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Sample records for genotyping human ancient

  1. A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites.

    PubMed

    Côté, Nathalie M L; Daligault, Julien; Pruvost, Mélanie; Bennett, E Andrew; Gorgé, Olivier; Guimaraes, Silvia; Capelli, Nicolas; Le Bailly, Matthieu; Geigl, Eva-Maria; Grange, Thierry

    2016-01-01

    Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of intact eggs and their proper identification. Genotyping via PCR-based approaches has the potential to achieve a precise species-level taxonomic determination. However, so far it has mostly been applied to individual eggs isolated from archeological samples. To increase the throughput and taxonomic accuracy, as well as reduce costs of genotyping methods, we adapted a PCR-based approach coupled with next-generation sequencing to perform precise taxonomic identification of parasitic helminths directly from archeological sediments. Our study of twenty-five 100 to 7,200 year-old archeological samples proved this to be a powerful, reliable and efficient approach for species determination even in the absence of preserved eggs, either as a stand-alone method or as a complement to microscopic studies.

  2. A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites

    PubMed Central

    Côté, Nathalie M. L.; Daligault, Julien; Pruvost, Mélanie; Bennett, E. Andrew; Gorgé, Olivier; Guimaraes, Silvia; Capelli, Nicolas; Le Bailly, Matthieu; Geigl, Eva-Maria; Grange, Thierry

    2016-01-01

    Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of intact eggs and their proper identification. Genotyping via PCR-based approaches has the potential to achieve a precise species-level taxonomic determination. However, so far it has mostly been applied to individual eggs isolated from archeological samples. To increase the throughput and taxonomic accuracy, as well as reduce costs of genotyping methods, we adapted a PCR-based approach coupled with next-generation sequencing to perform precise taxonomic identification of parasitic helminths directly from archeological sediments. Our study of twenty-five 100 to 7,200 year-old archeological samples proved this to be a powerful, reliable and efficient approach for species determination even in the absence of preserved eggs, either as a stand-alone method or as a complement to microscopic studies. PMID:26752051

  3. Ancient human microbiomes

    PubMed Central

    Warinner, Christina; Speller, Camilla; Collins, Matthew J.; Lewis, Cecil M.

    2015-01-01

    Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and therefore, we lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today. PMID:25559298

  4. Ancient human microbiomes.

    PubMed

    Warinner, Christina; Speller, Camilla; Collins, Matthew J; Lewis, Cecil M

    2015-02-01

    Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today. PMID:25559298

  5. Ancient Admixture in Human History

    PubMed Central

    Patterson, Nick; Moorjani, Priya; Luo, Yontao; Mallick, Swapan; Rohland, Nadin; Zhan, Yiping; Genschoreck, Teri; Webster, Teresa; Reich, David

    2012-01-01

    Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean “Iceman.” PMID:22960212

  6. Ancient admixture in human history.

    PubMed

    Patterson, Nick; Moorjani, Priya; Luo, Yontao; Mallick, Swapan; Rohland, Nadin; Zhan, Yiping; Genschoreck, Teri; Webster, Teresa; Reich, David

    2012-11-01

    Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean "Iceman."

  7. The Echoes of Ancient Humans

    ERIC Educational Resources Information Center

    Watzman, Haim

    2006-01-01

    Several artifacts found at the Gesher Benot Ya'aqov, or Daughters of Jacob Bridge, archaeological site in Israel provide a picture of ancient human ancestors that is different from the once accepted by most scholars. The discoveries by Israeli archaeologist Naama Goren-Inbar suggest that humans developed language and other key abilities far…

  8. Ancient DNA and human history.

    PubMed

    Slatkin, Montgomery; Racimo, Fernando

    2016-06-01

    We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history.

  9. Ancient DNA and human history

    PubMed Central

    Slatkin, Montgomery; Racimo, Fernando

    2016-01-01

    We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history. PMID:27274045

  10. Ancient DNA and human history.

    PubMed

    Slatkin, Montgomery; Racimo, Fernando

    2016-06-01

    We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history. PMID:27274045

  11. Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity

    PubMed Central

    Müller, Romy; Roberts, Charlotte A.; Brown, Terence A.

    2014-01-01

    The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second–nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth–nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis. PMID:24573854

  12. Re-inventing ancient human DNA.

    PubMed

    Knapp, Michael; Lalueza-Fox, Carles; Hofreiter, Michael

    2015-01-01

    For a long time, the analysis of ancient human DNA represented one of the most controversial disciplines in an already controversial field of research. Scepticism in this field was only matched by the long-lasting controversy over the authenticity of ancient pathogen DNA. This ambiguous view on ancient human DNA had a dichotomous root. On the one hand, the interest in ancient human DNA is great because such studies touch on the history and evolution of our own species. On the other hand, because these studies are dealing with samples from our own species, results are easily compromised by contamination of the experiments with modern human DNA, which is ubiquitous in the environment. Consequently, some of the most disputed studies published - apart maybe from early reports on million year old dinosaur or amber DNA - reported DNA analyses from human subfossil remains. However, the development of so-called next- or second-generation sequencing (SGS) in 2005 and the technological advances associated with it have generated new confidence in the genetic study of ancient human remains. The ability to sequence shorter DNA fragments than with PCR amplification coupled to traditional Sanger sequencing, along with very high sequencing throughput have both reduced the risk of sequencing modern contamination and provided tools to evaluate the authenticity of DNA sequence data. The field is now rapidly developing, providing unprecedented insights into the evolution of our own species and past human population dynamics as well as the evolution and history of human pathogens and epidemics. Here, we review how recent technological improvements have rapidly transformed ancient human DNA research from a highly controversial subject to a central component of modern anthropological research. We also discuss potential future directions of ancient human DNA research.

  13. Genomic correlates of atherosclerosis in ancient humans.

    PubMed

    Zink, Albert; Wann, L Samuel; Thompson, Randall C; Keller, Andreas; Maixner, Frank; Allam, Adel H; Finch, Caleb E; Frohlich, Bruno; Kaplan, Hillard; Lombardi, Guido P; Sutherland, M Linda; Sutherland, James D; Watson, Lucia; Cox, Samantha L; Miyamoto, Michael I; Narula, Jagat; Stewart, Alexandre F R; Thomas, Gregory S; Krause, Johannes

    2014-06-01

    Paleogenetics offers a unique opportunity to study human evolution, population dynamics, and disease evolution in situ. Although histologic and computed x-ray tomographic investigations of ancient mummies have clearly shown that atherosclerosis has been present in humans for more than 5,000 years, limited data are available on the presence of genetic predisposition for cardiovascular disease in ancient human populations. In a previous whole-genome study of the Tyrolean Iceman, a 5,300-year-old glacier mummy from the Alps, an increased risk for coronary heart disease was detected. The Iceman's genome revealed several single nucleotide polymorphisms that are linked with cardiovascular disease in genome-wide association studies. Future genetic studies of ancient humans from various geographic origins and time periods have the potential to provide more insights into the presence and possible changes of genetic risk factors in our ancestors. The study of ancient humans and a better understanding of the interaction between environmental and genetic influences on the development of heart diseases may lead to a more effective prevention and treatment of the most common cause of death in the modern world. PMID:25667090

  14. Genomic correlates of atherosclerosis in ancient humans.

    PubMed

    Zink, Albert; Wann, L Samuel; Thompson, Randall C; Keller, Andreas; Maixner, Frank; Allam, Adel H; Finch, Caleb E; Frohlich, Bruno; Kaplan, Hillard; Lombardi, Guido P; Sutherland, M Linda; Sutherland, James D; Watson, Lucia; Cox, Samantha L; Miyamoto, Michael I; Narula, Jagat; Stewart, Alexandre F R; Thomas, Gregory S; Krause, Johannes

    2014-06-01

    Paleogenetics offers a unique opportunity to study human evolution, population dynamics, and disease evolution in situ. Although histologic and computed x-ray tomographic investigations of ancient mummies have clearly shown that atherosclerosis has been present in humans for more than 5,000 years, limited data are available on the presence of genetic predisposition for cardiovascular disease in ancient human populations. In a previous whole-genome study of the Tyrolean Iceman, a 5,300-year-old glacier mummy from the Alps, an increased risk for coronary heart disease was detected. The Iceman's genome revealed several single nucleotide polymorphisms that are linked with cardiovascular disease in genome-wide association studies. Future genetic studies of ancient humans from various geographic origins and time periods have the potential to provide more insights into the presence and possible changes of genetic risk factors in our ancestors. The study of ancient humans and a better understanding of the interaction between environmental and genetic influences on the development of heart diseases may lead to a more effective prevention and treatment of the most common cause of death in the modern world.

  15. Palaeoparasitology - Human Parasites in Ancient Material.

    PubMed

    Araújo, Adauto; Reinhard, Karl; Ferreira, Luiz Fernando

    2015-01-01

    Parasite finds in ancient material launched a new field of science: palaeoparasitology. Ever since the pioneering studies, parasites were identified in archaeological and palaeontological remains, some preserved for millions of years by fossilization. However, the palaeoparasitological record consists mainly of parasites found specifically in human archaeological material, preserved in ancient occupation sites, from prehistory until closer to 2015. The results include some helminth intestinal parasites still commonly found in 2015, such as Ascaris lumbricoides, Trichuris trichiura and hookworms, besides others such as Amoebidae and Giardia intestinalis, as well as viruses, bacteria, fungi and arthropods. These parasites as a whole provide important data on health, diet, climate and living conditions among ancient populations. This chapter describes the principal findings and their importance for knowledge on the origin and dispersal of infectious diseases.

  16. Palaeoparasitology - Human Parasites in Ancient Material.

    PubMed

    Araújo, Adauto; Reinhard, Karl; Ferreira, Luiz Fernando

    2015-01-01

    Parasite finds in ancient material launched a new field of science: palaeoparasitology. Ever since the pioneering studies, parasites were identified in archaeological and palaeontological remains, some preserved for millions of years by fossilization. However, the palaeoparasitological record consists mainly of parasites found specifically in human archaeological material, preserved in ancient occupation sites, from prehistory until closer to 2015. The results include some helminth intestinal parasites still commonly found in 2015, such as Ascaris lumbricoides, Trichuris trichiura and hookworms, besides others such as Amoebidae and Giardia intestinalis, as well as viruses, bacteria, fungi and arthropods. These parasites as a whole provide important data on health, diet, climate and living conditions among ancient populations. This chapter describes the principal findings and their importance for knowledge on the origin and dispersal of infectious diseases. PMID:26597072

  17. The retrieval of ancient human DNA sequences.

    PubMed Central

    Handt, O.; Krings, M.; Ward, R. H.; Pääbo, S.

    1996-01-01

    DNA was extracted from approximately 600-year-old human remains found at an archaeological site in the southwestern United States, and mtDNA fragments were amplified by PCR. When these fragments were sequenced directly, multiple sequences seemed to be present. From three representative individuals, DNA fragments of different lengths were quantified and short overlapping amplification products cloned. When amplifications started from <40 molecules, clones contained several different sequences. In contrast, when they were initiated by a few thousand molecules, unambiguous and reproducible results were achieved. These results show that more experimental work than is often applied is necessary to ensure that DNA sequences amplified from ancient human remains are authentic. In particular, quantitation of the numbers of amplifiable molecules is a useful tool to determine the role of contaminating contemporary molecules and PCR errors in amplifications from ancient DNA. Images Figure 1 PMID:8755923

  18. Clinical significance of human papillomavirus genotyping.

    PubMed

    Choi, Youn Jin; Park, Jong Sup

    2016-03-01

    Cervical cancer is the fourth most common cancer in women worldwide, and the human papillomavirus (HPV) is the main causative agent for its development. HPV is a heterogeneous virus, and a persistent infection with a high-risk HPV contributes to the development of cancer. In recent decades, great advances have been made in understanding the molecular biology of HPV, and HPV's significance in cervical cancer prevention and management has received increased attention. In this review, we discuss the role of HPV genotyping in cervical cancer by addressing: clinically important issues in HPV virology; the current application of HPV genotyping in clinical medicine; and potential future uses for HPV genotyping.

  19. Human uses of ultrasound: ancient and modern.

    PubMed

    Wade, G

    2000-03-01

    For untold millennia certain animals have used ultrasound to probe places where light is unavailable, echo-locating bats being among the most adept. With ultrasonics, bats can quickly and safely 'see' at night in pursuing insects or flying in dark caves. Unable to hear ultrasound, humans have nevertheless made use of it. They did this anciently by taming wolves, with their keen ultrasonic hearing, for aiding in the hunt. Currently, they are doing this by developing technology to detect, generate and process ultrasound for searching in air or other gases, in water or other liquids, and in solids. The story of these technological developments is a large and fascinating mirror of human history involving the advent of such discoveries and inventions as magnetostriction, piezoelectricity, sonar, ultrasonic microscopy, etc.--the list is long. By now we are skilled in probing for underwater objects, the internal structure in materials, organs inside the human body, etc.--again the list is long. A number of different ultrasonic systems can be categorized into one of three key generic approaches: pulse-echo exploration, intensity mapping, and phase-amplitude measurement. In addition, each of these categories can be combined with the others to produce hybrid systems for which an unambiguous categorization is difficult or impossible. Challenging problems remain but solutions are being found. New principles and techniques are being discovered that will improve the use of ultrasound. Employing tomo-holographic techniques to reduce ambiguity in probing three-dimensional objects, near-field techniques to boost resolution and using limited-diffraction beams to provide image construction with ultra high frame rates are cases in point.

  20. Is atherosclerosis fundamental to human aging? Lessons from ancient mummies.

    PubMed

    Clarke, Emily M; Thompson, Randall C; Allam, Adel H; Wann, L Samuel; Lombardi, Guido P; Sutherland, M Linda; Sutherland, James D; Cox, Samantha L; Soliman, Muhammad Al-Tohamy; Abd el-Maksoud, Gomaa; Badr, Ibrahem; Miyamoto, Michael I; Frohlich, Bruno; Nur el-din, Abdel-Halim; Stewart, Alexandre F R; Narula, Jagat; Zink, Albert R; Finch, Caleb E; Michalik, David E; Thomas, Gregory S

    2014-05-01

    Case reports from Johan Czermak, Marc Ruffer, and others a century or more ago demonstrated ancient Egyptians had atherosclerosis three millennia ago. The Horus study team extended their findings, demonstrating that atherosclerosis was prevalent among 76 ancient Egyptian mummies and among 61 mummies from each of the ancient cultures of Peru, the American Southwest, and the Aleutian Islands. These findings challenge the assumption that atherosclerosis is a modern disease caused by present day risk factors. An extensive autopsy of an ancient Egyptian teenage male weaver named Nakht found that he was infected with four parasites: Schistosoma haematobium, Taenia species, Trichinella spiralis, and Plasmodium falciparum. Modern day patients with chronic inflammatory disease such as rheumatoid arthritis, systemic lupus erythematosus, and human immunodeficiency virus experience premature atherosclerosis. Could the burden of chronic inflammatory disease have been a risk factor for atherosclerosis in these ancient cultures? The prevalence of atherosclerosis in four diverse ancient cultures is consistent with atherosclerosis being fundamental to aging. The impact of risk factors in modern times, and potentially in ancient times, suggests a strong gene-environmental interplay: human genes provide a vulnerability to atherosclerosis, the environment determines when and if atherosclerosis becomes manifest clinically.

  1. Ancient human genomics: the methodology behind reconstructing evolutionary pathways.

    PubMed

    Marciniak, Stephanie; Klunk, Jennifer; Devault, Alison; Enk, Jacob; Poinar, Hendrik N

    2015-02-01

    High-throughput sequencing (HTS) has radically altered approaches to human evolutionary research. Recent contributions highlight that HTS is able to reach depths of the human lineage previously thought to be impossible. In this paper, we outline the methodological advances afforded by recent developments in DNA recovery, data output, scalability, speed, and resolution of the current sequencing technology. We review and critically evaluate the 'DNA pipeline' for ancient samples: from DNA extraction, to constructing immortalized sequence libraries, to enrichment strategies (e.g., polymerase chain reaction [PCR] and hybridization capture), and finally, to bioinformatic analyses of sequence data. We argue that continued evaluations and improvements to this process are essential to ensure sequence data validity. Also, we highlight the role of contamination and authentication in ancient DNA-HTS, which is particularly relevant to ancient human genomics, since sequencing the genomes of hominins such as Homo erectus and Homo heidelbergensis may soon be within the realm of possibility. PMID:25601038

  2. Pathogens and host immunity in the ancient human oral cavity

    PubMed Central

    Warinner, Christina; Matias Rodrigues, João F.; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y.; Tito, Raul Y.; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar-García, Domingo C.; Eppler, Elisabeth; Seiler, Roger; Hansen, Lars; Samaniego Castruita, José Alfredo; Barkow-Oesterreicher, Simon; Teoh, Kai Yik; Kelstrup, Christian; Olsen, Jesper V.; Nanni, Paolo; Kawai, Toshihisa; Willerslev, Eske; von Mering, Christian; Lewis, Cecil M.; Collins, Matthew J.; Gilbert, M. Thomas P.; Rühli, Frank; Cappellini, Enrico

    2014-01-01

    Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize: (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) the first evidence of ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, “red-complex” pathogens, and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity, and diet, thereby extending the direct investigation of common diseases into the human evolutionary past. PMID:24562188

  3. Pathogens and host immunity in the ancient human oral cavity.

    PubMed

    Warinner, Christina; Rodrigues, João F Matias; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y; Tito, Raul Y; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar-García, Domingo C; Eppler, Elisabeth; Seiler, Roger; Hansen, Lars H; Castruita, José Alfredo Samaniego; Barkow-Oesterreicher, Simon; Teoh, Kai Yik; Kelstrup, Christian D; Olsen, Jesper V; Nanni, Paolo; Kawai, Toshihisa; Willerslev, Eske; von Mering, Christian; Lewis, Cecil M; Collins, Matthew J; Gilbert, M Thomas P; Rühli, Frank; Cappellini, Enrico

    2014-04-01

    Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity and diet, thereby extending direct investigation of common diseases into the human evolutionary past.

  4. Diversity of Human Clock Genotypes and Consequences

    PubMed Central

    Zhang, Luoying; Ptáček, Louis J.; Fu, Ying-Hui

    2014-01-01

    The molecular clock consists of a number of genes that form transcriptional and post-transcriptional feedback loops, which function together to generate circadian oscillations that give rise to circadian rhythms of our behavioral and physiological processes. Genetic variations in these clock genes have been shown to be associated with phenotypic effects in a repertoire of biological processes, such as diurnal preference, sleep, metabolism, mood regulation, addiction, and fertility. Consistently, rodent models carrying mutations in clock genes also demonstrate similar phenotypes. Taken together, these studies suggest that human clock-gene variants contribute to the phenotypic differences observed in various behavioral and physiological processes, although to validate this requires further characterization of the molecular consequences of these polymorphisms. Investigating the diversity of human genotypes and the phenotypic effects of these genetic variations shall advance our understanding of the function of the circadian clock and how we can employ the clock to improve our overall health. PMID:23899594

  5. The Characterization of Helicobacter pylori DNA Associated with Ancient Human Remains Recovered from a Canadian Glacier

    PubMed Central

    Swanston, Treena; Haakensen, Monique; Deneer, Harry; Walker, Ernest G.

    2011-01-01

    Helicobacter pylori is a gram-negative bacterium that colonizes the stomach of nearly half of the world's population. Genotypic characterization of H. pylori strains involves the analysis of virulence-associated genes, such as vacA, which has multiple alleles. Previous phylogenetic analyses have revealed a connection between modern H. pylori strains and the movement of ancient human populations. In this study, H. pylori DNA was amplified from the stomach tissue of the Kwäday Dän Ts'ìnchi individual. This ancient individual was recovered from the Samuel Glacier in Tatshenshini-Alsek Park, British Columbia, Canada on the traditional territory of the Champagne and Aishihik First Nations and radiocarbon dated to a timeframe of approximately AD 1670 to 1850. This is the first ancient H. pylori strain to be characterized with vacA sequence data. The Tatshenshini H. pylori strain has a potential hybrid vacA m2a/m1d middle (m) region allele and a vacA s2 signal (s) region allele. A vacA s2 allele is more commonly identified with Western strains, and this suggests that European strains were present in northwestern Canada during the ancient individual's time. Phylogenetic analysis indicated that the vacA m1d region of the ancient strain clusters with previously published novel Native American strains that are closely related to Asian strains. This indicates a past connection between the Kwäday Dän Ts'ìnchi individual and the ancestors who arrived in the New World thousands of years ago. PMID:21359221

  6. Phylogenetic evidence that two distinct Trichuris genotypes infect both humans and non-human primates.

    PubMed

    Ravasi, Damiana F; O'Riain, Mannus J; Davids, Faezah; Illing, Nicola

    2012-01-01

    Although there has been extensive debate about whether Trichuris suis and Trichuris trichiura are separate species, only one species of the whipworm T. trichiura has been considered to infect humans and non-human primates. In order to investigate potential cross infection of Trichuris sp. between baboons and humans in the Cape Peninsula, South Africa, we sequenced the ITS1-5.8S-ITS2 region of adult Trichuris sp. worms isolated from five baboons from three different troops, namely the Cape Peninsula troop, Groot Olifantsbos troop and Da Gama Park troop. This region was also sequenced from T. trichiura isolated from a human patient from central Africa (Cameroon) for comparison. By combining this dataset with Genbank records for Trichuris isolated from other humans, non-human primates and pigs from several different countries in Europe, Asia, and Africa, we confirmed the identification of two distinct Trichuris genotypes that infect primates. Trichuris sp. isolated from the Peninsula baboons fell into two distinct clades that were found to also infect human patients from Cameroon, Uganda and Jamaica (named the CP-GOB clade) and China, Thailand, the Czech Republic, and Uganda (named the DG clade), respectively. The divergence of these Trichuris clades is ancient and precedes the diversification of T. suis which clustered closely to the CP-GOB clade. The identification of two distinct Trichuris genotypes infecting both humans and non-human primates is important for the ongoing treatment of Trichuris which is estimated to infect 600 million people worldwide. Currently baboons in the Cape Peninsula, which visit urban areas, provide a constant risk of infection to local communities. A reduction in spatial overlap between humans and baboons is thus an important measure to reduce both cross-transmission and zoonoses of helminthes in Southern Africa.

  7. Human tuberculosis predates domestication in ancient Syria.

    PubMed

    Baker, Oussama; Lee, Oona Y-C; Wu, Houdini H T; Besra, Gurdyal S; Minnikin, David E; Llewellyn, Gareth; Williams, Christopher M; Maixner, Frank; O'Sullivan, Niall; Zink, Albert; Chamel, Bérénice; Khawam, Rima; Coqueugniot, Eric; Helmer, Daniel; Le Mort, Françoise; Perrin, Pascale; Gourichon, Lionel; Dutailly, Bruno; Pálfi, György; Coqueugniot, Hélène; Dutour, Olivier

    2015-06-01

    The question of pre-neolithic tuberculosis is still open in paleopathological perspective. One of the major interests is to explore what type of infection could have existed around the early stage of animal domestication. Paleopathological lesions evoking skeletal TB were observed on five human skeletons coming from two PPNB sites in Syria, which belongs to the geographical cradle of agriculture. These sites represent respectively pre-domestication phase (Dja'de el Mughara, Northern Syria, 8800-8300 BCE cal.) and early domestication phase (Tell Aswad, Southern Syria, 8200-7600 BCE cal.). MicroCT scan analyses were performed on two specimens (one per site) and revealed microscopic changes in favor of TB infection. Detection of lipid biomarkers is positive for two specimens (one per site). Initial molecular analysis further indicates the presence of TB in one individual from Dja'de. Interestingly, no morphological evidence of TB was observed on animal remains of wild and newly domesticated species, discovered in these sites. These observations strongly suggest the presence of human tuberculosis before domestication and at its early stages.

  8. Human tuberculosis predates domestication in ancient Syria.

    PubMed

    Baker, Oussama; Lee, Oona Y-C; Wu, Houdini H T; Besra, Gurdyal S; Minnikin, David E; Llewellyn, Gareth; Williams, Christopher M; Maixner, Frank; O'Sullivan, Niall; Zink, Albert; Chamel, Bérénice; Khawam, Rima; Coqueugniot, Eric; Helmer, Daniel; Le Mort, Françoise; Perrin, Pascale; Gourichon, Lionel; Dutailly, Bruno; Pálfi, György; Coqueugniot, Hélène; Dutour, Olivier

    2015-06-01

    The question of pre-neolithic tuberculosis is still open in paleopathological perspective. One of the major interests is to explore what type of infection could have existed around the early stage of animal domestication. Paleopathological lesions evoking skeletal TB were observed on five human skeletons coming from two PPNB sites in Syria, which belongs to the geographical cradle of agriculture. These sites represent respectively pre-domestication phase (Dja'de el Mughara, Northern Syria, 8800-8300 BCE cal.) and early domestication phase (Tell Aswad, Southern Syria, 8200-7600 BCE cal.). MicroCT scan analyses were performed on two specimens (one per site) and revealed microscopic changes in favor of TB infection. Detection of lipid biomarkers is positive for two specimens (one per site). Initial molecular analysis further indicates the presence of TB in one individual from Dja'de. Interestingly, no morphological evidence of TB was observed on animal remains of wild and newly domesticated species, discovered in these sites. These observations strongly suggest the presence of human tuberculosis before domestication and at its early stages. PMID:25819157

  9. Ancient origins of human developmental plasticity.

    PubMed

    Crespi, Erica J; Denver, Robert J

    2005-01-01

    Animals have the ability to alter development, physiology, growth, and behavior in response to different environmental conditions. These responses represent critical assessments of both external and internal factors. For example, the timing of metamorphosis, hatching, or birth depends on the trade-offs between growth opportunity and mortality risk in the developmental habitat. Physiological sensors compute these trade-offs as a function of energy balance and environmental stress, and effectors initiate physiological, developmental, and behavioral responses to these determinations. The neuroendocrine stress axis provides a means for animals to integrate information from multiple sources and to respond accordingly. Considerable evidence now supports the view that the secretion of hormones critical to development (corticosteroid and thyroid hormones) is controlled by a common neuroendocrine stress pathway involving corticotropin-releasing factor (CRF) and related peptides. CRF produced in the hypothalamus stimulates the biosynthesis and secretion of both thyroid and corticosteroid hormones, leading to accelerated tadpole metamorphosis. Similarly, in mammals CRF of fetal and placental origin has been shown to influence the timing of birth. Studies in several experimental animal models and in humans show that early life experience can have long-term phenotypic consequences. Furthermore, there is evidence that phenotypic expression is strongly influenced by the actions of stress hormones produced during development. The integrated neuroendocrine response to stress, and its role in timing critical life history transitions and establishing long-term phenotypic expression, arose early in the evolution of vertebrates.

  10. Global proficiency study of human papillomavirus genotyping.

    PubMed

    Eklund, Carina; Zhou, Tiequn; Dillner, Joakim

    2010-11-01

    Internationally comparable quality assurance of Human Papillomavirus (HPV) DNA detection and typing methods is essential for evaluation of HPV vaccines and effective monitoring and implementation of HPV vaccination programs. Therefore, the World Health Organization (WHO) HPV Laboratory Network (LabNet) designed an international proficiency study. Following announcement at the WHO website, the responding laboratories performed HPV typing using one or more of their usual assays on 43 coded samples composed of titration series of purified plasmids of 16 HPV types (HPV6, -11, -16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, and -68). Detection of at least 50 IU of HPV16 or HPV18 DNA and of 500 genome equivalents (GE) of the other 14 HPV types (in samples with single and multiple HPV types) was considered proficient. Fifty-four laboratories worldwide submitted a total of 84 data sets. More than 21 HPV-genotyping assays were used. Commonly used methods were Linear Array, Lineblot, InnoLiPa, Clinical Array, type-specific real-time PCR, PCR-Luminex and microarray assays. The major oncogenic HPV types (HPV16 and -18) were detected in 89.7% (70/78) and 92.2% (71/77) of the data sets, respectively. HPV types 56, 59, and 68 were the least commonly detected types (in less than 80% of the data sets). Twenty-eight data sets reported multiple false-positive results and were considered nonproficient. In conclusion, we found that international proficiency studies, traceable to international standards, allow standardized quality assurance for different HPV-typing assays and enable the comparison of data generated from different laboratories worldwide.

  11. Improved Calibration of the Human Mitochondrial Clock Using Ancient Genomes

    PubMed Central

    Rieux, Adrien; Eriksson, Anders; Li, Mingkun; Sobkowiak, Benjamin; Weinert, Lucy A.; Warmuth, Vera; Ruiz-Linares, Andres; Manica, Andrea; Balloux, François

    2014-01-01

    Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties around these rates, with substantial variation among recent published estimates. Substitution rates have traditionally been estimated by associating dated events to the root (e.g., the divergence between humans and chimpanzees) or to internal nodes in a phylogenetic tree (e.g., first entry into the Americas). The recent availability of ancient mitochondrial DNA sequences allows for a more direct calibration by assigning the age of the sequenced samples to the tips within the human phylogenetic tree. But studies also vary greatly in the methodology employed and in the sequence panels analyzed, making it difficult to tease apart the causes for the differences between previous estimates. To clarify this issue, we compiled a comprehensive data set of 350 ancient and modern human complete mitochondrial DNA genomes, among which 146 were generated for the purpose of this study and estimated substitution rates using calibrations based both on dated nodes and tips. Our results demonstrate that, for the same data set, estimates based on individual dated tips are far more consistent with each other than those based on nodes and should thus be considered as more reliable. PMID:25100861

  12. Dispersal time for ancient human migrations: Americas and Europe colonization

    NASA Astrophysics Data System (ADS)

    Flores, J. C.

    2007-07-01

    I apply the recently proposed intermittence strategy to investigate the ancient human migrations in the world. That is, the Americas colonization (Bering-bridge and Pacific-coast theories) and Neanderthal replacement in Europe around 45000 years before the present. Using a mathematical equation related to diffusion and ballistic motion, I calculate the colonization time in all these cases in good agreement with archeological data (including Neolithic transition in Europe). Moreover, to support these calculations, I obtain analytically the effective speed of colonization in Europe veff=0.62 [km/yr] and related to the Aurignacian culture propagation.

  13. PCR-based approach to distinguish group A human rotavirus genotype 1 vs. genotype 2 genes.

    PubMed

    McKell, Allison O; Nichols, Joshua C; McDonald, Sarah M

    2013-12-01

    Group A rotaviruses (RVs) are eleven-segmented, double-stranded RNA viruses and important causes of severe diarrhea in children. A full-genome classification system is readily used to describe the genetic makeup of individual RV strains. In this system, each viral gene is assigned a specific genotype based upon its nucleotide sequence and established percent identity cut-off values. However, a faster and more cost-effective approach to determine RV gene genotypes is to utilize specific oligonucleotide primer sets in RT-PCR/PCR. Such primer sets and PCR-based genotyping methods have already been developed for the VP7-, VP6-, VP4- and NSP4-coding gene segments. In this study, primers were developed for the remaining seven RV gene segments, which encode proteins VP1, VP2, VP3, NSP1, NSP2, NSP3, and NSP5/6. Specifically, primers were designed to distinguish the two most common human RV genotypes (1 vs. 2) for these genes and were validated on several cell culture-adapted human and animal RV strains, as well as on human RVs from clinical fecal specimens. As such, primer sets now exist for all eleven genes of common human RVs, allowing for the identification of reassortant strains with mixed constellations of both genotype 1 and 2 genes using a rapid and economical RT-PCR/PCR method. PMID:24012969

  14. Almost all human genes resulted from ancient duplication.

    PubMed

    Britten, Roy J

    2006-12-12

    Results of protein sequence comparison at open criterion show a very large number of relationships that have, up to now, gone unreported. The relationships suggest many ancient events of gene duplication. It is well known that gene duplication has been a major process in the evolution of genomes. A collection of human genes that have known functions have been examined for a history of gene duplications detected by means of amino acid sequence similarity by using BLASTp with an expectation of two or less (open criterion). Because the collection of genes in build 35 includes sets of transcript variants, all genes of known function were collected, and only the longest transcription variant was included, yielding a 13,298-member library called KGMV (for known genes maximum variant). When all lengths of matches are accepted, >97% of human genes show significant matches to each other. Many form matches with a large number of other different proteins, showing that most genes are made up from parts of many others as a result of ancient events of duplication. To support the use of the open criterion, all of the members of the KGMV library were twice replaced with random protein sequences of the same length and average composition, and all were compared with each other with BLASTp at expectation two or less. The set of matches averaged 0.35% of that observed for the KGMV set of proteins. PMID:17146051

  15. Resequencing Microarray Technology for Genotyping Human Papillomavirus in Cervical Smears

    PubMed Central

    Berthet, Nicolas; Falguières, Michael; Filippone, Claudia; Bertolus, Chloé; Bole-Feysot, Christine; Brisse, Sylvain; Gessain, Antoine; Heard, Isabelle; Favre, Michel

    2014-01-01

    There are more than 40 human papillomaviruses (HPVs) belonging to the alpha genus that cause sexually transmitted infections; these infections are among the most frequent and can lead to condylomas and anogenital intra-epithelial neoplasia. At least 18 of these viruses are causative agents of anogenital carcinomas. We evaluated the performance of a resequencing microarray for the detection and genotyping of alpha HPV of clinical significance using cloned HPV DNA. To reduce the number of HPV genotypes tiled on microarray, we used reconstructed ancestral sequences (RASs) as they are more closely related to the various genotypes than the current genotypes are among themselves. The performance of this approach was tested by genotyping with a set of 40 cervical smears already genotyped using the commercial PapilloCheck kit. The results of the two tests were concordant for 70% (28/40) of the samples and compatible for 30% (12/40). Our findings indicate that RASs were able to detect and identify one or several HPV in clinical samples. Associating RASs with homonym sequences improved the genotyping of HPV present in cases of multiple infection. In conclusion, we demonstrate the diagnostic potential of resequencing technology for genotyping of HPV, and illustrate its value both for epidemiological studies and for monitoring the distribution of HPV in the post-vaccination era. PMID:25383888

  16. Ancient Human Migration after Out-of-Africa

    PubMed Central

    Shriner, Daniel; Tekola-Ayele, Fasil; Adeyemo, Adebowale; Rotimi, Charles N.

    2016-01-01

    The serial founder model of modern human origins predicts that the phylogeny of ancestries exhibits bifurcating, tree-like behavior. Here, we tested this prediction using three methods designed to investigate gene flow in autosome-wide genotype data from 3,528 unrelated individuals from 163 global samples. Specifically, we investigated whether Cushitic ancestry has an East African or Middle Eastern origin. We found evidence for non-tree-like behavior in the form of four migration events. First, we found that Cushitic ancestry is a mixture of ancestries closely related to Arabian ancestry and Nilo-Saharan or Omotic ancestry. We found evidence for additional migration events in the histories of: 1) Indian and Arabian ancestries, 2) Kalash ancestry, and 3) Native American and Northern European ancestries. These findings, based on analysis of ancestry of present-day humans, reveal migration in the distant past and provide new insights into human history. PMID:27212471

  17. Ancient Human Migration after Out-of-Africa.

    PubMed

    Shriner, Daniel; Tekola-Ayele, Fasil; Adeyemo, Adebowale; Rotimi, Charles N

    2016-01-01

    The serial founder model of modern human origins predicts that the phylogeny of ancestries exhibits bifurcating, tree-like behavior. Here, we tested this prediction using three methods designed to investigate gene flow in autosome-wide genotype data from 3,528 unrelated individuals from 163 global samples. Specifically, we investigated whether Cushitic ancestry has an East African or Middle Eastern origin. We found evidence for non-tree-like behavior in the form of four migration events. First, we found that Cushitic ancestry is a mixture of ancestries closely related to Arabian ancestry and Nilo-Saharan or Omotic ancestry. We found evidence for additional migration events in the histories of: 1) Indian and Arabian ancestries, 2) Kalash ancestry, and 3) Native American and Northern European ancestries. These findings, based on analysis of ancestry of present-day humans, reveal migration in the distant past and provide new insights into human history. PMID:27212471

  18. Genotype constellation and evolution of group A rotaviruses infecting humans.

    PubMed

    Matthijnssens, Jelle; Van Ranst, Marc

    2012-08-01

    Numerous rotavirus group A (RVA) strains with distinct G-genotype and P-genotype combinations have been described infecting humans worldwide. However, the increasing amount of complete RVA genome data which have become available, suggest that only RVA strains with 2 discrete genotype constellations have been successful in sustaining infection of humans worldwide over longer periods of time. Those genotype constellations have been designated I1-R1-C1-M1-A1-N1-T1-E1-H1 and I2-R2-C2-M2-A2-N2-T2-E2-H2 and are also known as Wa-like and DS-1-like, respectively. RVAs of other genotype constellations which were able to spread to a limited extent in the human population are AU-1-related RVA strains (I3-R3-C3-M3-A3/A12-N3-T3-E3-H3/H6) in combination with G3P[9] or G12P[9], and neonatal G10P[11] RVA strains in India (bovine×human Wa-like reassortants). On the basis of the analysis of complete genomes, it is suggested that the overall genetic diversity of epidemiologically widespread human RVA strains is more limited than generally assumed. This conclusion has consequences for how we look at host range restriction and the criteria according to which the effectiveness of RVA universal mass vaccination programs is assessed.

  19. Synchrotron Study of Strontium in Modern and Ancient Human Bones

    NASA Astrophysics Data System (ADS)

    Pingitore, N. E.; Cruz-Jimenez, G.

    2001-05-01

    Archaeologists use the strontium in human bone to reconstruct diet and migration in ancient populations. Because mammals discriminate against strontium relative to calcium, carnivores show lower bone Sr/Ca ratios than herbivores. Thus, in a single population, bone Sr/Ca ratios can discriminate a meat-rich from a vegetarian diet. Also, the ratio of 87-Sr to 86-Sr in soils varies with the underlying geology; incorporated into the food chain, this local signature becomes embedded in our bones. The Sr isotopic ratio in the bones of individuals or populations which migrate to a different geologic terrane will gradually change as bone remodels. In contrast, the isotopic ratio of tooth enamel is fixed at an early age and is not altered later in life. Addition of Sr to bone during post-mortem residence in moist soil or sediment compromises application of the Sr/Ca or Sr-isotope techniques. If this post-mortem Sr resides in a different atomic environment than the Sr deposited in vivo, x-ray absorption spectroscopy could allow us to distinguish pristine from contaminated, and thus unreliable, samples. Initial examination of a suite of modern and ancient human and animal bones by extended x-ray absorption fine structure (EXAFS) showed no obvious differences between the fresh and buried materials. We note, with obvious concern, that the actual location of Sr in modern bone is controversial: there is evidence both that Sr substitutes for Ca and that Sr is sorbed on the surfaces of bone crystallites. Additional material is being studied.

  20. Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins.

    PubMed

    Eriksson, Anders; Manica, Andrea

    2012-08-28

    Recent comparisons between anatomically modern humans and ancient genomes of other hominins have raised the tantalizing, and hotly debated, possibility of hybridization. Although several tests of hybridization have been devised, they all rely on the degree to which different modern populations share genetic polymorphisms with the ancient genomes of other hominins. However, spatial population structure is expected to generate genetic patterns similar to those that might be attributed to hybridization. To investigate this problem, we take Neanderthals as a case study, and build a spatially explicit model of the shared history of anatomically modern humans and this hominin. We show that the excess polymorphism shared between Eurasians and Neanderthals is compatible with scenarios in which no hybridization occurred, and is strongly linked to the strength of population structure in ancient populations. Thus, we recommend caution in inferring admixture from geographic patterns of shared polymorphisms, and argue that future attempts to investigate ancient hybridization between humans and other hominins should explicitly account for population structure.

  1. Genotyping of Coxiella burnetii from domestic ruminants and human in Hungary: indication of various genotypes

    PubMed Central

    2014-01-01

    Background Information about the genotypic characteristic of Coxiella burnetii from Hungary is lacking. The aim of this study is to describe the genetic diversity of C. burnetii in Hungary and compare genotypes with those found elsewhere. A total of 12 samples: (cattle, n = 6, sheep, n = 5 and human, n = 1) collected from across Hungary were studied by a 10-loci multispacer sequence typing (MST) and 6-loci multiple-locus variable-number of tandem repeat analysis (MLVA). Phylogenetic relationships among MST genotypes show how these Hungarian samples are related to others collected around the world. Results Three MST genotypes were identified: sequence type (ST) 20 has also been identified in ruminants from other European countries and the USA, ST28 was previously identified in Kazakhstan, and the proposed ST37 is novel. All MST genotypes yielded different MLVA genotypes and three different MLVA genotypes were identified within ST20 samples alone. Two novel MLVA types 0-9-5-5-6-2 (AG) and 0-8-4-5-6-2 (AF) (Ms23-Ms24-Ms27-Ms28-Ms33-Ms34) were defined in the ovine materials correlated with ST28 and ST37. Samples from different parts of the phylogenetic tree were associated with different hosts, suggesting host-specific adaptations. Conclusions Even with the limited number of samples analysed, this study revealed high genetic diversity among C. burnetii in Hungary. Understanding the background genetic diversity will be essential in identifying and controlling outbreaks. PMID:24885415

  2. Genotype × age interaction in human transcriptional ageing

    PubMed Central

    Kent, Jack W.; Göring, Harald H. H.; Charlesworth, Jac C.; Drigalenko, Eugene; Diego, Vincent P.; Curran, Joanne E.; Johnson, Matthew P.; Dyer, Thomas D.; Cole, Shelley A.; Jowett, Jeremy B. M.; Mahaney, Michael C.; Comuzzie, Anthony G.; Almasy, Laura; Moses, Eric K.; Blangero, John; Williams-Blangero, Sarah

    2012-01-01

    Individual differences in biological ageing (i.e., the rate of physiological response to the passage of time) may be due in part to genotype-specific variation in gene action. However, the sources of heritable variation in human age-related gene expression profiles are largely unknown. We have profiled genome-wide expression in peripheral blood mononuclear cells from 1,240 individuals in large families and found 4,472 human autosomal transcripts, representing ~4,349 genes, significantly correlated with age. We identified 623 transcripts that show genotype by age interaction in addition to a main effect of age, defining a large set of novel candidates for characterization of the mechanisms of differential biological ageing. We applied a novel SNP genotype×age interaction test to one of these candidates, the ubiquilin-like gene UBQLNL, and found evidence of joint cis-association and genotype by age interaction as well as trans-genotype by age interaction for UBQLNL expression. Both UBQLNL expression levels at recruitment and cis genotype are associated with longitudinal cancer risk in our study cohort. PMID:22871458

  3. First Ancient Mitochondrial Human Genome from a Prepastoralist Southern African

    PubMed Central

    Smith, Andrew B.; Hayes, Vanessa M.

    2014-01-01

    The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semidesert regions of Namibia and Botswana, whereas archeological, historical, and genetic evidence promotes a once broader southerly dispersal of click-speaking peoples including southward migrating pastoralists and indigenous marine-foragers. No genetic data have been recovered from the indigenous peoples that once sustained life along the southern coastal waters of Africa prepastoral arrival. In this study we generate a complete mitochondrial genome from a 2,330-year-old male skeleton, confirmed through osteological and archeological analysis as practicing a marine-based forager existence. The ancient mtDNA represents a new L0d2c lineage (L0d2c1c) that is today, unlike its Khoe-language based sister-clades (L0d2c1a and L0d2c1b) most closely related to contemporary indigenous San-speakers (specifically Ju). Providing the first genomic evidence that prepastoral Southern African marine foragers carried the earliest diverged maternal modern human lineages, this study emphasizes the significance of Southern African archeological remains in defining early modern human origins. PMID:25212860

  4. Hydroarchaeology: Measuring the Ancient Human Impact on the Palenque Watershed

    NASA Astrophysics Data System (ADS)

    French, K. D.; Duffy, C. J.

    2010-03-01

    Palenque, one of the best known Classic Maya centers, has what is arguably the most unique and intricate system of water management known anywhere in the Maya Lowlands. Years of archaeological research, including intensive mapping between 1997 and 2000, reveal that this major center, situated on a narrow escarpment at the base of a high mountain range in northern Chiapas, Mexico, began as a modest settlement about AD 100. Then, during the seventh and eighth centuries, Palenque experienced explosive growth, mushrooming into a dense community with an estimated population of 6000 and approximately 1500 structures — residences, palaces, and temples¬ - under a series of powerful rulers. This process of "urban" growth led to obvious changes in landcover. In order to better understand the effects that landcover and climate change have on the availability of water for an ancient city a new approach is required. In this paper we explore a hydroarchaeological approach that utilizes simulated daily paleoclimate data, watershed modeling, and traditional archaeology to view the response of ancient human impact within the watershed surrounding Palenque. There is great potential for watershed-climate modeling in developing plausible scenarios of water use and supply, and the effect of extreme conditions (flood and drought), all of which cannot be fully represented by atmosphere-based climate and weather projections. The first objective of the paper is to test the hypothesis that drought was a major cause for Palenque’s collapse. Did the Maya abandon Palenque in search of water? Secondly, we evaluate the hydraulic design of the water management features at Palenque against extreme meteorological events. How successful was the hydraulic engineering of the Maya in coping with droughts and floods? The archaeological implications for this non-invasive "virtual" method are many, including detecting periods of stress within a community, estimating population by developing caps

  5. A test for ancient selective sweeps and an application to candidate sites in modern humans.

    PubMed

    Racimo, Fernando; Kuhlwilm, Martin; Slatkin, Montgomery

    2014-12-01

    We introduce a new method to detect ancient selective sweeps centered on a candidate site. We explored different patterns produced by sweeps around a fixed beneficial mutation, and found that a particularly informative statistic measures the consistency between majority haplotypes near the mutation and genotypic data from a closely related population. We incorporated this statistic into an approximate Bayesian computation (ABC) method that tests for sweeps at a candidate site. We applied this method to simulated data and show that it has some power to detect sweeps that occurred more than 10,000 generations in the past. We also applied it to 1,000 Genomes and Complete Genomics data combined with high-coverage Denisovan and Neanderthal genomes to test for sweeps in modern humans since the separation from the Neanderthal-Denisovan ancestor. We tested sites at which humans are fixed for the derived (i.e., nonchimpanzee allele) whereas the Neanderthal and Denisovan genomes are homozygous for the ancestral allele. We observe only weak differences in statistics indicative of selection between functional categories. When we compare patterns of scaled diversity or use our ABC approach, we fail to find a significant difference in signals of classic selective sweeps between regions surrounding nonsynonymous and synonymous changes, but we detect a slight enrichment for reduced scaled diversity around splice site changes. We also present a list of candidate sites that show high probability of having undergone a classic sweep in the modern human lineage since the split from Neanderthals and Denisovans. PMID:25172957

  6. A test for ancient selective sweeps and an application to candidate sites in modern humans.

    PubMed

    Racimo, Fernando; Kuhlwilm, Martin; Slatkin, Montgomery

    2014-12-01

    We introduce a new method to detect ancient selective sweeps centered on a candidate site. We explored different patterns produced by sweeps around a fixed beneficial mutation, and found that a particularly informative statistic measures the consistency between majority haplotypes near the mutation and genotypic data from a closely related population. We incorporated this statistic into an approximate Bayesian computation (ABC) method that tests for sweeps at a candidate site. We applied this method to simulated data and show that it has some power to detect sweeps that occurred more than 10,000 generations in the past. We also applied it to 1,000 Genomes and Complete Genomics data combined with high-coverage Denisovan and Neanderthal genomes to test for sweeps in modern humans since the separation from the Neanderthal-Denisovan ancestor. We tested sites at which humans are fixed for the derived (i.e., nonchimpanzee allele) whereas the Neanderthal and Denisovan genomes are homozygous for the ancestral allele. We observe only weak differences in statistics indicative of selection between functional categories. When we compare patterns of scaled diversity or use our ABC approach, we fail to find a significant difference in signals of classic selective sweeps between regions surrounding nonsynonymous and synonymous changes, but we detect a slight enrichment for reduced scaled diversity around splice site changes. We also present a list of candidate sites that show high probability of having undergone a classic sweep in the modern human lineage since the split from Neanderthals and Denisovans.

  7. Ancient human genome sequence of an extinct Palaeo-Eskimo

    PubMed Central

    Rasmussen, Morten; Li, Yingrui; Lindgreen, Stinus; Pedersen, Jakob Skou; Albrechtsen, Anders; Moltke, Ida; Metspalu, Mait; Metspalu, Ene; Kivisild, Toomas; Gupta, Ramneek; Bertalan, Marcelo; Nielsen, Kasper; Gilbert, M. Thomas P.; Wang, Yong; Raghavan, Maanasa; Campos, Paula F.; Kamp, Hanne Munkholm; Wilson, Andrew S.; Gledhill, Andrew; Tridico, Silvana; Bunce, Michael; Lorenzen, Eline D.; Binladen, Jonas; Guo, Xiaosen; Zhao, Jing; Zhang, Xiuqing; Zhang, Hao; Li, Zhuo; Chen, Minfeng; Orlando, Ludovic; Kristiansen, Karsten; Bak, Mads; Tommerup, Niels; Bendixen, Christian; Pierre, Tracey L.; Grønnow, Bjarne; Meldgaard, Morten; Andreasen, Claus; Fedorova, Sardana A.; Osipova, Ludmila P.; Higham, Thomas F. G.; Ramsey, Christopher Bronk; Hansen, Thomas v. O.; Nielsen, Finn C.; Crawford, Michael H.; Brunak, Søren; Sicheritz-Pontén, Thomas; Villems, Richard; Nielsen, Rasmus; Krogh, Anders; Wang, Jun; Willerslev, Eske

    2013-01-01

    We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit. PMID:20148029

  8. Ancient DNA and the rewriting of human history: be sparing with Occam's razor.

    PubMed

    Haber, Marc; Mezzavilla, Massimo; Xue, Yali; Tyler-Smith, Chris

    2016-01-11

    Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA.

  9. Hepatitis E Virus Genotype 3 in Humans and Swine, Bolivia

    PubMed Central

    Cavallo, Annalisa; Gonzales, José Luis; Bonelli, Sara Irene; Valda, Ybar; Pieri, Angela; Segundo, Higinio; Ibañez, Ramón; Mantella, Antonia; Bartalesi, Filippo; Tolari, Francesco; Bartoloni, Alessandro

    2011-01-01

    We determined the seroprevalence of hepatitis E virus (HEV) in persons in 2 rural communities in southeastern Bolivia and the presence of HEV in human and swine fecal samples. HEV seroprevalence was 6.3%, and HEV genotype 3 strains with high sequence homology were detected. PMID:21801630

  10. Ancient DNA and the human settlement of the Pacific: a review.

    PubMed

    Matisoo-Smith, Elizabeth

    2015-02-01

    The Pacific region provides unique opportunities to study human evolution including through analyses of ancient DNA. While some of the earliest studies involving ancient DNA from skeletal remains focused on Pacific samples, in the following 25 years, several factors meant that little aDNA research, particularly research focused on human populations, has emerged. This paper briefly presents the genetic evidence for population origins, reviews what ancient DNA work has been undertaken to address human history and evolution in the Pacific region, and argues that the future is bright but research requires a collaborative approach between academic disciplines but also with local communities.

  11. Human papillomavirus genotypes distribution in cervical samples from Uruguayan women.

    PubMed

    Ramas, Viviana; Mirazo, Santiago; Bonilla, Sylvia; Mendoza, Laura; Lago, Olga; Basiletti, Jorge; González, Joaquin; Picconi, Maria Alejandra; Arbiza, Juan

    2013-05-01

    Persistent infection with high-risk human papillomavirus (HPV) causes cervical preneoplasic lesions and invasive cervical cancer. This study evaluated the prevalence and distribution of HPV genotypes in cervical exfoliated cells from Uruguayan women. Five hundred sixty-eight cervical specimens were examined by PCR using MY09/11 primer set, and were genotyped by restriction enzyme digestion (RFLP). Some of the samples which remained undetermined were reanalyzed by PGMY PCR combined with reverse line blot hybridization. Overall, about 42% of samples were positive for HPV; 96% in high-grade squamous intraepithelial lesion, 66% in low-grade squamous intraepithelial lesion, 15% in atypical squamous cells of undetermined significance, and 19% in samples negative for intraepithelial lesion or malignancy. HPV 16 was the most commonly found genotype, followed by HPV 68 and 58. Within low risk-HPV genotypes 6, 61, and 11 were the most frequent. This is the first cross-sectional study, accounting for prevalence and genotype distribution of HPV in Uruguayan women.

  12. A Rapid Genotyping Assay for Segregating Human Olfactory Receptor Pseudogenes

    PubMed Central

    Hinkley, Craig S.; Ismaili, Lindita

    2012-01-01

    Variation in odor perception between individuals is initiated by binding of “odorant” molecules to olfactory receptors (ORs) located in the nasal cavity. To determine the mechanism for variation in odor perception, identification of specific ligands for a large number of ORs is required. However, it has been difficult to identify specific ligands, and ligands have been identified for only 2–3% of the hundreds of mammalian ORs. One way to increase the number of identified ligands is to take advantage of >60 human OR genes that are segregating as a result of a single nucleotide polymorphism, between a functional intact allele and a nonfunctional pseudogene allele. Potential ligands for these ORs can be identified by correlating odor perception of an individual with their genotype [intact/intact (I/I) vs. pseudogene/pseudogene (P/P)] for an OR gene. For this type of study, genotypes must be determined for a large number of individuals. We have developed a PCR-based assay to distinguish between the intact and pseudogene alleles of 49 segregating human OR genes and to determine an individual's genotype for these genes. To facilitate rapid determination of genotypes for a large number of individuals, the assay uses a small number of simple steps and equipment commonly found in most molecular biology and biochemistry laboratories. Although this assay was developed to distinguish between polymorphisms in OR genes, it can easily be adapted for use in distinguishing single nucleotide polymorphisms in any gene or chromosomal locus. PMID:23002384

  13. Human papillomavirus genotyping and integration in ovarian cancer Saudi patients

    PubMed Central

    2013-01-01

    Background Human papillomavirus (HPV) is associated with different malignancies but its role in the pathogenesis of ovarian cancer is controversial. This study investigated the prevalence, genotyping and physical state of HPV in ovarian cancer Saudi patients. Methods Hundred formalin fixed paraffin embedded (FFPE) ovarian carcinoma tissues and their normal adjacent tissues (NAT) were included in the study. HPV was detected by nested polymerase chain reaction (PCR) using degenerated HPVL1 consensus primer pairs MY09/MY11 and GP5+/GP6 + to amplify a broad spectrum of HPV genotypes in a single reaction. The HPV positive samples were further genotyped using DNA sequencing. The physical state of the virus was identified using Amplification of Papillomavirus Oncogene Transcripts (APOT) assay in the samples positive for HPV16 and/or HPV18. Results High percentage of HPV (42%) was observed in ovarian carcinoma compared to 8% in the NAT. The high-risk HPV types 16, 18 and 45 were highly associated with the advanced stages of tumor, while low-risk types 6 and 11 were present in NAT. In malignant tissues, HPV-16 was the most predominant genotype followed by HPV-18 and -45. The percentage of viral integration into the host genome was significantly high (61.1%) compared to 38.9% episomal in HPV positive tumors tissues. In HPV18 genotype the percentage of viral integration was 54.5% compared to 45.5% episomal. Conclusion The high risk HPV genotypes in ovarian cancer may indicate its role in ovarian carcinogenesis. The HPV vaccination is highly recommended to reduce this type of cancer. PMID:24252426

  14. Human platelet antigen genotyping of platelet donors in southern Brazil.

    PubMed

    Merzoni, J; Fagundes, I S; Lunardi, L W; Lindenau, J D-R; Gil, B C; Jobim, M; Dias, V G; Merzoni, L; Sekine, L; Onsten, T G H; Jobim, L F

    2015-10-01

    Human platelet antigens (HPA) are immunogenic structures that result from single nucleotide polymorphisms (SNPs) leading to single amino acid substitutions. This study sought to determine the allele and genotype frequencies of HPA-1, HPA-2, HPA-3, HPA-4, HPA-5 and HPA-15 in platelet donors from the state of Rio Grande do Sul (RS), Brazil, and compare their allele frequencies to those observed in other populations. HPA genotyping was performed by PCR-SSP method. The study sample comprised 201 platelet donors (167 Caucasians and 34 non-Caucasians). Allele 'a' was that most commonly found for HPA-1 to 5 in both groups. The HPA-15ab genotype predominated over homozygous genotypes of this system. Fisher's exact test revealed statistically significant differences for the HPA-5 system, with a greater prevalence of the HPA-5b allele in non-Caucasians. The neighbour-joining method and principal components analysis revealed genetic proximity between our Caucasian group and European populations. We conclude that the allele frequencies of HPA-1 to 5 and HPA-15 found in our Caucasian sample are similar to those reported for European populations. These findings corroborate the ethnic makeup of the population of RS. The higher frequency of the HPA-5b allele found in the non-Caucasian group of our sample suggests the possibility of allosensitization in patients who receive platelet transfusions from genetically incompatible donors.

  15. Resources for Popular Culture in Ancient, Medieval and Renaissance Humanities.

    ERIC Educational Resources Information Center

    Schroeder, Fred E. H.

    1996-01-01

    Notes that there are few readily accessible resources for teachers who wish to include popular culture in their ancient, medieval, or renaissance history lessons. Goes on to partially remedy this situation by providing a review of print sources of information on popular culture. Also mentions useful films and artifacts. (DSK)

  16. Genetic Diversity within Human Erythroviruses: Identification of Three Genotypes

    PubMed Central

    Servant, Annabelle; Laperche, Syria; Lallemand, Francis; Marinho, Valérie; De Saint Maur, Guillemette; Meritet, Jean François; Garbarg-Chenon, Antoine

    2002-01-01

    B19 virus is a human virus belonging to the genus Erythrovirus. The genetic diversity among B19 virus isolates has been reported to be very low, with less than 2% nucleotide divergence in the whole genome sequence. We have previously reported the isolation of a human erythrovirus isolate, termed V9, whose sequence was markedly distinct (>11% nucleotide divergence) from that of B19 virus. To date, the V9 isolate remains the unique representative of a new variant in the genus Erythrovirus, and its taxonomic position is unclear. We report here the isolation of 11 V9-related viruses. A prospective study conducted in France between 1999 and 2001 indicates that V9-related viruses actually circulate at a significant frequency (11.4%) along with B19 viruses. Analysis of the nearly full-length genome sequence of one V9-related isolate (D91.1) indicates that the D91.1 sequence clusters together with but is notably distant from the V9 sequence (5.3% divergence) and is distantly related to B19 virus sequences (13.8 to 14.2% divergence). Additional phylogenetic analysis of partial sequences from the V9-related isolates combined with erythrovirus sequences available in GenBank indicates that the erythrovirus group is more diverse than thought previously and can be divided into three well-individualized genotypes, with B19 viruses corresponding to genotype 1 and V9-related viruses being distributed into genotypes 2 and 3. PMID:12186896

  17. Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins

    PubMed Central

    Adcock, Gregory J.; Dennis, Elizabeth S.; Easteal, Simon; Huttley, Gavin A.; Jermiin, Lars S.; Peacock, W. James; Thorne, Alan

    2001-01-01

    DNA from ancient human remains provides perspectives on the origin of our species and the relationship between molecular and morphological variation. We report analysis of mtDNA from the remains of 10 ancient Australians. These include the morphologically gracile Lake Mungo 3 [≈60 thousand years (ka) before present] and three other gracile individuals from Holocene deposits at Willandra Lakes (<10 ka), all within the skeletal range of living Australians, and six Pleistocene/early Holocene individuals (15 to <8 ka) from Kow Swamp with robust morphologies outside the skeletal range of contemporary indigenous Australians. Lake Mungo 3 is the oldest (Pleistocene) “anatomically modern” human from whom DNA has been recovered. His mtDNA belonged to a lineage that only survives as a segment inserted into chromosome 11 of the nuclear genome, which is now widespread among human populations. This lineage probably diverged before the most recent common ancestor of contemporary human mitochondrial genomes. This timing of divergence implies that the deepest known mtDNA lineage from an anatomically modern human occurred in Australia; analysis restricted to living humans places the deepest branches in East Africa. The other ancient Australian individuals we examined have mtDNA sequences descended from the most recent common ancestor of living humans. Our results indicate that anatomically modern humans were present in Australia before the complete fixation of the mtDNA lineage now found in all living people. Sequences from additional ancient humans may further challenge current concepts of modern human origins. PMID:11209053

  18. Insights into Ancient Human Populations and their Environment through Stable Isotope Analysis

    NASA Astrophysics Data System (ADS)

    Macko, S. A.

    2011-12-01

    Fundamental to the understanding of human history is the ability to make interpretations based on artifacts and other remains which are used to gather information about an ancient population. Sequestered in the organic matrices of these remains can be information concerning incidence of disease, population interactions, genetic defects and diet. Stable isotopes have long been used to interpret diet and trophic interactions in modern ecosystems. We suggest that the isotope compositions of a commonly overlooked material, human hair, is an ideal tool to be used in gleaning information, especially on human diets, about ancient civilizations. Hair can be well-preserved and is amenable to routine measurements of 13C, 15N and 34S isotope analyses and distinguishing sources of nutrition. We have isotopically characterized hair from both modern and ancient individuals. There is a wide diversity in isotope values owing, at least partially, to the levels of seafood, corn-fed animals and other grains in diet. Using these isotope tracers, new information regarding historical figures (George Washington, 1799 AD) to perhaps the most ancient of mummies, the Chinchorro of Chile (more than 7000 BP) as well as the Moche of Peru (1500 BP) and the best preserved mummy, the Neolithic Ice Man of the Oetztaler Alps (5200 BP), have been deciphered. It appears that the often-overlooked hair in archaeological sites represents a significant approach for understanding ancient human communities and their environments, as well as new perspectives on our use of our own modern nutritional sources.

  19. Enterobius vermicularis: ancient DNA from North and South American human coprolites.

    PubMed

    Iñiguez, Alena M; Reinhard, Karl J; Araújo, Adauto; Ferreira, Luiz Fernando; Vicente, Ana Carolina P

    2003-01-01

    A molecular paleoparasitological diagnostic approach was developed for Enterobius vermicularis. Ancient DNA was extracted from 27 coprolites from archaeological sites in Chile and USA. Enzymatic amplification of human mtDNA sequences confirmed the human origin. We designed primers specific to the E. vermicularis 5S ribosomal RNA spacer region and they allowed reproducible polymerase chain reaction identification of ancient material. We suggested that the paleoparasitological microscopic identification could accompany molecular diagnosis, which also opens the possibility of sequence analysis to understand parasite-host evolution.

  20. Aspects of Ancient Mitochondrial DNA Analysis in Different Populations for Understanding Human Evolution

    PubMed Central

    Nesheva, DV

    2014-01-01

    The evolution of modern humans is a long and difficult process which started from their first appearance and continues to the present day. The study of the genetic origin of populations can help to determine population kinship and to better understand the gradual changes of the gene pool in space and time. Mitochondrial DNA (mtDNA) is a proper tool for the determination of the origin of populations due to its high evolutionary importance. Ancient mitochondrial DNA retrieved from museum specimens, archaeological finds and fossil remains can provide direct evidence for population origins and migration processes. Despite the problems with contaminations and authenticity of ancient mitochondrial DNA, there is a developed set of criteria and platforms for obtaining authentic ancient DNA. During the last two decades, the application of different methods and techniques for analysis of ancient mitochondrial DNA gave promising results. Still, the literature is relatively poor with information for the origin of human populations. Using comprehensive phylogeographic and population analyses we can observe the development and formation of the contemporary populations. The aim of this study was to shed light on human migratory processes and the formation of populations based on available ancient mtDNA data. PMID:25741209

  1. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.

    PubMed

    Der Sarkissian, Clio; Balanovsky, Oleg; Brandt, Guido; Khartanovich, Valery; Buzhilova, Alexandra; Koshel, Sergey; Zaporozhchenko, Valery; Gronenborn, Detlef; Moiseyev, Vyacheslav; Kolpakov, Eugen; Shumkin, Vladimir; Alt, Kurt W; Balanovska, Elena; Cooper, Alan; Haak, Wolfgang

    2013-01-01

    North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across

  2. Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe

    PubMed Central

    Der Sarkissian, Clio; Balanovsky, Oleg; Brandt, Guido; Khartanovich, Valery; Buzhilova, Alexandra; Koshel, Sergey; Zaporozhchenko, Valery; Gronenborn, Detlef; Moiseyev, Vyacheslav; Kolpakov, Eugen; Shumkin, Vladimir; Alt, Kurt W.; Balanovska, Elena; Cooper, Alan; Haak, Wolfgang

    2013-01-01

    North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across

  3. DRD4 genotype predicts longevity in mouse and human

    PubMed Central

    Grady, Deborah L.; Thanos, Panayotis K.; Corrada, Maria M.; Barnett, Jeffrey C.; Ciobanu, Valentina; Shustarovich, Diana; Napoli, Anthony; Moyzis, Alexandra G.; Grandy, David; Rubinstein, Marcelo; Wang, Gene-Jack; H.Kawas, Claudia; Chen, Chuansheng; Dong, Qi; Wang, Eric; Volkow, Nora D.; Moyzis, Robert K.

    2013-01-01

    Longevity is influenced by genetic and environmental factors. The brain's dopamine system may be particularly relevant, since it modulates traits (e.g., sensitivity to reward, incentive motivation, sustained effort) that impact behavioral responses to the environment. In particular, the dopamine D4 receptor (DRD4) has been shown to moderate the impact of environments on behavior and health. We tested the hypothesis that the DRD4 gene influences longevity and that its impact is mediated through environmental effects. Surviving participants of a 30 year-old population-based health survey (N=310, age range 90–109; the 90+ Study) were genotyped/resequenced at the DRD4 gene, and compared to a European ancestry-matched younger population (N=2902, age range 7–45). We found that the oldest-old population had a 66% increase in individuals carrying the DRD4 7R allele relative to the younger sample (p=3.5 × 10−9), and that this genotype was strongly correlated with increased levels of physical activity. Consistent with these results, DRD4 knockout mice, when compared to wild-type and heterozygous mice, displayed a 7–9.7% decrease in lifespan, reduced spontaneous locomotor activity, and no lifespan increase when reared in an enriched environment. These results support the hypothesis that DRD4 gene variants contribute to longevity in humans and in mice, and suggest that this effect is mediated by shaping behavioral responses to the environment. PMID:23283341

  4. Ancient Humans Influenced the Current Spatial Genetic Structure of Common Walnut Populations in Asia.

    PubMed

    Pollegioni, Paola; Woeste, Keith E; Chiocchini, Francesca; Del Lungo, Stefano; Olimpieri, Irene; Tortolano, Virginia; Clark, Jo; Hemery, Gabriel E; Mapelli, Sergio; Malvolti, Maria Emilia

    2015-01-01

    Common walnut (Juglans regia L) is an economically important species cultivated worldwide for its wood and nuts. It is generally accepted that J. regia survived and grew spontaneously in almost completely isolated stands in its Asian native range after the Last Glacial Maximum. Despite its natural geographic isolation, J. regia evolved over many centuries under the influence of human management and exploitation. We evaluated the hypothesis that the current distribution of natural genetic resources of common walnut in Asia is, at least in part, the product of ancient anthropogenic dispersal, human cultural interactions, and afforestation. Genetic analysis combined with ethno-linguistic and historical data indicated that ancient trade routes such as the Persian Royal Road and Silk Road enabled long-distance dispersal of J. regia from Iran and Trans-Caucasus to Central Asia, and from Western to Eastern China. Ancient commerce also disrupted the local spatial genetic structure of autochthonous walnut populations between Tashkent and Samarkand (Central-Eastern Uzbekistan), where the northern and central routes of the Northern Silk Road converged. A significant association between ancient language phyla and the genetic structure of walnut populations is reported even after adjustment for geographic distances that could have affected both walnut gene flow and human commerce over the centuries. Beyond the economic importance of common walnut, our study delineates an alternative approach for understanding how the genetic resources of long-lived perennial tree species may be affected by the interaction of geography and human history.

  5. Ancient Humans Influenced the Current Spatial Genetic Structure of Common Walnut Populations in Asia.

    PubMed

    Pollegioni, Paola; Woeste, Keith E; Chiocchini, Francesca; Del Lungo, Stefano; Olimpieri, Irene; Tortolano, Virginia; Clark, Jo; Hemery, Gabriel E; Mapelli, Sergio; Malvolti, Maria Emilia

    2015-01-01

    Common walnut (Juglans regia L) is an economically important species cultivated worldwide for its wood and nuts. It is generally accepted that J. regia survived and grew spontaneously in almost completely isolated stands in its Asian native range after the Last Glacial Maximum. Despite its natural geographic isolation, J. regia evolved over many centuries under the influence of human management and exploitation. We evaluated the hypothesis that the current distribution of natural genetic resources of common walnut in Asia is, at least in part, the product of ancient anthropogenic dispersal, human cultural interactions, and afforestation. Genetic analysis combined with ethno-linguistic and historical data indicated that ancient trade routes such as the Persian Royal Road and Silk Road enabled long-distance dispersal of J. regia from Iran and Trans-Caucasus to Central Asia, and from Western to Eastern China. Ancient commerce also disrupted the local spatial genetic structure of autochthonous walnut populations between Tashkent and Samarkand (Central-Eastern Uzbekistan), where the northern and central routes of the Northern Silk Road converged. A significant association between ancient language phyla and the genetic structure of walnut populations is reported even after adjustment for geographic distances that could have affected both walnut gene flow and human commerce over the centuries. Beyond the economic importance of common walnut, our study delineates an alternative approach for understanding how the genetic resources of long-lived perennial tree species may be affected by the interaction of geography and human history. PMID:26332919

  6. Ancient Humans Influenced the Current Spatial Genetic Structure of Common Walnut Populations in Asia

    PubMed Central

    Pollegioni, Paola; Woeste, Keith E.; Chiocchini, Francesca; Del Lungo, Stefano; Olimpieri, Irene; Tortolano, Virginia; Clark, Jo; Hemery, Gabriel E.; Mapelli, Sergio; Malvolti, Maria Emilia

    2015-01-01

    Common walnut (Juglans regia L) is an economically important species cultivated worldwide for its wood and nuts. It is generally accepted that J. regia survived and grew spontaneously in almost completely isolated stands in its Asian native range after the Last Glacial Maximum. Despite its natural geographic isolation, J. regia evolved over many centuries under the influence of human management and exploitation. We evaluated the hypothesis that the current distribution of natural genetic resources of common walnut in Asia is, at least in part, the product of ancient anthropogenic dispersal, human cultural interactions, and afforestation. Genetic analysis combined with ethno-linguistic and historical data indicated that ancient trade routes such as the Persian Royal Road and Silk Road enabled long-distance dispersal of J. regia from Iran and Trans-Caucasus to Central Asia, and from Western to Eastern China. Ancient commerce also disrupted the local spatial genetic structure of autochthonous walnut populations between Tashkent and Samarkand (Central-Eastern Uzbekistan), where the northern and central routes of the Northern Silk Road converged. A significant association between ancient language phyla and the genetic structure of walnut populations is reported even after adjustment for geographic distances that could have affected both walnut gene flow and human commerce over the centuries. Beyond the economic importance of common walnut, our study delineates an alternative approach for understanding how the genetic resources of long-lived perennial tree species may be affected by the interaction of geography and human history. PMID:26332919

  7. An ancient founder mutation in PROKR2 impairs human reproduction.

    PubMed

    Avbelj Stefanija, Magdalena; Jeanpierre, Marc; Sykiotis, Gerasimos P; Young, Jacques; Quinton, Richard; Abreu, Ana Paula; Plummer, Lacey; Au, Margaret G; Balasubramanian, Ravikumar; Dwyer, Andrew A; Florez, Jose C; Cheetham, Timothy; Pearce, Simon H; Purushothaman, Radhika; Schinzel, Albert; Pugeat, Michel; Jacobson-Dickman, Elka E; Ten, Svetlana; Latronico, Ana Claudia; Gusella, James F; Dode, Catherine; Crowley, William F; Pitteloud, Nelly

    2012-10-01

    Congenital gonadotropin-releasing hormone (GnRH) deficiency manifests as absent or incomplete sexual maturation and infertility. Although the disease exhibits marked locus and allelic heterogeneity, with the causal mutations being both rare and private, one causal mutation in the prokineticin receptor, PROKR2 L173R, appears unusually prevalent among GnRH-deficient patients of diverse geographic and ethnic origins. To track the genetic ancestry of PROKR2 L173R, haplotype mapping was performed in 22 unrelated patients with GnRH deficiency carrying L173R and their 30 first-degree relatives. The mutation's age was estimated using a haplotype-decay model. Thirteen subjects were informative and in all of them the mutation was present on the same ~123 kb haplotype whose population frequency is ≤10%. Thus, PROKR2 L173R represents a founder mutation whose age is estimated at approximately 9000 years. Inheritance of PROKR2 L173R-associated GnRH deficiency was complex with highly variable penetrance among carriers, influenced by additional mutations in the other PROKR2 allele (recessive inheritance) or another gene (digenicity). The paradoxical identification of an ancient founder mutation that impairs reproduction has intriguing implications for the inheritance mechanisms of PROKR2 L173R-associated GnRH deficiency and for the relevant processes of evolutionary selection, including potential selective advantages of mutation carriers in genes affecting reproduction.

  8. Human evolution in Siberia: from frozen bodies to ancient DNA

    PubMed Central

    2010-01-01

    Background The Yakuts contrast strikingly with other populations from Siberia due to their cattle- and horse-breeding economy as well as their Turkic language. On the basis of ethnological and linguistic criteria as well as population genetic studies, it has been assumed that they originated from South Siberian populations. However, many questions regarding the origins of this intriguing population still need to be clarified (e.g. the precise origin of paternal lineages and the admixture rate with indigenous populations). This study attempts to better understand the origins of the Yakuts by performing genetic analyses on 58 mummified frozen bodies dated from the 15th to the 19th century, excavated from Yakutia (Eastern Siberia). Results High quality data were obtained for the autosomal STRs, Y-chromosomal STRs and SNPs and mtDNA due to exceptional sample preservation. A comparison with the same markers on seven museum specimens excavated 3 to 15 years ago showed significant differences in DNA quantity and quality. Direct access to ancient genetic data from these molecular markers combined with the archaeological evidence, demographical studies and comparisons with 166 contemporary individuals from the same location as the frozen bodies helped us to clarify the microevolution of this intriguing population. Conclusion We were able to trace the origins of the male lineages to a small group of horse-riders from the Cis-Baïkal area. Furthermore, mtDNA data showed that intermarriages between the first settlers with Evenks women led to the establishment of genetic characteristics during the 15th century that are still observed today. PMID:20100333

  9. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false In vitro human immunodeficiency virus (HIV) drug... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. (a) Identification. The in vitro HIV drug resistance genotype assay is a device that consists of nucleic acid...

  10. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false In vitro human immunodeficiency virus (HIV) drug... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. (a) Identification. The in vitro HIV drug resistance genotype assay is a device that consists of nucleic acid...

  11. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false In vitro human immunodeficiency virus (HIV) drug... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. (a) Identification. The in vitro HIV drug resistance genotype assay is a device that consists of nucleic acid...

  12. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false In vitro human immunodeficiency virus (HIV) drug... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. (a) Identification. The in vitro HIV drug resistance genotype assay is a device that consists of nucleic acid...

  13. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false In vitro human immunodeficiency virus (HIV) drug... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. (a) Identification. The in vitro HIV drug resistance genotype assay is a device that consists of nucleic acid...

  14. Human papillomavirus genotypes in human immunodeficiency virus-positive patients with anal pathology in Madrid, Spain

    PubMed Central

    2013-01-01

    Background We studied anal specimens to determine the distribution of human papillomavirus (HPV) genotypes and co-infection occurrence. This information will contribute to the knowledge of HPV genotype distributions and provide an estimate of the prevalence of different oncogenic HPV genotypes found in patients in Madrid (Spain). Methods We studied a total of 82 anal biopsies from the Hospital General Universitario Gregorio Marañón of Madrid. These included 4 specimens with benign lesions, 52 specimens with low-grade anal squamous intraepithelial lesion, 24 specimens with high-grade anal squamous intraepithelial lesions and 2 specimens with invasive anal carcinoma. HPV genotyping was performed with PCR amplification and reverse dot blot hybridization. Results We detected 33 different HPV genotypes, including 16 HPVs associated with a high risk of carcinogenesis, 3 HPVs associated with a highly likely risk of carcinogenesis and 14 HPVs associated with a low-risk of carcinogenesis. In two specimens, an uncharacterized HPV genotype was detected. The most frequent HPV genotypes found were HPV-16 (10.3%; 95% CI: 6.6%-15.1%), HPV-52 (8.5%; 95% CI: 5.2%-13%) and HPV-43/44 (7.6%; 95% CI: 4.5%-11.9%). HPV-18 was only detected in 0.9% (95% CI: 0.1%-3.2%) of the total viruses detected in all lesions. HPV co-infections were found in 83.9% of all types of lesions. The majority of cases (90.2%) were concomitantly infected with the human immunodeficiency virus (HIV). Conclusion The prevalence of high-risk carcinogenic genotypes in anal pathological samples was remarkable. Therefore, further studies that include a greater number of samples, particularly invasive carcinoma cases are needed to evaluate the potential influence of these HPV genotypes in the appearance of anal carcinomas. Also, the influence of other accompanying infections should be evaluated clarify the appearance of this type of carcinoma. Virtual slides The virtual slide(s) for this article can be found here

  15. Ancient gene flow from early modern humans into Eastern Neanderthals

    PubMed Central

    Kuhlwilm, Martin; Gronau, Ilan; Hubisz, Melissa J.; de Filippo, Cesare; Prado-Martinez, Javier; Kircher, Martin; Fu, Qiaomei; Burbano, Hernán A.; Lalueza-Fox, Carles; de la Rasilla, Marco; Rosas, Antonio; Rudan, Pavao; Brajkovic, Dejana; Kucan, Željko; Gušic, Ivan; Marques-Bonet, Tomas; Andrés, Aida M.; Viola, Bence; Pääbo, Svante; Meyer, Matthias; Siepel, Adam; Castellano, Sergi

    2016-01-01

    It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here, we analyze the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and of modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously reported. PMID:26886800

  16. Ancient gene flow from early modern humans into Eastern Neanderthals.

    PubMed

    Kuhlwilm, Martin; Gronau, Ilan; Hubisz, Melissa J; de Filippo, Cesare; Prado-Martinez, Javier; Kircher, Martin; Fu, Qiaomei; Burbano, Hernán A; Lalueza-Fox, Carles; de la Rasilla, Marco; Rosas, Antonio; Rudan, Pavao; Brajkovic, Dejana; Kucan, Željko; Gušic, Ivan; Marques-Bonet, Tomas; Andrés, Aida M; Viola, Bence; Pääbo, Svante; Meyer, Matthias; Siepel, Adam; Castellano, Sergi

    2016-02-25

    It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000-65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.

  17. Ancient gene flow from early modern humans into Eastern Neanderthals.

    PubMed

    Kuhlwilm, Martin; Gronau, Ilan; Hubisz, Melissa J; de Filippo, Cesare; Prado-Martinez, Javier; Kircher, Martin; Fu, Qiaomei; Burbano, Hernán A; Lalueza-Fox, Carles; de la Rasilla, Marco; Rosas, Antonio; Rudan, Pavao; Brajkovic, Dejana; Kucan, Željko; Gušic, Ivan; Marques-Bonet, Tomas; Andrés, Aida M; Viola, Bence; Pääbo, Svante; Meyer, Matthias; Siepel, Adam; Castellano, Sergi

    2016-02-25

    It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000-65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought. PMID:26886800

  18. Prior infection of pigs with a genotype 3 swine hepatitis E virus (HEV) protects against subsequent challenges with homologous and heterologous genotypes 3 and 4 human HEV.

    PubMed

    Sanford, Brenton J; Dryman, Barbara A; Huang, Yao-Wei; Feagins, Alicia R; Leroith, Tanya; Meng, Xiang-Jin

    2011-07-01

    Hepatitis E virus (HEV) is an important human pathogen. At least four recognized and two putative genotypes of mammalian HEV have been reported: genotypes 1 and 2 are restricted to humans whereas genotypes 3 and 4 are zoonotic. The current experimental vaccines are all based on a single strain of HEV, even though multiple genotypes of HEV are co-circulating in some countries and thus an individual may be exposed to more than one genotype. Genotypes 3 and 4 swine HEV is widespread in pigs and known to infect humans. Therefore, it is important to know if prior infection with a genotype 3 swine HEV will confer protective immunity against subsequent exposure to genotypes 3 and 4 human and swine HEV. In this study, specific-pathogen-free pigs were divided into 4 groups of 6 each. Pigs in the three treatment groups were each inoculated with a genotype 3 swine HEV, and 12 weeks later, challenged with the same genotype 3 swine HEV, a genotype 3 human HEV, and a genotype 4 human HEV, respectively. The control group was inoculated and challenged with PBS buffer. Weekly sera from all pigs were tested for HEV RNA and IgG anti-HEV, and weekly fecal samples were also tested for HEV RNA. The pigs inoculated with swine HEV became infected as evidenced by fecal virus shedding and viremia, and the majority of pigs also developed IgG anti-HEV prior to challenge at 12 weeks post-inoculation. After challenge, viremia was not detected and only two pigs challenged with swine HEV had 1-week fecal virus shedding, suggesting that prior infection with a genotype 3 swine HEV prevented pigs from developing viremia and fecal virus shedding after challenges with homologous and heterologous genotypes 3 and 4 HEV. The results from this study have important implications for future development of an effective HEV vaccine.

  19. Direct evidence of milk consumption from ancient human dental calculus

    PubMed Central

    Warinner, C.; Hendy, J.; Speller, C.; Cappellini, E.; Fischer, R.; Trachsel, C.; Arneborg, J.; Lynnerup, N.; Craig, O. E.; Swallow, D. M.; Fotakis, A.; Christensen, R. J.; Olsen, J. V.; Liebert, A.; Montalva, N.; Fiddyment, S.; Charlton, S.; Mackie, M.; Canci, A.; Bouwman, A.; Rühli, F.; Gilbert, M. T. P.; Collins, M. J.

    2014-01-01

    Milk is a major food of global economic importance, and its consumption is regarded as a classic example of gene-culture evolution. Humans have exploited animal milk as a food resource for at least 8500 years, but the origins, spread, and scale of dairying remain poorly understood. Indirect lines of evidence, such as lipid isotopic ratios of pottery residues, faunal mortality profiles, and lactase persistence allele frequencies, provide a partial picture of this process; however, in order to understand how, where, and when humans consumed milk products, it is necessary to link evidence of consumption directly to individuals and their dairy livestock. Here we report the first direct evidence of milk consumption, the whey protein β-lactoglobulin (BLG), preserved in human dental calculus from the Bronze Age (ca. 3000 BCE) to the present day. Using protein tandem mass spectrometry, we demonstrate that BLG is a species-specific biomarker of dairy consumption, and we identify individuals consuming cattle, sheep, and goat milk products in the archaeological record. We then apply this method to human dental calculus from Greenland's medieval Norse colonies, and report a decline of this biomarker leading up to the abandonment of the Norse Greenland colonies in the 15th century CE. PMID:25429530

  20. Direct evidence of milk consumption from ancient human dental calculus.

    PubMed

    Warinner, C; Hendy, J; Speller, C; Cappellini, E; Fischer, R; Trachsel, C; Arneborg, J; Lynnerup, N; Craig, O E; Swallow, D M; Fotakis, A; Christensen, R J; Olsen, J V; Liebert, A; Montalva, N; Fiddyment, S; Charlton, S; Mackie, M; Canci, A; Bouwman, A; Rühli, F; Gilbert, M T P; Collins, M J

    2014-01-01

    Milk is a major food of global economic importance, and its consumption is regarded as a classic example of gene-culture evolution. Humans have exploited animal milk as a food resource for at least 8500 years, but the origins, spread, and scale of dairying remain poorly understood. Indirect lines of evidence, such as lipid isotopic ratios of pottery residues, faunal mortality profiles, and lactase persistence allele frequencies, provide a partial picture of this process; however, in order to understand how, where, and when humans consumed milk products, it is necessary to link evidence of consumption directly to individuals and their dairy livestock. Here we report the first direct evidence of milk consumption, the whey protein β-lactoglobulin (BLG), preserved in human dental calculus from the Bronze Age (ca. 3000 BCE) to the present day. Using protein tandem mass spectrometry, we demonstrate that BLG is a species-specific biomarker of dairy consumption, and we identify individuals consuming cattle, sheep, and goat milk products in the archaeological record. We then apply this method to human dental calculus from Greenland's medieval Norse colonies, and report a decline of this biomarker leading up to the abandonment of the Norse Greenland colonies in the 15(th) century CE.

  1. Direct evidence of milk consumption from ancient human dental calculus.

    PubMed

    Warinner, C; Hendy, J; Speller, C; Cappellini, E; Fischer, R; Trachsel, C; Arneborg, J; Lynnerup, N; Craig, O E; Swallow, D M; Fotakis, A; Christensen, R J; Olsen, J V; Liebert, A; Montalva, N; Fiddyment, S; Charlton, S; Mackie, M; Canci, A; Bouwman, A; Rühli, F; Gilbert, M T P; Collins, M J

    2014-01-01

    Milk is a major food of global economic importance, and its consumption is regarded as a classic example of gene-culture evolution. Humans have exploited animal milk as a food resource for at least 8500 years, but the origins, spread, and scale of dairying remain poorly understood. Indirect lines of evidence, such as lipid isotopic ratios of pottery residues, faunal mortality profiles, and lactase persistence allele frequencies, provide a partial picture of this process; however, in order to understand how, where, and when humans consumed milk products, it is necessary to link evidence of consumption directly to individuals and their dairy livestock. Here we report the first direct evidence of milk consumption, the whey protein β-lactoglobulin (BLG), preserved in human dental calculus from the Bronze Age (ca. 3000 BCE) to the present day. Using protein tandem mass spectrometry, we demonstrate that BLG is a species-specific biomarker of dairy consumption, and we identify individuals consuming cattle, sheep, and goat milk products in the archaeological record. We then apply this method to human dental calculus from Greenland's medieval Norse colonies, and report a decline of this biomarker leading up to the abandonment of the Norse Greenland colonies in the 15(th) century CE. PMID:25429530

  2. How microbial ancient DNA, found in association with human remains, can be interpreted.

    PubMed Central

    Rollo, F; Marota, I

    1999-01-01

    The analysis of the DNA of ancient micro-organisms in archaeological and palaeontological human remains can contribute to the understanding of issues as different as the spreading of a new disease, a mummification process or the effect of diets on historical human populations. The quest for this type of DNA, however, can represent a particularly demanding task. This is mainly due to the abundance and diffusion of bacteria, fungi, yeasts, algae and protozoans in the most diverse environments of the present-day biosphere and the resulting difficulty in distinguishing between ancient and modern DNA. Nevertheless, at least under some special circumstances, by using rigorous protocols, which include an archaeometric survey of the specimens and evaluation of the palaeoecological consistency of the results of DNA sequence analysis, glimpses of the composition of the original microbial flora (e.g. colonic flora) can be caught in ancient human remains. Potentials and pitfalls of this research field are illustrated by the results of research works performed on prehistoric, pre-Columbian and Renaissance human mummies. PMID:10091251

  3. Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans

    PubMed Central

    Slatkin, Montgomery

    2016-01-01

    When sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters—including drift times and admixture rates—for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called ‘Demographic Inference with Contamination and Error’ (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (>3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%. PMID:27049965

  4. Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans.

    PubMed

    Racimo, Fernando; Renaud, Gabriel; Slatkin, Montgomery

    2016-04-01

    When sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters-including drift times and admixture rates-for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called 'Demographic Inference with Contamination and Error' (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (>3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%.

  5. Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans.

    PubMed

    Racimo, Fernando; Renaud, Gabriel; Slatkin, Montgomery

    2016-04-01

    When sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters-including drift times and admixture rates-for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called 'Demographic Inference with Contamination and Error' (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (>3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%. PMID:27049965

  6. Echinococcus granulosus sensu lato genotypes infecting humans--review of current knowledge.

    PubMed

    Alvarez Rojas, Cristian A; Romig, Thomas; Lightowlers, Marshall W

    2014-01-01

    Genetic variability in the species group Echinococcus granulosus sensu lato is well recognised as affecting intermediate host susceptibility and other biological features of the parasites. Molecular methods have allowed discrimination of different genotypes (G1-10 and the 'lion strain'), some of which are now considered separate species. An accumulation of genotypic analyses undertaken on parasite isolates from human cases of cystic echinococcosis provides the basis upon which an assessment is made here of the relative contribution of the different genotypes to human disease. The allocation of samples to G-numbers becomes increasingly difficult, because much more variability than previously recognised exists in the genotypic clusters G1-3 (=E. granulosus sensu stricto) and G6-10 (Echinococcus canadensis). To accommodate the heterogeneous criteria used for genotyping in the literature, we restrict ourselves to differentiate between E. granulosus sensu stricto (G1-3), Echinococcus equinus (G4), Echinococcus ortleppi (G5) and E. canadensis (G6-7, G8, G10). The genotype G1 is responsible for the great majority of human cystic echinococcosis worldwide (88.44%), has the most cosmopolitan distribution and is often associated with transmission via sheep as intermediate hosts. The closely related genotypes G6 and G7 cause a significant number of human infections (11.07%). The genotype G6 was found to be responsible for 7.34% of infections worldwide. This strain is known from Africa and Asia, where it is transmitted mainly by camels (and goats), and South America, where it appears to be mainly transmitted by goats. The G7 genotype has been responsible for 3.73% of human cases of cystic echinococcosis in eastern European countries, where the parasite is transmitted by pigs. Some of the samples (11) could not be identified with a single specific genotype belonging to E. canadensis (G6/10). Rare cases of human cystic echinococcosis have been identified as having been caused by

  7. Neonate human remains: a window of opportunity to the molecular study of ancient syphilis.

    PubMed

    Montiel, Rafael; Solórzano, Eduvigis; Díaz, Nancy; Álvarez-Sandoval, Brenda A; González-Ruiz, Mercedes; Cañadas, Mari Pau; Simões, Nelson; Isidro, Albert; Malgosa, Assumpció

    2012-01-01

    Ancient DNA (aDNA) analysis can be a useful tool in bacterial disease diagnosis in human remains. However, while the recovery of Mycobacterium spp. has been widely successful, several authors report unsuccessful results regarding ancient treponemal DNA, casting doubts on the usefulness of this technique for the diagnosis of ancient syphilis. Here, we present results from an analysis of four newborn specimens recovered from the crypt of "La Ermita de la Soledad" (XVI-XVII centuries), located in the province of Huelva in the southwest of Spain. We extracted and analyzed aDNA in three independent laboratories, following specific procedures generally practiced in the aDNA field, including cloning of the amplified DNA fragments and sequencing of several clones. This is the most ancient case, reported to date, from which detection of DNA from T. pallidum subspecies pallidum has been successful in more than one individual, and we put forward a hypothesis to explain this result, taking into account the course of the disease in neonate individuals. PMID:22567153

  8. Neonate Human Remains: A Window of Opportunity to the Molecular Study of Ancient Syphilis

    PubMed Central

    Montiel, Rafael; Solórzano, Eduvigis; Díaz, Nancy; Álvarez-Sandoval, Brenda A.; González-Ruiz, Mercedes; Cañadas, Mari Pau; Simões, Nelson; Isidro, Albert; Malgosa, Assumpció

    2012-01-01

    Ancient DNA (aDNA) analysis can be a useful tool in bacterial disease diagnosis in human remains. However, while the recovery of Mycobacterium spp. has been widely successful, several authors report unsuccessful results regarding ancient treponemal DNA, casting doubts on the usefulness of this technique for the diagnosis of ancient syphilis. Here, we present results from an analysis of four newborn specimens recovered from the crypt of “La Ermita de la Soledad” (XVI–XVII centuries), located in the province of Huelva in the southwest of Spain. We extracted and analyzed aDNA in three independent laboratories, following specific procedures generally practiced in the aDNA field, including cloning of the amplified DNA fragments and sequencing of several clones. This is the most ancient case, reported to date, from which detection of DNA from T. pallidum subspecies pallidum has been successful in more than one individual, and we put forward a hypothesis to explain this result, taking into account the course of the disease in neonate individuals. PMID:22567153

  9. Human adaptation and population differentiation in the light of ancient genomes

    PubMed Central

    Key, Felix M.; Fu, Qiaomei; Romagné, Frédéric; Lachmann, Michael; Andrés, Aida M.

    2016-01-01

    The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation. PMID:26988143

  10. Human adaptation and population differentiation in the light of ancient genomes.

    PubMed

    Key, Felix M; Fu, Qiaomei; Romagné, Frédéric; Lachmann, Michael; Andrés, Aida M

    2016-01-01

    The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles--especially those associated with pigmentation--are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation. PMID:26988143

  11. Human adaptation and population differentiation in the light of ancient genomes.

    PubMed

    Key, Felix M; Fu, Qiaomei; Romagné, Frédéric; Lachmann, Michael; Andrés, Aida M

    2016-03-18

    The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles--especially those associated with pigmentation--are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation.

  12. Comparison of genetic distance measures using human SNP genotype data.

    PubMed

    Libiger, Ondrej; Nievergelt, Caroline M; Schork, Nicholas J

    2009-08-01

    Quantification of the genetic distance between populations is instrumental in many genetic research initiatives, and a large number of formulas for this purpose have been proposed. However, selection of an appropriate measure for assessing genetic distance between real-world human populations that diverged as a result of mechanisms that are not fully known can be a challenging task. We compared results from nine widely used genetic distance measures to high-density whole-genome SNP genotype data obtained on individuals from 51 world populations. Using population trees and generalized analysis of molecular variance, we found that contradictory inferences could be drawn from analyses that used different distance measures. We determined the grouping of the distance measures in terms of similarity and consistency of their values using concordance, consistency, and Procrustes analyses. Overall, the Cavalli-Sforza and Edwards distance measure differed the most from the other measures. Wright's F(ST) for diploid data, the Latter and Reynolds distances, and Nei's minimum distance measures each yielded values that were most consistent with the other eight distance measures in terms of ordering populations based on genetic distance. The Cavalli-Sforza and Edwards distance and Nei's geometric distance were least consistent. Simulation studies showed that the Cavalli-Sforza and Edwards distance is relatively more sensitive in distinguishing genetically similar populations and that the Reynolds genetic distance provides the highest sensitivity for highly divergent populations. Finally, our study suggests that using the Cavalli-Sforza and Edwards distance may provide less power for studies concerning human migration history.

  13. Phylogenetic analysis of human parvovirus B19, indicating two subgroups of genotype 1 in Vietnamese patients.

    PubMed

    Toan, Nguyen L; Duechting, Anja; Kremsner, Peter G; Song, Le H; Ebinger, Martin; Aberle, Susanne; Binh, Vu Q; Duy, Dinh Ng; Torresi, Joseph; Kandolf, Reinhard; Bock, C-Thomas

    2006-10-01

    Recently, three distinct genotypes (1, 2 and 3) of human parvovirus B19 (B19) have been identified. However, the characteristics and distribution of B19 genotypes in Vietnam have not been investigated. Phylogenetic analysis using 49 subgenomic NS1/VP1u regions and two coding NS1-VP1/VP2 regions has been applied to investigate the prevalence of B19 genotypes in Vietnamese patients co-infected with Hepatitis B virus. Genetic analysis of the subgenomic NS1/VP1u region of B19 revealed that two genotypes of B19 were identified in these populations, with predominance of genotype 1 (47/49, 96 %) followed by genotype 2 (2/49, 4 %), but not genotype 3. Further, phylogenetic analysis of subgenomic B19 genomes revealed two major subgroups within genotype 1 (B19-1A and B19-1B) with an estimated nucleotide difference of >5 % between each subgroup, forming different branches. The mean percentage of amino acid variation between subgroup B19-1A and B19-1B was >2 % of the NS1, VP1 and VP2 proteins. Our results indicated that two of the three known genotypes of B19 were present in Vietnamese patients, with genotype 1 predominating, and that this genotype can be classified into at least two subgroups, B19-1A and B19-1B.

  14. Illumina human exome genotyping array clustering and quality control

    PubMed Central

    Guo, Yan; He, Jing; Zhao, Shilin; Wu, Hui; Zhong, Xue; Sheng, Quanhu; Samuels, David C; Shyr, Yu; Long, Jirong

    2015-01-01

    With the rise of high-throughput sequencing technology, traditional genotyping arrays are gradually being replaced by sequencing technology. Against this trend, Illumina has introduced an exome genotyping array that provides an alternative approach to sequencing, especially suited to large-scale genome-wide association studies (GWASs). the exome genotyping array targets the exome plus rare single-nucleotide polymorphisms (SNPs), a feature that makes it substantially more challenging to process than previous genotyping arrays that targeted common SNPs. Researchers have struggled to generate a reliable protocol for processing exome genotyping array data. The Vanderbilt epidemiology center, in cooperation with Vanderbilt Technologies for Advanced Genomics Analysis and Research Design (VANGARD), has developed a thorough exome chip–processing protocol. The protocol was developed during the processing of several large exome genotyping array-based studies, which included over 60,000 participants combined. The protocol described herein contains detailed clustering techniques and robust quality control procedures, and it can benefit future exome genotyping array–based GWASs. PMID:25321409

  15. A code of ethics for evidence-based research with ancient human remains.

    PubMed

    Kreissl Lonfat, Bettina M; Kaufmann, Ina Maria; Rühli, Frank

    2015-06-01

    As clinical research constantly advances and the concept of evolution becomes a strong and influential part of basic medical research, the absence of a discourse that deals with the use of ancient human remains in evidence-based research is becoming unbearable. While topics such as exhibition and excavation of human remains are established ethical fields of discourse, when faced with instrumentalization of ancient human remains for research (i.e., ancient DNA extractions for disease marker analyses) the answers from traditional ethics or even more practical fields of bio-ethics or more specific biomedical ethics are rare to non-existent. The Centre for Evolutionary Medicine at the University of Zurich solved their needs for discursive action through the writing of a self-given code of ethics which was written in dialogue with the researchers at the Institute and was published online in Sept. 2011: http://evolutionäremedizin.ch/coe/. The philosophico-ethical basis for this a code of conduct and ethics and the methods are published in this article.

  16. Human stewardship or ruining cultural landscapes of the ancient Tula wells, southern Ethiopia.

    PubMed

    Tiki, Waktole; Oba, Gufu; Tvedt, Terje

    2011-01-01

    This article uses the concepts of "human stewardship" and "ruined landscape" as a theoretical framework for analysing the community's perception of landscape change in the ancient tula well system of Borana in southern Ethiopia. The ancient tula well system, the main permanent water source, has been in operation for more than five centuries and it closely links human activity and the environment. The welfare of the tula well system and the performance of the Borana pastoral system are directly related. Borana management of the tula wells uses concepts such as laaf aadaa seeraa and laaf bade to differentiate between ‘land managed by customary laws’ (hereafter human stewardship) and ‘lost’ or ‘ruined’ land (laaf bade). The cultural landscapes of the ancient wells have undergone changes from ecosystems featuring ‘human stewardship’ (before the 1960s), that is, laaf aadaa seeraa to ‘ruined landscapes’ (after the 1960s), that is, laaf bade. Our interest is in understanding how the Borana perceive the impact of land use changes from these two conceptual perspectives. In group discussions, key informant interviews and household surveys across five of the nine well clusters, we found that the society described the changed tula cultural landscape in terms of drivers of well dynamics (i.e. use and disuse), break up of land use zonations, patterns of human settlement (traditional versus peri-urban), expansion of crop cultivation, and changes in environmental quality. Using the two concepts, we analysed linkages between changing patterns of land use that transformed the system from laaf aadaa seeraa, which ensured human stewardship, to laaf bade, which resulted in ruined landscapes. From these we analysed environmental narratives that showed how the society differentiated the past human stewardship that ensured sustainable landscape management from the present ruining of tula well cultural landscapes. PMID:21560273

  17. Human stewardship or ruining cultural landscapes of the ancient Tula wells, southern Ethiopia.

    PubMed

    Tiki, Waktole; Oba, Gufu; Tvedt, Terje

    2011-01-01

    This article uses the concepts of "human stewardship" and "ruined landscape" as a theoretical framework for analysing the community's perception of landscape change in the ancient tula well system of Borana in southern Ethiopia. The ancient tula well system, the main permanent water source, has been in operation for more than five centuries and it closely links human activity and the environment. The welfare of the tula well system and the performance of the Borana pastoral system are directly related. Borana management of the tula wells uses concepts such as laaf aadaa seeraa and laaf bade to differentiate between ‘land managed by customary laws’ (hereafter human stewardship) and ‘lost’ or ‘ruined’ land (laaf bade). The cultural landscapes of the ancient wells have undergone changes from ecosystems featuring ‘human stewardship’ (before the 1960s), that is, laaf aadaa seeraa to ‘ruined landscapes’ (after the 1960s), that is, laaf bade. Our interest is in understanding how the Borana perceive the impact of land use changes from these two conceptual perspectives. In group discussions, key informant interviews and household surveys across five of the nine well clusters, we found that the society described the changed tula cultural landscape in terms of drivers of well dynamics (i.e. use and disuse), break up of land use zonations, patterns of human settlement (traditional versus peri-urban), expansion of crop cultivation, and changes in environmental quality. Using the two concepts, we analysed linkages between changing patterns of land use that transformed the system from laaf aadaa seeraa, which ensured human stewardship, to laaf bade, which resulted in ruined landscapes. From these we analysed environmental narratives that showed how the society differentiated the past human stewardship that ensured sustainable landscape management from the present ruining of tula well cultural landscapes.

  18. Human Herpesvirus 8 Genotype E in Patients with Kaposi Sarcoma, Peru

    PubMed Central

    Cassar, Olivier; Blondot, Marie-Lise; Mohanna, Salim; Jouvion, Gregory; Bravo, Francisco; Maco, Vicente; Duprez, Renan; Huerre, Michel; Gotuzzo, Eduardo

    2010-01-01

    To determine human herpesvirus 8 (HHV-8) K1 genotypes in patients with Kaposi sarcoma (KS) from Peru, we characterized HHV-8 in 25 KS biopsy samples. Our findings of 8 A, 1 B, 14 C, and 2 E subtypes showed high HHV-8 diversity in these patients and association between E genotype and KS development. PMID:20735933

  19. Human Papillomavirus Genotype Distribution in Invasive Cervical Cancer in Pakistan

    PubMed Central

    Loya, Asif; Serrano, Beatriz; Rasheed, Farah; Tous, Sara; Hassan, Mariam; Clavero, Omar; Raza, Muhammad; De Sanjosé, Silvia; Bosch, F. Xavier; Alemany, Laia

    2016-01-01

    Few studies have assessed the burden of human papillomavirus (HPV) infection in Pakistan. We aim to provide specific information on HPV-type distribution in invasive cervical cancer (ICC) in the country. A total of 280 formalin-fixed paraffin-embedded tissue blocks were consecutively selected from Shaukat Khanum Memorial Cancer Hospital and Research Centre (Lahore, Pakistan). HPV-DNA was detected by SPF10 broad-spectrum PCR followed by DNA enzyme immunoassay and genotyping by LiPA25. HPV-DNA prevalence was 87.5% (95%CI: 83.0–91.1), with 96.1% of cases histologically classified as squamous cell carcinoma. Most of the HPV-DNA positive cases presented single infections (95.9%). HPV16 was the most common type followed by HPV18 and 45. Among HPV-DNA positive, a significantly higher contribution of HPV16/18 was detected in Pakistan (78.4%; 72.7–83.3), compared to Asia (71.6%; 69.9–73.4) and worldwide (70.8%; 69.9–71.8) and a lower contribution of HPVs31/33/45/52/58 (11.1%; 7.9–15.7 vs. 19.8%; 18.3–21.3 and 18.5%; 17.7–19.3). HPV18 or HPV45 positive ICC cases were significantly younger than cases infected by HPV16 (mean age: 43.3, 44.4, 50.5 years, respectively). A routine cervical cancer screening and HPV vaccination program does not yet exist in Pakistan; however, the country could benefit from national integrated efforts for cervical cancer prevention and control. Calculated estimations based on our results show that current HPV vaccine could potentially prevent new ICC cases. PMID:27483322

  20. Ancient human genomes suggest three ancestral populations for present-day Europeans

    PubMed Central

    Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa; Renaud, Gabriel; Mallick, Swapan; Kirsanow, Karola; Sudmant, Peter H.; Schraiber, Joshua G.; Castellano, Sergi; Lipson, Mark; Berger, Bonnie; Economou, Christos; Bollongino, Ruth; Fu, Qiaomei; Bos, Kirsten I.; Nordenfelt, Susanne; Li, Heng; de Filippo, Cesare; Prüfer, Kay; Sawyer, Susanna; Posth, Cosimo; Haak, Wolfgang; Hallgren, Fredrik; Fornander, Elin; Rohland, Nadin; Delsate, Dominique; Francken, Michael; Guinet, Jean-Michel; Wahl, Joachim; Ayodo, George; Babiker, Hamza A.; Bailliet, Graciela; Balanovska, Elena; Balanovsky, Oleg; Barrantes, Ramiro; Bedoya, Gabriel; Ben-Ami, Haim; Bene, Judit; Berrada, Fouad; Bravi, Claudio M.; Brisighelli, Francesca; Busby, George B. J.; Cali, Francesco; Churnosov, Mikhail; Cole, David E. C.; Corach, Daniel; Damba, Larissa; van Driem, George; Dryomov, Stanislav; Dugoujon, Jean-Michel; Fedorova, Sardana A.; Romero, Irene Gallego; Gubina, Marina; Hammer, Michael; Henn, Brenna M.; Hervig, Tor; Hodoglugil, Ugur; Jha, Aashish R.; Karachanak-Yankova, Sena; Khusainova, Rita; Khusnutdinova, Elza; Kittles, Rick; Kivisild, Toomas; Klitz, William; Kučinskas, Vaidutis; Kushniarevich, Alena; Laredj, Leila; Litvinov, Sergey; Loukidis, Theologos; Mahley, Robert W.; Melegh, Béla; Metspalu, Ene; Molina, Julio; Mountain, Joanna; Näkkäläjärvi, Klemetti; Nesheva, Desislava; Nyambo, Thomas; Osipova, Ludmila; Parik, Jüri; Platonov, Fedor; Posukh, Olga; Romano, Valentino; Rothhammer, Francisco; Rudan, Igor; Ruizbakiev, Ruslan; Sahakyan, Hovhannes; Sajantila, Antti; Salas, Antonio; Starikovskaya, Elena B.; Tarekegn, Ayele; Toncheva, Draga; Turdikulova, Shahlo; Uktveryte, Ingrida; Utevska, Olga; Vasquez, René; Villena, Mercedes; Voevoda, Mikhail; Winkler, Cheryl; Yepiskoposyan, Levon; Zalloua, Pierre; Zemunik, Tatijana; Cooper, Alan; Capelli, Cristian; Thomas, Mark G.; Ruiz-Linares, Andres; Tishkoff, Sarah A.; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Comas, David; Sukernik, Rem; Metspalu, Mait; Meyer, Matthias; Eichler, Evan E.; Burger, Joachim; Slatkin, Montgomery; Pääbo, Svante; Kelso, Janet; Reich, David; Krause, Johannes

    2014-01-01

    We sequenced the genomes of a ~7,000 year old farmer from Germany and eight ~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other ancient genomes1–4 with 2,345 contemporary humans to show that most present Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations’ deep relationships and show that EEF had ~44% ancestry from a “Basal Eurasian” population that split prior to the diversification of other non-African lineages. PMID:25230663

  1. Ancient human genomes suggest three ancestral populations for present-day Europeans.

    PubMed

    Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa; Renaud, Gabriel; Mallick, Swapan; Kirsanow, Karola; Sudmant, Peter H; Schraiber, Joshua G; Castellano, Sergi; Lipson, Mark; Berger, Bonnie; Economou, Christos; Bollongino, Ruth; Fu, Qiaomei; Bos, Kirsten I; Nordenfelt, Susanne; Li, Heng; de Filippo, Cesare; Prüfer, Kay; Sawyer, Susanna; Posth, Cosimo; Haak, Wolfgang; Hallgren, Fredrik; Fornander, Elin; Rohland, Nadin; Delsate, Dominique; Francken, Michael; Guinet, Jean-Michel; Wahl, Joachim; Ayodo, George; Babiker, Hamza A; Bailliet, Graciela; Balanovska, Elena; Balanovsky, Oleg; Barrantes, Ramiro; Bedoya, Gabriel; Ben-Ami, Haim; Bene, Judit; Berrada, Fouad; Bravi, Claudio M; Brisighelli, Francesca; Busby, George B J; Cali, Francesco; Churnosov, Mikhail; Cole, David E C; Corach, Daniel; Damba, Larissa; van Driem, George; Dryomov, Stanislav; Dugoujon, Jean-Michel; Fedorova, Sardana A; Gallego Romero, Irene; Gubina, Marina; Hammer, Michael; Henn, Brenna M; Hervig, Tor; Hodoglugil, Ugur; Jha, Aashish R; Karachanak-Yankova, Sena; Khusainova, Rita; Khusnutdinova, Elza; Kittles, Rick; Kivisild, Toomas; Klitz, William; Kučinskas, Vaidutis; Kushniarevich, Alena; Laredj, Leila; Litvinov, Sergey; Loukidis, Theologos; Mahley, Robert W; Melegh, Béla; Metspalu, Ene; Molina, Julio; Mountain, Joanna; Näkkäläjärvi, Klemetti; Nesheva, Desislava; Nyambo, Thomas; Osipova, Ludmila; Parik, Jüri; Platonov, Fedor; Posukh, Olga; Romano, Valentino; Rothhammer, Francisco; Rudan, Igor; Ruizbakiev, Ruslan; Sahakyan, Hovhannes; Sajantila, Antti; Salas, Antonio; Starikovskaya, Elena B; Tarekegn, Ayele; Toncheva, Draga; Turdikulova, Shahlo; Uktveryte, Ingrida; Utevska, Olga; Vasquez, René; Villena, Mercedes; Voevoda, Mikhail; Winkler, Cheryl A; Yepiskoposyan, Levon; Zalloua, Pierre; Zemunik, Tatijana; Cooper, Alan; Capelli, Cristian; Thomas, Mark G; Ruiz-Linares, Andres; Tishkoff, Sarah A; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Comas, David; Sukernik, Rem; Metspalu, Mait; Meyer, Matthias; Eichler, Evan E; Burger, Joachim; Slatkin, Montgomery; Pääbo, Svante; Kelso, Janet; Reich, David; Krause, Johannes

    2014-09-18

    We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.

  2. Ancient human genomes suggest three ancestral populations for present-day Europeans.

    PubMed

    Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa; Renaud, Gabriel; Mallick, Swapan; Kirsanow, Karola; Sudmant, Peter H; Schraiber, Joshua G; Castellano, Sergi; Lipson, Mark; Berger, Bonnie; Economou, Christos; Bollongino, Ruth; Fu, Qiaomei; Bos, Kirsten I; Nordenfelt, Susanne; Li, Heng; de Filippo, Cesare; Prüfer, Kay; Sawyer, Susanna; Posth, Cosimo; Haak, Wolfgang; Hallgren, Fredrik; Fornander, Elin; Rohland, Nadin; Delsate, Dominique; Francken, Michael; Guinet, Jean-Michel; Wahl, Joachim; Ayodo, George; Babiker, Hamza A; Bailliet, Graciela; Balanovska, Elena; Balanovsky, Oleg; Barrantes, Ramiro; Bedoya, Gabriel; Ben-Ami, Haim; Bene, Judit; Berrada, Fouad; Bravi, Claudio M; Brisighelli, Francesca; Busby, George B J; Cali, Francesco; Churnosov, Mikhail; Cole, David E C; Corach, Daniel; Damba, Larissa; van Driem, George; Dryomov, Stanislav; Dugoujon, Jean-Michel; Fedorova, Sardana A; Gallego Romero, Irene; Gubina, Marina; Hammer, Michael; Henn, Brenna M; Hervig, Tor; Hodoglugil, Ugur; Jha, Aashish R; Karachanak-Yankova, Sena; Khusainova, Rita; Khusnutdinova, Elza; Kittles, Rick; Kivisild, Toomas; Klitz, William; Kučinskas, Vaidutis; Kushniarevich, Alena; Laredj, Leila; Litvinov, Sergey; Loukidis, Theologos; Mahley, Robert W; Melegh, Béla; Metspalu, Ene; Molina, Julio; Mountain, Joanna; Näkkäläjärvi, Klemetti; Nesheva, Desislava; Nyambo, Thomas; Osipova, Ludmila; Parik, Jüri; Platonov, Fedor; Posukh, Olga; Romano, Valentino; Rothhammer, Francisco; Rudan, Igor; Ruizbakiev, Ruslan; Sahakyan, Hovhannes; Sajantila, Antti; Salas, Antonio; Starikovskaya, Elena B; Tarekegn, Ayele; Toncheva, Draga; Turdikulova, Shahlo; Uktveryte, Ingrida; Utevska, Olga; Vasquez, René; Villena, Mercedes; Voevoda, Mikhail; Winkler, Cheryl A; Yepiskoposyan, Levon; Zalloua, Pierre; Zemunik, Tatijana; Cooper, Alan; Capelli, Cristian; Thomas, Mark G; Ruiz-Linares, Andres; Tishkoff, Sarah A; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Comas, David; Sukernik, Rem; Metspalu, Mait; Meyer, Matthias; Eichler, Evan E; Burger, Joachim; Slatkin, Montgomery; Pääbo, Svante; Kelso, Janet; Reich, David; Krause, Johannes

    2014-09-18

    We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages. PMID:25230663

  3. Suppression of Langerhans cell activation is conserved amongst human papillomavirus α and β genotypes, but not a µ genotype.

    PubMed

    Da Silva, Diane M; Movius, Carly A; Raff, Adam B; Brand, Heike E; Skeate, Joseph G; Wong, Michael K; Kast, W Martin

    2014-03-01

    Human papillomavirus (HPV) has evolved mechanisms that allow it to evade the human immune system. Studies have shown HPV-mediated suppression of activation of Langerhans cells (LC) is a key mechanism through which HPV16 evades initial immune surveillance. However, it has not been established whether high- and low-risk mucosal and cutaneous HPV genotypes share a common mechanism of immune suppression. Here, we demonstrate that LC exposed to capsids of HPV types 18, 31, 45, 11, (alpha-papillomaviruses) and HPV5 (beta-papillomavirus) similarly suppress LC activation, including lack of costimulatory molecule expression, lack of cytokine and chemokine secretion, lack of migration, and deregulated cellular signaling. In contrast, HPV1 (mu-papillomavirus) induced costimulatory molecule and cytokine upregulation, but LC migration and cellular signaling was suppressed. These results suggest that alpha and beta HPV genotypes, and partially a mu genotype, share a conserved mechanism of immune escape that enables these viruses to remain undetected in the absence of other inflammatory events.

  4. A Genetic Variant of Hepatitis B Virus Divergent from Known Human and Ape Genotypes Isolated from a Japanese Patient and Provisionally Assigned to New Genotype J▿ †

    PubMed Central

    Tatematsu, Kanako; Tanaka, Yasuhito; Kurbanov, Fuat; Sugauchi, Fuminaka; Mano, Shuhei; Maeshiro, Tatsuji; Nakayoshi, Tomokuni; Wakuta, Moriaki; Miyakawa, Yuzo; Mizokami, Masashi

    2009-01-01

    Hepatitis B virus (HBV) of a novel genotype (J) was recovered from an 88-year-old Japanese patient with hepatocellular carcinoma who had a history of residing in Borneo during the World War II. It was divergent from eight human (A to H) and four ape (chimpanzee, gorilla, gibbon, and orangutan) HBV genotypes, as well as from a recently proposed ninth human genotype I, by 9.9 to 16.5% of the entire genomic sequence and did not have evidence of recombination with any of the nine human genotypes and four nonhuman genotypes. Based on a comparison of the entire nucleotide sequence against 1,440 HBV isolates reported, HBV/J was nearest to the gibbon and orangutan genotypes (mean divergences of 10.9 and 10.7%, respectively). Based on a comparison of four open reading frames, HBV/J was closer to gibbon/orangutan genotypes than to human genotypes in the P and large S genes and closest to Australian aboriginal strains (HBV/C4) and orangutan-derived strains in the S gene, whereas it was closer to human than ape genotypes in the C gene. HBV/J shared a deletion of 33 nucleotides at the start of preS1 region with C4 and gibbon genotypes, had an S-gene sequence similar to that of C4, and expressed the ayw subtype. Efficient infection, replication, and antigen expression by HBV/J were experimentally established in two chimeric mice with the liver repopulated for human hepatocytes. The HBV DNA sequence recovered from infected mice was identical to that in the inoculum. Since HBV/J is positioned phylogenetically in between human and ape genotypes, it may help to trace the origin of HBV and merits further epidemiological surveys. PMID:19640977

  5. The discovery of the body: human dissection and its cultural contexts in ancient Greece.

    PubMed Central

    von Staden, H.

    1992-01-01

    In the first half of the third century B.C, two Greeks, Herophilus of Chalcedon and his younger contemporary Erasistratus of Ceos, became the first and last ancient scientists to perform systematic dissections of human cadavers. In all probability, they also conducted vivisections of condemned criminals. Their anatomical and physiological discoveries were extraordinary. The uniqueness of these events presents an intriguing historical puzzle. Animals had been dissected by Aristotle in the preceding century (and partly dissected by other Greeks in earlier centuries), and, later, Galen (second century A.D.) and others again systematically dissected numerous animals. But no ancient scientists ever seem to have resumed systematic human dissection. This paper explores, first, the cultural factors--including traditional Greek attitudes to the corpse and to the skin, also as manifested in Greek sacred laws--that may have prevented systematic human dissection during almost all of Greek antiquity, from the Pre-Socratic philosopher-scientists of the sixth and fifth centuries B.C. to distinguished Greek physicians of the later Roman Empire. Second, the exceptional constellation of cultural, political, and social circumstances in early Alexandria that might have emboldened Herophilus to overcome the pressures of cultural traditions and to initiate systematic human dissection, is analyzed. Finally, the paper explores possible reasons for the mysteriously abrupt disappearance of systematic human dissection from Greek science after the death of Erasistratus and Herophilus. PMID:1285450

  6. VP4 genotyping of human rotavirus in the United States.

    PubMed Central

    Santos, N; Riepenhoff-Talty, M; Clark, H F; Offit, P; Gouvea, V

    1994-01-01

    The VP4 (P) and VP7 (G) types of 171 rotavirus isolates obtained from children with diarrhea in the United States were characterized by PCR typing assays. Strains P1G1 predominated (71%); this was followed by strains P1G3 (20%) and P2G2 and P1G4 (2% each). Mixed types were identified in five (3%) specimens. Two (1%) strains bearing the P3 genotype (P3G1 and P3G2) were found in children with severe dehydrating diarrhea, although the P3 genotype has been regarded as a possible marker for virus attenuation. Images PMID:8126181

  7. Three Point Bending Test of Human Femoral Tissue: An Essay in Ancient and Modern Bones

    NASA Astrophysics Data System (ADS)

    González-Bárcenas, L. A.; Trejo-Camacho, H.; Suárez-Estrella, I.; Heredia, A.; Magaña, C.; Bucio, L.; Orozco, E.

    2003-09-01

    Some procedures for characterising the mechanical properties of femur diaphysis are reviewed here. We have used the three point bending test to measure the relative rupture modulus of ancient healthy human tissues (1250, 800, 614, and 185 years BP) as well as recent bones. The maximum resistance to fracture was measured applying a force (by a wedge) over the femoral inner surface. The maximum rupture strength was about 150 MPa for recent bone and decreased as the antiquity increased. The typical anisotropy that is observed in this kind of tissues is due to the anisotropical orientation of fibres as well as the textured orientation of the apatite crystals over the collagen fibres. Therefore we found that ancient bones show less fracture strength probably due to an abiotic crystal growth phenomenon during the diagenesis process. By LVSEM analysis we have found that in recent samples the fracture surface is irregular due to the crosslinking interactions between the collagen molecules, in comparison with the ancient samples, where a smooth surface is clearly appreciated as the antiquity of the sample increases. The results reported here strongly suggest that these composites should contain a fibrillar phase as a matrix constituted mainly by a natural polymer (i.e. collagen, cellulose, etc.). Moreover, this composite must have a minimum rupture strength of about 150 MPa.

  8. Molecular study on human tuberculosis in three geographically distinct and time delineated populations from ancient Egypt.

    PubMed Central

    Zink, A. R.; Grabner, W.; Reischl, U.; Wolf, H.; Nerlich, A. G.

    2003-01-01

    We describe the molecular identification of human tuberculosis (TB) from vertebral bone tissue samples from three different populations of ancient Egypt. The specimens were obtained from the predynastic to early dynastic necropolis of Abydos (7 individuals, c. 3500-2650 B.C.), from a Middle Kingdom to Second Intermediate Period tomb of the necropolis of Thebes-West (37. c. 2100-1550 B.C.) and from five further Theban tombs used in the New Kingdom and the Late Period (39, c. 1450-500 B.C.). A total of 18 cases tested positive for the presence of ancient DNA (aDNA) of the M. tuberculosis complex. Out of the 9 cases with typical macromorphological signs of tuberculous spondylitis, 6 were positive for mycobacterial aDNA (66.7%). Of 24 cases with non-specific pathological alterations, 5 provided a positive result (20.8%). In 50 cases of normally appearing vertebral bones 7 tested positive (14.0%). There were only minor differences in the frequencies between the three populations. These data strongly support the notion that tuberculosis was present and prevalent in ancient Egypt since very early periods of this civilization. The unexpectedly high rate of mycobacterial aDNA in normal bone samples is presumably due to a pre- to perimortal systemic spread of the bacteria and indicates a generalized infection by M. tuberculosis. PMID:12729192

  9. Genotype and ancestry modulate brain's DAT availability in healthy humans

    SciTech Connect

    Shumay, E.; Shumay, E.; Chen, J.; Fowler, J.S.; Volkow, N.D.

    2011-08-01

    The dopamine transporter (DAT) is a principal regulator of dopaminergic neurotransmission and its gene (the SLC6A3) is a strong biological candidate gene for various behavioral- and neurological disorders. Intense investigation of the link between the SLC6A3 polymorphisms and behavioral phenotypes yielded inconsistent and even contradictory results. Reliance on objective brain phenotype measures, for example, those afforded by brain imaging, might critically improve detection of DAT genotype-phenotype association. Here, we tested the relationship between the DAT brain availability and the SLC6A3 genotypes using an aggregate sample of 95 healthy participants of several imaging studies. These studies employed positron emission tomography (PET) with [{sup 11}C] cocaine wherein the DAT availability was estimated as Bmax/Kd; while the genotype values were obtained on two repeat polymorphisms - 3-UTR- and intron 8- VNTRs. The main findings are the following: (1) both polymorphisms analyzed as single genetic markers and in combination (haplotype) modulate DAT density in midbrain; (2) ethnic background and age influence the strength of these associations; and (3) age-related changes in DAT availability differ in the 3-UTR and intron8 - genotype groups.

  10. Documenting the diet in ancient human populations through stable isotope analysis of hair.

    PubMed

    Macko, S A; Engel, M H; Andrusevich, V; Lubec, G; O'Connell, T C; Hedges, R E

    1999-01-29

    Fundamental to the understanding of human history is the ability to make interpretations based on artefacts and other remains which are used to gather information about an ancient population. Sequestered in the organic matrices of these remains can be information, for example, concerning incidence of disease, genetic defects and diet. Stable isotopic compositions, especially those made on isolates of collagen from bones, have been used to help suggest principal dietary components. A significant problem in the use of collagen is its long-term stability, and the possibility of isotopic alteration during early diagenesis, or through contaminating condensation reactions. In this study, we suggest that a commonly overlooked material, human hair, may represent an ideal material to be used in addressing human diets of ancient civilizations. Through the analysis of the amino-acid composition of modern hair, as well as samples that were subjected to radiation (thus simulating ageing of the hair) and hair from humans that is up to 5200 years old, we have observed little in the way of chemical change. The principal amino acids observed in all of these samples are essentially identical in relative abundances and content. Dominating the compositions are serine, glutamic acid, threonine, glycine and leucine, respectively accounting for approximately 15%, 17%, 10%, 8% and 8% of the total hydrolysable amino acids. Even minor components (for example, alanine, valine, isoleucine) show similar constancy between the samples of different ages. This constancy clearly indicates minimal alteration of the amino-acid composition of the hair. Further, it would indicate that hair is well preserved and is amenable to isotopic analysis as a tool for distinguishing sources of nutrition. Based on this observation, we have isotopically characterized modern individuals for whom the diet has been documented. Both stable nitrogen and carbon isotope compositions were assessed, and together provide an

  11. Documenting the diet in ancient human populations through stable isotope analysis of hair.

    PubMed Central

    Macko, S A; Engel, M H; Andrusevich, V; Lubec, G; O'Connell, T C; Hedges, R E

    1999-01-01

    Fundamental to the understanding of human history is the ability to make interpretations based on artefacts and other remains which are used to gather information about an ancient population. Sequestered in the organic matrices of these remains can be information, for example, concerning incidence of disease, genetic defects and diet. Stable isotopic compositions, especially those made on isolates of collagen from bones, have been used to help suggest principal dietary components. A significant problem in the use of collagen is its long-term stability, and the possibility of isotopic alteration during early diagenesis, or through contaminating condensation reactions. In this study, we suggest that a commonly overlooked material, human hair, may represent an ideal material to be used in addressing human diets of ancient civilizations. Through the analysis of the amino-acid composition of modern hair, as well as samples that were subjected to radiation (thus simulating ageing of the hair) and hair from humans that is up to 5200 years old, we have observed little in the way of chemical change. The principal amino acids observed in all of these samples are essentially identical in relative abundances and content. Dominating the compositions are serine, glutamic acid, threonine, glycine and leucine, respectively accounting for approximately 15%, 17%, 10%, 8% and 8% of the total hydrolysable amino acids. Even minor components (for example, alanine, valine, isoleucine) show similar constancy between the samples of different ages. This constancy clearly indicates minimal alteration of the amino-acid composition of the hair. Further, it would indicate that hair is well preserved and is amenable to isotopic analysis as a tool for distinguishing sources of nutrition. Based on this observation, we have isotopically characterized modern individuals for whom the diet has been documented. Both stable nitrogen and carbon isotope compositions were assessed, and together provide an

  12. Ancient population structure in Phoenix dactylifera revealed by genome-wide genotyping of geographically diverse date palm cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The date palm was one of the earliest cultivated fruit trees and is intimately tied to the history of human migration. With no true known wild ancestor little is known about the genetic origins and the effect of human cultivation on the date palm. Recent genome projects have just begun to provide th...

  13. Genetic history of Southeast Asian populations as revealed by ancient and modern human mitochondrial DNA analysis.

    PubMed

    Lertrit, Patcharee; Poolsuwan, Samerchai; Thosarat, Rachanie; Sanpachudayan, Thitima; Boonyarit, Hathaichanoke; Chinpaisal, Chatchai; Suktitipat, Bhoom

    2008-12-01

    The 360 base-pair fragment in HVS-1 of the mitochondrial genome were determined from ancient human remains excavated at Noen U-loke and Ban Lum-Khao, two Bronze and Iron Age archaeological sites in Northeastern Thailand, radio-carbon dated to circa 3,500-1,500 years BP and 3,200-2,400 years BP, respectively. These two neighboring populations were parts of early agricultural communities prevailing in northeastern Thailand from the fourth millennium BP onwards. The nucleotide sequences of these ancient samples were compared with the sequences of modern samples from various ethnic populations of East and Southeast Asia, encompassing four major linguistic affiliations (Altaic, Sino-Tibetan, Tai-Kadai, and Austroasiatic), to investigate the genetic relationships and history among them. The two ancient samples were most closely related to each other, and next most closely related to the Chao-Bon, an Austroasiatic-speaking group living near the archaeological sites, suggesting that the genetic continuum may have persisted since prehistoric times in situ among the native, perhaps Austroasiatic-speaking population. Tai-Kadai groups formed close affinities among themselves, with a tendency to be more closely related to other Southeast Asian populations than to populations from further north. The Tai-Kadai groups were relatively distant from all groups that have presumably been in Southeast Asia for longer-that is, the two ancient groups and the Austroasiatic-speaking groups, with the exception of the Khmer group. This finding is compatible with the known history of the Thais: their late arrival in Southeast Asia from southern China after the 10th-11th century AD, followed by a period of subjugation under the Khmers.

  14. Human cadaveric dissection: a historical account from ancient Greece to the modern era

    PubMed Central

    2015-01-01

    The review article attempts to focus on the practice of human cadaveric dissection during its inception in ancient Greece in 3rd century BC, revival in medieval Italy at the beginning of 14th century and subsequent evolution in Europe and the United States of America over the centuries. The article highlights on the gradual change in attitude of religious authorities towards human dissection, the shift in the practice of human dissection being performed by barber surgeons to the anatomist himself dissecting the human body and the enactment of prominent legislations which proved to be crucial milestones during the course of the history of human cadaveric dissection. It particularly emphasizes on the different means of procuring human bodies which changed over the centuries in accordance with the increasing demand due to the rise in popularity of human dissection as a tool for teaching anatomy. Finally, it documents the rise of body donation programs as the source of human cadavers for anatomical dissection from the second half of the 20th century. Presently innovative measures are being introduced within the body donation programs by medical schools across the world to sensitize medical students such that they maintain a respectful, compassionate and empathetic attitude towards the human cadaver while dissecting the same. Human dissection is indispensable for a sound knowledge in anatomy which can ensure safe as well as efficient clinical practice and the human dissection lab could possibly be the ideal place to cultivate humanistic qualities among future physicians in the 21st century. PMID:26417475

  15. Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence.

    PubMed

    Gokcumen, Omer; Zhu, Qihui; Mulder, Lubbertus C F; Iskow, Rebecca C; Austermann, Christian; Scharer, Christopher D; Raj, Towfique; Boss, Jeremy M; Sunyaev, Shamil; Price, Alkes; Stranger, Barbara; Simon, Viviana; Lee, Charles

    2013-04-01

    Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10⁻¹⁵). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003) and positive Tajima's D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human-Neandertal divergence and is evolving under balancing selection, especially among European populations. PMID

  16. Experimental study of human-induced effects on floor slab of an ancient Tibetan structure

    NASA Astrophysics Data System (ADS)

    Yang, Na; Guo, Ting; Law, S. S.

    2012-12-01

    With the opening of ancient Tibetan structures to visitors worldwide, human load has become the principal live load on these structures. This project studies the properties of the floor structure of an ancient Tibetan building and its behavior under human-induced load effects. Tests were conducted with static and dynamic crowd load, including stepping and jogging by people at a fixed position. The tests show that the floor structure does not behave as a continuous slab. It takes the load from local areas with minimal load transference properties. The acceleration response shows significant peaks when the footstep frequency is close to the natural frequency of the structure, but the human jogging excitation frequency does not have any obvious effect on the structural response. The elastic modulus of the Agatu material is estimated to be close to zero from the measured natural frequency of the slab. The Agatu material is concluded to be a discrete compacted material with insignificant contribution to the structural rigidity of the floor slab.

  17. Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone.

    PubMed

    Pinhasi, Ron; Fernandes, Daniel; Sirak, Kendra; Novak, Mario; Connell, Sarah; Alpaslan-Roodenberg, Songül; Gerritsen, Fokke; Moiseyev, Vyacheslav; Gromov, Andrey; Raczky, Pál; Anders, Alexandra; Pietrusewsky, Michael; Rollefson, Gary; Jovanovic, Marija; Trinhhoang, Hiep; Bar-Oz, Guy; Oxenham, Marc; Matsumura, Hirofumi; Hofreiter, Michael

    2015-01-01

    The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of

  18. Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone

    PubMed Central

    Pinhasi, Ron; Fernandes, Daniel; Sirak, Kendra; Novak, Mario; Connell, Sarah; Alpaslan-Roodenberg, Songül; Gerritsen, Fokke; Moiseyev, Vyacheslav; Gromov, Andrey; Raczky, Pál; Anders, Alexandra; Pietrusewsky, Michael; Rollefson, Gary; Jovanovic, Marija; Trinhhoang, Hiep; Bar-Oz, Guy; Oxenham, Marc; Matsumura, Hirofumi; Hofreiter, Michael

    2015-01-01

    The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of

  19. Multiple instances of ancient balancing selection shared between humans and chimpanzees*

    PubMed Central

    Gao, Ziyue; Pfeifer, Susanne; Ségurel, Laure; Auton, Adam; Venn, Oliver; Bowden, Rory; Bontrop, Ronald; Wall, Jeffrey D.; Sella, Guy; Donnelly, Peter; McVean, Gilean

    2013-01-01

    Instances in which natural selection maintains genetic variation in a population over millions of years are thought to be extremely rare. We conducted a genome-wide scan for long-lived balancing selection by looking for combinations of SNPs shared between humans and chimpanzees. In addition to the major histocompatibility complex (MHC), we identified 125 regions in which the same haplotypes are segregating in the two species, all but two of which are non-coding. In six cases, there is evidence for an ancestral polymorphism that persisted to the present in humans and chimpanzees. Regions with shared haplotypes are significantly enriched for membrane glycoproteins, and a similar trend is seen among shared coding polymorphisms. These findings indicate that ancient balancing selection has shaped human variation and point to genes involved in host-pathogen interactions as common targets. PMID:23413192

  20. The prevalence and genotype diversity of Human Rotavirus A circulating in Thailand, 2011-2014.

    PubMed

    Chieochansin, Thaweesak; Vutithanachot, Viboonsak; Phumpholsup, Tikumporn; Posuwan, Nawarat; Theamboonlers, Apiradee; Poovorawan, Yong

    2016-01-01

    Human rotavirus A (RVA) is the major infectious virus causing acute watery diarrhea in children, especially those younger than 5 years of age, and is a major public health problem in Thailand. Outbreaks of this virus have been reported worldwide. Besides the common genotypes, unusual genotypes providing evidence of inter-species transmission have also been described. Therefore, the aim of this study was to investigate the prevalence and genotypes of RVA in Thailand. A total of 688 samples were collected from children who were hospitalized with acute diarrhea in Chumphae Hospital in Khon Kaen and Chulalongkorn Hospital in Bangkok. RVA was detected using one-step RT-PCR and the genotypes were evaluated by sequencing. Overall, 204 of the 688 samples (30%) were positive for RVA. Nine genotypes were identified: three common in humans (G1P[8] [53%], G2P[4] [18%], G3P[8] [12%]), one feline-like (G3P[9] [1%]), four porcine-like (G4P[6] [0.5%], G5P[6] [0.5%], G9P[8] [0.5%], G12P[6] [1.5%]), and one bovine-like (G8P[8] [13%]). The variation in virus genotypes and the animal-like genotypes detected in this study suggested that a high diversity of RVA types is circulating in the Thai population. Therefore, continuous molecular epidemiological monitoring of RVA is essential and has implications for the national vaccination program.

  1. Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects.

    PubMed

    Thèves, Catherine; Senescau, Alice; Vanin, Stefano; Keyser, Christine; Ricaut, François Xavier; Alekseev, Anatoly N; Dabernat, Henri; Ludes, Bertrand; Fabre, Richard; Crubézy, Eric

    2011-01-01

    Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in eastern Siberia, dating from the end of 17(th) to the 19(th) century, we propose a methodology that includes the: 1) amplification of all 16S rDNA gene sequences present in each sample; 2) identification of all bacterial DNA sequences with a degree of identity ≥ 95%, according to quality criteria; 3) identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4) establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1) the correct identification of bacterial molecular sequence signatures by quality criteria; 2) the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3) the distribution of bacterial species for each subject and for each burial; and 4) the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17(th) century to the early 18(th) century.

  2. Echinococcus granulosus sensu lato GENOTYPES IN DOMESTIC LIVESTOCK AND HUMANS IN GOLESTAN PROVINCE, IRAN.

    PubMed

    Sharbatkhori, Mitra; Tanzifi, Asal; Rostami, Sima; Rostami, Masoomeh; Fasihi Harandi, Majid

    2016-01-01

    Cystic echinococcosis (CE) is a globally parasitic zoonosis caused by larval stages of Echinococcus granulosus. This study investigated E. granulosus genotypes isolated from livestock and humans in the Golestan province, northern Iran, southeast of the Caspian sea, using partial sequencing data of the cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase 1 (nad1) mitochondrial genes. Seventy E. granulosus isolates were collected from animals in slaughterhouses: 18 isolates from sheep, 40 from cattle, nine from camels, two from buffaloes and one from a goat, along with four human isolates (formalin-fixed, paraffin-embedded tissues) from CE patients of provincial hospitals. All isolates were successfully analysed by PCR amplification and sequencing. The sequence analysis found four E. granulosus genotypes among the 74 CE isolates: G1 (78.3%), G2 (2.7%), G3 (15%) and G6 (4%). The G1-G3 complex genotype was found in all of the sheep, goat, cattle and buffalo isolates. Among the nine camel isolates, the frequency of G1-G3 and G6 genotypes were 66.7% and 33.3%, respectively. All four human CE isolates belonged to E. granulosus sensu stricto. This study reports the first occurrence of the G2 genotype in cattle from Iran and confirms the previously reported G3 genotype in camels in the same country. PMID:27253740

  3. Echinococcus granulosus sensu lato GENOTYPES IN DOMESTIC LIVESTOCK AND HUMANS IN GOLESTAN PROVINCE, IRAN

    PubMed Central

    SHARBATKHORI, Mitra; TANZIFI, Asal; ROSTAMI, Sima; ROSTAMI, Masoomeh; HARANDI, Majid FASIHI

    2016-01-01

    Cystic echinococcosis (CE) is a globally parasitic zoonosis caused by larval stages of Echinococcus granulosus. This study investigated E. granulosus genotypes isolated from livestock and humans in the Golestan province, northern Iran, southeast of the Caspian sea, using partial sequencing data of the cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase 1 (nad1) mitochondrial genes. Seventy E. granulosus isolates were collected from animals in slaughterhouses: 18 isolates from sheep, 40 from cattle, nine from camels, two from buffaloes and one from a goat, along with four human isolates (formalin-fixed, paraffin-embedded tissues) from CE patients of provincial hospitals. All isolates were successfully analysed by PCR amplification and sequencing. The sequence analysis found four E. granulosus genotypes among the 74 CE isolates: G1 (78.3%), G2 (2.7%), G3 (15%) and G6 (4%). The G1-G3 complex genotype was found in all of the sheep, goat, cattle and buffalo isolates. Among the nine camel isolates, the frequency of G1-G3 and G6 genotypes were 66.7% and 33.3%, respectively. All four human CE isolates belonged to E. granulosus sensu stricto. This study reports the first occurrence of the G2 genotype in cattle from Iran and confirms the previously reported G3 genotype in camels in the same country. PMID:27253740

  4. Echinococcus granulosus sensu lato GENOTYPES IN DOMESTIC LIVESTOCK AND HUMANS IN GOLESTAN PROVINCE, IRAN.

    PubMed

    Sharbatkhori, Mitra; Tanzifi, Asal; Rostami, Sima; Rostami, Masoomeh; Fasihi Harandi, Majid

    2016-01-01

    Cystic echinococcosis (CE) is a globally parasitic zoonosis caused by larval stages of Echinococcus granulosus. This study investigated E. granulosus genotypes isolated from livestock and humans in the Golestan province, northern Iran, southeast of the Caspian sea, using partial sequencing data of the cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase 1 (nad1) mitochondrial genes. Seventy E. granulosus isolates were collected from animals in slaughterhouses: 18 isolates from sheep, 40 from cattle, nine from camels, two from buffaloes and one from a goat, along with four human isolates (formalin-fixed, paraffin-embedded tissues) from CE patients of provincial hospitals. All isolates were successfully analysed by PCR amplification and sequencing. The sequence analysis found four E. granulosus genotypes among the 74 CE isolates: G1 (78.3%), G2 (2.7%), G3 (15%) and G6 (4%). The G1-G3 complex genotype was found in all of the sheep, goat, cattle and buffalo isolates. Among the nine camel isolates, the frequency of G1-G3 and G6 genotypes were 66.7% and 33.3%, respectively. All four human CE isolates belonged to E. granulosus sensu stricto. This study reports the first occurrence of the G2 genotype in cattle from Iran and confirms the previously reported G3 genotype in camels in the same country.

  5. Genotypes and Mouse Virulence of Toxoplasma gondii Isolates from Animals and Humans in China

    PubMed Central

    Liu, Daohua; Huo, Xingxing; Gao, Jiangmei; Song, Xiaorong; Xu, Xiucai; Huang, Kaiquan; Liu, Wenqi; Wang, Yong; Lu, Fangli; Lun, Zhao-Rong; Luo, Qingli; Wang, Xuelong; Shen, Jilong

    2013-01-01

    Background Recent population structure studies of T. gondii revealed that a few major clonal lineages predominated in different geographical regions. T. gondii in South America is genetically and biologically divergent, whereas this parasite is remarkably clonal in North America and Europe with a few major lineages including Types I, II and III. Information on genotypes and mouse virulence of T. gondii isolates from China is scarce and insufficient to investigate its population structure, evolution, and transmission. Methodology/Principal Findings Genotyping of 23 T. gondii isolates from different hosts using 10 markers for PCR-restriction fragment length polymorphism analyses (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) revealed five genotypes; among them three genotypes were atypical and two were archetypal. Fifteen strains belong to the Chinese 1 lineage, which has been previously reported as a widespread lineage from swine, cats, and humans in China. Two human isolates fall into the type I and II lineages and the remaining isolates belong to two new atypical genotypes (ToxoDB#204 and #205) which has never been reported in China. Our results show that these genotypes of T. gondii isolates are intermediately or highly virulent in mice except for the strain TgCtwh6, which maintained parasitemia in mice for 35 days post infection although it possesses the uniform genotype of Chinese 1. Additionally, phylogenetic network analyses of all isolates of genotype Chinese 1 are identical, and there is no variation based on the sequence data generated for four introns (EF1, HP2, UPRT1 and UPRT7) and two dense granule proteins (GRA6 and GRA7). Conclusion/Significance A limited genetic diversity was found and genotype Chinese 1 (ToxoDB#9) is dominantly circulating in mainland China. The results will provide a useful profile for deep insight to the population structure, epidemiology and biological characteristics of T. gondii in China. PMID:23308233

  6. Source tracking identifies deer and geese as vectors of human-infectious Cryptosporidium genotypes in an urban/suburban watershed.

    PubMed

    Jellison, Kristen L; Lynch, Amy E; Ziemann, Joseph M

    2009-06-15

    This study identified Cryptosporidium genotypes in the Wissahickon watershed from May 2005 to April 2008. We analyzed 129 samples from Wissahickon Creek, 83 effluent samples from wastewater treatment plants (WWTPs), and 240 fecal droppings. Genotyping was based on the hypervariable region of the 18S rRNA gene. Oocysts were detected year-round, independent of wet weather events, in 22% of Wissahickon Creek samples, 5% of WWTP effluents, and 7% of fecal samples. Of the genotypes detected, 67% were human-infectious: 30% C. hominis or C. hominis-like, 12% C. parvum, 14% cervine genotype, 9% skunk genotype, and 1% chipmunk I genotype. Similar genotype profiles were detected in Wissahickon Creek each year, and human-infectious genotypes were detected year-round. Unusual genotypes detected in a deer (a C. hominis-like genotype) and geese (C. hominis-like genotypes, C. parvum, and muskrat genotype I) show that these animals are vectors of human-infectious genotypes in this watershed. Results suggest that deer, geese, and WWTPs are appropriate targets for source water protection in the Wissahickon watershed.

  7. Source tracking identifies deer and geese as vectors of human-infectious Cryptosporidium genotypes in an urban/suburban watershed.

    PubMed

    Jellison, Kristen L; Lynch, Amy E; Ziemann, Joseph M

    2009-06-15

    This study identified Cryptosporidium genotypes in the Wissahickon watershed from May 2005 to April 2008. We analyzed 129 samples from Wissahickon Creek, 83 effluent samples from wastewater treatment plants (WWTPs), and 240 fecal droppings. Genotyping was based on the hypervariable region of the 18S rRNA gene. Oocysts were detected year-round, independent of wet weather events, in 22% of Wissahickon Creek samples, 5% of WWTP effluents, and 7% of fecal samples. Of the genotypes detected, 67% were human-infectious: 30% C. hominis or C. hominis-like, 12% C. parvum, 14% cervine genotype, 9% skunk genotype, and 1% chipmunk I genotype. Similar genotype profiles were detected in Wissahickon Creek each year, and human-infectious genotypes were detected year-round. Unusual genotypes detected in a deer (a C. hominis-like genotype) and geese (C. hominis-like genotypes, C. parvum, and muskrat genotype I) show that these animals are vectors of human-infectious genotypes in this watershed. Results suggest that deer, geese, and WWTPs are appropriate targets for source water protection in the Wissahickon watershed. PMID:19603633

  8. Identification of potentially human-pathogenic Enterocytozoon bieneusi genotypes in various birds.

    PubMed

    Lobo, Maria Luísa; Xiao, Lihua; Cama, Vitaliano; Magalhães, Nuno; Antunes, Francisco; Matos, Olga

    2006-11-01

    Enterocytozoon bieneusi was detected in 24 of 83 samples from birds of the orders Columbiformes, Passeriformes, and Psittaciformes. It was identical to or closely related to the Peru6 genotype, which was previously found in humans in Peru. Thus, various birds can be a significant source of environmental contamination by potentially human-pathogenic E. bieneusi.

  9. Identification of Potentially Human-Pathogenic Enterocytozoon bieneusi Genotypes in Various Birds▿

    PubMed Central

    Lobo, Maria Luísa ; Xiao, Lihua; Cama, Vitaliano; Magalhães, Nuno; Antunes, Francisco; Matos, Olga

    2006-01-01

    Enterocytozoon bieneusi was detected in 24 of 83 samples from birds of the orders Columbiformes, Passeriformes, and Psittaciformes. It was identical to or closely related to the Peru6 genotype, which was previously found in humans in Peru. Thus, various birds can be a significant source of environmental contamination by potentially human-pathogenic E. bieneusi. PMID:16936045

  10. The Caucasus as an asymmetric semipermeable barrier to ancient human migrations.

    PubMed

    Yunusbayev, Bayazit; Metspalu, Mait; Järve, Mari; Kutuev, Ildus; Rootsi, Siiri; Metspalu, Ene; Behar, Doron M; Varendi, Kärt; Sahakyan, Hovhannes; Khusainova, Rita; Yepiskoposyan, Levon; Khusnutdinova, Elza K; Underhill, Peter A; Kivisild, Toomas; Villems, Richard

    2012-01-01

    The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture. PMID:21917723

  11. Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans.

    PubMed

    Barber, Matthew F; Kronenberg, Zev; Yandell, Mark; Elde, Nels C

    2016-05-01

    Lactoferrin is a multifunctional mammalian immunity protein that limits microbial growth through sequestration of nutrient iron. Additionally, lactoferrin possesses cationic protein domains that directly bind and inhibit diverse microbes. The implications for these dual functions on lactoferrin evolution and genetic conflicts with microbes remain unclear. Here we show that lactoferrin has been subject to recurrent episodes of positive selection during primate divergence predominately at antimicrobial peptide surfaces consistent with long-term antagonism by bacteria. An abundant lactoferrin polymorphism in human populations and Neanderthals also exhibits signatures of positive selection across primates, linking ancient host-microbe conflicts to modern human genetic variation. Rapidly evolving sites in lactoferrin further correspond to molecular interfaces with opportunistic bacterial pathogens causing meningitis, pneumonia, and sepsis. Because microbes actively target lactoferrin to acquire iron, we propose that the emergence of antimicrobial activity provided a pivotal mechanism of adaptation sparking evolutionary conflicts via acquisition of new protein functions. PMID:27203426

  12. Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans

    PubMed Central

    Kronenberg, Zev; Yandell, Mark; Elde, Nels C.

    2016-01-01

    Lactoferrin is a multifunctional mammalian immunity protein that limits microbial growth through sequestration of nutrient iron. Additionally, lactoferrin possesses cationic protein domains that directly bind and inhibit diverse microbes. The implications for these dual functions on lactoferrin evolution and genetic conflicts with microbes remain unclear. Here we show that lactoferrin has been subject to recurrent episodes of positive selection during primate divergence predominately at antimicrobial peptide surfaces consistent with long-term antagonism by bacteria. An abundant lactoferrin polymorphism in human populations and Neanderthals also exhibits signatures of positive selection across primates, linking ancient host-microbe conflicts to modern human genetic variation. Rapidly evolving sites in lactoferrin further correspond to molecular interfaces with opportunistic bacterial pathogens causing meningitis, pneumonia, and sepsis. Because microbes actively target lactoferrin to acquire iron, we propose that the emergence of antimicrobial activity provided a pivotal mechanism of adaptation sparking evolutionary conflicts via acquisition of new protein functions. PMID:27203426

  13. A Laboratory Exercise for Genotyping Two Human Single Nucleotide Polymorphisms

    ERIC Educational Resources Information Center

    Fernando, James; Carlson, Bradley; LeBard, Timothy; McCarthy, Michael; Umali, Finianne; Ashton, Bryce; Rose, Ferrill F., Jr.

    2016-01-01

    The dramatic decrease in the cost of sequencing a human genome is leading to an era in which a wide range of students will benefit from having an understanding of human genetic variation. Since over 90% of sequence variation between humans is in the form of single nucleotide polymorphisms (SNPs), a laboratory exercise has been devised in order to…

  14. Analysis of Genotype-Phenotype Correlations in Human Holoprosencephaly

    PubMed Central

    Solomon, Benjamin D.; Mercier, Sandra; Vélez, Jorge I.; Pineda-Alvarez, Daniel E.; Wyllie, Adrian; Zhou, Nan; Dubourg, Christèle; David, Veronique; Odent, Sylvie; Roessler, Erich; Muenke, Maximilian

    2009-01-01

    Since the discovery of the first gene causing holoprosencephaly (HPE), over 500 patients with mutations in genes associated with non-chromosomal, non-syndromic HPE have been described, with detailed descriptions available in over 300. Comprehensive clinical analysis of these individuals allows examination for the presence of genotype-phenotype correlations. These correlations allow a degree of differentiation between patients with mutations in different HPE-associated genes and for the application of functional studies to determine intragenic correlations. These early correlations are an important advance in the understanding of the clinical aspects of this disease, and in general argue for continued analysis of the genetic and clinical findings of large cohorts of patients with rare diseases in order to better inform both basic biological insight and care and counseling for affected patients and families. PMID:20104608

  15. Human genotype-phenotype databases: aims, challenges and opportunities.

    PubMed

    Brookes, Anthony J; Robinson, Peter N

    2015-12-01

    Genotype-phenotype databases provide information about genetic variation, its consequences and its mechanisms of action for research and health care purposes. Existing databases vary greatly in type, areas of focus and modes of operation. Despite ever larger and more intricate datasets--made possible by advances in DNA sequencing, omics methods and phenotyping technologies--steady progress is being made towards integrating these databases rather than using them as separate entities. The consequential shift in focus from single-gene variants towards large gene panels, exomes, whole genomes and myriad observable characteristics creates new challenges and opportunities in database design, interpretation of variant pathogenicity and modes of data representation and use. PMID:26553330

  16. Toward a new history and geography of human genes informed by ancient DNA.

    PubMed

    Pickrell, Joseph K; Reich, David

    2014-09-01

    Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture, and population replacement subsequent to the initial out-of-Africa expansion have altered the genetic structure of most of the world's human populations. In light of this we argue that it is time to critically reevaluate current models of the peopling of the globe, as well as the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.

  17. Biomolecular identification of ancient Mycobacterium tuberculosis complex DNA in human remains from Britain and continental Europe.

    PubMed

    Müller, Romy; Roberts, Charlotte A; Brown, Terence A

    2014-02-01

    Tuberculosis is known to have afflicted humans throughout history and re-emerged towards the end of the 20th century, to an extent that it was declared a global emergency in 1993. The aim of this study was to apply a rigorous analytical regime to the detection of Mycobacterium tuberculosis complex (MTBC) DNA in 77 bone and tooth samples from 70 individuals from Britain and continental Europe, spanning the 1st-19th centuries AD. We performed the work in dedicated ancient DNA facilities designed to prevent all types of modern contamination, we checked the authenticity of all products obtained by the polymerase chain reaction, and we based our conclusions on up to four replicate experiments for each sample, some carried out in an independent laboratory. We identified 12 samples that, according to our strict criteria, gave definite evidence for the presence of MTBC DNA, and another 22 that we classified as "probable" or "possible." None of the definite samples came from vertebrae displaying lesions associated with TB. Instead, eight were from ribs displaying visceral new bone formation, one was a tooth from a skeleton with rib lesions, one was taken from a skeleton with endocranial lesions, one from an individual with lesions to the sacrum and sacroiliac joint and the last was from an individual with no lesions indicative of TB or possible TB. Our results add to information on the past temporal and geographical distribution of TB and affirm the suitability of ribs for studying ancient TB.

  18. Toward a new history and geography of human genes informed by ancient DNA

    PubMed Central

    Pickrell, Joseph K.; Reich, David

    2014-01-01

    Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture and population replacement subsequent to the initial out-of-Africa expansion have altered the genetic structure of most of the world’s human populations. In light of this, we argue that it is time to critically re-evaluate current models of the peopling of the globe, as well as the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically-known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection. PMID:25168683

  19. Microarrays for Genotyping Human Group A Rotavirus by Multiplex Capture and Type-Specific Primer Extension

    PubMed Central

    Lovmar, Lovisa; Fock, Caroline; Espinoza, Felix; Bucardo, Filemon; Syvänen, Ann-Christine; Bondeson, Kåre

    2003-01-01

    Human group A rotavirus (HRV) is the major cause of severe gastroenteritis in infants worldwide. HRV shares the feature of a high degree of genetic diversity with many other RNA viruses, and therefore, genotyping of this organism is more complicated than genotyping of more stable DNA viruses. We describe a novel microarray-based method that allows high-throughput genotyping of RNA viruses with a high degree of polymorphism by multiplex capture and type-specific extension on microarrays. Denatured reverse transcription (RT)-PCR products derived from two outer capsid genes of clinical isolates of HRV were hybridized to immobilized capture oligonucleotides representing the most commonly occurring P and G genotypes on a microarray. Specific primer extension of the type-specific capture oligonucleotides was applied to incorporate the fluorescent nucleotide analogue cyanine 5-labeled dUTP as a detectable label. Laser scanning and fluorescence detection of the microarrays was followed by visual or computer-assisted interpretation of the fluorescence patterns generated on the microarrays. Initially, the method detected HRV in all 40 samples and correctly determined both the G and the P genotypes of 35 of the 40 strains analyzed. After modification by inclusion of additional capture oligonucleotides specific for the initially unassigned genotypes, all genotypes could be correctly defined. The results of genotyping with the microarray fully agreed with the results obtained by nucleotide sequence analysis and sequence-specific multiplex RT-PCR. Owing to its robustness, simplicity, and general utility, the microarray-based method may gain wide applicability for the genotyping of microorganisms, including highly variable RNA and DNA viruses. PMID:14605152

  20. Microarrays for genotyping human group a rotavirus by multiplex capture and type-specific primer extension.

    PubMed

    Lovmar, Lovisa; Fock, Caroline; Espinoza, Felix; Bucardo, Filemon; Syvänen, Ann-Christine; Bondeson, Kåre

    2003-11-01

    Human group A rotavirus (HRV) is the major cause of severe gastroenteritis in infants worldwide. HRV shares the feature of a high degree of genetic diversity with many other RNA viruses, and therefore, genotyping of this organism is more complicated than genotyping of more stable DNA viruses. We describe a novel microarray-based method that allows high-throughput genotyping of RNA viruses with a high degree of polymorphism by multiplex capture and type-specific extension on microarrays. Denatured reverse transcription (RT)-PCR products derived from two outer capsid genes of clinical isolates of HRV were hybridized to immobilized capture oligonucleotides representing the most commonly occurring P and G genotypes on a microarray. Specific primer extension of the type-specific capture oligonucleotides was applied to incorporate the fluorescent nucleotide analogue cyanine 5-labeled dUTP as a detectable label. Laser scanning and fluorescence detection of the microarrays was followed by visual or computer-assisted interpretation of the fluorescence patterns generated on the microarrays. Initially, the method detected HRV in all 40 samples and correctly determined both the G and the P genotypes of 35 of the 40 strains analyzed. After modification by inclusion of additional capture oligonucleotides specific for the initially unassigned genotypes, all genotypes could be correctly defined. The results of genotyping with the microarray fully agreed with the results obtained by nucleotide sequence analysis and sequence-specific multiplex RT-PCR. Owing to its robustness, simplicity, and general utility, the microarray-based method may gain wide applicability for the genotyping of microorganisms, including highly variable RNA and DNA viruses.

  1. Monitoring DNA Contamination in Handled vs. Directly Excavated Ancient Human Skeletal Remains

    PubMed Central

    Pilli, Elena; Modi, Alessandra; Serpico, Ciro; Achilli, Alessandro; Lancioni, Hovirag; Lippi, Barbara; Bertoldi, Francesca; Gelichi, Sauro; Lari, Martina; Caramelli, David

    2013-01-01

    Bones, teeth and hair are often the only physical evidence of human or animal presence at an archaeological site; they are also the most widely used sources of samples for ancient DNA (aDNA) analysis. Unfortunately, the DNA extracted from ancient samples, already scarce and highly degraded, is widely susceptible to exogenous contaminations that can affect the reliability of aDNA studies. We evaluated the molecular effects of sample handling on five human skeletons freshly excavated from a cemetery dated between the 11 to the 14th century. We collected specimens from several skeletal areas (teeth, ribs, femurs and ulnas) from each individual burial. We then divided the samples into two different sets: one labeled as “virgin samples” (i.e. samples that were taken by archaeologists under contamination-controlled conditions and then immediately sent to the laboratory for genetic analyses), and the second called “lab samples”(i.e. samples that were handled without any particular precautions and subject to normal washing, handling and measuring procedures in the osteological lab). Our results show that genetic profiles from “lab samples” are incomplete or ambiguous in the different skeletal areas while a different outcome is observed in the “virgin samples” set. Generally, all specimens from different skeletal areas in the exception of teeth present incongruent results between “lab” and “virgin” samples. Therefore teeth are less prone to contamination than the other skeletal areas we analyzed and may be considered a material of choice for classical aDNA studies. In addition, we showed that bones can also be a good candidate for human aDNA analysis if they come directly from the excavation site and are accompanied by a clear taphonomic history. PMID:23372650

  2. New genetic and linguistic analyses show ancient human influence on baobab evolution and distribution in Australia.

    PubMed

    Rangan, Haripriya; Bell, Karen L; Baum, David A; Fowler, Rachael; McConvell, Patrick; Saunders, Thomas; Spronck, Stef; Kull, Christian A; Murphy, Daniel J

    2015-01-01

    This study investigates the role of human agency in the gene flow and geographical distribution of the Australian baobab, Adansonia gregorii. The genus Adansonia is a charismatic tree endemic to Africa, Madagascar, and northwest Australia that has long been valued by humans for its multiple uses. The distribution of genetic variation in baobabs in Africa has been partially attributed to human-mediated dispersal over millennia, but this relationship has never been investigated for the Australian species. We combined genetic and linguistic data to analyse geographic patterns of gene flow and movement of word-forms for A. gregorii in the Aboriginal languages of northwest Australia. Comprehensive assessment of genetic diversity showed weak geographic structure and high gene flow. Of potential dispersal vectors, humans were identified as most likely to have enabled gene flow across biogeographic barriers in northwest Australia. Genetic-linguistic analysis demonstrated congruence of gene flow patterns and directional movement of Aboriginal loanwords for A. gregorii. These findings, along with previous archaeobotanical evidence from the Late Pleistocene and Holocene, suggest that ancient humans significantly influenced the geographic distribution of Adansonia in northwest Australia.

  3. New genetic and linguistic analyses show ancient human influence on baobab evolution and distribution in Australia.

    PubMed

    Rangan, Haripriya; Bell, Karen L; Baum, David A; Fowler, Rachael; McConvell, Patrick; Saunders, Thomas; Spronck, Stef; Kull, Christian A; Murphy, Daniel J

    2015-01-01

    This study investigates the role of human agency in the gene flow and geographical distribution of the Australian baobab, Adansonia gregorii. The genus Adansonia is a charismatic tree endemic to Africa, Madagascar, and northwest Australia that has long been valued by humans for its multiple uses. The distribution of genetic variation in baobabs in Africa has been partially attributed to human-mediated dispersal over millennia, but this relationship has never been investigated for the Australian species. We combined genetic and linguistic data to analyse geographic patterns of gene flow and movement of word-forms for A. gregorii in the Aboriginal languages of northwest Australia. Comprehensive assessment of genetic diversity showed weak geographic structure and high gene flow. Of potential dispersal vectors, humans were identified as most likely to have enabled gene flow across biogeographic barriers in northwest Australia. Genetic-linguistic analysis demonstrated congruence of gene flow patterns and directional movement of Aboriginal loanwords for A. gregorii. These findings, along with previous archaeobotanical evidence from the Late Pleistocene and Holocene, suggest that ancient humans significantly influenced the geographic distribution of Adansonia in northwest Australia. PMID:25830225

  4. New Genetic and Linguistic Analyses Show Ancient Human Influence on Baobab Evolution and Distribution in Australia

    PubMed Central

    Rangan, Haripriya; Bell, Karen L.; Baum, David A.; Fowler, Rachael; McConvell, Patrick; Saunders, Thomas; Spronck, Stef; Kull, Christian A.; Murphy, Daniel J.

    2015-01-01

    This study investigates the role of human agency in the gene flow and geographical distribution of the Australian baobab, Adansonia gregorii. The genus Adansonia is a charismatic tree endemic to Africa, Madagascar, and northwest Australia that has long been valued by humans for its multiple uses. The distribution of genetic variation in baobabs in Africa has been partially attributed to human-mediated dispersal over millennia, but this relationship has never been investigated for the Australian species. We combined genetic and linguistic data to analyse geographic patterns of gene flow and movement of word-forms for A. gregorii in the Aboriginal languages of northwest Australia. Comprehensive assessment of genetic diversity showed weak geographic structure and high gene flow. Of potential dispersal vectors, humans were identified as most likely to have enabled gene flow across biogeographic barriers in northwest Australia. Genetic-linguistic analysis demonstrated congruence of gene flow patterns and directional movement of Aboriginal loanwords for A. gregorii. These findings, along with previous archaeobotanical evidence from the Late Pleistocene and Holocene, suggest that ancient humans significantly influenced the geographic distribution of Adansonia in northwest Australia. PMID:25830225

  5. [Genotyping of Giardia intestinalis strains isolated from humans in Aydin, Turkey].

    PubMed

    Ertuğ, Sema; Ertabaklar, Hatice; Özlem Çalışkan, Serçin; Malatyalı, Erdoğan; Bozdoğan, Bülent

    2016-01-01

    Giardia intestinalis which is a flagellate, intestinal protozoon of humans and a variety of mammalian species, shows worldwide distribution. To date, eight genotypes of the parasite have been identified. Among these genotypes, assemblage A and B have zoonotic characteristics with low host specificity, thus they are responsible for the human infections. The aim of this study was to identify G.intestinalis genotypes in Aydin, located in Aegean region of Turkey. A total of 40 stool samples that were found positive for G.intestinalis by direct microscopic examination, from Adnan Menderes University, Research and Training Hospital, Parasitology Laboratory from January 2011 to December 2014 were included in the study. DNA isolation from stool samples performed with commercial kit (QIAamp DNA Stool Mini Kit, Qiagen, Germany) followed by polymerase chain reaction (PCR) for G.intestinalis 16S rRNA and beta-giardin genes and then the amplicons were sequenced. Out of 40 isolates 11 (27.5%) were positive with 16S rRNA PCR and 10 (25%) were positive with beta-giardin PCR. Of 21 sequenced amplicons, 10 (47.6%) of them showed 98%-100% similarity with reference sequences and their genotypes could be identified. The distribution of genotypes were as follows: cluster A1 (n: 3), cluster A2 (n: 3), cluster A3 (n: 2) and assemblage B (n: 2). In the light of our results the isolates detected in humans might be zoonotic origin. In accordance with the previous reports in Turkey, assemblage A (8/10) was more common than assemblage B (2/10). In the present study, 10 (25%) out of 40 isolates could be genotyped and sequencing of beta-giardin gene yielded more effective results than sequencing of 16S rRNA for the determination of assemblages. The present study indicated that, there is a need for prospective studies with extended number of cases allowing the comparison of the two genes used for G.intestinalis genotyping.

  6. Ancient genomics

    PubMed Central

    Der Sarkissian, Clio; Allentoft, Morten E.; Ávila-Arcos, María C.; Barnett, Ross; Campos, Paula F.; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J.; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D.; Moreno-Mayar, J. Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M. Thomas P.; Willerslev, Eske; Orlando, Ludovic

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. PMID:25487338

  7. Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation.

    PubMed

    Mondal, Mayukh; Casals, Ferran; Xu, Tina; Dall'Olio, Giovanni M; Pybus, Marc; Netea, Mihai G; Comas, David; Laayouni, Hafid; Li, Qibin; Majumder, Partha P; Bertranpetit, Jaume

    2016-09-01

    To shed light on the peopling of South Asia and the origins of the morphological adaptations found there, we analyzed whole-genome sequences from 10 Andamanese individuals and compared them with sequences for 60 individuals from mainland Indian populations with different ethnic histories and with publicly available data from other populations. We show that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves of migration. We also show that populations from South and Southeast Asia harbor a small proportion of ancestry from an unknown extinct hominin, and this ancestry is absent from Europeans and East Asians. The footprints of adaptive selection in the genomes of the Andamanese show that the characteristic distinctive phenotypes of this population (including very short stature) do not reflect an ancient African origin but instead result from strong natural selection on genes related to human body size. PMID:27455350

  8. Ancient origin of a deletion in human BST2/Tetherin that confers protection against viral zoonoses.

    PubMed

    Sauter, Daniel; Vogl, Michael; Kirchhoff, Frank

    2011-11-01

    Bone marrow stromal antigen 2 (BST2)/Tetherin is an antiviral factor that blocks the release of enveloped virions from infected cells. Recent data suggest that efficient BST2 antagonism was a prerequisite for the global spread of HIV/AIDS. Most simian immunodeficiency viruses (SIVs), including the direct precursors of HIV, use their Nef protein to antagonize BST2 of their respective host species. Human BST2, however, contains a five amino acid deletion in its cytoplasmic domain that confers resistance to Nef. Thus, this antiviral factor constitutes a major barrier to effective zoonotic transmissions of SIVs to humans. Here, we show that this protective deletion has already been present in Neanderthal and Denisovan BST2 and thus evolved at least 800,000 years ago. This ancient origin helps to explain why effectively spreading zoonotic transmissions of SIVs to humans have been rare, although SIVs are widespread in African nonhuman primates and humans must have been exposed to these viruses many times.

  9. Human papillomavirus genotypes and their association with cervical neoplasia in a cohort of Western Australian women.

    PubMed

    Brestovac, Brian; Harnett, Gerry B; Smith, David W; Shellam, Geoffrey R; Frost, Felicity A

    2005-05-01

    Human papillomavirus (HPV) is known to be the cause of almost all cervical cancers. The genotypes have been classified into high and low risk types according to their oncogenic potential. However, data for many of the genotypes are limited and some (HPV-26, 53, and 66) have no agreed status. A study was undertaken to determine the HPV genotype distribution in women of Western Australia and the association with cervical neoplasia. Liquid based cervical samples from a cohort of 282 Western Australian women were tested for HPV DNA by PCR followed by DNA sequencing to determine HPV genotypes. HPV-53 and HPV-16 were the most common genotypes found in this population. In addition 86 archived liquid based cervical samples from women with cervical intraepithelial neoplasia grades 1-3 (CIN 1-3) were tested for HPV DNA. Also 32 archived paraffin biopsy samples from women with squamous cell carcinoma were also tested. HPV-16 was the most common genotype found in these samples. Of the cohort of Western Australian women tested, 27% were found to contain HPV and approximately half of these contained known high-risk HPV genotypes, but only 30% of these were types 16 or 18. The data from this study indicate that HPV-53 is not oncogenic based on an R value and odds ratio (OR) of zero. The data also suggest that HPV-73 may be oncogenic, while HPV-66 is unlikely to be. Two high-risk HPV genotypes that are associated with the Asian region (HPV-52 and HPV-58) were found in Western Australian women suggesting a possible epidemiological link between women in these countries.

  10. Low-Density microarray technologies for rapid human norovirus genotyping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Human noroviruses (HuNoV) are the most common cause of food borne disease and viruses are likely responsible for a large proportion of foodborne diseases of unknown etiology. Recent advancements in molecular biology, bioinformatics, epidemiology, and risk analysis have aided the study of these agent...

  11. Low-density microarray technologies for rapid human norovirus genotyping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Human noroviruses cause up to 21 million cases of foodborne disease in the United States annually and are the most common cause of acute gastroenteritis in industrialized countries. To reduce the burden of foodborne disease associated with viruses, the use of low density DNA microarrays in conjuncti...

  12. A revised timescale for human evolution based on ancient mitochondrial genomes

    PubMed Central

    Johnson, Philip L.F.; Bos, Kirsten; Lari, Martina; Bollongino, Ruth; Sun, Chengkai; Giemsch, Liane; Schmitz, Ralf; Burger, Joachim; Ronchitelli, Anna Maria; Martini, Fabio; Cremonesi, Renata G.; Svoboda, Jiří; Bauer, Peter; Caramelli, David; Castellano, Sergi; Reich, David; Pääbo, Svante; Krause, Johannes

    2016-01-01

    Summary Background Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought. Result Here we use mitochondrial genome sequences from 10 securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) of less than 62,000-95,000 years ago. Conclusion Though single loci like mitochondrial DNA (mtDNA) can only provide biased estimates of population split times, they can provide valid upper bounds; our results exclude most of the older dates for African and non-African split times recently suggested by de novo mutation rate estimates in the nuclear genome. PMID:23523248

  13. Modeling ancient Egyptian mummification on fresh human tissue: macroscopic and histological aspects.

    PubMed

    Papageorgopoulou, Christina; Shved, Natallia; Wanek, Johann; Rühli, Frank J

    2015-06-01

    Many studies have been concerned with the ancient Egyptian mummification method; nevertheless, little effort has been made to explore it experimentally. The goal of this study is to apply evidence-based diagnostic criteria and state-of-the art methodology in order to improve knowledge on soft tissues preservation and postmortem alterations. Two human lower limbs (LL) from a female donor were (1) "naturally" mummified by dry heat and (2) artificially in natron. At specific time intervals a macroscopic and radiological examination of the LL was performed and skin and muscle samples were taken for histological and biomolecular analysis. Temperature, humidity, pH, and weight of the LL were systematically measured. The mummification by dry heat was stopped after 7 days due to unexpected lack of mummification progress. The mummification in natron was completed successfully after 208 days. The humidity, the external temperature, and the pH were proven with Pearson correlation and principal component analysis as important factors for the mummification process. The steady removal of water from the tissues through the natron has prevented the putrefaction. This is also evident in the absence of bacteria or fungi through the microbiological analysis. The histological analysis revealed very good preservation of the skin and the muscle tissues. In the muscular sample certain degree of structural disintegration can be seen, particularly affecting the epimysium whilst in the skin samples the epidermis, especially the stratum corneum, is mostly affected. The samples show better preservation compared with ancient Egyptian sections and other mummified tissues from historic or forensic context.

  14. Evidence that the Echinococcus granulosus G6 genotype has an affinity for the brain in humans.

    PubMed

    Sadjjadi, S M; Mikaeili, F; Karamian, M; Maraghi, S; Sadjjadi, F S; Shariat-Torbaghan, S; Kia, E B

    2013-10-01

    The present study investigates the molecular characteristics of cerebral Echinococcus cysts. A total of 10 specimens of cerebral Echinococcus cysts, including six formalin-fixed paraffin blocks and four intact cerebral cysts, were used for this study. The target DNA was successfully amplified from eight samples and sequenced. BLAST analysis indicated that sequenced isolates belong to the Echinococcus granulosus (G6) genotype. All of the eight sampled brain cysts belonged to the G6 genotype, while all of the eight liver cysts belonged to G1. This is a strong indication that G6 has a higher affinity for the human brain than G1.

  15. Human papillomavirus (HPV) infection and genotype frequency in the oral mucosa of newborns in Milan, Italy.

    PubMed

    Martinelli, M; Zappa, A; Bianchi, S; Frati, E; Colzani, D; Amendola, A; Tanzi, E

    2012-06-01

    Human papillomavirus (HPV) causes cutaneous and mucosal infections in both adults and children. In order to evaluate HPV prevalence and the spectrum of genotypes in the oral cavity of paediatric subjects, a retrospective study was carried out on oral-pharyngeal swabs collected from 177 newborns aged 0-6 months. HPV-DNA was detected by a nested-PCR; the viral typing was made through DNA sequencing. HPV infection was identified in 25 subjects (14.1%) and the sequence analysis showed eight distinct genotypes. These data confirm HPV detection in newborn oral mucosa. Further investigations are needed to clarify the methods of HPV acquisition.

  16. From genotype to human β cell phenotype and beyond

    PubMed Central

    Marchetti, Piero; Syed, Farooq; Suleiman, Mara; Bugliani, Marco; Marselli, Lorella

    2012-01-01

    Polygenic type 2 diabetes mellitus (T2DM) is a multi-factorial disease due to the interplay between genes and the environment. Over the years, several genes/loci have been associated with this type of diabetes, with the majority of them being related to β cell dysfunction. In this review, the available information on how polymorphisms in T2DM-associated genes/loci do directly affect the properties of human islet cells are presented and discussed, including some clinical implications and the role of epigenetic mechanisms. PMID:23073174

  17. Detection of rare and possibly carcinogenic human papillomavirus genotypes as single infections in invasive cervical cancer.

    PubMed

    Geraets, Daan; Alemany, Laia; Guimera, Nuria; de Sanjose, Silvia; de Koning, Maurits; Molijn, Anco; Jenkins, David; Bosch, Xavier; Quint, Wim

    2012-12-01

    The contribution of carcinogenic human papillomavirus (HPV) types to the burden of cervical cancer has been well established. However, the role and contribution of phylogenetically related HPV genotypes and rare variants remains uncertain. In a recent global study of 8977 HPV-positive invasive cervical carcinomas (ICCs), the genotype remained unidentified in 3.7% by the HPV SPF10 PCR-DEIA-LiPA25 (version 1) algorithm. The 331 ICC specimens with unknown genotype were analysed by a novel sequence methodology, using multiple selected short regions in L1. This demonstrated HPV genotypes that have infrequently or never been detected in ICC, ie HPV26, 30, 61, 67, 68, 69, 73 and 82, and rare variants of HPV16, 18, 26, 30, 34, 39, 56, 67, 68, 69, 82 and 91. These are not identified individually by LiPA25 and only to some extent by other HPV genotyping assays. Most identified genotypes have a close phylogenetic relationship with established carcinogenic HPVs and have been classified as possibly carcinogenic by IARC. Except for HPV85, all genotypes in α-species 5, 6, 7, 9 and 11 were encountered as single infections in ICCs. These species of established and possibly carcinogenic HPV types form an evolutionary clade. We have shown that the possibly carcinogenic types were detected only in squamous cell carcinomas, which were often keratinizing and diagnosed at a relatively higher mean age (55.3 years) than those associated with established carcinogenic types (50.9 years). The individual frequency of the possibly carcinogenic types in ICCs is low, but together they are associated with 2.25% of the 8338 included ICCs with a single HPV type. This fraction is greater than seven of the established carcinogenic types individually. This study provides evidence that possibly carcinogenic HPV types occur as single infections in invasive cervical cancer, strengthening the circumstantial evidence of a carcinogenic role.

  18. Detection and genotyping of human papillomavirus in breast cancer tissues from Iraqi patients.

    PubMed

    Ali, S H M; Al-Alwan, N A S; Al-Alwany, S H M

    2014-06-18

    Studies have suggested a possible link between breast cancer pathogenesis and human papillomavirus (HPV) infection. This study in Iraq used in situ hybridization to detect the frequency and genotyping of HPV in tissue specimens from 129 patients diagnosed with malignant breast cancer, 24 with benign breast tumours and 20 healthy controls. In the breast cancer group, cocktail HPV genotypes were detected in 60 (46.5%) archived tissue blocks. Of these, genotypes 16 (55.5%), 18 (58.4%), 31 (65.0%) and 33 (26.6%) were detected. Mixed HPV genotypes 16 + 18, 16 + 18 + 31, 16 + 18 + 33, 18 + 33, 16 + 31 and 18 + 31 were found in 5.0%, 25.0%, 8.3%, 7.7%, 10.0% and 13.3% of cancer cases respectively. Only 3 benign breast tumour tissues (12.5%) and none of the healthy breast tissue specimens were HPV-DNA-positive. The detection of high-oncogenic HPV genotypes in patients with breast cancer supports the hypothesis of an etiologic role for the virus in breast cancer development.

  19. Human phenylalanine hydroxylase mutations and hyperphenylalaninemia phenotypes: a metanalysis of genotype-phenotype correlations.

    PubMed Central

    Kayaalp, E; Treacy, E; Waters, P J; Byck, S; Nowacki, P; Scriver, C R

    1997-01-01

    We analyzed correlations between mutant genotypes at the human phenylalanine hydroxylase locus (gene symbol PAH) and the corresponding hyperphenylalaninemia (HPA) phenotypes (notably, phenylketonuria [OMIM 261600]). We used reports, both published and in the PAH Mutation Analysis Consortium Database, on 365 patients harboring 73 different PAH mutations in 161 different genotypes. HPA phenotypes were classified as phenylketonuria (PKU), variant PKU, and non-PKU HPA. By analysis both of homoallelic mutant genotypes and of "functionally hemizygous" heteroallelic genotypes, we characterized the phenotypic effect of 48 of the 73 different, largely missense mutations. Among those with consistent in vivo expression, 24 caused PKU, 3 caused variant PKU, and 10 caused non-PKU HPA. However, 11 mutations were inconsistent in their effect: 9 appeared in two different phenotype classes, and 2 (I65T and Y414C) appeared in all three classes. Seven mutations were inconsistent in phenotypic effect when in vitro (unit-protein) expression was compared with the corresponding in vivo phenotype (an emergent property). We conclude that the majority of PAH mutations confer a consistent phenotype and that this is concordant with their effects, when known, predicted from in vitro expression analysis. However, significant inconsistencies, both between in vitro and in vivo phenotypes and between different individuals with similar PAH genotypes, reveal that the HPA-phenotype is more complex than that predicted by Mendelian inheritance of alleles at the PAH locus. PMID:9399896

  20. Paleogenomics: Investigation of an ancient family of repetitive sequences present in great numbers in human genome

    SciTech Connect

    Zietkiewicz, E.; Labuda, D.; Jurka, J.

    1994-09-01

    Paleogenomics is the research activity aiming to reconstruct ancient genetic events and/or structures from the {open_quotes}fossil{close_quotes} genomic record. With about 120,000 copies, mammalian interspersed repeats, MIRs, represent the second most abundant family of short interspersed repeats in human DNA, only outnumbered by Alu elements. MIR consensus sequence of 100 nucleotides was reconstructed from 455 mutated copies preserved in contemporary genome (GenBank release 69). As no division into subfamilies was observed, we assume that this consensus represents an ancestral MIR sequence. To find out how far MIRs can be traced down the phylogenetic tree, we examined their distribution in a variety of mammalian and non-mammalian DNAs. Oligonucleotide primers based on the MIR consensus were used, one at a time, for PCR amplification of the genomic fragments flanked by MIR repeats (inter-MIR-PCR). Significant amplification in DNA samples from a variety of placental orders as well as marsupials and monotremes indicates that MIRs originated in early mammals. Sequence analysis is consistent with their proliferation during the Mesozoic era. Electrophoretic profiles of inter-MIR-PCR products are distinct among different species. Intra-species comparison of multiple human samples reveals polymorphic bands segregating as Mendelian traits which can be used as genetic markers in both mapping and fingerprinting.

  1. Direct genotyping of animal and human isolates of Toxoplasma gondii from Colombia (South America).

    PubMed

    Gallego, Carolina; Saavedra-Matiz, Carlos; Gómez-Marín, Jorge Enrique

    2006-02-01

    Genetic analysis of the SAG2 locus was performed to determine the prevalence of the main genotypes of Toxoplasma gondii (SAG2 types I, II, and III) associated with humans, cats, birds and guinea pig toxoplasmosis in Colombia. This typing was directly performed on clinical samples and autopsy material from human or animals. A total of 50 from 146 samples were positive by specific B1 Toxoplasma PCR assay and then were analyzed by restriction fragment length polymorphism in PCR-amplified SAG2 products. Characterization of the SAG2 gene was successful in 33 (66%) of the samples. Genotyping indicated that 31 (93.9%) were SAG2 type I, 1 was SAG2 type III and 1 was atypical. In birds and cats all samples were SAG2 type I. Results support a predominance of the Toxoplasma SAG2 type I circulating in human and animals in South America.

  2. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

    PubMed Central

    Ozga, Andrew T.; Nieves‐Colón, Maria A.; Honap, Tanvi P.; Sankaranarayanan, Krithivasan; Hofman, Courtney A.; Milner, George R.; Lewis, Cecil M.; Stone, Anne C.

    2016-01-01

    ABSTRACT Objectives Archaeological dental calculus is a rich source of host‐associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. Materials and Methods Extracted DNA from six individuals at the 700‐year‐old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in‐solution capture techniques, followed by Illumina high‐throughput sequencing. Results Full mitogenomes (7–34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92–100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. Discussion Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220–228, 2016. © 2016 The Authors American Journal of Physical Anthropology

  3. Human beta-globin gene polymorphisms characterized in DNA extracted from ancient bones 12,000 years old.

    PubMed Central

    Béraud-Colomb, E; Roubin, R; Martin, J; Maroc, N; Gardeisen, A; Trabuchet, G; Goosséns, M

    1995-01-01

    Analyzing the nuclear DNA from ancient human bones is an essential step to the understanding of genetic diversity in current populations, provided that such systematic studies are experimentally feasible. This article reports the successful extraction and amplification of nuclear DNA from the beta-globin region from 5 of 10 bone specimens up to 12,000 years old. These have been typed for beta-globin frameworks by sequencing through two variable positions and for a polymorphic (AT) chi (T) gamma microsatellite 500 bp upstream of the beta-globin gene. These specimens of human remains are somewhat older than those analyzed in previous nuclear gene sequencing reports and considerably older than those used to study high-copy-number human mtDNA. These results show that the systematic study of nuclear DNA polymorphisms of ancient populations is feasible. Images Figure 2 Figure 3 PMID:8533755

  4. Differences in Genotypes of Helicobacter pylori from Different Human Populations

    PubMed Central

    Kersulyte, Dangeruta; Mukhopadhyay, Asish K.; Velapatiño, Billie; Su, WanWen; Pan, ZhiJun; Garcia, Claudia; Hernandez, Virginia; Valdez, Yanet; Mistry, Rajesh S.; Gilman, Robert H.; Yuan, Yuan; Gao, Hua; Alarcón, Teresa; López-Brea, Manuel; Balakrish Nair, G.; Chowdhury, Abhijit; Datta, Simanti; Shirai, Mutsunori; Nakazawa, Teruko; Ally, Reidwaan; Segal, Isidore; Wong, Benjamin C. Y.; Lam, S. K.; Olfat, Farzad O.; Borén, Thomas; Engstrand, Lars; Torres, Olga; Schneider, Roberto; Thomas, Julian E.; Czinn, Steven; Berg, Douglas E.

    2000-01-01

    DNA motifs at several informative loci in more than 500 strains of Helicobacter pylori from five continents were studied by PCR and sequencing to gain insights into the evolution of this gastric pathogen. Five types of deletion, insertion, and substitution motifs were found at the right end of the H. pylori cag pathogenicity island. Of the three most common motifs, type I predominated in Spaniards, native Peruvians, and Guatemalan Ladinos (mixed Amerindian-European ancestry) and also in native Africans and U.S. residents; type II predominated among Japanese and Chinese; and type III predominated in Indians from Calcutta. Sequences in the cagA gene and in vacAm1 type alleles of the vacuolating cytotoxin gene (vacA) of strains from native Peruvians were also more like those from Spaniards than those from Asians. These indications of relatedness of Latin American and Spanish strains, despite the closer genetic relatedness of Amerindian and Asian people themselves, lead us to suggest that H. pylori may have been brought to the New World by European conquerors and colonists about 500 years ago. This thinking, in turn, suggests that H. pylori infection might have become widespread in people quite recently in human evolution. PMID:10809702

  5. Comparison of INNO-LiPA HPV Genotyping v2 with PCR product subcloning and sequencing for identification of genital human papillomavirus genotypes in African women.

    PubMed

    Didelot-Rousseau, Marie-Noëlle; Courgnaud, Valérie; Nagot, Nicolas; Ouedraogo, Abdoulaye; Konate, Issouf; Mayaud, Philippe; Weiss, Helen; Van de Perre, Philippe; Segondy, Michel

    2006-08-01

    The performance characteristics of the INNO-LiPA Genotyping v2 test for human papillomavirus (HPV) identification were assessed by comparing results with those obtained by PCR product sequencing after subcloning, in genital samples from 20 highly sexually exposed African women. The INNO-LiPA HPV Genotyping v2 test identified more HPV types than subcloning/sequencing (56 versus 37, respectively). Overall, 86.5% (32/37) of the HPV types identified by subcloning/sequencing were identified by the INNO-LiPA HPV Genotyping v2 test, whereas 57.1% (32/56) of the HPV types identified by the INNO-LiPA HPV Genotyping v2 test were identified by subcloning/sequencing. Of the 20 clinical samples tested, 7 had identical types detected under both methods and a further 11 had more types detected under INNO-LiPA HPV Genotyping v2 than subcloning/sequencing. Of the remaining two samples, the same number of types were detected under both methods, but different types were detected. INNO-LiPA HPV Genotyping v2 test appears as a valid method for identifying HPV subtypes in women with multiple HPV infection. PMID:16675035

  6. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    PubMed Central

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed M. Vargas; Parker, Brian J.; Rasmussen, Morten; Lindgreen, Stinus; Lilje, Berit; Tobin, Desmond J.; Kelly, Theresa K.; Vang, Søren; Andersson, Robin; Jones, Peter A.; Hoover, Cindi A.; Tikhonov, Alexei; Prokhortchouk, Egor; Rubin, Edward M.; Sandelin, Albin; Gilbert, M. Thomas P.; Krogh, Anders; Willerslev, Eske; Orlando, Ludovic

    2014-01-01

    Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues. Using ancient methylation information, we estimated the age at death of the Saqqaq individual and illustrate how epigenetic information can be used to infer ancient gene expression. Similar epigenetic signatures were found in other fossil material, such as 110,000- to 130,000-yr-old bones, supporting the contention that ancient epigenomic information can be reconstructed from a deep past. Our findings lay the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time, as well as providing an original window into modern epigenomics. PMID:24299735

  7. Prevalence and genotype distribution of human papillomavirus among Hakka women in China

    PubMed Central

    Zeng, Xiang-Xing; Yan, Li-Xiang; Huang, Xiu-Xia; He, Cai-Hua; Liu, Wei-Guo; Yuan, Wen-Qing; Qiu, Yan-Ping

    2016-01-01

    Background Human papillomavirus (HPV) infection is the primary risk factor for cervical cancer. HPV genotypes are associated with varying degrees of pathogenicity. To better formulate strategies for cervical cancer prevention, we investigated the population-specific distribution of HPV genotypes, including those with high carcinogenicity. Methods From January to December 2012, a cervical cancer-screening program for HPV infection in Hakka women of Heyuan City Guangdong province was conducted. Of 736,000 women residents, 8,284 volunteers were recruited. The cytology specimens of 107 women were not adequate and excluded. Thus, 8,177 women submitted to polymerase chain reaction (PCR) sequencing of 16 HPV genotypes via MassARRAY spectrometry. Results Risk stratification based on genotypes indicated that the prevalence of overall, high-risk, and low-risk HPV infections was 12.27%, 14.20%, and 0.79%, respectively. Of the 1,003 women positively infected, 82.75% were infected with a single HPV type; 17.25% were infected with ≥2 types. Analysis revealed a U-shaped curve in HPV prevalence that correlated with age group, with peaks at ages 18–24 y (22.03%) and 60–65 y (25%). The most frequently detected HPV genotype was HPV-52 (26.81%), and then HPV-16 (17.54%), HPV-58 (14.25%), HPV-18 (10.16%), HPV-68 (8.27%), HPV-39 (5.68%), and HPV-51 (5.38%). Conclusions HPV-52 is the most prevalent genotype infecting Hakka women. Therefore, vaccination against HPV-52 is imperative. The prevalence of HPV infection is highest in the younger (18–24 y) and older (60–65 y) age groups, indicating that screening for HPV in Hakka women should be performed early and maintained in the elderly. PMID:27570770

  8. Human papilloma virus genotypes in women from Nayarit, Mexico, with squamous intraepithelial lesions and cervical cancer

    PubMed Central

    Ortega-Cervantes, Laura; Aguilar-Lemarroy, Adriana; Rojas-García, Aurora Elizabeth; Barrón-Vivanco, Briscia Socorro; Vallejo-Ruiz, Verónica; León, David Cantú-De; Hernández, Yael Yvette Bernal; Jáuregui-Martínez, Armando; Medina-Díaz, Irma Martha

    2016-01-01

    Objective In Mexico cervical cancer (CC) is the most common cause of death from neoplasia in women. Study aimed to analyze the current distribution of Human papillomavirus (HPV) types in women from Nayarit, Mexico, with Squamous intraepithelial lesions (SIL) and Cervical cancer (CC). Methodology Between January 2011 and July 2013, cervical samples were collected from female residents of the Mexican state of Nayarit and were analyzed by means of a LINEAR ARRAY® HPV genotyping test. Data analyses were performed using Stata ver. 8.0 statistical software. Results Of the samples analyzed, 91.2%, HPV DNA was detected. Of these positive samples, 82% were High-risk (HR) viral types. The most prevalent HPV genotypes identified were 16, 58, 31, 18, and 70. Forty two percent of participants had a single infection, while 23 and 26% of participants were infected with two or more HPV genotypes, respectively. HPV 16 was the most prevalent genotype identified and was frequently present as a co-infection with HPV types 18, 51, 52, 59, 66, or 70. Conclusion Women <20 years of age were most often infected with HPV, and the HPV Quadrivalent vaccine (types 16, 18, 6, and 11), currently available in Mexico, no confers protection against a subset of the HPV genotypes identified in the present study (58, 31, 70, and 35). Thus, it is important evaluate the geographical distribution of specific HPV genotypes in all health of center across Mexico in order to implement a successful vaccination program and to diagnose CC in its early stages. PMID:27610056

  9. Human papilloma virus genotypes in women from Nayarit, Mexico, with squamous intraepithelial lesions and cervical cancer

    PubMed Central

    Ortega-Cervantes, Laura; Aguilar-Lemarroy, Adriana; Rojas-García, Aurora Elizabeth; Barrón-Vivanco, Briscia Socorro; Vallejo-Ruiz, Verónica; León, David Cantú-De; Hernández, Yael Yvette Bernal; Jáuregui-Martínez, Armando; Medina-Díaz, Irma Martha

    2016-01-01

    Objective In Mexico cervical cancer (CC) is the most common cause of death from neoplasia in women. Study aimed to analyze the current distribution of Human papillomavirus (HPV) types in women from Nayarit, Mexico, with Squamous intraepithelial lesions (SIL) and Cervical cancer (CC). Methodology Between January 2011 and July 2013, cervical samples were collected from female residents of the Mexican state of Nayarit and were analyzed by means of a LINEAR ARRAY® HPV genotyping test. Data analyses were performed using Stata ver. 8.0 statistical software. Results Of the samples analyzed, 91.2%, HPV DNA was detected. Of these positive samples, 82% were High-risk (HR) viral types. The most prevalent HPV genotypes identified were 16, 58, 31, 18, and 70. Forty two percent of participants had a single infection, while 23 and 26% of participants were infected with two or more HPV genotypes, respectively. HPV 16 was the most prevalent genotype identified and was frequently present as a co-infection with HPV types 18, 51, 52, 59, 66, or 70. Conclusion Women <20 years of age were most often infected with HPV, and the HPV Quadrivalent vaccine (types 16, 18, 6, and 11), currently available in Mexico, no confers protection against a subset of the HPV genotypes identified in the present study (58, 31, 70, and 35). Thus, it is important evaluate the geographical distribution of specific HPV genotypes in all health of center across Mexico in order to implement a successful vaccination program and to diagnose CC in its early stages.

  10. Distribution and chemical speciation of arsenic in ancient human hair using synchrotron radiation.

    PubMed

    Kakoulli, Ioanna; Prikhodko, Sergey V; Fischer, Christian; Cilluffo, Marianne; Uribe, Mauricio; Bechtel, Hans A; Fakra, Sirine C; Marcus, Matthew A

    2014-01-01

    Pre-Columbian populations that inhabited the Tarapacá mid river valley in the Atacama Desert in Chile during the Middle Horizon and Late Intermediate Period (AD 500-1450) show patterns of chronic poisoning due to exposure to geogenic arsenic. Exposure of these people to arsenic was assessed using synchrotron-based elemental X-ray fluorescence mapping, X-ray absorption spectroscopy, X-ray diffraction and Fourier transform infrared spectromicroscopy measurements on ancient human hair. These combined techniques of high sensitivity and specificity enabled the discrimination between endogenous and exogenous processes that has been an analytical challenge for archeological studies and criminal investigations in which hair is used as a proxy of premortem metabolism. The high concentration of arsenic mainly in the form of inorganic As(III) and As(V) detected in the hair suggests chronic arsenicism through ingestion of As-polluted water rather than external contamination by the deposition of heavy metals due to metallophilic soil microbes or diffusion of arsenic from the soil. A decrease in arsenic concentration from the proximal to the distal end of the hair shaft analyzed may indicate a change in the diet due to mobility, though chemical or microbiologically induced processes during burial cannot be entirely ruled out. PMID:24320096

  11. Distribution and chemical speciation of arsenic in ancient human hair using synchrotron radiation.

    PubMed

    Kakoulli, Ioanna; Prikhodko, Sergey V; Fischer, Christian; Cilluffo, Marianne; Uribe, Mauricio; Bechtel, Hans A; Fakra, Sirine C; Marcus, Matthew A

    2014-01-01

    Pre-Columbian populations that inhabited the Tarapacá mid river valley in the Atacama Desert in Chile during the Middle Horizon and Late Intermediate Period (AD 500-1450) show patterns of chronic poisoning due to exposure to geogenic arsenic. Exposure of these people to arsenic was assessed using synchrotron-based elemental X-ray fluorescence mapping, X-ray absorption spectroscopy, X-ray diffraction and Fourier transform infrared spectromicroscopy measurements on ancient human hair. These combined techniques of high sensitivity and specificity enabled the discrimination between endogenous and exogenous processes that has been an analytical challenge for archeological studies and criminal investigations in which hair is used as a proxy of premortem metabolism. The high concentration of arsenic mainly in the form of inorganic As(III) and As(V) detected in the hair suggests chronic arsenicism through ingestion of As-polluted water rather than external contamination by the deposition of heavy metals due to metallophilic soil microbes or diffusion of arsenic from the soil. A decrease in arsenic concentration from the proximal to the distal end of the hair shaft analyzed may indicate a change in the diet due to mobility, though chemical or microbiologically induced processes during burial cannot be entirely ruled out.

  12. SNP genotyping of animal and human derived isolates of Mycobacterium avium subsp. paratuberculosis.

    PubMed

    Wynne, James W; Beller, Christie; Boyd, Victoria; Francis, Barry; Gwoźdź, Jacek; Carajias, Marios; Heine, Hans G; Wagner, Josef; Kirkwood, Carl D; Michalski, Wojtek P

    2014-08-27

    Mycobacterium avium subsp. paratuberculosis (MAP) is the aetiological agent of Johne's disease (JD), a chronic granulomatous enteritis that affects ruminants worldwide. While the ability of MAP to cause disease in animals is clear, the role of this bacterium in human inflammatory bowel diseases remains unresolved. Previous whole genome sequencing of MAP isolates derived from human and three animal hosts showed that human isolates were genetically similar and showed a close phylogenetic relationship to one bovine isolate. In contrast, other animal derived isolates were more genetically diverse. The present study aimed to investigate the frequency of this human strain across 52 wild-type MAP isolates, collected predominantly from Australia. A Luminex based SNP genotyping approach was utilised to genotype SNPs that had previously been shown to be specific to the human, bovine or ovine isolate types. Fourteen SNPs were initially evaluated across a reference panel of isolates with known genotypes. A subset of seven SNPs was chosen for analysis within the wild-type collection. Of the seven SNPs, three were found to be unique to paediatric human isolates. No wild-type isolates contain these SNP alleles. Interestingly, and in contrast to the paediatric isolates, three additional adult human isolates (derived from adult Crohn's disease patients) also did not contain these SNP alleles. Furthermore we identified two SNPs, which demonstrate extensive polymorphism within the animal-derived MAP isolates. One of which appears unique to ovine and a single camel isolate. From this study we suggest the existence of genetic heterogeneity between human derived MAP isolates, some of which are highly similar to those derived from bovine hosts, but others of which are more divergent.

  13. Chlamydophila psittaci genotype E/B transmission from African grey parrots to humans.

    PubMed

    Harkinezhad, Taher; Verminnen, Kristel; Van Droogenbroeck, Caroline; Vanrompay, Daisy

    2007-08-01

    Thirty-six birds from a parrot relief and breeding centre, as well as the manager, were examined for the presence of Chlamydophila psittaci. In the relief unit, 5 of 20 African grey parrots showed depression, ruffled feathers, loss of weight and mild dyspnoea. The birds received no antibiotic treatment. Birds of the breeding unit, 14 blue and gold macaws and 2 green-winged macaws, were healthy. They received doxycycline at the start of each breeding season. The manager complained of shortness of breath but took no medication. Using a nested PCR enzyme immunoassay (EIA), Cp. psittaci was detected in the faeces of all five sick birds, as well as in a nasal and pharyngeal swab from the manager. The veterinarian and her assistant became infected while sampling the parrots, as pharyngeal and nasal swabs from both were positive by nested PCR/EIA after visiting the parrot relief and breeding centre, but they showed no clinical signs of infection. Bacteria could be isolated from three of five nested PCR/EIA-positive birds, the manager and the veterinarian, but not from the veterinary assistant. Using an ompA genotype-specific real-time PCR, Cp. psittaci genotype E/B was identified as the transmitted strain. All breeding birds tested negative for Cp. psittaci. This is believed to be the first report on Cp. psittaci genotype E/B transmission from parrots to humans. In contradiction to genotype A strains, which are thought to be highly virulent to both birds and men, the currently described genotype E/B strain apparently caused no severe clinical symptoms in either parrots or humans.

  14. Genotyping of Echinococcus granulosus from domestic animals and humans from Ardabil Province, northwest Iran.

    PubMed

    Pezeshki, A; Akhlaghi, L; Sharbatkhori, M; Razmjou, E; Oormazdi, H; Mohebali, M; Meamar, A R

    2013-12-01

    Cystic echinococcosis is endemic in Iran, particularly in Ardabil Province, where it causes health and economic problems. The genetic pattern of Echinococcus granulosus has been determined in most parts of Iran, except in this area. In the present investigation, 55 larval isolates were collected from humans (11), sheep (19), goats (4) and cattle (21). For analysis of the genetic characteristics of E. granulosus isolates, DNA sequencing of mitochondrial cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) genes was applied. Fifty isolates were successfully analysed, with 92% (46) and 8% (4) identified as G1 and G3 genotypes, respectively. The sequence analyses of the isolates displayed nine characteristic profiles in cox1 sequences and eight characteristic profiles in nad1 sequences. Based on these results, the sheep strain (G1 genotype) was the most prevalent in humans, sheep, goats and cattle. The buffalo strain (G3 genotype) was not only demonstrated in sheep (1 isolate) and cattle (1 isolate), but also for the first time in two human isolates. These findings will provide information for local control of echinococcosis.

  15. Easy and fast detection and genotyping of high-risk human papillomavirus by dedicated DNA microarrays.

    PubMed

    Albrecht, Valérie; Chevallier, Anne; Magnone, Virginie; Barbry, Pascal; Vandenbos, Fanny; Bongain, André; Lefebvre, Jean-Claude; Giordanengo, Valérie

    2006-11-01

    Persistent cervical high-risk human papillomavirus (HPV) infection is correlated with an increased risk of developing a high-grade cervical intraepithelial lesion. A two-step method was developed for detection and genotyping of high-risk HPV. DNA was firstly amplified by asymmetrical PCR in the presence of Cy3-labelled primers and dUTP. Labelled DNA was then genotyped using DNA microarray hybridization. The current study evaluated the technical efficacy of laboratory-designed HPV DNA microarrays for high-risk HPV genotyping on 57 malignant and non-malignant cervical smears. The approach was evaluated for a broad range of cytological samples: high-grade squamous intraepithelial lesions (HSIL), low-grade squamous intraepithelial lesions (LSIL) and atypical squamous cells of high-grade (ASC-H). High-risk HPV was also detected in six atypical squamous cells of undetermined significance (ASC-US) samples; among them only one cervical specimen was found uninfected, associated with no histological lesion. The HPV oligonucleotide DNA microarray genotyping detected 36 infections with a single high-risk HPV type and 5 multiple infections with several high-risk types. Taken together, these results demonstrate the sensitivity and specificity of the HPV DNA microarray approach. This approach could improve clinical management of patients with cervical cytological abnormalities. PMID:16879879

  16. Evaluation of the Editing Process in Human Immunodeficiency Virus Type 1 Genotyping

    PubMed Central

    Huang, Diana D.; Eshleman, Susan H.; Brambilla, Donald J.; Palumbo, Paul E.; Bremer, James W.

    2003-01-01

    Sequencing-based human immunodeficiency virus type 1 (HIV-1) genotyping assays require subjective interpretation (editing) of sequence data from multiple primers to form consensus sequences and identify antiretroviral drug resistance mutations. We assessed interlaboratory variations in editing and their impact on the recognition of resistance mutations. Six samples were analyzed in a central laboratory by using a research-use-only HIV-1 genotyping system previously produced by Applied Biosystems. The electronic files of individual primer sequences from the samples were sent to 10 laboratories to compare sequence editing strategies. Each sequence data set included sequences from seven primers spanning protease codons 1 to 99 and reverse transcriptase codons 1 to 320. Each laboratory generated a consensus sequence for each sample and completed a questionnaire about editing strategy. The amount of editing performed, the concordance of consensus sequences among the laboratories, and the identification of resistance mutations were evaluated. Sequence agreement was high among the laboratories despite wide variations in editing strategies. All laboratories identified 66 (88%) of 75 resistance mutations in the samples. Nonconcordant identifications were made for 9 (12%) of the 75 mutations, all of which required editing for identification. These results indicate a need for standardized editing guidelines in genotyping assays. Proficiency in editing should be assessed in training and included in quality control programs for HIV-1 genotyping. PMID:12843074

  17. High-risk human papillomavirus genotypes in cervical lesions and vaccination challenges in China.

    PubMed

    Xu, Qiu-Xiang; Zhang, Zhen-Yu

    2015-01-01

    Cervical cancer, mostly progressing from cervical intraepithelial neoplasia, is a major cause of morbidity and mortality in Chinese women. This is largely due to high prevalence of high-risk human papillomaviruses (hr-HPVs) in the population. The prevalence of hr-HPV DNA in women and in cervical lesions women ranged from 9.9% to 17.% and from 50.5% to 70.9% in different regions of China, respectively. The most common genotypes somewhat differ between regions throughout the country and from those in many other countries. This may be a challenge to cervical cancer screening and prevention in China. Combined detection of particular HPV genotypes should be recommended in all geographical regions in China and greater attention must be paid to specific hr-HPV types during cervical cancer screening and follow-up of cervical lesions. Besides, vaccination for prevention of cervical cancer by particular HPV genotypes, has not been introduced to China so far. Updated knowledge on prevalent HPV genotypes should be provided to public health organizations to help with the development of more effective HPV vaccines, which can protect Chinese women against HPV types prevalent in local China and thus have a substantial impact on the cervical cancer burden.

  18. Prevalence and genotype distribution of human papillomavirus infection in asymptomatic women in Liaoning province, China.

    PubMed

    Xue, Hui; Lin, Xuyong; Li, Tianren; Yan, Xiaoxia; Guo, Kejun; Zhang, Yi

    2015-07-01

    Infection by human papillomavirus (HPV) is a necessary cause of cervical cancer. The purpose of this study was to investigate the prevalence and genotype distribution of HPV infection in Chinese women who were asymptomatic for cervical diseases. Cervical cytology samples were collected from 6479 asymptomatic Chinese women of Liaoning province, and tested for various HPV genotypes using a chip hybridization assay. HPV was found in 10.3% of all the asymptomatic women studied, with the prevalence of high risk HPV (HR HPV) and low risk HPV (LR HPV) being 9.5% and 1.1%, respectively. HPV genotypes 16, 52, and 58 were found the most frequently genotypes in the HR HPV positive women, and were present in 26.2%, 19.4% and 13.8%, respectively. A graph of HR HPV positive infection rates as a function of age is U-shaped, with a peak in women less than 30 years old and a second peak among women older than 50 years. Nearly half of the women infected with either HR HPV or LR HPV presented a normal looking cervix upon visual examination. The current study demonstrates that the epidemiology of HPV infection in asymptomatic Chinese women in Liaoning province is different from that in women from other regions, even from patients with cervical lesions in the same region. These findings could be used to guide the generation and design of an HPV vaccine for this population.

  19. Human Endometrial Side Population Cells Exhibit Genotypic, Phenotypic and Functional Features of Somatic Stem Cells

    PubMed Central

    Cervelló, Irene; Gil-Sanchis, Claudia; Mas, Aymara; Delgado-Rosas, Francisco; Martínez-Conejero, José Antonio; Galán, Amparo; Martínez-Romero, Alicia; Martínez, Sebastian; Navarro, Ismael; Ferro, Jaime; Horcajadas, José Antonio; Esteban, Francisco José; O'Connor, José Enrique; Pellicer, Antonio; Simón, Carlos

    2010-01-01

    During reproductive life, the human endometrium undergoes around 480 cycles of growth, breakdown and regeneration should pregnancy not be achieved. This outstanding regenerative capacity is the basis for women's cycling and its dysfunction may be involved in the etiology of pathological disorders. Therefore, the human endometrial tissue must rely on a remarkable endometrial somatic stem cells (SSC) population. Here we explore the hypothesis that human endometrial side population (SP) cells correspond to somatic stem cells. We isolated, identified and characterized the SP corresponding to the stromal and epithelial compartments using endometrial SP genes signature, immunophenotyping and characteristic telomerase pattern. We analyzed the clonogenic activity of SP cells under hypoxic conditions and the differentiation capacity in vitro to adipogenic and osteogenic lineages. Finally, we demonstrated the functional capability of endometrial SP to develop human endometrium after subcutaneous injection in NOD-SCID mice. Briefly, SP cells of human endometrium from epithelial and stromal compartments display genotypic, phenotypic and functional features of SSC. PMID:20585575

  20. Prevalence and genotype distribution of cervical human papillomavirus (HPV) among women in urban Tianjin, China.

    PubMed

    Chen, Xiujie; Wallin, Keng-Ling; Duan, Meng; Gharizadeh, Baback; Zheng, Biying; Qu, Pengpeng

    2015-11-01

    To investigate the prevalence and genotype distribution of human papillomavirus (HPV) infection among women in urban Tianjin, China. A cervical cancer screening program for 2,000 women aged 21-65 years old was performed in urban Tianjin from April to October in 2013. The program included ThinPrep cytologic tests (TCT), HPV DNA detection and genotyping using nested polymerase chain reaction (PCR) combined with Pyrosequencing technology. Colposcopy examination and biopsy were needed if TCT reported greater or equal atypical cells of undetermined significance (ASCUS). One thousand nine hundred seventy-eight women were enrolled in the final study, 14.71% (291/1,978) of women were tested HPV positive. Of HPV-positive specimens, 248 (85.22%) and 43 (14.78%) were infected with high- and low-risk HPV genotypes, respectively. Twenty-eight types of HPV were detected in all, the most frequently detected types were HPV16, 58, 18, and 66 orderly. The single infection rate was 92.28% among HPV-positive samples while the multiple infection rate was 7.72%. Among multiple infection models, HPV16 was the most common type co-infection with other types. This study is, to our knowledge, the first population-based survey to provide data on HPV infection and genotype distribution among women in urban Tianjin, China. There was a high prevalence of HPV infection in this area, and HPV16, 58, 18, 66 were the most frequently detected genotypes. Our study provide important information regarding the necessity of early cervical cancer screenings and prophylactic HPV vaccinations, and the knowledge of HPV distribution can also inform us about the HPV ecological change after the vaccination.

  1. Distribution of genital wart human papillomavirus genotypes in China: a multi-center study.

    PubMed

    Chang, Lihong; Ci, Puwa; Shi, Jufang; Zhai, Kan; Feng, Xiaoli; Colombara, Danny; Wang, Wei; Qiao, Youlin; Chen, Wen; Wu, Yuping

    2013-10-01

    Although it is understood that low-risk human papillomavirus (HPV) genotypes are associated with genital warts, there have been very few published studies reporting the genotype-specific prevalence of HPV among Chinese population. The aim of the study was to assess the prevalence of HPV genotypes in genital warts across China, and thus to evaluate the potential benefit of a quadrivalent HPV vaccine in this population. The tissue samples of a total of 1,005 genital warts cases were collected from seven geographical regions of China. HPV genotypes were analyzed using the general primer PCR and sequence-based typing method. Prevalence differences between sexes, geographical regions and age groups were assessed. The overall prevalence of HPV DNA in genital warts patients was 88.7% (891/1,005). Low-risk genotypes predominated, with a prevalence of 78.1% (785/1,005). The most prevalent genotypes were HPV-6 (41.3%), HPV-11 (37.6%) and HPV-16 (10.4%). Among HPV positive patients, single infections were more frequent (866/891, 97.2%) than co-infections (25/891, 2.8%). Both the overall prevalence of HPV DNA and that of HPV-6/-11/-16 (positive for any of the three types) decreased with age (P-trend = 0.010 and P-trend = 0.025, respectively). The prevalence of HPV-6/-11 (positive for either HPV type) and HPV-16 varied by geographic region (P = 0.003 and P ≤ 0.001, respectively). The prevalence of HPV-16 in female patients between urban and rural areas showed a marginally significant difference (P = 0.05). In sum, the results provide strong evidence that, in China, the most prevalent HPV genotypes in genital warts are HPV-6, HPV-11 and HPV-16. This indicates that a quadrivalent HPV vaccine may decrease the incidence of genital warts in the future.

  2. Microarray based comparative genotyping of gentamicin resistant Escherichia coli strains from food animals and humans.

    PubMed

    Szmolka, Ama; Anjum, Muna F; La Ragione, Roberto M; Kaszanyitzky, Eva J; Nagy, Béla

    2012-04-23

    Recent data from the European and Hungarian Antimicrobial Resistance Monitoring Systems have indicated that the routine use of gentamicin in human and veterinary medicine frequently leads to the selection of gentamicin resistance in Escherichia coli. The aim of this study was to provide molecular characterization of gentamicin resistance in clinical and commensal E. coli strains representing humans and food producing animals by genotyping for antimicrobial resistance and virulence using a miniaturized microarray. All 50 strains tested proved to be multidrug resistant defined as resistance to three or more antimicrobial classes. Antimicrobial resistances genes such as aadA1-like, strB, bla(TEM), sul1 and tet(A) or tet(B), and corresponding phenotypes (streptomycin-, ampicillin-, sulfamethoxazole- and tetracycline resistance) were detected in >50% of isolates regardless of the host or clinical background. However, certain genes encoding gentamicin resistance such as aac(6')-Ib and ant(2″)-Ia as well as catB3-like genes for phenicol resistance were only detected in human isolates. Among virulence genes, the increased serum survival gene iss was predominant in all host groups. Although the majority of gentamicin resistant E. coli strains were characterized by diverse antimicrobial resistance, and virulence gene patterns, accentuated links between catB3-like, aac(6')-Ib, bla(CTX-M-1) and sat genes could be detected in human strains. Further resistance/virulence gene associations (tet(A) with iroN and iss) were detected in poultry strains. In conclusion, the simultaneous characterization of antimicrobial resistance and virulence genotypes of representative clinical and commensal strains of E. coli should be useful for the identification of emerging genotypes with human and or animal health implications.

  3. Ancient cellular structures and modern humans: change of survival strategies before prolonged low solar activity period

    NASA Astrophysics Data System (ADS)

    Ragulskaya, Mariya; Rudenchik, Evgeniy; Gromozova, Elena; Voychuk, Sergei; Kachur, Tatiana

    The study of biotropic effects of modern space weather carries the information about the rhythms and features of adaptation of early biological systems to the outer space influence. The influence of cosmic rays, ultraviolet waves and geomagnetic field on early life has its signs in modern biosphere processes. These phenomena could be experimentally studied on present-day biological objects. Particularly inorganic polyphosphates, so-called "fossil molecules", attracts special attention as the most ancient molecules which arose in inanimate nature and have been accompanying biological objects at all stages of evolution. Polyphosphates-containing graves of yeast's cells of Saccharomyces cerevisiae strain Y-517, , from the Ukrainian Collection of Microorganisms was studied by daily measurements during 2000-2013 years. The IZMIRAN daily data base of physiological parameters dynamics during 2000-2013 years were analyzed simultaneously (25 people). The analysis showed significant simultaneous changes of the statistical parameters of the studied biological systems in 2004 -2006. The similarity of simultaneous changes of adaptation strategies of human organism and the cell structures of Saccharomyces cerevisiae during the 23-24 cycles of solar activity are discussed. This phenomenon could be due to a replacement of bio-effective parameters of space weather during the change from 23rd to 24th solar activity cycle and nonstandard geophysical peculiarities of the 24th solar activity cycle. It could be suggested that the observed similarity arose as the optimization of evolution selection of the living systems in expectation of probable prolonged period of low solar activity (4-6 cycles of solar activity).

  4. Widespread presence of human BOULE homologs among animals and conservation of their ancient reproductive function.

    PubMed

    Shah, Chirag; Vangompel, Michael J W; Naeem, Villian; Chen, Yanmei; Lee, Terrance; Angeloni, Nicholas; Wang, Yin; Xu, Eugene Yujun

    2010-07-15

    Sex-specific traits that lead to the production of dimorphic gametes, sperm in males and eggs in females, are fundamental for sexual reproduction and accordingly widespread among animals. Yet the sex-biased genes that underlie these sex-specific traits are under strong selective pressure, and as a result of adaptive evolution they often become divergent. Indeed out of hundreds of male or female fertility genes identified in diverse organisms, only a very small number of them are implicated specifically in reproduction in more than one lineage. Few genes have exhibited a sex-biased, reproductive-specific requirement beyond a given phylum, raising the question of whether any sex-specific gametogenesis factors could be conserved and whether gametogenesis might have evolved multiple times. Here we describe a metazoan origin of a conserved human reproductive protein, BOULE, and its prevalence from primitive basal metazoans to chordates. We found that BOULE homologs are present in the genomes of representative species of each of the major lineages of metazoans and exhibit reproductive-specific expression in all species examined, with a preponderance of male-biased expression. Examination of Boule evolution within insect and mammalian lineages revealed little evidence for accelerated evolution, unlike most reproductive genes. Instead, purifying selection was the major force behind Boule evolution. Furthermore, loss of function of mammalian Boule resulted in male-specific infertility and a global arrest of sperm development remarkably similar to the phenotype in an insect boule mutation. This work demonstrates the conservation of a reproductive protein throughout eumetazoa, its predominant testis-biased expression in diverse bilaterian species, and conservation of a male gametogenic requirement in mice. This shows an ancient gametogenesis requirement for Boule among Bilateria and supports a model of a common origin of spermatogenesis.

  5. The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data

    PubMed Central

    Kodama, Yuichi; Mashima, Jun; Kosuge, Takehide; Katayama, Toshiaki; Fujisawa, Takatomo; Kaminuma, Eli; Ogasawara, Osamu; Okubo, Kousaku; Takagi, Toshihisa; Nakamura, Yasukazu

    2015-01-01

    The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information. Since October 2013, DDBJ Center has operated the Japanese Genotype-phenotype Archive (JGA) in collaboration with our partner institute, the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency. DDBJ Center provides the JGA database system which securely stores genotype and phenotype data collected from individuals whose consent agreements authorize data release only for specific research use. NBDC has established guidelines and policies for sharing human-derived data and reviews data submission and usage requests from researchers. In addition to the JGA project, DDBJ Center develops Semantic Web technologies for data integration and sharing in collaboration with the Database Center for Life Science. This paper describes the overview of the JGA project, updates to the DDBJ databases, and services for data retrieval, analysis and integration. PMID:25477381

  6. First detection and genotyping of human-associated microsporidia in wild waterfowl of Slovakia.

    PubMed

    Malčeková, B; Valenčáková, A; Molnár, L; Kočišová, A

    2013-03-01

    A total of 47 avian faecal samples of wild waterfowl (great cormorant - Phalacrocorax carbo, great crested grebe - Podiceps cristatus, white stork - Ciconia ciconia) trapped in the eastern Slovakia were screened for the presence of human pathogenic microsporidia by microscopy and real-time SYBR Green PCR method using species primers and sequenced. Microscopic analysis showed presence in 32 samples (29 cormorants, 3 dippers). Microsporidial DNA (Encephalitozoon cuniculi genotype I) was identified in 19 faeces samples (40.4%) namely cormorants in 17 out of 40, one dipper of 5 and a stork out of 2. The present work describes three new host species of the bird population in microsporidium Encephalitozoon cuniculi genotype I which confirms the theory of low specificity of this species. PMID:23377906

  7. Human Papillomavirus Prevalence and Genotype Distribution among HIV-Infected Women in Korea

    PubMed Central

    Park, Eun Kyoung; Cho, Heerim; Lee, Seung Geun; Lee, Sang Yeup; Kim, Ki Hyung; Lee, Chang Hun; Chung, Joo Seop; Kwak, Ihm Soo

    2014-01-01

    The epidemiology on human papillomavirus (HPV) among human immunodeficiency virus (HIV)-infected women in Korea is not well established. A retrospective study was conducted to determine the prevalence and genotype distribution of HPV infection among HIV-infected women in Korea. HPV DNA genotype and cervical cytology were examined in 60 HIV-positive women and 1,938 HIV-negative women. HPV genotypes were analyzed by using a HPV DNA chip. HIV-infected women had higher prevalence of high-risk HPV (hr-HPV) infection (30% vs 4.9%, adjusted odds ratio [AOR], 6.96; 95% confidence interval [CI], 3.63-13.34, P<0.001) and abnormal cervical cytology (18.3% vs 1.8%, AOR, 10.94; 95% CI, 5.18-23.1, P<0.001) compared with controls. The most common hr-HPV genotype detected in HIV-infected women was HPV 16 (10%), followed by 18 (6.7%) and 52 (5%). Prevalence of quadrivalent vaccine-preventable types (HPV 6, 11, 16, and 18) was 21.7% and 2.3% in HIV-positive women and HIV-negative women, respectively. Age was a significant risk factor for hr-HPV infection in HIV-infected women (P=0.039). The presence of hr-HPV was significantly associated with abnormal cervical cytology (P<0.001). These findings suggest that HPV testing for cervical cancer screening in HIV-infected women would be necessary, particularly among young age group. PMID:24431902

  8. Genotyping of human papillomavirus in paraffin embedded cervical tissue samples from women in Ethiopia and the Sudan.

    PubMed

    Abate, Ebba; Aseffa, Abraham; El-Tayeb, Muntasir; El-Hassan, Ibrahim; Yamuah, Lawrence; Mihret, Wude; Bekele, Liku; Ashenafi, Senait; El-Dawi, Nadia; Belayneh, Meseret; El-Hassan, Ahmed; Engers, Howard

    2013-02-01

    Cervical cancer is the most frequent female malignancy in most developing countries. Previous studies have demonstrated a strong association of human papillomavirus (HPV) infection with dysplasia and carcinoma of the uterine cervix. The objective of this study was to identify the prevailing HPV genotypes responsible for the development of cervical cancer among women in Ethiopia and the Sudan. A molecular characterization of HPV was done on 245 paraffin embedded cervical biopsy samples collected from the two countries. Amplification of HPV and subsequent genotyping was done using SPF10 primers and Line probe assay. Of samples collected from Ethiopian patients, 93% (149/160) and 13% (21/160) had high risk and low risk HPV genotypes, respectively. Among samples collected from the Sudan, 94% (80/85) harbored high risk and 11.7% (10/85) low risk HPV genotypes. Human papillomavirus 16 was the most frequent genotype identified in samples from Ethiopia (91%, 136/149) and the Sudan (82.5%, 66/80). HPV 52, 58, and 18 were the second, third and fourth common genotypes identified in Ethiopia, whereas HPV 18, 45, and 52 were the second, third, and fourth genotypes identified in samples collected from the Sudan. Thus, individuals living in different geographical localities should receive vaccines based on the specific genotypes circulating in the area and a vaccine targeting HPV 16, 18, 45, 52, and 58 may be optimal for the control of cervical cancer in the two countries.

  9. Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: Clues from human phylogeography

    PubMed Central

    Mokrousov, Igor; Ly, Ho Minh; Otten, Tatiana; Lan, Nguyen Ngoc; Vyshnevskyi, Boris; Hoffner, Sven; Narvskaya, Olga

    2005-01-01

    We suggest that the evolution of the population structure of microbial pathogens is influenced by that of modern humans. Consequently, the timing of hallmark changes in bacterial genomes within the last 100,000 yr may be attempted by comparison with relevant human migrations. Here, we used a lineage within Mycobacterium tuberculosis, a Beijing genotype, as a model and compared its phylogeography with human demography and Y chromosome-based phylogeography. We hypothesize that two key events shaped the early history of the Beijing genotype: (1) its Upper Palaeolithic origin in the Homo sapiens sapiens K-M9 cluster in Central Asia, and (2) primary Neolithic dispersal of the secondary Beijing NTF::IS6110 lineage by Proto-Sino-Tibetan farmers within east Asia (human O-M214/M122 haplogroup). The independent introductions of the Beijing strains from east Asia to northern Eurasia and South Africa were likely historically recent, whereas their differential dissemination within these areas has been influenced by demographic and climatic factors. PMID:16169923

  10. Sentinel-base DNA genotyping using multiple sequencing primers for high-risk human papillomaviruses

    PubMed Central

    Gharizadeh, Baback; Zheng, Biying; Akhras, Michael; Ghaderi, Mehran; Jejelowo, Olufisayo; Strander, Björn; Nyrén, Pål; Wallin, Keng-Ling; Pourmand, Nader

    2009-01-01

    Despite the various technologies in place for genotyping human papillomaviruses (HPV), clinical use and clinical research demand a method that is fast, more reliable and cost-effective. The technology described here represents a breakthrough development in that direction. By combining the method of multiple sequencing primers with DNA sequencing, we have developed a rapid assay for genotyping HPV that relies on the identification of a single, type-specific ‘sentinel’ base. As described here, the prototype assay has been developed to recognize the 12 most high-risk HPV types (HPV-16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58 and 59) and is capable of recognizing and simultaneously genotyping multiple HPV co-infections. By providing sequence information on multiple HPV infections, this method eliminates the need for labor- and cost-intensive PCR cloning. These proof-of-concept studies establish the assay to be accurate, reliable, rapid, flexible, and cost-effective, providing evidence of the feasibility this technique for use in clinical settings. PMID:16516439

  11. Genotype distribution characteristics of high-risk human papillomaviruses in women from Shanghai, China.

    PubMed

    Gu, Y; Yi, M; Xu, Y; Zhao, H; Fu, F; Zhang, Y

    2016-05-01

    High-risk human papillomaviruses (HPVs) are highly prevalent worldwide, and HPV genotype distribution varies regionally. Molecular surveys of HPVs are important for effective HPV control and prevention. Fifteen high-risk HPV strains (16, 18, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68) and six low-risk HPV strains (HPV6, 11, 42, 43, 44, CP8304) were detected by cervical cytology from 10 501 subjects. High-risk HPVs, low-risk HPVs, and both high- and low-risk HPVs were detected in 14·5%, 2·8%, and 2·4% of cases, respectively. Of 1782 subjects with high-risk HPV infection, 75·5%, 18·1%, and 6·4% were infected with one, two, and ⩾3 strains of high-risk HPVs, respectively. HPV52, HPV16, and HPV58 were the top three most dominant high-risk HPV genotypes in our population with positivity rates of 23·0%, 17·7% and 16·9%, respectively. Multiple infection was common, with significantly higher co-infection rates of HPV58/HPV33 (12·9%) and HPV58/HPV52 (11·3%). Further data comparisons showed that HPV genotype distribution varied markedly between domestic and international regions. In conclusion, a monolithic vaccination strategy is obviously impractical, and regional HPV surveillance is essential to optimize current HPV control and prevention.

  12. Human papillomavirus prevalence and genotypes distribution among female outpatients in Qingdao, East China.

    PubMed

    Bi, Qingqing; Zhang, Lei; Zhao, Ziyun; Mu, Xiaofeng; Zhang, Meilian; Wang, Peng

    2015-12-01

    Persistent infection with human papillomavirus, especially high risk ones, is a necessary cause of cervical cancer. This study aimed to investigate the distribution of HPV genotypes in female outpatients from Qingdao, East China. A total of 4,534 cervical swabs from women visiting this medical institution for gynecologic care were included. HPV genotypes were examined by a PCR-based hybridization gene chip assay and liquid-based cytology analysis was used to evaluate cervical cytology. The overall HPV prevalence in this study was 32.2% (1,459/4,534). A total of 23 HPV genotypes were identified and the five most prevalent ones were HPV16 (16.1%), HPV52 (8.9%), HPV58 (7.9%), HPV6 (7.0%), and HPV53 (6.5%). Age-specific prevalence of HPV exhibited one peak at the youngest age group and the HPV positive rate decreased gradually with age growth. But high risk HPV infections were more prevalent among aged women. Besides, association between cervical cytology and HPV infection was also determined, 27.2% (1124/4,126) of women with normal cytology were HPV positive while 82.1% (335/408) of women with abnormal cytology were HPV positive. These findings give new epidemiological data and may provide guidance for the vaccination program in this area.

  13. Prevalence and genotype distribution of human papillomavirus among women from Henan, China.

    PubMed

    Wang, Xiao-Chuan; Sun, Liang-Qi; Ma, Li; Li, Hua-Xin; Wang, Xiu-Li; Wang, Xin; Yun, Tian; Meng, Nian-Long; Lv, Da-Le

    2014-01-01

    Human papillomavirus (HPV) infection has been implicated as a causative of cervical cancer. In the present study, a total of 578 samples from females attending the gynecological outpatient clinic in Henan province, China, were collected and the HPV genotypes were detected by gene chip and flow-through hybridization. Overall, 44.5% (257/578) females were found to be HPV DNA positive, and the high risk HPV (HR-HPV) rate was 35.1% (203/578). The first peak of HR-HPV infection appeared in the >60 year-old group (55.0%), and the second was within the 51-55 year-old group (50.0%) (χ2=19.497, p<0.05). HPV 16 was the most prevalent genotype (9.2%), followed by HPV 52 (7.8%), HPV 6 (6.9%), HPV 11 (5.9%) and HPV 42 (5.0%). The single type HPV infection was 30.4%, with the five majority prevalent genotype HPV 16 (16.5%), HPV 52 (14.3%), HPV 6 (12.6%), HPV 42 (8.6%), HPV 31 (5.1%). The multiple-type HPV infections were 14.0%, and HPV 16 was the most prevalent type (29.6%), followed by HPV 52 (24.7%), HPV 6 (22.2%), HPV 11 (22.2%), HPV 42 (17.3%) and HPV 39 (17.3%).

  14. Rapid method for growth hormone receptor exon 3 delete (GHRd3) SNP genotyping from archival human placental samples.

    PubMed

    Pelekanos, Rebecca A; Sardesai, Varda S; Dekker Nitert, Marloes; Callaway, Leonie K; Fisk, Nicholas M; Jeffery, Penny L

    2015-08-01

    Analysis of archival samples from cohorts of pregnant women may be key to discovering prognosticators of stillbirth and pregnancy/perinatal complications. Growth hormone (GH) and its receptor (GHR) are pivotal in feto-placental development and pregnancy maintenance. We report a rapid, optimized method for genotyping the GHR full-length versus exon 3-deleted isoform (GHRd3). TaqMan single nucleotide polymorphism (SNP) genotyping proved superior to standard multiplex polymerase chain reaction (PCR) in allele detection and GHR genotyping from archived samples, including those with poor genomic deoxyribonucleic acid quality/quantity such as formalin fixed, paraffin embedded, blood, and serum. Furthermore, this assay is suitable for high through put 96 or 384-well plate quantitative PCR machines with automated genotype calling software. The TaqMan genotyping assay can increase the data obtained from precious archival human samples.

  15. Human papillomavirus genotypes distribution in 175 invasive cervical cancer cases from Brazil

    PubMed Central

    2013-01-01

    Background Invasive cervical cancer is the second most common malignant tumor affecting Brazilian women. Knowledge on Human Papillomavirus (HPV) genotypes in invasive cervical cancer cases is crucial to guide the introduction and further evaluate the impact of new preventive strategies based on HPV. We aimed to provide updated comprehensive data about the HPV types’ distribution in patients with invasive cervical cancer. Methods Fresh tumor tissue samples of histologically confirmed invasive cervical cancer were collected from 175 women attending two cancer reference hospitals from São Paulo State: ICESP and Hospital de Câncer de Barretos. HPV detection and genotyping were performed by the Linear Array HPV Genotyping Test (Roche Molecular Diagnostics, Pleasanton,USA). Results 170 out of 172 valid samples (99%) were HPV DNA positive. The most frequent types were HPV16 (77.6%), HPV18 (12.3%), HPV31 (8.8%), HPV33 (7.1%) and HPV35 (5.9%). Most infections (75%) were caused by individual HPV types. Women with adenocarcinoma were not younger than those with squamous cell carcinoma, as well, as women infected with HPV33 were older than those infected by other HPV types. Some differences between results obtained in the two hospitals were observed: higher overall prevalence of HPV16, absence of single infection by HPV31 and HPV45 was verified in HC-Barretos in comparison to ICESP patients. Conclusions To our knowledge, this is one of the largest studies made with fresh tumor tissues of invasive cervical cancer cases in Brazil. This study depicted a distinct HPV genotype distribution between two centers that may reflect the local epidemiology of HPV transmission among these populations. Due to the impact of these findings on cervical cancer preventive strategies, extension of this investigation to routine screening populations is warranted. PMID:23883423

  16. Human neutrophil alloantigen genotype frequencies among blood donors with Turkish and German descent.

    PubMed

    Hauck, B; Philipp, A; Eckstein, R; Ott, S; Zimmermann, R; Dengler, T; Zingsem, J

    2011-12-01

    Antibodies against the human neutrophil antigens (HNA) are able to stimulate transfusion reactions, autoimmune and neonatal neutropenia. The aim of this study was to determine the HNA allele frequencies in the largest ethnic minority group in Germany in comparison with the German population for predicting the risk of alloimmunization and associated transfusion reactions, as well as the risk of developing neonatal neutropenia for the newborn of racial mixed couples. However, there exists no data about HNA genotype distribution in Turkish population. DNA was isolated from blood samples of 119 German and 118 Turkish blood donors and typed them for HNA-1, -3, -4, and -5 by using a commercial polymerase chain reaction kit with sequence-specific primers (SSP-PCR) and compared the HNA genotype distribution of both groups. In German blood donors, the gene frequencies for HNA-1a and HNA-1b were 0.391 and 0.601, for HNA-3a and -3b, 0.744 and 0.256, for HNA-4a and -4b, 0.908 and 0.092, and for HNA-5a and -5bw, 0.731 and 0.269. In Turkish blood donors, we observed 0.420/0.564, 0.737/0.263, 0.881/0.119, and 0.754/0.246 for HNA-1a/1b, -3a/3b, -4a/4b, and -5a/5bw. No statistic significant difference between genotypes in these populations was observed. This study is the first to report HNA gene frequencies in a Turkish population. It showed that there is no difference of HNA genotype in blood donors with Turkish descent in comparison with German blood donors. The alternating transfusion of blood and blood components is no increased risk for developing alloantibodies against HNA antigens. In pregnancy of mixed couples no special screening programs for HNA are necessary.

  17. Clinical Effect of Human Papillomavirus Genotypes in Patients With Cervical Cancer Undergoing Primary Radiotherapy

    SciTech Connect

    Wang, Chun-Chieh; Lai, Chyong-Huey; Huang, Huei-Jean; Chao, Angel; Chang, Chee-Jen; Chang, Ting-Chang; Chou, Hung-Hsueh; Hong, Ji-Hong

    2010-11-15

    Purpose: To study the prognostic value of the human papillomavirus (HPV) genotypes in cervical cancer patients undergoing radiotherapy. Patients and Methods: A total of 1,010 patients with cervical cancer after radiotherapy between 1993 and 2000 were eligible for this study. The HPV genotypes were determined by a genechip, which detects 38 types of HPV. The patient characteristics and treatment outcomes were analyzed using the Cox regression hazard model and classification and regression tree decision tree method. Results: A total of 25 genotypes of HPV were detected in 992 specimens (98.2%). The leading 8 types were HPV16, 58, 18, 33, 52, 39, 31, and 45. These types belong to two high-risk HPV species: alpha-7 (HPV18, 39, 45) and alpha-9 (HPV16, 31, 33, 52, 58). Three HPV-based risk groups, which were independent of established prognostic factors, such as International Federation of Gynecology and Obstetrics stage, age, pathologic features, squamous cell carcinoma antigen, and lymph node metastasis, were associated with the survival outcomes. The high-risk group consisted of the patients without HPV infection or the ones infected with the alpha-7 species only. Patients co-infected with the alpha-7 and alpha-9 species belonged to the medium-risk group, and the others were included in the low-risk group. Conclusion: The results of the present study have confirmed the prognostic value of HPV genotypes in cervical cancer treated with radiotherapy. The different effect of the alpha-7 and alpha-9 species on the radiation response deserves additional exploration.

  18. The 2010 global proficiency study of human papillomavirus genotyping in vaccinology.

    PubMed

    Eklund, Carina; Forslund, Ola; Wallin, Keng-Ling; Zhou, Tiequn; Dillner, Joakim

    2012-07-01

    Accurate and internationally comparable human papillomavirus (HPV) DNA genotyping is essential both for evaluation of HPV vaccines and for effective monitoring and implementation of vaccination programs. The World Health Organization (WHO) HPV Laboratory Network (LabNet) regularly issues international proficiency studies. The 2010 HPV genotyping proficiency panel for HPV vaccinology contained 43 coded samples composed of purified plasmids of 16 HPV types (HPV types 6, 11, 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68a and 68b) and 3 coded extraction controls. Proficient typing was defined as detection in both single and multiple infections of 50 international units (IU) of HPV type 16 (HPV-16) and HPV-18 DNA and 500 genome equivalents (GE) for the other 14 HPV types. Ninety-eight laboratories worldwide submitted a total of 132 data sets. Twenty-four different HPV genotyping assay methods were used, with Linear Array being the most commonly used. Other major assays used were a line blot assay (Inno-LiPa), CLART, type-specific real-time PCR, PCR Luminex, and different microarray assays. Altogether, 72 data sets were proficient for detection of more than 1 type, and only 26 data sets proficiently detected all 16 HPV types. The major oncogenic HPV types, 16 and 18, were proficiently detected in 95.0% (114/120) and 87.0% (94/108) of data sets, respectively. Forty-six data sets reported multiple false-positive results and were considered nonproficient. A trend toward increased sensitivity of assays was seen for the 41 laboratories that participated in both 2008 and 2010. In conclusion, continued global proficiency studies will be required for establishing comparable and reliable HPV genotyping services for vaccinology worldwide.

  19. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

    PubMed Central

    2015-01-01

    Understanding the functional consequences of genetic variation, and how it affects complex human disease and quantitative traits, remains a critical challenge for biomedicine. We present an analysis of RNA sequencing data from 1641 samples across 43 tissues from 175 individuals, generated as part of the pilot phase of the Genotype-Tissue Expression (GTEx) project. We describe the landscape of gene expression across tissues, catalog thousands of tissue-specific and shared regulatory expression quantitative trait loci (eQTL) variants, describe complex network relationships, and identify signals from genome-wide association studies explained by eQTLs. These findings provide a systematic understanding of the cellular and biological consequences of human genetic variation and of the heterogeneity of such effects among a diverse set of human tissues. PMID:25954001

  20. A two-step real-time PCR assay for quantitation and genotyping of human parvovirus 4.

    PubMed

    Väisänen, E; Lahtinen, A; Eis-Hübinger, A M; Lappalainen, M; Hedman, K; Söderlund-Venermo, M

    2014-01-01

    Human parvovirus 4 (PARV4) of the family Parvoviridae was discovered in a plasma sample of a patient with an undiagnosed acute infection in 2005. Currently, three PARV4 genotypes have been identified, however, with an unknown clinical significance. Interestingly, these genotypes seem to differ in epidemiology. In Northern Europe, USA and Asia, genotypes 1 and 2 have been found to occur mainly in persons with a history of injecting drug use or other parenteral exposure. In contrast, genotype 3 appears to be endemic in sub-Saharan Africa, where it infects children and adults without such risk behaviour. In this study, a novel straightforward and cost-efficient molecular assay for both quantitation and genotyping of PARV4 DNA was developed. The two-step method first applies a single-probe pan-PARV4 qPCR for screening and quantitation of this relatively rare virus, and subsequently, only the positive samples undergo a real-time PCR-based multi-probe genotyping. The new qPCR-GT method is highly sensitive and specific regardless of the genotype, and thus being suitable for studying the clinical impact and occurrence of the different PARV4 genotypes.

  1. Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains

    PubMed Central

    2013-01-01

    Background DNA analysis of ancient skeletal remains is invaluable in evolutionary biology for exploring the history of species, including humans. Contemporary human bones and teeth, however, are relevant in forensic DNA analyses that deal with the identification of perpetrators, missing persons, disaster victims or family relationships. They may also provide useful information towards unravelling controversies that surround famous historical individuals. Retrieving information about a deceased person’s externally visible characteristics can be informative in both types of DNA analyses. Recently, we demonstrated that human eye and hair colour can be reliably predicted from DNA using the HIrisPlex system. Here we test the feasibility of the novel HIrisPlex system at establishing eye and hair colour of deceased individuals from skeletal remains of various post-mortem time ranges and storage conditions. Methods Twenty-one teeth between 1 and approximately 800 years of age and 5 contemporary bones were subjected to DNA extraction using standard organic protocol followed by analysis using the HIrisPlex system. Results Twenty-three out of 26 bone DNA extracts yielded the full 24 SNP HIrisPlex profile, therefore successfully allowing model-based eye and hair colour prediction. HIrisPlex analysis of a tooth from the Polish general Władysław Sikorski (1881 to 1943) revealed blue eye colour and blond hair colour, which was positively verified from reliable documentation. The partial profiles collected in the remaining three cases (two contemporary samples and a 14th century sample) were sufficient for eye colour prediction. Conclusions Overall, we demonstrate that the HIrisPlex system is suitable, sufficiently sensitive and robust to successfully predict eye and hair colour from ancient and contemporary skeletal remains. Our findings, therefore, highlight the HIrisPlex system as a promising tool in future routine forensic casework involving skeletal remains, including

  2. Bio-Anthropological Studies on Human Skeletons from the 6th Century Tomb of Ancient Silla Kingdom in South Korea

    PubMed Central

    Lee, Won-Joon; Woo, Eun Jin; Oh, Chang Seok; Yoo, Jeong A.; Kim, Yi-Suk; Hong, Jong Ha; Yoon, A. Young; Wilkinson, Caroline M.; Ju, Jin Og; Choi, Soon Jo; Lee, Soong Doek; Shin, Dong Hoon

    2016-01-01

    In November and December 2013, unidentified human skeletal remains buried in a mokgwakmyo (a traditional wooden coffin) were unearthed while conducting an archaeological investigation near Gyeongju, which was the capital of the Silla Kingdom (57 BCE– 660 CE) of ancient Korea. The human skeletal remains were preserved in relatively intact condition. In an attempt to obtain biological information on the skeleton, physical anthropological, mitochondrial DNA, stable isotope and craniofacial analyses were carried out. The results indicated that the individual was a female from the Silla period, of 155 ± 5 cm height, who died in her late thirties. The maternal lineage belonged to the haplogroup F1b1a, typical for East Asia, and the diet had been more C3- (wheat, rice and potatoes) than C4-based (maize, millet and other tropical grains). Finally, the face of the individual was reconstructed utilizing the skull (restored from osseous fragments) and three-dimensional computerized modeling system. This study, applying multi-dimensional approaches within an overall bio-anthropological analysis, was the first attempt to collect holistic biological information on human skeletal remains dating to the Silla Kingdom period of ancient Korea. PMID:27249220

  3. An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree

    PubMed Central

    Mendez, Fernando L.; Krahn, Thomas; Schrack, Bonnie; Krahn, Astrid-Maria; Veeramah, Krishna R.; Woerner, August E.; Fomine, Forka Leypey Mathew; Bradman, Neil; Thomas, Mark G.; Karafet, Tatiana M.; Hammer, Michael F.

    2013-01-01

    We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins. PMID:23453668

  4. Planet Earth, Humans, Gravity and Their Connection to Natural Medicine-Essence from a 5000 Yrs Old Ancient Pedagogy

    NASA Astrophysics Data System (ADS)

    Lakshmanan, S.; Monsanto, C.; Radjendirane, B.

    2015-12-01

    According to the Ancient Indian Science, the fundamental constituents of planet earth are the five elements (Solid, Liquid, Heat, Air and Akash (subtlest energy field)). The same five elements constitute the human body. The Chinese and many other native traditions have used their deep understanding of these elements to live in balance with the planet. David Suzuki has elaborated on this key issue in his classic book, The Legacy: "Today we are in a state of crisis, and we must join together to respond to that crisis. If we do so, Suzuki envisions a future in which we understand that we are the Earth and live accordingly. All it takes is imagination and a determination to live within our, and the planet's, means". Gravity, the common force that connects both the body and earth plays a major role in the metabolism as well as the autonomous function of different organs in the body. Gravity has a direct influence on the fruits and vegetables that are grown on the planet as well. As a result, there is a direct relationship among gravity, food and human health. My talk will cover the missing link between the Earth's Gravity and the human health. A new set of ancient axioms will be used to address this and many other issues that are remain as "major unsolved problems" linking modern Geophysical and Health sciences.

  5. An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree.

    PubMed

    Mendez, Fernando L; Krahn, Thomas; Schrack, Bonnie; Krahn, Astrid-Maria; Veeramah, Krishna R; Woerner, August E; Fomine, Forka Leypey Mathew; Bradman, Neil; Thomas, Mark G; Karafet, Tatiana M; Hammer, Michael F

    2013-03-01

    We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237-581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

  6. Bio-Anthropological Studies on Human Skeletons from the 6th Century Tomb of Ancient Silla Kingdom in South Korea.

    PubMed

    Lee, Won-Joon; Woo, Eun Jin; Oh, Chang Seok; Yoo, Jeong A; Kim, Yi-Suk; Hong, Jong Ha; Yoon, A Young; Wilkinson, Caroline M; Ju, Jin Og; Choi, Soon Jo; Lee, Soong Doek; Shin, Dong Hoon

    2016-01-01

    In November and December 2013, unidentified human skeletal remains buried in a mokgwakmyo (a traditional wooden coffin) were unearthed while conducting an archaeological investigation near Gyeongju, which was the capital of the Silla Kingdom (57 BCE- 660 CE) of ancient Korea. The human skeletal remains were preserved in relatively intact condition. In an attempt to obtain biological information on the skeleton, physical anthropological, mitochondrial DNA, stable isotope and craniofacial analyses were carried out. The results indicated that the individual was a female from the Silla period, of 155 ± 5 cm height, who died in her late thirties. The maternal lineage belonged to the haplogroup F1b1a, typical for East Asia, and the diet had been more C3- (wheat, rice and potatoes) than C4-based (maize, millet and other tropical grains). Finally, the face of the individual was reconstructed utilizing the skull (restored from osseous fragments) and three-dimensional computerized modeling system. This study, applying multi-dimensional approaches within an overall bio-anthropological analysis, was the first attempt to collect holistic biological information on human skeletal remains dating to the Silla Kingdom period of ancient Korea. PMID:27249220

  7. Giant magnetoimpedance-based microchannel system for quick and parallel genotyping of human papilloma virus type 16/18

    NASA Astrophysics Data System (ADS)

    Yang, Hao; Chen, Lei; Lei, Chong; Zhang, Ju; Li, Ding; Zhou, Zhi-Min; Bao, Chen-Chen; Hu, Heng-Yao; Chen, Xiang; Cui, Feng; Zhang, Shuang-Xi; Zhou, Yong; Cui, Da-Xiang

    2010-07-01

    Quick and parallel genotyping of human papilloma virus (HPV) type 16/18 is carried out by a specially designed giant magnetoimpedance (GMI) based microchannel system. Micropatterned soft magnetic ribbon exhibiting large GMI ratio serves as the biosensor element. HPV genotyping can be determined by the changes in GMI ratio in corresponding detection region after hybridization. The result shows that this system has great potential in future clinical diagnostics and can be easily extended to other biomedical applications based on molecular recognition.

  8. Genotype analysis of faecal and blood isolates of Salmonella dublin from humans in England and Wales.

    PubMed Central

    Chowdry, N.; Threlfall, E. J.; Rowe, B.; Stanley, J.

    1993-01-01

    An analysis of genotype was made for representative strains of Salmonella dublin. The collection consisted primarily of strains isolated from humans in England and Wales, and were of both intestinal and extra-intestinal origin. Three genetic elements were characterized by DNA hybridization. They were the spvBC genes, extrachromosomal virulence determinants, the salmonella-specific insertion sequence IS200, and the 16S ribosomal RNA genes, a phylogenetic marker. Two clones of S. dublin (SdRI and SdRII) which shared an identical IS200 profile, were identified on the basis of restriction fragment length polymorphism at the 16S rRNA locus. With one exception, all strains harboured a 52 MDa plasmid which contained a conserved 3.7 kbp Hind III fragment homologous to the spvBC mouse-virulence genes of S. typhimurium. However, a single plasmid-free strain of SdRI, isolated from a patient with septicaemia exhibited no spc homology. In SdRI there was no observable genotype distinction between strains causing gastroenteritis or bacteraemia. In contrast, none of the strains of SdRII were from cases of bacteraemia, and all human isolates of this clone were from cases of gastroenteritis. Images Fig. 1 Fig. 2 PMID:8097167

  9. Multiple-Locus Variable-Number Tandem-Repeat Analysis Genotyping of Human Brucella Isolates from Turkey▿†

    PubMed Central

    Kılıç, Selçuk; Ivanov, Ivan N.; Durmaz, Rıza; Bayraktar, Mehmet Refik; Ayaşlıoğlu, Ergin; Uyanık, M. Hamidullah; Alışkan, Hikmet; Yaşar, Ekrem; Bayramoğlu, Gülçin; Arslantürk, Ahmet; Vergnaud, Gilles; Kantardjiev, Todor V.

    2011-01-01

    A multiple-locus variable-number tandem-repeat analysis (MLVA) was applied to investigate the epidemiological relationship and genetic diversity among 162 human Brucella isolates collected from all geographic regions of Turkey in an 8-year period (2001 to 2008). The isolates were genotyped by using an MLVA assay developed in Orsay, France (MLVA-16Orsay) including eight minisatellite (panel 1) and eight microsatellite (panel 2, subdivided into 2A and 2B) markers. Panels 1 and 2A distinguish 14 genotypes; two of these represented 85% of the strains. Panel 2B displayed a very high discriminatory power. Three loci from panel 2B had diversity index values higher than 0.74. MLVA-16Orsay yielded 105 genotypes; 73 were represented by a unique isolate, and 32 included two to eight isolates. The isolates from different patients within the same outbreak or from the same patient before first-line therapy and after relapse showed identical genotypes. A number of MLVA genotypes appeared to be partially restricted to some geographic areas and displayed no annual variation, possibly reflecting persistence of genotypes in certain areas for a time span of at least a decade. This study, representing the first molecular typing results of human Brucella isolates from Turkey, indicated that Turkish human Brucella melitensis isolates were most closely related to the neighboring countries' isolates included in the East Mediterranean group. PMID:21795514

  10. Multiple-locus variable-number tandem-repeat analysis genotyping of human Brucella isolates from Turkey.

    PubMed

    Kiliç, Selçuk; Ivanov, Ivan N; Durmaz, Riza; Bayraktar, Mehmet Refik; Ayaslioglu, Ergin; Uyanik, M Hamidullah; Aliskan, Hikmet; Yasar, Ekrem; Bayramoglu, Gülçin; Arslantürk, Ahmet; Vergnaud, Gilles; Kantardjiev, Todor V

    2011-09-01

    A multiple-locus variable-number tandem-repeat analysis (MLVA) was applied to investigate the epidemiological relationship and genetic diversity among 162 human Brucella isolates collected from all geographic regions of Turkey in an 8-year period (2001 to 2008). The isolates were genotyped by using an MLVA assay developed in Orsay, France (MLVA-16(Orsay)) including eight minisatellite (panel 1) and eight microsatellite (panel 2, subdivided into 2A and 2B) markers. Panels 1 and 2A distinguish 14 genotypes; two of these represented 85% of the strains. Panel 2B displayed a very high discriminatory power. Three loci from panel 2B had diversity index values higher than 0.74. MLVA-16(Orsay) yielded 105 genotypes; 73 were represented by a unique isolate, and 32 included two to eight isolates. The isolates from different patients within the same outbreak or from the same patient before first-line therapy and after relapse showed identical genotypes. A number of MLVA genotypes appeared to be partially restricted to some geographic areas and displayed no annual variation, possibly reflecting persistence of genotypes in certain areas for a time span of at least a decade. This study, representing the first molecular typing results of human Brucella isolates from Turkey, indicated that Turkish human Brucella melitensis isolates were most closely related to the neighboring countries' isolates included in the East Mediterranean group.

  11. Burying dogs in ancient Cis-Baikal, Siberia: temporal trends and relationships with human diet and subsistence practices.

    PubMed

    Losey, Robert J; Garvie-Lok, Sandra; Leonard, Jennifer A; Katzenberg, M Anne; Germonpré, Mietje; Nomokonova, Tatiana; Sablin, Mikhail V; Goriunova, Olga I; Berdnikova, Natalia E; Savel'ev, Nikolai A

    2013-01-01

    The first objective of this study is to examine temporal patterns in ancient dog burials in the Lake Baikal region of Eastern Siberia. The second objective is to determine if the practice of dog burial here can be correlated with patterns in human subsistence practices, in particular a reliance on terrestrial mammals. Direct radiocarbon dating of a suite of the region's dog remains indicates that these animals were given burial only during periods in which human burials were common. Dog burials of any kind were most common during the Early Neolithic (∼7-8000 B.P.), and rare during all other time periods. Further, only foraging groups seem to have buried canids in this region, as pastoralist habitation sites and cemeteries generally lack dog interments, with the exception of sacrificed animals. Stable carbon and nitrogen isotope data indicate that dogs were only buried where and when human diets were relatively rich in aquatic foods, which here most likely included river and lake fish and Baikal seal (Phoca sibirica). Generally, human and dog diets appear to have been similar across the study subregions, and this is important for interpreting their radiocarbon dates, and comparing them to those obtained on the region's human remains, both of which likely carry a freshwater old carbon bias. Slight offsets were observed in the isotope values of dogs and humans in our samples, particularly where both have diets rich in aquatic fauna. This may result from dietary differences between people and their dogs, perhaps due to consuming fish of different sizes, or even different tissues from the same aquatic fauna. This paper also provides a first glimpse of the DNA of ancient canids in Northeast Asia.

  12. Burying Dogs in Ancient Cis-Baikal, Siberia: Temporal Trends and Relationships with Human Diet and Subsistence Practices

    PubMed Central

    Losey, Robert J.; Garvie-Lok, Sandra; Leonard, Jennifer A.; Katzenberg, M. Anne; Germonpré, Mietje; Nomokonova, Tatiana; Sablin, Mikhail V.; Goriunova, Olga I.; Berdnikova, Natalia E.; Savel’ev, Nikolai A.

    2013-01-01

    The first objective of this study is to examine temporal patterns in ancient dog burials in the Lake Baikal region of Eastern Siberia. The second objective is to determine if the practice of dog burial here can be correlated with patterns in human subsistence practices, in particular a reliance on terrestrial mammals. Direct radiocarbon dating of a suite of the region’s dog remains indicates that these animals were given burial only during periods in which human burials were common. Dog burials of any kind were most common during the Early Neolithic (∼7–8000 B.P.), and rare during all other time periods. Further, only foraging groups seem to have buried canids in this region, as pastoralist habitation sites and cemeteries generally lack dog interments, with the exception of sacrificed animals. Stable carbon and nitrogen isotope data indicate that dogs were only buried where and when human diets were relatively rich in aquatic foods, which here most likely included river and lake fish and Baikal seal (Phoca sibirica). Generally, human and dog diets appear to have been similar across the study subregions, and this is important for interpreting their radiocarbon dates, and comparing them to those obtained on the region’s human remains, both of which likely carry a freshwater old carbon bias. Slight offsets were observed in the isotope values of dogs and humans in our samples, particularly where both have diets rich in aquatic fauna. This may result from dietary differences between people and their dogs, perhaps due to consuming fish of different sizes, or even different tissues from the same aquatic fauna. This paper also provides a first glimpse of the DNA of ancient canids in Northeast Asia. PMID:23696851

  13. Network Modules of the Cross-Species Genotype-Phenotype Map Reflect the Clinical Severity of Human Diseases.

    PubMed

    Han, Seong Kyu; Kim, Inhae; Hwang, Jihye; Kim, Sanguk

    2015-01-01

    Recent advances in genome sequencing techniques have improved our understanding of the genotype-phenotype relationship between genetic variants and human diseases. However, genetic variations uncovered from patient populations do not provide enough information to understand the mechanisms underlying the progression and clinical severity of human diseases. Moreover, building a high-resolution genotype-phenotype map is difficult due to the diverse genetic backgrounds of the human population. We built a cross-species genotype-phenotype map to explain the clinical severity of human genetic diseases. We developed a data-integrative framework to investigate network modules composed of human diseases mapped with gene essentiality measured from a model organism. Essential and nonessential genes connect diseases of different types which form clusters in the human disease network. In a large patient population study, we found that disease classes enriched with essential genes tended to show a higher mortality rate than disease classes enriched with nonessential genes. Moreover, high disease mortality rates are explained by the multiple comorbid relationships and the high pleiotropy of disease genes found in the essential gene-enriched diseases. Our results reveal that the genotype-phenotype map of a model organism can facilitate the identification of human disease-gene associations and predict human disease progression.

  14. Network Modules of the Cross-Species Genotype-Phenotype Map Reflect the Clinical Severity of Human Diseases

    PubMed Central

    Han, Seong Kyu; Kim, Inhae; Hwang, Jihye; Kim, Sanguk

    2015-01-01

    Recent advances in genome sequencing techniques have improved our understanding of the genotype-phenotype relationship between genetic variants and human diseases. However, genetic variations uncovered from patient populations do not provide enough information to understand the mechanisms underlying the progression and clinical severity of human diseases. Moreover, building a high-resolution genotype-phenotype map is difficult due to the diverse genetic backgrounds of the human population. We built a cross-species genotype-phenotype map to explain the clinical severity of human genetic diseases. We developed a data-integrative framework to investigate network modules composed of human diseases mapped with gene essentiality measured from a model organism. Essential and nonessential genes connect diseases of different types which form clusters in the human disease network. In a large patient population study, we found that disease classes enriched with essential genes tended to show a higher mortality rate than disease classes enriched with nonessential genes. Moreover, high disease mortality rates are explained by the multiple comorbid relationships and the high pleiotropy of disease genes found in the essential gene-enriched diseases. Our results reveal that the genotype-phenotype map of a model organism can facilitate the identification of human disease-gene associations and predict human disease progression. PMID:26301634

  15. Cryptococcus gattii in the United States: Genotypic Diversity of Human and Veterinary Isolates

    PubMed Central

    Lockhart, Shawn R.; Iqbal, Naureen; Harris, Julie R.; Grossman, Nina T.; DeBess, Emilio; Wohrle, Ron; Marsden-Haug, Nicola; Vugia, Duc J.

    2013-01-01

    Background Cryptococcusgattii infections are being reported in the United States (US) with increasing frequency. Initially, US reports were primarily associated with an ongoing C. gattii outbreak in the Pacific Northwest (PNW) states of Washington and Oregon, starting in 2004. However, reports of C. gattii infections in patients from other US states have been increasing since 2009. Whether this is due to increasing frequency of disease, greater recognition within the clinical community, or both is currently unknown. Methodology/Principal Findings During 2005–2013, a total of 273 C. gattii isolates from human and veterinary sources in 16 US states were collected. Of these, 214 (78%) were from the Pacific Northwest (PNW) and comprised primarily the clonal C. gattii genotypes VGIIa (64%), VGIIc (21%) and VGIIb (9%). The 59 isolates from outside the PNW were predominantly molecular types VGIII (44%) and VGI (41%). Genotyping using multilocus sequence typing revealed small clusters, including a cluster of VGI isolates from the southeastern US, and an unrelated cluster of VGI isolates and a large cluster of VGIII isolates from California. Most of the isolates were mating type MATα, including all of the VGII isolates, but one VGI and three VGIII isolates were mating type MATa. Conclusions/Significance We provide the most comprehensive report to date of genotypic diversity of US C. gattii isolates both inside and outside of the PNW. C. gattii may have multiple endemic regions in the US, including a previously-unrecognized endemic region in the southeast. Regional clusters exist both in California and the Southeastern US. VGII strains associated with the PNW outbreak do not appear to have spread substantially beyond the PNW. PMID:24019979

  16. Epidemiology and genotype distribution of high risk human papillomavirus in population of hospital opportunistic screening

    PubMed Central

    Liu, Ying-Qiao; He, Xin; Xu, Sha-Sha; Qu, Jiu-Xin; Wang, Yue; Diao, Xiao-Li; Liu, Jun; Wang, Shu-Zhen

    2015-01-01

    This study aimed to determine the prevalence of high-risk human papillomavirus (HR-HPV) in population of hospital opportunistic screening and to identify the correlation of prevalent genotypes and cervical cytological abnormalities. A cross-sectional study was employed between July 2013 and July 2014 in the Chaoyang hospital, in Beijing. Cervical samples were collected for the Type-specific HPV and the cervical cytological analyses in the population of hospital opportunistic screening. Total of 8975 samples from female patients aged 17-86 years were tested. Of these, 10.4% were infected by HR-HPV, the highest prevalence of HR-HPV in the youngest group and decreasing with aging (X2=19.68, P=0.02). Of these, 78.73% were single infections and 21.27% were multiple infections. Age-specific prevalence of multiple HPV exhibited a “U” shaped curve (X2=19.98, P=0.018). The most prevalent genotype is HPV 52, then descending order of frequency were HPV-58, 16, 39, 51, 56, 59, 18, 31, 33, 35, 68 and 45. 15.9% had an abnormal cytology in HR-HPV positive women, vs 4.13% in HR-HPV negative women. The prevalence of HR-HPV were 9.2%, 26.8%, 32%, 35.3% and 36.4% in normal cell, ASCUS, LSIL, ASC-H and HSIL, respectively (X2=234.67, P=0.000). Women with HPV 52, 16, 18, 58, 39, 51, 59, 56, 33, 31 infections related to the abnormal cytology, while the HPV68, 45, 35 didn’t. The prevalent characteristic in population of the hospital opportunistic screening is similar to the population of cervical screen, But the most five prevalent genotype in rank are different .Women with HR-HPV infections were more likely to have the cervical abnormal cytology. PMID:26629105

  17. Bead-based multiplex genotyping of 58 cutaneous human papillomavirus types.

    PubMed

    Michael, K M; Forslund, O; Bacevskij, O; Waterboer, T; Bravo, I G; Pawlita, M; Schmitt, M

    2011-10-01

    Cutaneous human papillomaviruses (HPVs) are a heterogeneous, nonmonophyletic assembly, comprising about 50 characterized types and at least 133 isolates putatively representing new types. Their natural history of infection and potential association with nonmelanoma skin cancer are not well understood. Several PCR systems have been developed that amplify a broad spectrum of cutaneous HPVs. However, amplicon genotyping by sequencing or reverse line blot assays are complex and not well suited for high-throughput analyses. We developed a novel multiplex cutaneous papillomavirus genotyping (McPG) assay for 38 defined and 20 putative cutaneous HPVs of the beta, gamma, mu, and nu genera. Viral DNA was amplified by the use of a modified single-tube nested "hanging-droplet" FAP PCR. The amplifiable papillomavirus (PV) spectrum was enlarged by the use of 9 outer and 13 inner primers. Biotinylated PCR products were hybridized to type-specific oligonucleotide probes coupled to fluorescence-labeled polystyrene beads and analyzed using Luminex technology. Analytical sensitivity was analyzed for 38 defined HPVs and was ≤100 genome copies for all types. Integrated β-globin primers allow for simultaneous DNA quality control. McPG is characterized by high reproducibility (κ= 0.84, 95% confidence interval = 0.79 to 0.88), good concordance with the original nested FAP PCR, followed by sequencing (70.2% complete or partial agreement) when 322 skin biopsy DNA samples were analyzed, and improved ability to detect multiple infections (on average 2.5 HPV types per HPV-positive sample compared to 1.7 HPV types with nested FAP-PCR). In conclusion, McPG is a powerful tool for genotyping multiple cutaneous HPVs in a high-throughput format and is thus suitable for large-scale epidemiological studies.

  18. Performance of commercial reverse line blot assays for human papillomavirus genotyping.

    PubMed

    Steinau, Martin; Onyekwuluje, Juanita M; Scarbrough, Mariela Z; Unger, Elizabeth R; Dillner, Joakim; Zhou, Tiequn

    2012-05-01

    The performance of three line blot assays (LBAs), the Linear Array HPV genotyping assay (LA) (Roche Diagnostics), INNO-LiPA HPV Genotyping Extra (LiPA) (Innogenetics), and the reverse hybridization assay (RH) (Qiagen), was evaluated using quantitated whole genomic human papillomavirus (HPV) plasmids (types 6, 11, 16, 18, 31, 33, 35, 39, 51, 52, 56, 58, 59, and 68b) as well as epidemiologic samples. In a plasmid titration series, LiPA and RH did not detect 50 international units (IU) of HPV type 18 (HPV18) in the presence of 5 × 10(4) IU or more of HPV16. HPV DNA (1 to 6 types) in the plasmid challenges at 50 IU or genome equivalents (GE) were identified with an accuracy of 99.9% by LA, 97.3% by LiPA, and 95.4% by RH, with positive reproducibility of 99.8% (kappa = 0.992), 88.2% (kappa = 0.928), and 88.1% (kappa = 0.926), respectively. Two instances of mistyping occurred with LiPA. Of the 120 epidemiologic samples, 76 were positive for high-risk types by LA, 90 by LiPA, and 69 by RH, with a positive reproducibility of 87.3% (kappa = 0.925), 83.9% (kappa = 0.899), and 90.2% (kappa = 0.942), respectively. Although the assays had good concordance in the clinical samples, the greater accuracy and specificity in the plasmid panel suggest that LA has an advantage for internationally comparable genotyping studies.

  19. Ancient Mtdna Sequences And Radiocarbon Dating Of Human Bones From The Chalcolithic Caves Of Wadi El-Makkukh.

    NASA Astrophysics Data System (ADS)

    Salamon, M.; Tzur, S.; Arensburg, B.; Zias, J.; Nagar, Y.; Weiner, S.; Boaretto, E.

    DNA from fossil human bones can provide valuable information for understanding intra- and inter-population relationships. Using the DNA preserved inside crystal aggregates from human fossil bones containing relatively large amounts of collagen, we demonstrate the presence of reproducible mtDNA control region sequences. Radiocarbon dates from each bone show that the burial caves were used for up to 600 years during the Chalcolithic period (5th-4th millennium BP). A comparison of the ancient DNA sequences with modern mtDNA databases indicates that all samples can most likely be assigned to the R haplogroup sub-clades, which are common in West-Eurasia. In four cases more precise and confident haplogroup identifications could be achieved (H, U3a and H6). The H haplogroup is present in three out of the four assigned ancient samples. This haplogroup is prevalent today in West - Eurasia. The results reported here tend to genetically link this Chalcolithic group of individuals to the current West Eurasian populations.

  20. Hidden Plasmodium falciparum parasites in human infections: different genotype distribution in the peripheral circulation and in the placenta.

    PubMed

    Schleiermacher, Dietlind; Le Hesran, Jean-Yves; Ndiaye, Jean-Louis; Perraut, Ronald; Gaye, Alioune; Mercereau-Puijalon, Odile

    2002-12-01

    Sequestration of the mature Plasmodium falciparum forms complicates detection, quantification and molecular analysis of human infections. Whether the circulating parasites represent all or only a subset of co-infecting genotypes is unclear. We have investigated this issue and compared placenta and peripheral blood msp1 and msp2 genotypes in 58 women delivering with an ICT-positive placenta in Guediawaye, Senegal. Most placenta (91%) and blood samples (98%) were multiply infected. Multiplicity of infection was positively correlated in both tissues. However, the placental and circulating genotype profiles differed markedly. Only 10% of matched peripheral blood/placenta samples had identical genotypes, whereas 74% had only partially concordant genotypes, with some alleles detected in both tissues, together with additional allele(s) detected in one tissue only. Eight women (14%) had totally discordant placental and peripheral blood genotypes. Thus, in the vast majority of cases, some sequestered genotypes remain hidden, undetected in the peripheral circulation, indicating that analysis of peripheral parasites generates a partial picture of a P. falciparum infection.

  1. Comparison of Hybribio GenoArray and Roche human papillomavirus (HPV) linear array for HPV genotyping in anal swab samples.

    PubMed

    Low, Huey Chi; Silver, Michelle I; Brown, Brandon J; Leng, Chan Yoon; Blas, Magaly M; Gravitt, Patti E; Woo, Yin Ling

    2015-02-01

    Human papillomavirus (HPV) is causally associated with anal cancer, as HPV DNA is detected in up to 90% of anal intraepithelial neoplasias and anal cancers. With the gradual increase of anal cancer rates, there is a growing need to establish reliable and clinically relevant methods to detect anal cancer precursors. In resource-limited settings, HPV DNA detection is a potentially relevant tool for anal cancer screening. Here, we evaluated the performance of the Hybribio GenoArray (GA) for genotyping HPV in anal samples, against the reference standard Roche Linear Array (LA). Anal swab samples were obtained from sexually active men who have sex with men. Following DNA extraction, each sample was genotyped using GA and LA. The overall interassay agreement, type-specific, and single and multiple genotype agreements were evaluated by kappa statistics and McNemar's χ(2) tests. Using GA and LA, 68% and 76% of samples were HPV DNA positive, respectively. There was substantial interassay agreements for the detection of all HPV genotypes (κ = 0.70, 86% agreement). Although LA was able to detect more genotypes per sample, the interassay agreement was acceptable (κ = 0.53, 63% agreement). GA had poorer specific detection of HPV genotypes 35, 42, and 51 (κ < 0.60). In conclusion, GA and LA showed good interassay agreement for the detection of most HPV genotypes in anal samples. However, the detection of HPV DNA in up to 76% of anal samples warrants further evaluation of its clinical significance. PMID:25502520

  2. Comparison of Hybribio GenoArray and Roche Human Papillomavirus (HPV) Linear Array for HPV Genotyping in Anal Swab Samples

    PubMed Central

    Silver, Michelle I.; Brown, Brandon J.; Leng, Chan Yoon; Blas, Magaly M.; Gravitt, Patti E.; Woo, Yin Ling

    2014-01-01

    Human papillomavirus (HPV) is causally associated with anal cancer, as HPV DNA is detected in up to 90% of anal intraepithelial neoplasias and anal cancers. With the gradual increase of anal cancer rates, there is a growing need to establish reliable and clinically relevant methods to detect anal cancer precursors. In resource-limited settings, HPV DNA detection is a potentially relevant tool for anal cancer screening. Here, we evaluated the performance of the Hybribio GenoArray (GA) for genotyping HPV in anal samples, against the reference standard Roche Linear Array (LA). Anal swab samples were obtained from sexually active men who have sex with men. Following DNA extraction, each sample was genotyped using GA and LA. The overall interassay agreement, type-specific, and single and multiple genotype agreements were evaluated by kappa statistics and McNemar's χ2 tests. Using GA and LA, 68% and 76% of samples were HPV DNA positive, respectively. There was substantial interassay agreements for the detection of all HPV genotypes (κ = 0.70, 86% agreement). Although LA was able to detect more genotypes per sample, the interassay agreement was acceptable (κ = 0.53, 63% agreement). GA had poorer specific detection of HPV genotypes 35, 42, and 51 (κ < 0.60). In conclusion, GA and LA showed good interassay agreement for the detection of most HPV genotypes in anal samples. However, the detection of HPV DNA in up to 76% of anal samples warrants further evaluation of its clinical significance. PMID:25502520

  3. HIGH-THROUGHPUT PHYLOGENOMICS: FROM ANCIENT DNA TO SIGNATURES OF HUMAN ANIMAL HUSBANDRY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We utilized the Illumina BovineSNP50 BeadChip with 54,693 single nucleotide polymorphism loci developed for Bos taurus taurus to rapidly genotype 677 individuals representing 61 Pecoran (horned ruminant) species diverged by up to 29 million years. We produced a completely bifurcating tree, the first...

  4. Ancient Egyptian herbal wines

    PubMed Central

    McGovern, Patrick E.; Mirzoian, Armen; Hall, Gretchen R.

    2009-01-01

    Chemical analyses of ancient organics absorbed into pottery jars from the beginning of advanced ancient Egyptian culture, ca. 3150 B.C., and continuing for millennia have revealed that a range of natural products—specifically, herbs and tree resins—were dispensed by grape wine. These findings provide chemical evidence for ancient Egyptian organic medicinal remedies, previously only ambiguously documented in medical papyri dating back to ca. 1850 B.C. They illustrate how humans around the world, probably for millions of years, have exploited their natural environments for effective plant remedies, whose active compounds have recently begun to be isolated by modern analytical techniques. PMID:19365069

  5. An efficient genotyping method for genome-modified animals and human cells generated with CRISPR/Cas9 system.

    PubMed

    Zhu, Xiaoxiao; Xu, Yajie; Yu, Shanshan; Lu, Lu; Ding, Mingqin; Cheng, Jing; Song, Guoxu; Gao, Xing; Yao, Liangming; Fan, Dongdong; Meng, Shu; Zhang, Xuewen; Hu, Shengdi; Tian, Yong

    2014-09-19

    The rapid generation of various species and strains of laboratory animals using CRISPR/Cas9 technology has dramatically accelerated the interrogation of gene function in vivo. So far, the dominant approach for genotyping of genome-modified animals has been the T7E1 endonuclease cleavage assay. Here, we present a polyacrylamide gel electrophoresis-based (PAGE) method to genotype mice harboring different types of indel mutations. We developed 6 strains of genome-modified mice using CRISPR/Cas9 system, and utilized this approach to genotype mice from F0 to F2 generation, which included single and multiplexed genome-modified mice. We also determined the maximal detection sensitivity for detecting mosaic DNA using PAGE-based assay as 0.5%. We further applied PAGE-based genotyping approach to detect CRISPR/Cas9-mediated on- and off-target effect in human 293T and induced pluripotent stem cells (iPSCs). Thus, PAGE-based genotyping approach meets the rapidly increasing demand for genotyping of the fast-growing number of genome-modified animals and human cell lines created using CRISPR/Cas9 system or other nuclease systems such as TALEN or ZFN.

  6. Diagnosis of Human Axillary Osmidrosis by Genotyping of the Human ABCC11 Gene: Clinical Practice and Basic Scientific Evidence

    PubMed Central

    Toyoda, Yu; Gomi, Tsuneaki; Nakagawa, Hiroshi; Nagakura, Makoto; Ishikawa, Toshihisa

    2016-01-01

    The importance of personalized medicine and healthcare is becoming increasingly recognized. Genetic polymorphisms associated with potential risks of various human genetic diseases as well as drug-induced adverse reactions have recently been well studied, and their underlying molecular mechanisms are being uncovered by functional genomics as well as genome-wide association studies. Knowledge of certain genetic polymorphisms is clinically important for our understanding of interindividual differences in drug response and/or disease risk. As such evidence accumulates, new clinical applications and practices are needed. In this context, the development of new technologies for simple, fast, accurate, and cost-effective genotyping is imperative. Here, we describe a simple isothermal genotyping method capable of detecting single nucleotide polymorphisms (SNPs) in the human ATP-binding cassette (ABC) transporter ABCC11 gene and its application to the clinical diagnosis of axillary osmidrosis. We have recently reported that axillary osmidrosis is linked with one SNP 538G>A in the ABCC11 gene. Our molecular biological and biochemical studies have revealed that this SNP greatly affects the protein expression level and the function of ABCC11. In this review, we highlight the clinical relevance and importance of this diagnostic strategy in axillary osmidrosis therapy. PMID:27057547

  7. Population-Level Effects of Human Papillomavirus Vaccination Programs on Infections with Nonvaccine Genotypes.

    PubMed

    Mesher, David; Soldan, Kate; Lehtinen, Matti; Beddows, Simon; Brisson, Marc; Brotherton, Julia M L; Chow, Eric P F; Cummings, Teresa; Drolet, Mélanie; Fairley, Christopher K; Garland, Suzanne M; Kahn, Jessica A; Kavanagh, Kimberley; Markowitz, Lauri; Pollock, Kevin G; Söderlund-Strand, Anna; Sonnenberg, Pam; Tabrizi, Sepehr N; Tanton, Clare; Unger, Elizabeth; Thomas, Sara L

    2016-10-01

    We analyzed human papillomavirus (HPV) prevalences during prevaccination and postvaccination periods to consider possible changes in nonvaccine HPV genotypes after introduction of vaccines that confer protection against 2 high-risk types, HPV16 and HPV18. Our meta-analysis included 9 studies with data for 13,886 girls and women ≤19 years of age and 23,340 women 20-24 years of age. We found evidence of cross-protection for HPV31 among the younger age group after vaccine introduction but little evidence for reductions of HPV33 and HPV45. For the group this same age group, we also found slight increases in 2 nonvaccine high-risk HPV types (HPV39 and HPV52) and in 2 possible high-risk types (HPV53 and HPV73). However, results between age groups and vaccines used were inconsistent, and the increases had possible alternative explanations; consequently, these data provided no clear evidence for type replacement. Continued monitoring of these HPV genotypes is important. PMID:27648688

  8. Genotyping of human parechoviruses in Iranian young children with aseptic meningitis and sepsis-like illness.

    PubMed

    Rahimi, Pooneh; Naser, Hakimeh Mahdian; Siadat, Seyed Davar; Sohrabi, Amir; Mostafavi, Ehsan; Motamedirad, Mahdieh; Bahramali, Golnaz; Sadat, Seyed Mehdi; Ardestani, Mehdi Shafiee

    2013-12-01

    Human parechoviruses (HPeV) are classified into 14 genotypes. HPeV1 and HPeV2 are the most prevalent genotypes in young children, which have been associated with mild to severe diseases. This study was conducted to investigate the involvement of HPeVs in aseptic meningitis and sepsis-like illness in Iran. Viral RNA was extracted from 148 cerebrospinal fluid samples from children <8 years old with primary diagnosis of aseptic meningitis and/or sepsis-like illness. Specific HPeV, HEV real-time PCR and HPeV typing were done to identify the infection rate of these viruses. HPeV and HEV were detected in 64 (43.24 %), 31 (20.94 %) of 148 patients with 10 (6.75 %) coinfection. VP1/VP3 junction region was successfully sequenced from 12 of the HPeV-positive specimens, and all of them were identified as HPeV1. HPeV was more prevalent than HEV in both aseptic meningitis and sepsis-like illness, so further studies are needed to understand the disease burden of HPeV infections, and clinical manifestations especially in specific illnesses of possible viral etiology. Direct detection of these viruses leads to reduce hospitalization and use of antibiotic, which are often followed by other complications in neonates and young children.

  9. Population-Level Effects of Human Papillomavirus Vaccination Programs on Infections with Nonvaccine Genotypes

    PubMed Central

    Soldan, Kate; Lehtinen, Matti; Beddows, Simon; Brisson, Marc; Brotherton, Julia M.L.; Chow, Eric P.F.; Cummings, Teresa; Drolet, Mélanie; Fairley, Christopher K.; Garland, Suzanne M.; Kahn, Jessica A.; Kavanagh, Kimberley; Markowitz, Lauri; Pollock, Kevin G.; Söderlund-Strand, Anna; Sonnenberg, Pam; Tabrizi, Sepehr N.; Tanton, Clare; Unger, Elizabeth; Thomas, Sara L.

    2016-01-01

    We analyzed human papillomavirus (HPV) prevalences during prevaccination and postvaccination periods to consider possible changes in nonvaccine HPV genotypes after introduction of vaccines that confer protection against 2 high-risk types, HPV16 and HPV18. Our meta-analysis included 9 studies with data for 13,886 girls and women ≤19 years of age and 23,340 women 20–24 years of age. We found evidence of cross-protection for HPV31 among the younger age group after vaccine introduction but little evidence for reductions of HPV33 and HPV45. For the group this same age group, we also found slight increases in 2 nonvaccine high-risk HPV types (HPV39 and HPV52) and in 2 possible high-risk types (HPV53 and HPV73). However, results between age groups and vaccines used were inconsistent, and the increases had possible alternative explanations; consequently, these data provided no clear evidence for type replacement. Continued monitoring of these HPV genotypes is important. PMID:27648688

  10. Prevalence of Human Papillomavirus Genotypes Among Women With High-Grade Cervical Lesions in Beijing, China.

    PubMed

    Xiao, Meizhu; Xu, Qiuxiang; Li, Hongyan; Gao, Huiqiao; Bie, Yachun; Zhang, Zhenyu

    2016-01-01

    The aim of the study is to investigate the prevalence of high-risk human papillomavirus (hr-HPV) genotypes among Han women with high-grade cervical lesions in Beijing, China.Cervical cell specimens from patients with histopathologically confirmed cervical lesions at 7 hospitals in Beijing were examined with a validated HPV kit for 13 hr-HPV genotypes during the study period. The patients were divided into a low-grade cervical lesions group (cervical intraepithelial neoplasia grade 1, CIN1) and a high-grade cervical lesions group (CIN2+, including cervical intraepithelial neoplasia grade 2, CIN2; cervical intraepithelial neoplasia grade 3, CIN3; squamous cervical cancer, SCC; and adenocarcinoma of the cervix, ACC) based on the histopathology results.A total of 2817 eligible patients were enrolled, including 610 cases identified as CIN1 and 2207 as CIN2+. The hr-HPV positive rates in the CIN1 and CIN2+ groups were 78.2% (477/610) and 93.3% (2060/2207), respectively. The most frequently detected genotypes were HPV16, 58, 52 and18 in the CIN1 group and HPV16, 58, 33, and 52 in the CIN2+ group, in descending order of prevalence. In addition, the prevalence of HPV18 among the patients with ACC was 28.6% (14/49), significantly >7.2% (54/752) prevalence among the SCC patients (P < 0.001). Additionally, significantly more women in the CIN2+ group had multiple infections compared with those in the CIN1 group (38.1% and 24.9%, respectively; P < 0.001). However, as the cervical lesion grade increased, the prevalence of multiple hr-HPV infections gradually deceased to 44.2% in the CIN2 patients, 36.7% in the CIN3 patients, and 35.3% in the cervical cancer (CC) patients, which included SCC and ACC patients. In cases of multiple hr-HPV infections in the CIN2+ group, double infections accounted for ∼76.6%, and HPV16+58, HPV16+52, and HPV16+18 were the most common combinations, in descending order. The most frequent combination for triple infections was HPV16+58+31, with

  11. Prevalence of Human Papillomavirus Genotypes Among Women With High-Grade Cervical Lesions in Beijing, China

    PubMed Central

    Xiao, Meizhu; Xu, Qiuxiang; Li, Hongyan; Gao, Huiqiao; Bie, Yachun; Zhang, Zhenyu

    2016-01-01

    Abstract The aim of the study is to investigate the prevalence of high-risk human papillomavirus (hr-HPV) genotypes among Han women with high-grade cervical lesions in Beijing, China. Cervical cell specimens from patients with histopathologically confirmed cervical lesions at 7 hospitals in Beijing were examined with a validated HPV kit for 13 hr-HPV genotypes during the study period. The patients were divided into a low-grade cervical lesions group (cervical intraepithelial neoplasia grade 1, CIN1) and a high-grade cervical lesions group (CIN2+, including cervical intraepithelial neoplasia grade 2, CIN2; cervical intraepithelial neoplasia grade 3, CIN3; squamous cervical cancer, SCC; and adenocarcinoma of the cervix, ACC) based on the histopathology results. A total of 2817 eligible patients were enrolled, including 610 cases identified as CIN1 and 2207 as CIN2+. The hr-HPV positive rates in the CIN1 and CIN2+ groups were 78.2% (477/610) and 93.3% (2060/2207), respectively. The most frequently detected genotypes were HPV16, 58, 52 and18 in the CIN1 group and HPV16, 58, 33, and 52 in the CIN2+ group, in descending order of prevalence. In addition, the prevalence of HPV18 among the patients with ACC was 28.6% (14/49), significantly >7.2% (54/752) prevalence among the SCC patients (P < 0.001). Additionally, significantly more women in the CIN2+ group had multiple infections compared with those in the CIN1 group (38.1% and 24.9%, respectively; P < 0.001). However, as the cervical lesion grade increased, the prevalence of multiple hr-HPV infections gradually deceased to 44.2% in the CIN2 patients, 36.7% in the CIN3 patients, and 35.3% in the cervical cancer (CC) patients, which included SCC and ACC patients. In cases of multiple hr-HPV infections in the CIN2+ group, double infections accounted for ∼76.6%, and HPV16+58, HPV16+52, and HPV16+18 were the most common combinations, in descending order. The most frequent combination for triple infections was HPV16

  12. Prevalence of Human Papillomavirus Genotypes Among Women With High-Grade Cervical Lesions in Beijing, China.

    PubMed

    Xiao, Meizhu; Xu, Qiuxiang; Li, Hongyan; Gao, Huiqiao; Bie, Yachun; Zhang, Zhenyu

    2016-01-01

    The aim of the study is to investigate the prevalence of high-risk human papillomavirus (hr-HPV) genotypes among Han women with high-grade cervical lesions in Beijing, China.Cervical cell specimens from patients with histopathologically confirmed cervical lesions at 7 hospitals in Beijing were examined with a validated HPV kit for 13 hr-HPV genotypes during the study period. The patients were divided into a low-grade cervical lesions group (cervical intraepithelial neoplasia grade 1, CIN1) and a high-grade cervical lesions group (CIN2+, including cervical intraepithelial neoplasia grade 2, CIN2; cervical intraepithelial neoplasia grade 3, CIN3; squamous cervical cancer, SCC; and adenocarcinoma of the cervix, ACC) based on the histopathology results.A total of 2817 eligible patients were enrolled, including 610 cases identified as CIN1 and 2207 as CIN2+. The hr-HPV positive rates in the CIN1 and CIN2+ groups were 78.2% (477/610) and 93.3% (2060/2207), respectively. The most frequently detected genotypes were HPV16, 58, 52 and18 in the CIN1 group and HPV16, 58, 33, and 52 in the CIN2+ group, in descending order of prevalence. In addition, the prevalence of HPV18 among the patients with ACC was 28.6% (14/49), significantly >7.2% (54/752) prevalence among the SCC patients (P < 0.001). Additionally, significantly more women in the CIN2+ group had multiple infections compared with those in the CIN1 group (38.1% and 24.9%, respectively; P < 0.001). However, as the cervical lesion grade increased, the prevalence of multiple hr-HPV infections gradually deceased to 44.2% in the CIN2 patients, 36.7% in the CIN3 patients, and 35.3% in the cervical cancer (CC) patients, which included SCC and ACC patients. In cases of multiple hr-HPV infections in the CIN2+ group, double infections accounted for ∼76.6%, and HPV16+58, HPV16+52, and HPV16+18 were the most common combinations, in descending order. The most frequent combination for triple infections was HPV16+58+31, with

  13. Genotypic characterization of Staphylococcus aureus isolated from bovines, humans, and food in Indonesia

    PubMed Central

    Tato, Syarifudin; Sugiyono, Ngalijan; Ariyanti, Dwi; Prabawati, Feny

    2011-01-01

    The present study determined the genetic relationships between 41 Staphyloccocus (S.) aureus isolates from bovines, humans, and food using a single enzyme amplified fragment length polymorphism (AFLP) technique. We evaluated the prevalence of staphylococcal enterotoxin (SE) genes and other virulence gene determinants by PCR. The identification of S. aureus was based on culturing and biochemical tests, and by amplifying a specific section of the 23S rRNA gene. PCR amplification of the SE genes (sea, seb, sec, see, seg, seh, and sei) singly or in combination was observed. Most isolates of bovine origin harbored hla (84%) and cap5 (74%), while most isolates from humans harbored hla (73%), cap8 (91%), and fnbA (100%). Strains from food sources were positive for hla (100%), cap5 (100%), and cap8 (64%) unlike isolates from humans or bovines. A single enzyme AFLP analysis revealed a correlation between AFLP clusters of some strains and the source of the isolates The genotypic results of the present study might help to better understand the distribution of prevalent S. aureus clones among humans, bovines, and food and will help control S. aureus infections in Indonesia. PMID:22127020

  14. Comparing different post-mortem human samples as DNA sources for downstream genotyping and identification.

    PubMed

    Calacal, Gayvelline C; Apaga, Dame Loveliness T; Salvador, Jazelyn M; Jimenez, Joseph Andrew D; Lagat, Ludivino J; Villacorta, Renato Pio F; Lim, Maria Cecilia F; Fortun, Raquel D R; Datar, Francisco A; De Ungria, Maria Corazon A

    2015-11-01

    The capability of DNA laboratories to perform genotyping procedures from post-mortem remains, including those that had undergone putrefaction, continues to be a challenge in the Philippines, a country characterized by very humid and warm conditions all year round. These environmental conditions accelerate the decomposition of human remains that were recovered after a disaster and those that were left abandoned after a crime. When considerable tissue decomposition of human remains has taken place, there is no other option but to extract DNA from bone and/or teeth samples. Routinely, femur shafts are obtained from recovered bodies for human identification because the calcium matrix protects the DNA contained in the osteocytes. In the Philippines, there is difficulty in collecting femur samples after natural disasters or even human-made disasters, because these events are usually characterized by a large number of fatalities. Identification of casualties is further delayed by limitation in human and material resources. Hence, it is imperative to test other types of biological samples that are easier to collect, transport, process and store. We analyzed DNA that were obtained from body fluid, bone marrow, muscle tissue, clavicle, femur, metatarsal, patella, rib and vertebral samples from five recently deceased untreated male cadavers and seven male human remains that were embalmed, buried for ∼ 1 month and then exhumed. The bodies had undergone different environmental conditions and were in various stages of putrefaction. A DNA extraction method utilizing a detergent-washing step followed by an organic procedure was used. The utility of bone marrow and vitreous fluid including bone marrow and vitreous fluid that was transferred on FTA(®) cards and subjected to autosomal STR and Y-STR DNA typing were also evaluated. DNA yield was measured and the presence or absence of PCR inhibitors in DNA extracts was assessed using Plexor(®)HY. All samples were amplified using

  15. Comparing different post-mortem human samples as DNA sources for downstream genotyping and identification.

    PubMed

    Calacal, Gayvelline C; Apaga, Dame Loveliness T; Salvador, Jazelyn M; Jimenez, Joseph Andrew D; Lagat, Ludivino J; Villacorta, Renato Pio F; Lim, Maria Cecilia F; Fortun, Raquel D R; Datar, Francisco A; De Ungria, Maria Corazon A

    2015-11-01

    The capability of DNA laboratories to perform genotyping procedures from post-mortem remains, including those that had undergone putrefaction, continues to be a challenge in the Philippines, a country characterized by very humid and warm conditions all year round. These environmental conditions accelerate the decomposition of human remains that were recovered after a disaster and those that were left abandoned after a crime. When considerable tissue decomposition of human remains has taken place, there is no other option but to extract DNA from bone and/or teeth samples. Routinely, femur shafts are obtained from recovered bodies for human identification because the calcium matrix protects the DNA contained in the osteocytes. In the Philippines, there is difficulty in collecting femur samples after natural disasters or even human-made disasters, because these events are usually characterized by a large number of fatalities. Identification of casualties is further delayed by limitation in human and material resources. Hence, it is imperative to test other types of biological samples that are easier to collect, transport, process and store. We analyzed DNA that were obtained from body fluid, bone marrow, muscle tissue, clavicle, femur, metatarsal, patella, rib and vertebral samples from five recently deceased untreated male cadavers and seven male human remains that were embalmed, buried for ∼ 1 month and then exhumed. The bodies had undergone different environmental conditions and were in various stages of putrefaction. A DNA extraction method utilizing a detergent-washing step followed by an organic procedure was used. The utility of bone marrow and vitreous fluid including bone marrow and vitreous fluid that was transferred on FTA(®) cards and subjected to autosomal STR and Y-STR DNA typing were also evaluated. DNA yield was measured and the presence or absence of PCR inhibitors in DNA extracts was assessed using Plexor(®)HY. All samples were amplified using

  16. Incorporation of Trace Elements in Ancient and Modern Human Bone: An X-Ray Absorption Spectroscopy Study

    NASA Astrophysics Data System (ADS)

    Pingitore, N. E.; Cruz-Jimenez, G.; Price, T. D.

    2001-12-01

    X-ray absorption spectroscopy (XAS) affords the opportunity to probe the atomic environment of trace elements in human bone. We are using XAS to investigate the mode(s) of incorporation of Sr, Zn, Pb, and Ba in both modern and ancient (and thus possibly altered) human and animal bone. Because burial and diagenesis may add trace elements to bone, we performed XAS analysis on samples of pristine contemporary and ancient, buried human and animal bone. We assume that deposition of these elements during burial occurs by processes distinct from those in vivo, and this will be reflected in their atomic environments. Archaeologists measure strontium in human and animal bone as a guide to diet. Carnivores show lower Sr/Ca ratios than their herbivore prey due to discrimination against Sr relative to Ca up the food chain. In an initial sample suite no difference was observed between modern and buried bone. Analysis of additional buried samples, using a more sensitive detector, revealed significant differences in the distance to the second and third neighbors of the Sr in some of the buried samples. Distances to the first neighbor, oxygen, were similar in all samples. Zinc is also used in paleo-diet studies. Initial x-ray absorption spectroscopy of a limited suite of bones did not reveal any differences between modern and buried samples. This may reflect the limited number of samples examined or the low levels of Zn in typical aqueous solutions in soils. Signals from barium and lead were too low to record useful XAS spectra. Additional samples will be studied for Zn, Ba, and Pb. We conducted our XAS experiments on beam lines 4-1 and 4-3 at the Stanford Synchrotron Radiation Laboratory. Data were collected in the fluorescence mode, using a Lytle detector and appropriate filter, and a solid state, 13-element Ge-detector.

  17. Study of Helicobacter pylori genotype status in cows, sheep, goats and human beings

    PubMed Central

    2014-01-01

    Background Helicobacter pylori is one of the most controversial bacteria in the world causing diverse gastrointestinal diseases. The transmission way of this bacterium still remains unknown. The possibility of zoonotic transmission of H. pylori has been suggested, but is not proven in nonprimate reservoirs. In the current survey, we investigate the presence of H. pylori in cow, sheep and goat stomach, determine the bacterium virulence factors and finally compare the human H. pylori virulence factors and animals in order to examine whether H. pylori might be transmitted from these animals to human beings. Methods This cross- sectional study was performed on 800 gastric biopsy specimens of cows, sheep, goats and human beings. The PCR assays was performed to detection of H. pylori, vacA and cagA genes. The PCR products of Ruminant’s samples with positive H. pylori were subjected to DNA sequencing analysis. Statistical tests were applied for data analysis. Results Overall 6 (3%) cows, 32 (16%) sheep and 164 (82%) human beings specimens were confirmed to be H. pylori positive; however we were not able to detect this bacterium in all 200 goat samples. The vacA s1a/m1a was the predominant H. pylori genotype in all three kinds of studied population. There was 3.4–8.4% variability and 92.9-98.5% homology between sheep and human samples. Conclusions Considering the high sequence homology among DNA of H. pylori isolated from sheep and human, our data suggest that sheep may act as a reservoir for H. pylori and in the some extent share the ancestral host for the bacteria with human. PMID:24708464

  18. Endocrinology in ancient Sparta.

    PubMed

    Tsoulogiannis, Ioannis N; Spandidos, Demetrios A

    2007-01-01

    This article attempts to analyze the crucial link between the plant Agnus castus and human health, particularly hormonal status, with special reference to the needs of the society of ancient Sparta. The ancient Spartans used Agnus both as a cure for infertility and as a remedy to treat battle wounds. These special properties were recognized by the sanctuary of Asclepios Agnita, which was located in Sparta, as well as by medical practitioners in Sparta during the classical, Hellenistic and Roman ages.

  19. Identification of Genotype 3 Hepatitis E Virus (HEV) in Serum and Fecal Samples from Pigs in Thailand and Mexico, Where Genotype 1 and 2 HEV Strains Are Prevalent in the Respective Human Populations

    PubMed Central

    Cooper, K.; Huang, F. F.; Batista, L.; Rayo, C. D.; Bezanilla, J. C.; Toth, T. E.; Meng, X. J.

    2005-01-01

    Hepatitis E virus (HEV), the causative agent of hepatitis E, is an important public health concern in many developing countries. Increasing evidence indicates that hepatitis E is a zoonotic disease. There exist four major genotypes of HEV, and HEV isolates identified in samples from pigs belong to either genotype 3 or 4. Genotype 1 and 2 HEVs are found exclusively in humans. To determine whether genotype 1 and 2 HEVs also exist in pigs, a universal reverse transcription-PCR assay that is capable of detecting all four HEV genotypes was used to test for the presence of HEV RNA in serum and/or fecal samples from pigs in Thailand, where genotype 1 human HEV is prevalent, and from pigs in Mexico, where genotype 2 human HEV was epidemic. In Thailand, swine HEV RNA was detected in sera from 10/26 pigs of 2 to 4 months of age but not in sera from 50 pigs of other ages. In Mexico, swine HEV RNA was detected in 8/125 sera and 28/92 fecal samples from 2- to 4-month-old pigs. Antibodies to swine HEV were also detected in about 81% of the Mexican pigs. A total of 44 swine HEV isolates were sequenced for the open reading frame 2 gene region. Sequence analyses revealed that all swine HEV isolates identified in samples from pigs in Thailand and Mexico belong to genotype 3. Phylogenetic analyses revealed that minor branches associated with geographic origin exist among the swine HEV isolates. The results indicated that genotype 1 or 2 swine HEV does not exist in pigs from countries where the respective human HEV genotype 1 or 2 is prevalent. It is likely that only genotype 3 and 4 HEV strains have zoonotic potential. PMID:15814985

  20. Cystic fibrosis mice carrying the missense mutation G551D replicate human genotype-phenotype correlations.

    PubMed Central

    Delaney, S J; Alton, E W; Smith, S N; Lunn, D P; Farley, R; Lovelock, P K; Thomson, S A; Hume, D A; Lamb, D; Porteous, D J; Dorin, J R; Wainwright, B J

    1996-01-01

    We have generated a mouse carrying the human G551D mutation in the cystic fibrosis transmembrane conductance regulator gene (CFTR) by a one-step gene targeting procedure. These mutant mice show cystic fibrosis pathology but have a reduced risk of fatal intestinal blockage compared with 'null' mutants, in keeping with the reduced incidence of meconium ileus in G551D patients. The G551D mutant mice show greatly reduced CFTR-related chloride transport, displaying activity intermediate between that of cftr(mlUNC) replacement ('null') and cftr(mlHGU) insertional (residual activity) mutants and equivalent to approximately 4% of wild-type CFTR activity. The long-term survival of these animals should provide an excellent model with which to study cystic fibrosis, and they illustrate the value of mouse models carrying relevant mutations for examining genotype-phenotype correlations. Images PMID:8605891

  1. Geographical distribution and risk association of human papillomavirus genotype 52-variant lineages.

    PubMed

    Zhang, Chuqing; Park, Jong-Sup; Grce, Magdalena; Hibbitts, Samantha; Palefsky, Joel M; Konno, Ryo; Smith-McCune, Karen K; Giovannelli, Lucia; Chu, Tang-Yuan; Picconi, María Alejandra; Piña-Sánchez, Patricia; Settheetham-Ishida, Wannapa; Coutlée, Francois; De Marco, Federico; Woo, Yin-Ling; Ho, Wendy C S; Wong, Martin C S; Chirenje, Mike Z; Magure, Tsitsi; Moscicki, Anna-Barbara; Sabol, Ivan; Fiander, Alison N; Chen, Zigui; Chan, Martin C W; Cheung, Tak-Hong; Burk, Robert D; Chan, Paul K S

    2014-11-15

    Human papillomavirus (HPV) genotype 52 is commonly found in Asian cases of cervical cancer but is rare elsewhere. Analysis of 611 isolates collected worldwide revealed a remarkable geographical distribution, with lineage B predominating in Asia (89.0% vs 0%-5.5%; P(corrected) < .001), whereas lineage A predominated in Africa, the Americas, and Europe. We propose that the name "Asian lineage" be used to denote lineage B, to signify this feature. Preliminary analysis suggested a higher disease risk for lineage B, although ethnogeographical confounders could not be excluded. Further studies are warranted to verify whether the reported high attribution of disease to HPV52 in Asia is due to the high prevalence of lineage B.

  2. Geographic distribution of human rotavirus VP4 genotypes and VP7 serotypes in five South African regions.

    PubMed Central

    Steele, A D; van Niekerk, M C; Mphahlele, M J

    1995-01-01

    The rotavirus outer capsid proteins elicit the production of neutralizing antibodies and are known to play a role in inducing resistance to disease. In this study, cDNA probes directed at the six most common human rotavirus VP7 serotypes (G1 to G4, G8, and G9) and five human rotavirus VP4 genotypes (P4, P6, P8, P9, and P10) were utilized. Hybridization analysis of 572 human rotavirus strains collected from five regions in South Africa was performed to determine the distribution of the VP7 serotypes and VP4 genotypes in nature. VP7 serotype G1 was identified most frequently, occurring in 51% of the rotavirus strains tested. VP7 serotypes G2 and G4 occurred in similar numbers, although their distribution varied regionally. Few serotype G3 strains and no G8 or G9 strains were identified. The P8 VP4 genotype occurred most frequently overall (66%), and the P4 genotype was detected next most frequently. The P6 genotype was identified in 28 symptomatically infected neonates and in 8 symptomatic infants. Few P9 strains were identified. The potential for reassortment events was demonstrated by dual infections with different viruses. PMID:7650177

  3. Human parechovirus infections and child myositis cases associated with genotype 3 in Osaka City, Japan, 2014.

    PubMed

    Yamamoto, Seiji P; Kaida, Atsushi; Naito, Takuto; Hosaka, Taisuke; Miyazato, Yusuke; Sumimoto, Shin-ichi; Kohdera, Urara; Ono, Atsushi; Kubo, Hideyuki; Iritani, Nobuhiro

    2015-11-01

    Human parechovirus (HPeV) infects humans early in life and typically causes asymptomatic or mild diseases such as gastrointestinal and respiratory illness but sometimes leads to more serious consequences in neonates and young infants. In 2014, we detected HPeV from 38 patients by real-time reverse transcription-PCR in Osaka City, Japan, and 33 HPeV strains were genotyped based on their VP1 sequences. HPeV genotype 3 (HPeV-3) was the most prevalent and accounted for 22 cases (66.7%) followed by nine HPeV-1 (27.3%), one HPeV-2 (3.0%) and one HPeV-4 (3.0%). Phylogenetic analysis revealed that detected HPeV-3 strains were divided into three genetically distinct groups. One was characterized by a novel single amino acid deletion mutation at the N terminus of the 2A protein as well as the VP1 sequence, whereas the others were closely related to HPeV-3 strains detected in Japan in either 2008 or 2011. These HPeV-3 groups were detected from patients with various symptoms including three myositis cases. Recent papers have demonstrated that HPeV-3 was the aetiological agent for epidemic myalgia exclusively among adults from Yamagata Prefecture in Japan. Here, we provide clinical details and episodes of three myositis patients including an adult and two children in Osaka City, Japan. Our results suggest that HPeV-3 is a causative agent of myositis not only in adults but also in children.

  4. Genotypic Characterization of Staphylococcus aureus Obtained from Humans and Bovine Mastitis Samples in India

    PubMed Central

    Prashanth, K; Rao, K Rajender; Reddy, PV Vivek; Saranathan, R; Makki, Abhijith R

    2011-01-01

    Aim and Background: Staphylococcus aureus is a major human pathogen that also causes important infections in cattle and sheep. The present study aimed to test genetic diversity among strains of S. aureus isolated from cattle (n=34) and humans (n=22) by DNA typing. Materials and Methods: Fluorescent amplified fragment length polymorphism (FAFLP) is the genotyping tool used in the study. The presence of the mecA and Panton-Valentine leukocidin (PVL) genes among these strain groups was also checked. Results: A dendrogram deduced from FAFLP showed that all the strains clustered into 10 groups (A–J) with a relative genetic divergence of less than 8%. Sixty-seven percent of the isolates from bovine sources clustered together in two clades (A and H), while another major cluster with 13 isolates (59%) (Cluster G) had all strains from a human host. The remaining strains from both the hosts clustered independently into smaller clusters with the exception of two strains of human origin, which clustered along with a bovine cluster. Thirteen strains belonging to cluster G were highly clonal. About 77% of strains obtained from human infections were methicillin-resistant S. aureus (MRSA), whereas only 29% of strains from bovine origin were MRSA. Only three strains from human origin showed PVL positive, while no strain from cattle had PVL genes. The complete absence of PVL genes in all the bovine strains in the study appears to be significant. Conclusions: FAFLP can be successfully applied to assess the genetic relationship of S. aureus isolates from different hosts. The study also provided the valuable epidemiological data on S. aureus from bovine sources in India, which is lacking. PMID:21731296

  5. Publishing SNP genotypes of human embryonic stem cell lines: policy statement of the International Stem Cell Forum Ethics Working Party.

    PubMed

    Knoppers, Bartha M; Isasi, Rosario; Benvenisty, Nissim; Kim, Ock-Joo; Lomax, Geoffrey; Morris, Clive; Murray, Thomas H; Lee, Eng Hin; Perry, Margery; Richardson, Genevra; Sipp, Douglas; Tanner, Klaus; Wahlström, Jan; de Wert, Guido; Zeng, Fanyi

    2011-09-01

    Novel methods and associated tools permitting individual identification in publicly accessible SNP databases have become a debatable issue. There is growing concern that current technical and ethical safeguards to protect the identities of donors could be insufficient. In the context of human embryonic stem cell research, there are no studies focusing on the probability that an hESC line donor could be identified by analyzing published SNP profiles and associated genotypic and phenotypic information. We present the International Stem Cell Forum (ISCF) Ethics Working Party's Policy Statement on "Publishing SNP Genotypes of Human Embryonic Stem Cell Lines (hESC)". The Statement prospectively addresses issues surrounding the publication of genotypic data and associated annotations of hESC lines in open access databases. It proposes a balanced approach between the goals of open science and data sharing with the respect for fundamental bioethical principles (autonomy, privacy, beneficence, justice and research merit and integrity).

  6. Relationship between pathogenicity for humans and stx genotype in Shiga toxin-producing Escherichia coli serotype O157.

    PubMed

    Kawano, K; Okada, M; Haga, T; Maeda, K; Goto, Y

    2008-03-01

    To examine the reason why people infected with Shiga toxin (Stx) producing Escherichia coli (STEC) O157 strains develop varying clinical manifestations, 65 STEC O157 isolates originating from 64 different occurrences of infection in Miyazaki Prefecture in 2001-2003 and their 79 infected individuals were analyzed by stx genotyping, quantitative analysis of reversed passive latex agglutination (RPLA), genomic DNA analysis using pulsed-field gel electrophoresis (PFGE), and clinical manifestations. The isolates were found to carry the following stx genes: stx2vha alone (60.0%), stx1/stx2 (27.7%), stx1/stx2vha (6.1%), stx2 alone (3.1%), and stx2/stx2vha (3.1%). No strain carried the stx1 gene alone. STEC strains carrying stx2 were more frequently associated with clinical manifestations of hemolytic-uremic syndrome (HUS) or bloody diarrhea than those carrying stx2vha. Clusters of PFGE banding patterns were correlated well with the stx genotypes. We conclude that stx genotype is one of the important factors of clinical outcome of STEC O157 infection and that pathogenicity for humans was higher in the stx2 genotype strains than in the stx2vha genotype strains, as reported previously by other researchers. Further, we newly found that four clusters identified by PFGE using restriction enzyme XbaI, stx genotypes and clinical manifestations were well correlated with each other.

  7. Fire Usage and Ancient Hominin Detoxification Genes: Protective Ancestral Variants Dominate While Additional Derived Risk Variants Appear in Modern Humans

    PubMed Central

    Alink, Gerrit M.; Scherjon, Fulco; MacDonald, Katharine; Smith, Alison C.; Nijveen, Harm; Roebroeks, Wil

    2016-01-01

    Studies of the defence capacity of ancient hominins against toxic substances may contribute importantly to the reconstruction of their niche, including their diets and use of fire. Fire usage implies frequent exposure to hazardous compounds from smoke and heated food, known to affect general health and fertility, probably resulting in genetic selection for improved detoxification. To investigate whether such genetic selection occurred, we investigated the alleles in Neanderthals, Denisovans and modern humans at gene polymorphisms well-known to be relevant from modern human epidemiological studies of habitual tobacco smoke exposure and mechanistic evidence. We compared these with the alleles in chimpanzees and gorillas. Neanderthal and Denisovan hominins predominantly possess gene variants conferring increased resistance to these toxic compounds. Surprisingly, we observed the same in chimpanzees and gorillas, implying that less efficient variants are derived and mainly evolved in modern humans. Less efficient variants are observable from the first early Upper Palaeolithic hunter-gatherers onwards. While not clarifying the deep history of fire use, our results highlight the long-term stability of the genes under consideration despite major changes in the hominin dietary niche. Specifically for detoxification gene variants characterised as deleterious by epidemiological studies, our results confirm the predominantly recent appearance reported for deleterious human gene variants, suggesting substantial impact of recent human population history, including pre-Holocene expansions. PMID:27655273

  8. Ancient Egypt.

    ERIC Educational Resources Information Center

    Evers, Virginia

    This four-week fourth grade social studies unit dealing with religious dimensions in ancient Egyptian culture was developed by the Public Education Religion Studies Center at Wright State University. It seeks to help students understand ancient Egypt by looking at the people, the culture, and the people's world view. The unit begins with outlines…

  9. Epstein-Barr Virus and Human Papillomavirus Infections and Genotype Distribution in Head and Neck Cancers

    PubMed Central

    Deng, Zeyi; Uehara, Takayuki; Maeda, Hiroyuki; Hasegawa, Masahiro; Matayoshi, Sen; Kiyuna, Asanori; Agena, Shinya; Pan, Xiaoli; Zhang, Chunlin; Yamashita, Yukashi; Xie, Minqiang; Suzuki, Mikio

    2014-01-01

    Objective To investigate the prevalence, genotypes, and prognostic values of Epstein-Barr virus (EBV) and human papillomavirus (HPV) infections in Japanese patients with different types of head and neck cancer (HNC). Methods and Materials HPV and EBV DNA, EBV genotypes and LMP-1 variants, and HPV mRNA expression were detected by PCR from fresh-frozen HNC samples. HPV genotypes were determined by direct sequencing, and EBV encoded RNA (EBER) was examined by in situ hybridization. Results Of the 209 HNC patients, 63 (30.1%) had HPV infection, and HPV-16 was the most common subtype (86.9%). HPV E6/E7 mRNA expression was found in 23 of 60 (38.3%) HPV DNA-positive cases detected. The site of highest prevalence of HPV was the oropharynx (45.9%). Among 146 (69.9%) HNCs in which EBV DNA was identified, 107 (73.3%) and 27 (18.5%) contained types A and B, respectively, and 124 (84.9%) showed the existence of del-LMP-1. However, only 13 (6.2%) HNCs were positive for EBER, 12 (92.3%) of which derived from the nasopharynx. Co-infection of HPV and EBER was found in only 1.0% of HNCs and 10.0% of NPCs. Kaplan-Meier survival analysis showed significantly better disease-specific and overall survival in the HPV DNA+/mRNA+ oropharyngeal squamous cell carcinoma (OPC) patients than in the other OPC patients (P = 0.027 and 0.017, respectively). Multivariate analysis showed that stage T1–3 (P = 0.002) and HPV mRNA-positive status (P = 0.061) independently predicted better disease-specific survival. No significant difference in disease-specific survival was found between the EBER-positive and -negative NPC patients (P = 0.155). Conclusions Our findings indicate that co-infection with HPV and EBV is rare in HNC. Oropharyngeal SCC with active HPV infection was related to a highly favorable outcome, while EBV status was not prognostic in the NPC cohort. PMID:25405488

  10. Prevalence and Genotyping of High Risk Human Papillomavirus in Cervical Cancer Samples from Punjab, Pakistan

    PubMed Central

    Siddiqa, Abida; Zainab, Maidah; Qadri, Ishtiaq; Bhatti, Muhammad Faraz; Parish, Joanna L.

    2014-01-01

    Cervical cancer is the third most common cause of cancer-related death in women worldwide. Infection with high-risk human papillomavirus (HPV) is established as the cause of cervical carcinoma, therefore, high risk HPV detection may have prognostic significance for the women who are at increased risk of disease progression. The paucity of data on the incidence of cervical cancer in Pakistan makes it difficult to determine disease burden. Even less information is available regarding the prevalent HPV strains in cervical specimens collected from this region. Cervical cancer is a neglected disease in Pakistan in terms of screening, prevention, and vaccination. Identification and accurate genotyping of the virus burden in cancer specimens is important to inform intervention policies for future management of HPV associated disease and to potentially stratify patients dependent on HPV status. In this study, detection and genotyping of HPV types 16 and 18 from 77 cervical specimens were carried out. Consensus primers GP5+/GP6+, which detect 44 genital HPV types, and type specific primers (TS16 and TS18) were used in conjunction with newly designed type specific primers. Using a combination of these methods of detection, a total of 94.81% (95% CI ±4.95) of cervical lesions were positive for HPV. Single infections of HPV16 were detected in 24.68% (95% CI ±9.63) of total samples and HPV18 was found in 25.97% (95% CI ±9.79) samples. Interestingly, a high proportion of samples (40.26%, 95% CI ±10.95) was positive for both HPV16 and 18, indicating a higher incidence of co-infection than previously reported for similar ethnic regions. The HPV genotype of 3.90% of HPV positive samples remained undetected, although these samples were positive with the GP5+/GP6+ primer set indicating infection with an HPV type other than 16 or 18. These data indicate that the overall incidence of high risk HPV infection in cervical cancer and intraepithelial neoplasia specimens in Punjab

  11. Prevalence and genotyping of high risk human papillomavirus in cervical cancer samples from Punjab, Pakistan.

    PubMed

    Siddiqa, Abida; Zainab, Maidah; Qadri, Ishtiaq; Bhatti, Muhammad Faraz; Parish, Joanna L

    2014-07-01

    Cervical cancer is the third most common cause of cancer-related death in women worldwide. Infection with high-risk human papillomavirus (HPV) is established as the cause of cervical carcinoma, therefore, high risk HPV detection may have prognostic significance for the women who are at increased risk of disease progression. The paucity of data on the incidence of cervical cancer in Pakistan makes it difficult to determine disease burden. Even less information is available regarding the prevalent HPV strains in cervical specimens collected from this region. Cervical cancer is a neglected disease in Pakistan in terms of screening, prevention, and vaccination. Identification and accurate genotyping of the virus burden in cancer specimens is important to inform intervention policies for future management of HPV associated disease and to potentially stratify patients dependent on HPV status. In this study, detection and genotyping of HPV types 16 and 18 from 77 cervical specimens were carried out. Consensus primers GP5+/GP6+, which detect 44 genital HPV types, and type specific primers (TS16 and TS18) were used in conjunction with newly designed type specific primers. Using a combination of these methods of detection, a total of 94.81% (95% CI ±4.95) of cervical lesions were positive for HPV. Single infections of HPV16 were detected in 24.68% (95% CI ±9.63) of total samples and HPV18 was found in 25.97% (95% CI ±9.79) samples. Interestingly, a high proportion of samples (40.26%, 95% CI ±10.95) was positive for both HPV16 and 18, indicating a higher incidence of co-infection than previously reported for similar ethnic regions. The HPV genotype of 3.90% of HPV positive samples remained undetected, although these samples were positive with the GP5+/GP6+ primer set indicating infection with an HPV type other than 16 or 18. These data indicate that the overall incidence of high risk HPV infection in cervical cancer and intraepithelial neoplasia specimens in Punjab

  12. Prevalence and genotype distribution of human papillomavirus infection of the cervix in Spain: the CLEOPATRE study.

    PubMed

    Castellsagué, Xavier; Iftner, Thomas; Roura, Esther; Vidart, José Antonio; Kjaer, Susanne K; Bosch, F Xavier; Muñoz, Nubia; Palacios, Santiago; San Martin Rodriguez, Maria; Serradell, Laurence; Torcel-Pagnon, Laurence; Cortes, Javier

    2012-06-01

    Human papillomavirus (HPV) infection is a necessary cause of cervical cancer. The aim of this study was to estimate the prevalence of cervical HPV infection and HPV type-specific distribution among women attending cervical cancer screening in Spain during 2007 and 2008. Women aged 18-65 years were recruited according to an age-stratified sampling method. Liquid-based cervical samples were collected and analyzed for cytology, HPV detection, and genotyping. HPV genotyping was determined using the INNO-LiPA HPV Genotyping Extra Reverse Hybridization Line Probe Assay. Prevalence estimates were age-standardized using 2001 Spanish census data. The present study included 3,261 women. Age-standardized HC2-based HPV prevalence was 14.3% (95% CI, 13.1-15.5) among women aged 18-65 years, and 28.8% (26.6-31.1) among women aged 18-25 years. High-risk HPV types were detected in 12.2% (95% CI, 11.1-13.4) of HPV-tested women, representing 84.0% of HPV-positive samples. Multiple infections were present in 4.1% (95% CI, 3.4-4.8) of HPV-tested women (25.0% of HPV-positive samples). The most common high-risk HPV-types among HPV-tested women were 16 (2.9%), 52 (1.8%), 51 (1.6%), 31 (1.3%), and 66 (1.2%). HPV-type 16 was present in 16.9% of HPV-positive samples. One or more of the HPV vaccine types 6/11/16/18 were detected in 3.8% of HPV-tested women (22.1% of HPV-positive samples). Though not a true population-based survey, this study provides valuable baseline data for future assessment of the impact of current HPV vaccination programs in Spain. The high prevalence of HPV infection among young women may reflect recent changes in sexual behavior.

  13. Changing Epidemiology of Hepatitis C Virus Genotype among Patients with Human Immunodeficiency Virus/Hepatitis C Virus Co-Infection in China

    PubMed Central

    Hu, Fengyu; Nie, Jingmin; Lan, Yun; Li, Huiqin; Lu, Ruichao; Gao, Yanqing; Song, Yuxia; Zhao, Qingxia; Zheng, Yuhuang; Tang, Xiaoping; Cai, Weiping

    2016-01-01

    Background Co-infection with hepatitis C virus (HCV) has become the most common cause of death in human immunodeficiency virus (HIV) infected patients on antiretroviral therapy. The distribution of HCV genotypes varies with geographical regions and time, and limited studies have focused on the HCV genotype in HIV/HCV co-infection. Methods The distribution of HCV genotypes was evaluated in 414 patients with HIV/HCV co-infection in three regions (South, Central and Northwest) of China from 2008 to 2010. The NS5B region of HCV was characterized using nested reverse transcription polymerase chain reaction. Nucleotide sequences obtained were subjected to phylogenetic analysis, and genotypes were assigned using published reference genotypes. Results Genotype 3 was the most prevalent HCV strain (36.2%), followed by genotype 6 (30.0%), genotype 1 (28.5%), genotype 2 (5.1%), and genotype 5 (0.2%). The distribution varied geographically. Genotype 6 (37.6%) was the predominant strain while genotype 1 (20.2%) was less common in the South compared to the Central and Northwest regions (all P < 0.001). The distribution also varied temporally. There was no significant difference in genotype distribution in Guangdong (a province in the South region), between patient cohorts from 2005–2008 and 2009–2010. However, outside Guangdong, genotypes 3 and 6a became significantly more prevalent (22.4% vs.42.2%, P< 0.001; 8.0% vs. 19.8%, P = 0.004), and genotype 1 less prevalent (54.4% vs.26.6%, P< 0.001) over time. Conclusion The most dramatic shift in genotypic distribution was the movement of HCV genotypes 3 and 6a outside of Guangdong in HIV/HCV co-infected patients. This movement appeared closely associated with transmission via injected drug use. PMID:27603929

  14. Inferences of Recent and Ancient Human Population History Using Genetic and Non-Genetic Data

    ERIC Educational Resources Information Center

    Kitchen, Andrew

    2008-01-01

    I have adopted complementary approaches to inferring human demographic history utilizing human and non-human genetic data as well as cultural data. These complementary approaches form an interdisciplinary perspective that allows one to make inferences of human history at varying timescales, from the events that occurred tens of thousands of years…

  15. GENOTYPE CHARACTERIZATION OF Leishmania (Viannia) braziliensis ISOLATED FROM HUMAN AND CANINE BIOPSIES WITH AMERICAN CUTANEOUS LEISHMANIASIS

    PubMed Central

    FERREIRA, Lasaro Teixeira; GOMES, Aparecida Helena de Souza; PEREIRA-CHIOCCOLA, Vera Lucia

    2015-01-01

    Introduction: American tegumentary leishmaniasis (ATL) can be caused by Leishmania (Viannia) braziliensis complex. The evolution of ATL initially results in lesions and can develop into disseminated or diffuse forms. The genetic diversity of L. (V.) braziliensis in some endemic areas of Brazil has been poorly studied, such as in the state of São Paulo. This study analyzed the genetic diversity of L. (V.) braziliensis isolates collected from patients and dogs with LTA from the state of São Paulo. Methods: Leishmaniasis diagnosis was determined by PCR. The 132 biopsies were collected in different regions of Sao Paulo State, Brazil (36 municipalities). The genetic characterization of L. (V.) braziliensis isolates was tested by RFLP-PCR using DNA extracted from biopsies. The primer set amplified a specific region of Leishmania internal transcribed spacers of the ribosomal DNA locus. Results: Of the 132 samples, 52 (40%) were completely genotyped by RFLP-PCR (44 from human patients and eight from dogs). The results showed nine distinct patterns. The majority of the genotyped samples were from Sorocaba (30), and the others were distributed among 14 other municipalities. The first pattern was more frequent (29 samples), followed by pattern 2 (nine samples) and pattern 3 (three samples). Patterns 4, 6, 7, 8 and 9 were composed of two samples each and pattern 5 of one sample. Conclusion: These results suggest that polymorphic strains of L. (V.) braziliensis circulate in the state of São Paulo. These data agree with studies from other regions of Brazil, showing great variability among the natural populations of endemic foci. PMID:26200968

  16. Attributing oncogenic human papillomavirus genotypes to high-grade cervical neoplasia: which type causes the lesion?

    PubMed

    van der Marel, Jacolien; Berkhof, Johannes; Ordi, Jaume; Torné, Aureli; Del Pino, Marta; van Baars, Romy; Schiffman, Mark; Wentzensen, Nicolas; Jenkins, David; Quint, Wim G V

    2015-04-01

    Human papillomavirus (HPV) is found in most women with high-grade cervical intraepithelial neoplasia (CIN) 2/3 in cervical cytology and biopsies. Multiple high-risk HPV (hrHPV) genotypes are present in 15% to 50% of cytology samples. We have shown by laser-capture microscopy (LCM)-polymerase chain reaction (PCR) that each lesion is associated with a single hrHPV type. Attribution of hrHPV types to CIN2/3 is important to understand the oncogenic role of different types and the limitations of cytologic typing. We studied hrHPV genotypes in 257 women with histologic CIN2/3 referred on the basis of abnormal cytology. HPV typing was done on cytology and CIN2/3 biopsies. If the whole-tissue section of the biopsy was positive for multiple hrHPV types, LCM-PCR was performed. We found 181 (70%) single and 71 (28%) multiple hrHPV infections in cytology, with 5 (2%) cases HPV-positive only on whole-tissue section PCR. Of cases with multiple cytologic hrHPV infections, 47/71 (66%) showed a single type in CIN2/3 lesions. In total, in 232 of 257 (90%) women with CIN2/3, a single hrHPV type caused CIN2/3. One was nonattributable on the LCM level. The remaining 24 women had 2 or more contiguous or separated lesions, each associated with a single hrHPV infection. The probability of HPV16 being present in CIN2/3, if detected in cytology, was 0.96 (95% confidence interval=0.90-0.98). LCM-PCR confirms that only 9% of histologic CIN2/3 is associated with multiple hrHPV types, much less than cytology would indicate, and each lesion was associated with a single hrHPV infection.

  17. Tracing the sources of human salmonellosis: a multi-model comparison of phenotyping and genotyping methods.

    PubMed

    Mughini-Gras, Lapo; Smid, Joost; Enserink, Remko; Franz, Eelco; Schouls, Leo; Heck, Max; van Pelt, Wilfrid

    2014-12-01

    Salmonella source attribution is usually performed using frequency-matched models, such as the (modified) Dutch and Hald models, based on phenotyping data, i.e. serotyping, phage typing, and antimicrobial resistance profiling. However, for practical and economic reasons, genotyping methods such as Multi-locus Variable Number of Tandem Repeats Analysis (MLVA) are gradually replacing traditional phenotyping of salmonellas beyond the serovar level. As MLVA-based source attribution of human salmonellosis using frequency-matched models is problematic due to the high variability of the genetic targets investigated, other models need to be explored. Using a comprehensive data set from the Netherlands in 2005-2013, this study aimed at attributing sporadic and domestic cases of Salmonella Typhimurium/4,[5],12:i:- and Salmonella Enteritidis to four putative food-producing animal sources (pigs, cattle, broilers, and layers/eggs) using the modified Dutch and Hald models (based on sero/phage typing data) in comparison with a widely applied population genetics model - the asymmetric island model (AIM) - supplied with MLVA data. This allowed us to compare model outcomes and to corroborate whether MLVA-based Salmonella source attribution using the AIM is able to provide sound, comparable results. All three models provided very similar results, confirming once more that most S. Typhimurium/4,[5],12:i:- and S. Enteritidis cases are attributable to pigs and layers/eggs, respectively. We concluded that MLVA-based source attribution using the AIM is a feasible option, at least for S. Typhimurium/4,[5],12:i:- and S. Enteritidis. Enough information seems to be contained in the MLVA profiles to trace the sources of human salmonellosis even in presence of imperfect temporal overlap between human and source isolates. Besides Salmonella, the AIM might also be applicable to other pathogens that do not always comply to clonal models. This would add further value to current surveillance

  18. IFNL3 genotype is associated with differential induction of IFNL3 in primary human hepatocytes

    PubMed Central

    Kurbanov, Fuat; Kim, Yonghak; Latanich, Rachel; Chaudhari, Pooja; El-Diwany, Ramy; Knabel, Matt; Kandathil, Abraham J; Cameron, Andrew; Cox, Andrea; Jang, Yoon-Young; Thomas, David L; Balagopal, Ashwin

    2016-01-01

    Background Lambda interferons (IFNLs) have potent antiviral activity against HCV, and polymorphisms within the IFNL gene cluster near the IFNL3 gene strongly predict spontaneous- and treatment-related HCV infection outcomes. The mechanism(s) linking IFNL polymorphisms and HCV control is currently elusive. Methods IFNL induction was studied in primary human hepatocytes (PHH) from 18 human donors, peripheral blood mononuclear cells (PBMCs) from 18 human donors, multiple cell lines and induced pluripotent stem cell-derived hepatocyte-like cells (iPSC-hepatocytes) from 7 human donors. After stimulation with intracellular RNA and infectious HCV, quantitative PCR (qPCR) primers and probes were designed to distinguish and quantify closely related IFNL messenger (m)RNAs from IFNL1, IFNL2 and IFNL3. Results PHH demonstrated the most potent induction of IFNLs, although had lower pre-stimulation levels compared to PBMCs, monocytes and cell lines. PHH stimulation with cytoplasmic poly I:C induced >1,000-fold expression of IFNL1, IFNL2 and IFNL3. PHH from donors who were homozygous for the favourable IFNL3 allele (IFNL3-CC) had higher IFNL3 induction compared to PHH from IFNL3-TT donors (P=0.03). Baseline IFNL mRNA expression and induction was also tested in iPSC-hepatocytes: iPSC-hepatocytes had significantly higher baseline expression of IFNLs compared to PHH (P<0.0001), and IFNL3 induction was marginally different in iPSC-hepatocytes by IFNL genotype (P=0.07). Conclusions Hepatocytes express IFNLs when stimulated by a synthetic viral RNA that signals the cell through the cytoplasm. IFNL induction may be greater in persons with the favourable IFNL3 allele. These data provide insight into the strong linkage between IFNL3 genetics and control of HCV infection. PMID:26109548

  19. Human keratin diseases: the increasing spectrum of disease and subtlety of the phenotype-genotype correlation.

    PubMed

    Irvine, A D; McLean, W H

    1999-05-01

    Keratins are obligate heterodimer proteins that form the intermediate filament cytoskeleton of all epithelial cells. Keratins are tissue and differentiation specific and are expressed in pairs of types I and II proteins. The spectrum of inherited human keratin diseases has steadily increased since the causative role of mutations in the basal keratinocyte keratins 5 and 14 in epidermolysis bullosa simplex (EBS) was first reported in 1991. At the time of writing, mutations in 15 epithelial keratins and two trichocyte keratins have been associated with human diseases which include EBS, bullous congenital ichthyosiform erythroderma, epidermolytic palmoplantar keratoderma, ichthyosis bullosa of Siemens, diffuse and focal non-epidermolytic palmoplantar keratoderma, pachyonychia congenita and monilethrix. Mutations in extracutaneous keratins have been reported in oral white sponge naevus and Meesmann's corneal dystrophy. New subtleties of phenotype-genotype correlation are emerging within the keratin diseases with widely varying clinical presentations attributable to similar mutations within the same keratin. Mutations in keratin-associated proteins have recently been reported for the first time. This article reviews clinical, ultrastructural and molecular aspects of all the keratin diseases described to date and delineates potential future areas of research in this field.

  20. Phenotypic and genotypic characterization of Vagococcus fluvialis, including strains isolated from human sources.

    PubMed Central

    Teixeira, L M; Carvalho, M G; Merquior, V L; Steigerwalt, A G; Brenner, D J; Facklam, R R

    1997-01-01

    This study presents phenotypic and genotypic data for seven isolates of Vagococcus fluvialis, including four strains recovered from human clinical sources, one strain isolated from an environmental source, and two strains isolated from pigs. On the basis of phenotypic characteristics, most isolates were initially classified as "unidentified enterococci," because they resembled atypical arginine-negative enterococcal species. All seven strains as well as the type strain of V. fluvialis reacted with the AccuProbe Enterococcus genetic probe. The seven isolates had virtually indistinguishable whole-cell protein profiles that were similar to that of the V. fluvialis type strain and distinct from those of Enterococcus and Lactococcus species. DNA-DNA reassociation experiments confirmed that the strains were V. fluvialis. They were 71% or more related to the V. fluvialis type strain under optimum and stringent conditions, with 2.5% or less divergence within related sequences. All strains were susceptible to ampicillin, cefotaxime, trimethoprim-sulfamethoxazole, and vancomycin and were resistant to clindamycin, lomefloxacin, and ofloxacin. Strain-to-strain variation was observed in relation to susceptibilities to 18 other antimicrobial agents. Chromosomal DNA was analyzed by pulsed-field gel electrophoresis (PFGE) after digestion with SmaI. Distinctive PFGE patterns were generated, suggesting the nonclonal nature of V. fluvialis strains. Although the number of strains was small, this report provides molecular characterization of V. fluvialis and the first evidence of a possible connection of this species with human infections. PMID:9350732

  1. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

    PubMed Central

    Warinner, Christina; Speller, Camilla; Collins, Matthew J.

    2015-01-01

    The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes. PMID:25487328

  2. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome.

    PubMed

    Warinner, Christina; Speller, Camilla; Collins, Matthew J

    2015-01-19

    The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.

  3. Human papillomavirus infections in women seeking cervical Papanicolaou cytology of Durango, Mexico: prevalence and genotypes

    PubMed Central

    Sánchez-Anguiano, Luis Francisco; Alvarado-Esquivel, Cosme; Reyes-Romero, Miguel Arturo; Carrera-Rodríguez, Margarita

    2006-01-01

    Background HPV infection in women from developing countries is an important public health problem. Therefore, we sought to determine the prevalences of HPV infection and HPV genotypes in a female population of Durango City, Mexico. Also to determine whether any socio-demographic characteristic from the women associated with HPV infection exists. Methods Four hundred and ninety eight women seeking cervical Papanicolaou examination in three public Health Centers were examined for HPV infection. All women were tested for HPV DNA PCR by using HPV universal primers. In addition, all positive HPV DNA PCR samples were further analyzed for genotyping of HPV genotype 16, 18 and 33. Socio-demographic characteristics from each participant were also obtained. Results Twenty-four out of four hundred and ninety-eight (4.8%) women were found infected by HPV. HPV genotype 16 was found in 18 out of the 24 (75%) infected women. Two of them were also coinfected by HPV genotype 18 (8.3%). In the rest 6 PCR positive women, genotyping for HPV genotypes 16, 18 and 33 were negative. Conclusion The prevalence of HPV in women of Durango City is low; however, most infected women have high risk HPV genotype. The women who were studied showed low frequency of risk factors for HPV infection and this may explain the low prevalence of HPV infection. The high frequency of high risk HPV genotypes observed might explain the high rate of mortality for cervical cancer in our region. PMID:16504014

  4. An ascorbic acid-enriched tomato genotype to fight UVA-induced oxidative stress in normal human keratinocytes.

    PubMed

    Petruk, Ganna; Raiola, Assunta; Del Giudice, Rita; Barone, Amalia; Frusciante, Luigi; Rigano, Maria Manuela; Monti, Daria Maria

    2016-10-01

    UVA radiations contribute up to 95% of the total UV exposure and are known to induce cell damage, leading to apoptosis. Since the benefic effects of ascorbic acid on human health are well known, a new tomato genotype (named DHO4), highly rich in ascorbic acid, has been recently obtained. Here, we compared the effects of ascorbic acid and hydrophilic DHO4 extracts in protecting human keratinocytes exposed to UVA stress. Keratinocytes were pre-incubated with ascorbic acid or with extracts from the ascorbic acid enriched tomato genotype and irradiated with UVA light. Then, ROS production, intracellular GSH and lipid peroxidation levels were quantified. Western blots were carried out to evaluate mitogen-activated protein kinases cascade, activation of caspase-3 and inflammation levels. We demonstrated that ROS, GSH and lipid peroxidation levels were not altered in cell exposed to UVA stress when cells were pre-treated with ascorbic acid or with tomato extracts. In addition, no evidence of apoptosis and inflammation were observed in irradiated pre-treated cells. Altogether, we demonstrated the ability of an ascorbic acid enriched tomato genotype to counteract UVA-oxidative stress on human keratinocytes. This protective effect is due to the high concentration of vitamin C that acts as free radical scavenger. This novel tomato genotype may be used as genetic material in breeding schemes to produce improved varieties with higher antioxidant levels.

  5. An ascorbic acid-enriched tomato genotype to fight UVA-induced oxidative stress in normal human keratinocytes.

    PubMed

    Petruk, Ganna; Raiola, Assunta; Del Giudice, Rita; Barone, Amalia; Frusciante, Luigi; Rigano, Maria Manuela; Monti, Daria Maria

    2016-10-01

    UVA radiations contribute up to 95% of the total UV exposure and are known to induce cell damage, leading to apoptosis. Since the benefic effects of ascorbic acid on human health are well known, a new tomato genotype (named DHO4), highly rich in ascorbic acid, has been recently obtained. Here, we compared the effects of ascorbic acid and hydrophilic DHO4 extracts in protecting human keratinocytes exposed to UVA stress. Keratinocytes were pre-incubated with ascorbic acid or with extracts from the ascorbic acid enriched tomato genotype and irradiated with UVA light. Then, ROS production, intracellular GSH and lipid peroxidation levels were quantified. Western blots were carried out to evaluate mitogen-activated protein kinases cascade, activation of caspase-3 and inflammation levels. We demonstrated that ROS, GSH and lipid peroxidation levels were not altered in cell exposed to UVA stress when cells were pre-treated with ascorbic acid or with tomato extracts. In addition, no evidence of apoptosis and inflammation were observed in irradiated pre-treated cells. Altogether, we demonstrated the ability of an ascorbic acid enriched tomato genotype to counteract UVA-oxidative stress on human keratinocytes. This protective effect is due to the high concentration of vitamin C that acts as free radical scavenger. This novel tomato genotype may be used as genetic material in breeding schemes to produce improved varieties with higher antioxidant levels. PMID:27599115

  6. Optimal sample storage and extraction procotols for reliable multilocus genotyping of the human parasite Schistosoma mansoni.

    PubMed

    Van den Broeck, F; Geldof, S; Polman, K; Volckaert, F A M; Huyse, T

    2011-08-01

    Genotyping individual larval stages and eggs of natural parasite populations is complicated by the difficulty of obtaining reliable genotypes from low quantity DNA template. A suitable storage and extraction protocol, together with a thorough quantification of genotyping errors are therefore crucial for molecular epidemiological studies. Here we test the robustness, handling time, ease of use, cost effectiveness and success rate of various fixation (Whatman FTA(®) Classic and Elute Cards, 70% EtOH and RNAlater(®)) and subsequent DNA extraction methods (commercial kits and proteinase K protocol). None of these methods require a cooling chain and are therefore suitable for field collection. Based on a multiplex microsatellite PCR with nine loci the success and reliability of each technique is evaluated by the proportion of samples with at least eight scored loci and the proportion of genotyping errors. If only the former is taken into account, FTA(®) Elute is recommended (83% success; 44% genotyping error; 0.2 €/sample; 1h 20 m handling time). However, when also considering the genotyping errors, handling time and ease of use, we opt for 70% EtOH with the 96-well plate technology followed by a simple proteinase K extraction (73% success; 0% genotyping error; 0.2 €/sample; 15m handling time). For eggs we suggest (1) to pool all eggs per person in 1.5 ml tubes filled with 70% EtOH for transport and (2) to identify each egg to species level prior to genotyping. To this end we extended the Rapid diagnostic PCR developed by Webster et al. (2010) with a S. mansoni-specific primer to discriminate between S. mansoni, S. haematobium and S. bovis in a single PCR reaction. The success rate of genotyping eggs was 75% (0% genotyping error). This is the first study to incorporate genotyping errors through re-amplification for the evaluation of schistosome sampling protocols and the identification of error-prone loci.

  7. Clusters of alpha satellite on human chromosome 21 are dispersed far onto the short arm and lack ancient layers.

    PubMed

    Ziccardi, William; Zhao, Chongjian; Shepelev, Valery; Uralsky, Lev; Alexandrov, Ivan; Andreeva, Tatyana; Rogaev, Evgeny; Bun, Christopher; Miller, Emily; Putonti, Catherine; Doering, Jeffrey

    2016-09-01

    Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the AS arrays, and compared them to AS arrays found on other chromosomes. We find that the majority of the HC21 AS sequences are present on the p-arm of the chromosome and are organized into at least five distinct isolated clusters which are distributed over a larger distance from the functional centromere than that typically seen for AS on other chromosomes. Using both phylogenetic and L1 element age estimations, we found that all of the HC21 AS clusters outside the functional centromere are of a similar relatively recent evolutionary origin. HC21 contains none of the ancient AS layers associated with early primate evolution which is present on other chromosomes, possibly due to the fact that the p-arm of HC21 and the other acrocentric chromosomes underwent substantial reorganization about 20 million years ago. PMID:27430641

  8. DNA detection and genotypic identification of potentially human-pathogenic microsporidia from asymptomatic pet parrots in South Korea as a risk factor for zoonotic emergence.

    PubMed

    Lee, So-Young; Lee, Sung-Seok; Lyoo, Young S; Park, Hee-Myung

    2011-12-01

    We detected and identified genotypes of human-pathogenic microsporidia in fecal samples from 51 asymptomatic captive-bred pet parrots in South Korea. Microsporidia were identified in 8 samples (15.7%); 7 parrots tested positive for Encephalitozoon hellem, and 1 parrot tested positive for both E. hellem and Encephalitozoon cuniculi. In genotypic identifications, E. hellem was present in genotypes 1A and 2B and E. cuniculi was present in genotype II. Pet parrots might be a source of human microsporidian infection.

  9. First report of an Acanthamoeba genotype T13 isolate as etiological agent of a keratitis in humans.

    PubMed

    Grün, Anna-Lena; Stemplewitz, Birthe; Scheid, Patrick

    2014-06-01

    Several strains of free-living amoebae (FLA) belonging to the genus Acanthamoeba are able to cause a painful sight-threatening disease of the cornea designated as Acanthamoeba keratitis (AK). In this case report, a 22-year-old woman, wearer of soft contact lenses, was treated after the initial examination, and follow-up laboratory results led to the diagnosis of Acanthamoeba keratitis. The patient recovered under the targeted therapy, demonstrating that the acanthamoebae were the etiological agents of the keratitis in this case. The acanthamoebae belonged morphologically to group II. Genotyping of the causative Acanthamoeba strain based on sequences of the PCR amplimer ASA.S1 amplified from 18S ribosomal DNA by using the genus-specific primers JDP1 and JDP2 followed. The phylogenetic comparison of ASA.S1 confirmed that the isolated Acanthamoeba strain is closely related to genotype T13 supported by pairwise sequence identities of 97.1-98.0% and bootstrap support of 980 replicates with reference sequences of genotype T13. These results regarding the Acanthamoeba keratitis-causing isolate KaBo expands the number of known pathogenic genotypes to 12. To our knowledge, this is the first report of a T13 Acanthamoeba genotype being associated with keratitis in humans. PMID:24802868

  10. Bacterial histo-blood group antigens contributing to genotype-dependent removal of human noroviruses with a microfiltration membrane.

    PubMed

    Amarasiri, Mohan; Hashiba, Satoshi; Miura, Takayuki; Nakagomi, Toyoko; Nakagomi, Osamu; Ishii, Satoshi; Okabe, Satoshi; Sano, Daisuke

    2016-05-15

    We demonstrated the genotype-dependent removal of human norovirus particles with a microfiltration (MF) membrane in the presence of bacteria bearing histo-blood group antigens (HBGAs). Three genotypes (GII.3, GII.4, and GII.6) of norovirus-like particles (NoVLPs) were mixed with three bacterial strains (Enterobacter sp. SENG-6, Escherichia coli O86:K61:B7, and Staphylococcus epidermidis), respectively, and the mixture was filtered with an MF membrane having a nominal pore size of 0.45 μm. All NoVLP genotypes were rejected by the MF membrane in the presence of Enterobacter sp. SENG-6, which excreted HBGAs as extracellular polymeric substances (EPS). This MF membrane removal of NoVLPs was not significant when EPS was removed from cells of Enterobacter sp. SENG-6. GII.6 NoVLP was not rejected with the MF membrane in the presence of E. coli O86:K61:B7, but the removal of EPS of E. coli O86:K61:B7 increased the removal efficiency due to the interaction of NoVLPs with the exposed B-antigen in lipopolysaccharide (LPS) of E. coli O86:K61:B7. No MF membrane removal of all three genotypes was observed when S. epidermidis, an HBGA-negative strain, was mixed with NoVLPs. These results demonstrate that the location of HBGAs on bacterial cells is an important factor in determining the genotype-dependent removal efficiency of norovirus particles with the MF membrane. The presence of HBGAs in mixed liquor suspended solids from a membrane bioreactor (MBR) pilot plant was confirmed by immune-transmission electron microscopy, which implies that bacterial HBGAs can contribute to the genotype-dependent removal of human noroviruses with MBR using MF membrane. PMID:27095709

  11. Genotyping of Campylobacter coli strains isolated in Brazil suggests possible contamination amongst environmental, human, animal and food sources.

    PubMed

    Gomes, Carolina N; Souza, Roberto A; Passaglia, Jaqueline; Duque, Sheila S; Medeiros, Marta I C; Falcão, Juliana P

    2016-01-01

    Campylobacter coli and Campylobacter jejuni are two of the most common causative agents of food-borne gastroenteritis in numerous countries worldwide. In Brazil, campylobacteriosis is under diagnosed and under-reported, and few studies have molecularly characterized Campylobacter spp. in this country. The current study genotyped 63 C. coli strains isolated from humans (n512), animals (n521), food (n510) and the environment (n520) between 1995 and 2011 in Brazil. The strains were genotyped using pulsed-field gel electrophoresis (PFGE), sequencing the short variable region (SVR) of the flaA gene ( flaA-SVR) and high-resolution melting analysis (HRMA) of the clustered regularly interspaced short palindromic repeat (CRISPR) locus to better understand C. coli genotypic diversity and compare the suitability of these three methods for genotyping this species. Additionally, the discrimination index (DI) of each of these methods was assessed. Some C. coli strains isolated from clinical and non-clinical origins presented ≥80 % genotypic similarity by PFGE and flaA-SVR sequencing. HRMA of the CRISPR locus revealed only four different melting profiles. In total, 22 different flaA-SVR alleles were detected. Of these, seven alleles, comprising gt1647–gt1653, were classified as novel. The most frequent genotypes were gt30 and gt1647. This distribution reveals the diversity of selected Brazilian isolates in comparison with the alleles described in the PubMLST database. The DIs for PFGE, flaA–SVR sequencing and CRISPR-HRMA were 0.986, 0.916 and 0.550, respectively. PFGE and flaA-SVR sequencing were suitable for subtyping C. coli strains, in contrast to CRISPR-HRMA. The high genomic similarity amongst some C. coli strains confirms the hypothesis that environmental and food sources potentially lead to human and animal contamination in Brazil.

  12. Ancient Civilizations.

    ERIC Educational Resources Information Center

    Web Feet K-8, 2000

    2000-01-01

    This subject guide includes Web sites and other resources on ancient civilizations with age levels and appropriate subject disciplines specified. Also includes CD-ROMs and software, videos, books, audios, magazines, professional resources, and a sample student assignment. (LRW)

  13. Distribution of Carcinogenic Human Papillomavirus Genotypes and Association to Cervical Lesions among Women in Fez (Morocco)

    PubMed Central

    Souho, Tiatou; El Fatemi, Hinde; Karim, Safae; El Rhazi, Karima; Bouchikhi, Chahrazed; Banani, Abdelaziz; Melhouf, Moulay Abdelilah; Benlemlih, Mohamed; Bennani, Bahia

    2016-01-01

    Objectives To determine the distribution of cervical high-risk human papillomavirus genotypes and their association to cellular abnormalities in women from Fez and its neighborhood. Methods Women attending the Hassan II University Hospital for cervical pap smears were recruited after an informed consent. Interviews and two cervical samples were performed for each woman. Cervical samples were used for cytological analysis and HPV DNA detection. HPV was typed using a method based on multiplex PCR with fluorescently labeled specific primers followed by capillary electrophoresis. The study was approved by the ethics committee of the Faculty of Medicine and Pharmacy of Fez. Results The HPV prevalence in the studied population was 43.1% and the most prevalent types were HPV 53 (23 cases); HPV 16 (20 cases); HPV 35 (18 cases); HPV 51 (10 cases) and HPV 56 (7 cases). From the 619 confirmed pap smears, 20% were abnormal. The cytological abnormalities were significantly associated to HPV infection, women age, number of pregnancies and parity (p < 0.05). Conclusion More attention should be given to HPV in Morocco because it represents an important public health concern. The distribution of carcinogenic HPV types in the studied population is different from the data in other regions but epidemiological studies in other Moroccan regions are required. PMID:26731415

  14. Detection of Human Papillomavirus Genotypes and Major BRCA Mutations in Familial Breast Cancer.

    PubMed

    Mohtasebi, Parinaz; Rassi, Hossein; Maleki, Fatemeh; Hajimohammadi, Sameh; Bagheri, Zahra; Fakhar Miandoab, Malihe; Naserbakht, Mahdieh

    2016-06-01

    Breast cancer is a multistep disease and infection with a DNA virus could play a role in one or more of the steps in this pathogenic process. High-risk human papillomaviruses (HPVs) are the causative agents of several cancers. In this study, we investigated HPV genotypes associated with breast cancer and its relationship with BRCA mutation for the detection of familial breast cancer. We analyzed 84 formalin-fixed, paraffin-embedded tissue blocks from 38 familial breast cancer and 46 nonfamilial breast cancer samples by multiplex polymerase chain reaction and clinical parameters. Overall prevalence of HPV infection was 27 of 84: 10 (37.03%) HPV-16, 9 (29.62%) HPV-18, 4 (14.81%) HPV-11, 1 (3.7%) HPV-31, 1 (3.7%) HPV-33, and 2 (7.4%) HPV35. Furthermore, 17 mtDNA4977 deletions and 5 5382insC mutations were detected from 38 familial breast cancer samples. Our results demonstrate that infection with HPV was prevalent among Iranian women with familial breast cancer and the testing of mtDNA4977 deletions and 5382insC mutations in combination with clinical parameters as major risk factors can serve in the identification of familial breast cancer. PMID:27186947

  15. Diversity of human parechoviruses in Bulgaria, 2011: Detection of rare genotypes 8 and 10.

    PubMed

    Mladenova, Zornitsa; Dikova, Antoaneta; Thongprachum, Aksara; Petrov, Petar; Pekova, Liliq; Komitova, Radka; Iturriza-Gomara, Miren; Ushijima, Hiroshi

    2015-12-01

    Human parechovirus (HPeV) infections are commonly asymptomatic but are also found in association with symptoms of the gastrointestinal and respiratory tract, or central nervous system. In order to study their distribution and genetic diversity in Bulgaria, specimens from 229 children aged <5years old hospitalized due to neurological manifestations (n=104) and acute gastroenteritis (n=125) were analyzed. Stool samples were tested using reverse transcription followed by real-time polymerase chain reaction toward the 5'UTR region, and the HPeVs detected were identified by PCR directed to VP1 followed by sequencing. HPeV infection rates of 1.9% and 7.2% were found in children presented with neurological symptoms or with acute diarrhea, respectively. Four different HPeV genotypes, HPeV-3 (n=2), HPeV-5 (n=2), HPeV-8 (n=1) and HPeV-10 (n=1) were identified. All but two HPeVs were detected in acute diarrheal cases, while a single HPeV-3 strain and an HPeV-8 strain were detected in association with facial palsy and encephalitis, respectively. This is the first report of HPeV-8 and HPeV-10 in Europe. PMID:26453770

  16. Ancient DNA.

    PubMed

    Willerslev, Eske; Cooper, Alan

    2005-01-01

    In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.

  17. Ancient DNA

    PubMed Central

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets. PMID:15875564

  18. Multilocus Genotyping of Human Giardia Isolates Suggests Limited Zoonotic Transmission and Association between Assemblage B and Flatulence in Children

    PubMed Central

    Lebbad, Marianne; Petersson, Ingvor; Karlsson, Lillemor; Botero-Kleiven, Silvia; Andersson, Jan O.; Svenungsson, Bo; Svärd, Staffan G.

    2011-01-01

    Background Giardia intestinalis is one of the most common diarrhea-related parasites in humans, where infection ranges from asymptomatic to acute or chronic disease. G. intestinalis consists of eight genetically distinct genotypes or assemblages, designated A–H, and assemblages A and B can infect humans. Giardiasis has been classified as a possible zoonotic disease but the role of animals in human disease transmission still needs to be proven. We tried to link different assemblages and sub-assemblages of G. intestinalis isolates from Swedish human patients to clinical symptoms and zoonotic transmission. Methodology/Principal Findings Multilocus sequence-based genotyping of 207 human Giardia isolates using three gene loci: ß-giardin, glutamate dehydrogenase (gdh), and triose phosphate isomerase (tpi) was combined with assemblage-specific tpi PCRs. This analysis identified 73 patients infected with assemblage A, 128 with assemblage B, and six with mixed assemblages A+B. Multilocus genotypes (MLGs) were easily determined for the assemblage A isolates, and most patients with this genotype had apparently been infected through anthroponotic transmission. However, we also found evidence of limited zoonotic transmission of Giardia in Sweden, since a few domestic human infections involved the same assemblage A MLGs previously reported in Swedish cats and ruminants. Assemblage B was detected more frequently than assemblage A and it was also more common in patients with suspected treatment failure. However, a large genetic variability made determination of assemblage B MLGs problematic. Correlation between symptoms and assemblages was found only for flatulence, which was significantly more common in children less than six years of age infected with assemblage B. Conclusions/Significance This study shows that certain assemblage A subtypes are potentially zoonotic and that flatulence is connected to assemblage B infections in young children. Determination of MLGs from

  19. Characterization of variant Creutzfeldt-Jakob disease prions in prion protein-humanized mice carrying distinct codon 129 genotypes.

    PubMed

    Takeuchi, Atsuko; Kobayashi, Atsushi; Ironside, James W; Mohri, Shirou; Kitamoto, Tetsuyuki

    2013-07-26

    To date, all clinical variant Creutzfeldt-Jakob disease (vCJD) patients are homozygous for methionine at polymorphic codon 129 (129M/M) of the prion protein (PrP) gene. However, the appearance of asymptomatic secondary vCJD infection in individuals with a PRNP codon 129 genotype other than M/M and transmission studies using animal models have raised the concern that all humans might be susceptible to vCJD prions, especially via secondary infection. To reevaluate this possibility and to analyze in detail the transmission properties of vCJD prions to transgenic animals carrying distinct codon 129 genotype, we performed intracerebral inoculation of vCJD prions to humanized knock-in mice carrying all possible codon 129 genotypes (129M/M, 129M/V, or 129V/V). All humanized knock-in mouse lines were susceptible to vCJD infection, although the attack rate gradually decreased from 129M/M to 129M/V and to 129V/V. The amount of PrP deposition including florid/amyloid plaques in the brain also gradually decreased from 129M/M to 129M/V and to 129V/V. The biochemical properties of protease-resistant abnormal PrP in the brain and transmissibility of these humanized mouse-passaged vCJD prions upon subpassage into knock-in mice expressing bovine PrP were not affected by the codon 129 genotype. These results indicate that individuals with the 129V/V genotype may be more susceptible to secondary vCJD infection than expected and may lack the neuropathological characteristics observed in vCJD patients with the 129M/M genotype. Besides the molecular typing of protease-resistant PrP in the brain, transmission studies using knock-in mice carrying bovine PrP may aid the differential diagnosis of secondary vCJD infection, especially in individuals with the 129V/V genotype.

  20. stx genotype and molecular epidemiological analyses of Shiga toxin-producing Escherichia coli O157:H7/H- in human and cattle isolates.

    PubMed

    Kawano, K; Ono, H; Iwashita, O; Kurogi, M; Haga, T; Maeda, K; Goto, Y

    2012-02-01

    The relationship between human diseases caused by infection with Shiga toxin (Stx)-producing Escherichia coli (STEC) O157 strains and O157 strains isolated from cattle was investigated in an area where stockbreeding is prolific. For this purpose, the stx genotypes, the molecular epidemiological characteristics of 268 STEC O157 strains including 211 human-origin strains and 57 cattle-origin strains, and clinical manifestations of 210 STEC-infected people were analyzed. Of 211 human-origin strains, 92 strains (44%) were of the stx1/stx2 genotype, and 74 strains (35%) were of the stx2c genotype. Most of the people infected with stx2c genotype strains presented no symptoms or mild symptoms such as slight diarrhea, except for 3 patients with bloody diarrhea. Of the 57 cattle-origin strains, 27 strains (47%) were of the stx2c genotype and 17 strains (30%) were of the stx1/stx2 genotype. Pulsed-field gel electrophoresis (PFGE) and insertion sequence (IS) analysis demonstrated that 11 isolates (41%) of the 27 cattle isolates of the stx2c genotype had high homology (>95% identity) with human isolates. These results suggest that some genetic patterns of the stx2c genotype strains might be preserved in cattle or their surrounding environment for several years, and during these periods, they might have opportunities to infect people through various routes. Because of the mild virulence of the stx2c genotype strains, they seemed to be transmitted asymptomatically from cattle to humans and then spread from person to person. It may be a public health concern. Further, they occasionally cause severe symptoms in humans; therefore, caution is warranted for infections by stx2c genotype O157 strains, in addition to stx2-possessing genotype O157 strains.

  1. Genotypic and phenotypic variation among Staphylococcus saprophyticus from human and animal isolates

    PubMed Central

    2010-01-01

    Background The main aim of this study was to examine the genotypic and phenotypic diversity of Staphylococcus saprophyticus isolates from human and animal origin. Findings In total, 236 clinical isolates and 15 animal isolates of S. saprophyticus were characterized in respect of the occurrence of 9 potential virulence genes and four surface properties. All strains were PCR positive for the regulatory genes agr, sar >it>A and rot as well as for the surface proteins UafA and Aas. Nearly 90% of the clinical isolates were found to possess the gene for the surface-associated lipase Ssp and 10% for the collagen binding MSCRAMM SdrI. All animal isolates were negative forsdrI. Lipolytic activity could be detected in 66% of the clinical and 46% of the animal isolates. Adherence to collagen type I was shown of 20% of the clinical strains and 6% of the strains of animal origin. Most S. saprophyticus strains showed hydrophobic properties and only few could agglutinate sheep erythrocytes. Conclusions We described a broad analysis of animal and human S. saprophyticus isolates regarding virulence genes and phenotypic properties such as lipase activity, hydrophobicity, and adherence. While S. saprophyticus strains from animal sources have prerequisites for colonization of the urinary tract like the D-serine-deaminase, out findings suggested that they need to acquire new genes e.g. MSCRAMMS for adherence like sdrI and to modulate their existing properties e.g. increasing the lipase activity or reducing hydrophobicity. These apparently important new genes or properties for virulence have to be further analyzed. PMID:20537181

  2. New Ancient Egyptian Human Mummies from the Valley of the Kings, Luxor: Anthropological, Radiological, and Egyptological Investigations

    PubMed Central

    Rühli, Frank; Ikram, Salima; Bickel, Susanne

    2015-01-01

    The Valley of the Kings (arab. Wadi al Muluk; KV) situated on the West Bank near Luxor (Egypt) was the site for royal and elite burials during the New Kingdom (ca. 1500–1100 BC), with many tombs being reused in subsequent periods. In 2009, the scientific project “The University of Basel Kings' Valley Project” was launched. The main purpose of this transdisciplinary project is the clearance and documentation of nonroyal tombs in the surrounding of the tomb of Pharaoh Thutmosis III (ca. 1479–1424 BC; KV 34). This paper reports on newly discovered ancient Egyptian human mummified remains originating from the field seasons 2010–2012. Besides macroscopic assessments, the remains were conventionally X-rayed by a portable X-ray unit in situ inside KV 31. These image data serve as basis for individual sex and age determination and for the study of probable pathologies and embalming techniques. A total of five human individuals have been examined so far and set into an Egyptological context. This project highlights the importance of ongoing excavation and science efforts even in well-studied areas of Egypt such as the Kings' Valley. PMID:26347313

  3. New Ancient Egyptian Human Mummies from the Valley of the Kings, Luxor: Anthropological, Radiological, and Egyptological Investigations.

    PubMed

    Rühli, Frank; Ikram, Salima; Bickel, Susanne

    2015-01-01

    The Valley of the Kings (arab. Wadi al Muluk; KV) situated on the West Bank near Luxor (Egypt) was the site for royal and elite burials during the New Kingdom (ca. 1500-1100 BC), with many tombs being reused in subsequent periods. In 2009, the scientific project "The University of Basel Kings' Valley Project" was launched. The main purpose of this transdisciplinary project is the clearance and documentation of nonroyal tombs in the surrounding of the tomb of Pharaoh Thutmosis III (ca. 1479-1424 BC; KV 34). This paper reports on newly discovered ancient Egyptian human mummified remains originating from the field seasons 2010-2012. Besides macroscopic assessments, the remains were conventionally X-rayed by a portable X-ray unit in situ inside KV 31. These image data serve as basis for individual sex and age determination and for the study of probable pathologies and embalming techniques. A total of five human individuals have been examined so far and set into an Egyptological context. This project highlights the importance of ongoing excavation and science efforts even in well-studied areas of Egypt such as the Kings' Valley.

  4. New Ancient Egyptian Human Mummies from the Valley of the Kings, Luxor: Anthropological, Radiological, and Egyptological Investigations.

    PubMed

    Rühli, Frank; Ikram, Salima; Bickel, Susanne

    2015-01-01

    The Valley of the Kings (arab. Wadi al Muluk; KV) situated on the West Bank near Luxor (Egypt) was the site for royal and elite burials during the New Kingdom (ca. 1500-1100 BC), with many tombs being reused in subsequent periods. In 2009, the scientific project "The University of Basel Kings' Valley Project" was launched. The main purpose of this transdisciplinary project is the clearance and documentation of nonroyal tombs in the surrounding of the tomb of Pharaoh Thutmosis III (ca. 1479-1424 BC; KV 34). This paper reports on newly discovered ancient Egyptian human mummified remains originating from the field seasons 2010-2012. Besides macroscopic assessments, the remains were conventionally X-rayed by a portable X-ray unit in situ inside KV 31. These image data serve as basis for individual sex and age determination and for the study of probable pathologies and embalming techniques. A total of five human individuals have been examined so far and set into an Egyptological context. This project highlights the importance of ongoing excavation and science efforts even in well-studied areas of Egypt such as the Kings' Valley. PMID:26347313

  5. Human Papillomavirus Genotyping Using Archival Vulval Dysplastic or Neoplastic Biopsy Tissues: Comparison between the INNO-LiPA and Linear Array Assays▿

    PubMed Central

    Tan, Sarah E.; Garland, Suzanne M.; Rumbold, Alice R.; Tabrizi, Sepehr N.

    2010-01-01

    The Roche Linear Array (LA) and Innogenetics INNO-LiPA human papillomavirus (HPV) genotyping assays were compared for paraffin-embedded vulval tissues. The LA detected amplifiable DNA in 28 (57%) out of 49 biopsy specimens, 20 (40%) being HPV genotyped, compared to 49 (100%) and 41 (83%), respectively, detected by the INNO-LiPA. The INNO-LiPA provides greater sensitivity for HPV genotyping in archival tissue. PMID:20181920

  6. Ancient human sialic acid variant restricts an emerging zoonotic malaria parasite

    PubMed Central

    Dankwa, Selasi; Lim, Caeul; Bei, Amy K.; Jiang, Rays H. Y.; Abshire, James R.; Patel, Saurabh D.; Goldberg, Jonathan M.; Moreno, Yovany; Kono, Maya; Niles, Jacquin C.; Duraisingh, Manoj T.

    2016-01-01

    Plasmodium knowlesi is a zoonotic parasite transmitted from macaques causing malaria in humans in Southeast Asia. Plasmodium parasites bind to red blood cell (RBC) surface receptors, many of which are sialylated. While macaques synthesize the sialic acid variant N-glycolylneuraminic acid (Neu5Gc), humans cannot because of a mutation in the enzyme CMAH that converts N-acetylneuraminic acid (Neu5Ac) to Neu5Gc. Here we reconstitute CMAH in human RBCs for the reintroduction of Neu5Gc, which results in enhancement of P. knowlesi invasion. We show that two P. knowlesi invasion ligands, PkDBPβ and PkDBPγ, bind specifically to Neu5Gc-containing receptors. A human-adapted P. knowlesi line invades human RBCs independently of Neu5Gc, with duplication of the sialic acid-independent invasion ligand, PkDBPα and loss of PkDBPγ. Our results suggest that absence of Neu5Gc on human RBCs limits P. knowlesi invasion, but that parasites may evolve to invade human RBCs through the use of sialic acid-independent pathways. PMID:27041489

  7. Molecular genotyping of human Ureaplasma species based on multiple-banded antigen (MBA) gene sequences.

    PubMed

    Kong, F; Ma, Z; James, G; Gordon, S; Gilbert, G L

    2000-09-01

    Ureaplasma urealyticum has been divided into 14 serovars. Recently, subdivision of U. urealyticum into two species has been proposed: U. parvum (previously U. urealyticum parvo biovar), comprising four serovars (1, 3, 6, 14) and U. urealyticum (previously U. urealyticum T-960 biovar), 10 serovars (2, 4, 5, 7-13). The multiple-banded antigen (MBA) genes of these species contain both species and serovar/subtype specific sequences. Based on whole sequences of the 5'-ends of MBA genes of U. parvum serovars and partial sequences of the 5'-ends of MBA genes of U. urealyticum serovars, we previously divided each of these species into three MBA genotypes. To further elucidate the relationships between serovars, we sequenced the whole 5'-ends of MBA genes of all 10 U. urealyticum serovars and partial repetitive regions of these genes from all serovars of U. parvum and U. urealyticum. For the first time, all four serovars of U. parvum were clearly differentiated from each other. In addition, the 10 serovars of U. urealyticum were divided into five MBA genotypes, as follows: MBA genotype A comprises serovars 2, 5, 8; MBA genotype B, serovar 10 only; MBA genotype C, serovars 4, 12, 13; MBA genotype D, serovar 9 only; and MBA genotype E comprises serovars 7 and 11. There were no sequence differences between members within each MBA genotype. Further work is required to identify other genes or other regions of the MBA genes that may be used to differentiate U. urealyticum serovars within MBA genotypes A, C and E. A better understanding of the molecular basis of serotype differentiation will help to improve subtyping methods for use in studies of the pathogenesis and epidemiology of these organisms.

  8. Full genomic characterization of a novel genotype combination, G4P[14], of a human rotavirus strain from Barbados.

    PubMed

    Tam, Ka Ian; Roy, Sunando; Esona, Mathew D; Jones, Starlene; Sobers, Stephanie; Morris-Glasgow, Victoria; Rey-Benito, Gloria; Gentsch, Jon R; Bowen, Michael D

    2014-12-01

    Since 2004, the Pan American Health Organization (PAHO) has carried out rotavirus surveillance in Latin America and the Caribbean. Here we report the characterization of human rotavirus with the novel G-P combination of G4P[14], detected through PAHO surveillance in Barbados. Full genome sequencing of strain RVA/Human-wt/BRB/CDC1133/2012/G4P[14] revealed that its genotype is G4-P[14]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The possession of a Genogroup 1 (Wa-like) backbone distinguishes this strain from other P[14] rotavirus strains. Phylogenetic analyses suggested that this strain was likely generated by genetic reassortment between human, porcine and possibly other animal rotavirus strains and identified 7 lineages within the P[14] genotype. The results of this study reinforce the potential role of interspecies transmission in generating human rotavirus diversity through reassortment. Continued surveillance is important to determine if rotavirus vaccines will protect against strains that express the P[14] rotavirus genotype.

  9. Full genomic characterization of a novel genotype combination, G4P[14], of a human rotavirus strain from Barbados.

    PubMed

    Tam, Ka Ian; Roy, Sunando; Esona, Mathew D; Jones, Starlene; Sobers, Stephanie; Morris-Glasgow, Victoria; Rey-Benito, Gloria; Gentsch, Jon R; Bowen, Michael D

    2014-12-01

    Since 2004, the Pan American Health Organization (PAHO) has carried out rotavirus surveillance in Latin America and the Caribbean. Here we report the characterization of human rotavirus with the novel G-P combination of G4P[14], detected through PAHO surveillance in Barbados. Full genome sequencing of strain RVA/Human-wt/BRB/CDC1133/2012/G4P[14] revealed that its genotype is G4-P[14]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The possession of a Genogroup 1 (Wa-like) backbone distinguishes this strain from other P[14] rotavirus strains. Phylogenetic analyses suggested that this strain was likely generated by genetic reassortment between human, porcine and possibly other animal rotavirus strains and identified 7 lineages within the P[14] genotype. The results of this study reinforce the potential role of interspecies transmission in generating human rotavirus diversity through reassortment. Continued surveillance is important to determine if rotavirus vaccines will protect against strains that express the P[14] rotavirus genotype. PMID:25251674

  10. Poor Prognosis Associated With Human Papillomavirus α7 Genotypes in Cervical Carcinoma Cannot Be Explained by Intrinsic Radiosensitivity

    SciTech Connect

    Hall, John S.; Iype, Rohan; Armenoult, Lucile S.C.; Taylor, Janet; Miller, Crispin J.; Davidson, Susan; Sanjose, Silvia de; Bosch, Xavier; Stern, Peter L.; West, Catharine M.L.

    2013-04-01

    Purpose: To investigate the relationship between human papillomavirus (HPV) genotype and outcome after radiation therapy and intrinsic radiosensitivity. Methods and Materials: HPV genotyping was performed on cervix biopsies by polymerase chain reaction using SPF-10 broad-spectrum primers, followed by deoxyribonucleic acid enzyme immunoassay and genotyping by reverse hybridization line probe assay (LiPA{sub 25}) (version 1) (n=202). PapilloCheck and quantitative reverse transcription-polymerase chain reaction were used to genotype cervix cancer cell lines (n=16). Local progression-free survival after radiation therapy alone was assessed using log-rank and Cox proportionate hazard analyses. Intrinsic radiosensitivity was measured as surviving fraction at 2 Gy (SF2) using clonogenic assays. Results: Of the 202 tumors, 107 (53.0%) were positive for HPV16, 29 (14.4%) for HPV18, 9 (4.5%) for HPV45, 23 (11.4%) for other HPV genotypes, and 22 (10.9%) were negative; 11 (5.5%) contained multiple genotypes, and 1 tumor was HPV X (0.5%). In 148 patients with outcome data, those with HPVα9-positive tumors had better local progression-free survival compared with α7 patients in univariate (P<.004) and multivariate (hazard ratio 1.54, 95% confidence interval 1.11-1.76, P=.021) analyses. There was no difference in the median SF2 of α9 and α7 cervical tumors (n=63). In the cell lines, 9 were α7 and 4 α9 positive and 3 negative. There was no difference in SF2 between α9 and α7 cell lines (n=14). Conclusion: The reduced radioresponsiveness of α7 cervical tumors is not related to intrinsic radiosensitivity.

  11. Comparison of Seegene Anyplex II HPV28 with the PGMY-CHUV assay for human papillomavirus genotyping.

    PubMed

    Estrade, C; Sahli, R

    2014-02-01

    The Anyplex II HPV28 (H28; Seegene) is a new semiquantitative real-time multiplex PCR assay for screening and genotyping 28 human papillomaviruses (HPV) in only 2 reaction wells. H28 was compared to the PGMY-CHUV assay (PG) with 309 archival DNA samples from cervical smears collected over 8 years in our laboratory. H28 and PG were fully concordant at the genotypic level on 228 (73.8%) out of 309 samples: 27 HPV negative and 201 HPV positive. The 201 fully concordant positive samples corresponded to single infections (n = 145) and to multiple infections (2 genotypes, n = 38; 3 to 5 genotypes, n = 18). The remaining 81 samples (26.2%) were either partially concordant (n = 64, 20.7%) or fully discordant (n = 17, 5.5%). While genotype-specific agreement was nearly perfect (κ = 0.877), HPV51 was significantly less well detected by H28 and the converse was observed for HPV40, -42, -54, and -68. Sequencing of PG amplicons confirmed HPV51 discordants and suggested the involvement of a possibly local HPV51 subtype. Mismatches in the PGMY09 primers to HPV68a explained most of the HPV68 discordants, confirming the specificity of H28 toward HPV68. With PG as a reference, the sensitivity and specificity of H28 were 93.4% and 99.0%, respectively. Considering H28 as a reference, the sensitivity and specificity of PG were 83.8% and 99.6%, respectively. H28 is a very sensitive and specific HPV genotyping assay suitable for research and clinical use as an adjunct to a clinically validated test. H28 semiquantitative readout ought to be evaluated for primary cervical cancer screening.

  12. Ancient, highly polymorphic human major histocompatibility complex DQA1 intron sequence

    SciTech Connect

    McGinnis, M.D.; Quinn, D.L.; Lebo, R.V.; Simons, M.J.

    1994-10-01

    A 438 basepair intron 1 sequence adjacent to exon 2 in the human major histocompatibility complex DQA1 gene defined 16 allelic variants in 69 individuals from wide ethnic backgrounds. In contrast, the most variable coding region spanned by the 247 basepair exon 2 defined 11 allelic variants. Our phylogenetic human intron 1 tree derived by the Bootstrap algorithm reflects the same relative allelic relationships as the reported DQA1 exon 2 have cosegregated since divergence of the human races. Comparison of human alleles to a Rhesus monkey DQA1 first intron sequence found only 10 nucleotide substitutions unique to Rhesus, with the other 428 positions (98%) found in at least one human allele. This high degree of homology reflects the evolutionary stability of intron sequences since these two species diverged over 20 million years ago. Because more intron 1 alleles exist than exon 2 alleles, these polymorphic introns can be used to improve tissue typing for transplantation, paternity testing, and forensics and to derive more complete phylogenetic trees. These results suggest that introns represent a previously underutilized polymorphic resource. 42 refs., 3 figs., 1 tab.

  13. Genotype distribution of human papillomavirus (HPV) in histological sections of cervical intraepithelial neoplasia and invasive cervical carcinoma in Madrid, Spain

    PubMed Central

    2012-01-01

    Background Human Papillomavirus (HPV) genotype distribution and co-infection occurrence was studied in cervical specimens from the city of Madrid (Spain), as a contribution to the knowledge of Human Papillomavirus genotype distribution and prevalence of carcinogenic HPV types in cervical lesions in Spain. Methods A total of 533 abnormal specimens, from the Hospital General Universitario “Gregorio Marañón” of Madrid, were studied. These included 19 benign lesions, 349 cervical intraepithelial neoplasias 1 (CIN1), 158 CIN2-3 and 7 invasive cervical carcinomas (ICC). HPV genotyping was performed using PCR and tube array hybridization. Results We detected 20 different HPV types: 13 carcinogenic high-risk HPV types (HR-HPVs), 2 probably carcinogenic high-risk HPV types (PHR-HPVs) and 5 carcinogenic low-risk HPV types (LR-HPVs). The most frequent HPV genotypes found in all specimens were HPV16 (26.0%), 31 (10.7%) and 58 (8.0%). HPV 18 was only detected in 5.0%. Co-infections were found in 30.7% of CIN 1 and 18.4% cases of CIN2-3. The highest percentage of HR HPVs was found in those specimens with a CIN2-3 lesion (93.7%). Conclusion As our study shows the current tetravalent vaccine could be effective in our geographical area for preventing all the invasive cervical carcinomas. In addition, upon the estimates of the important presence of other HR-HPV types – such as 31, 58, 33 and 52 – in different preneoplasic lesions the effectiveness of HPV vaccination in our geographical area, and others with similar genotype distribution, should be limited. PMID:23167826

  14. Comparative genotypic and pathogenic examination of Campylobacter concisus isolates from diarrheic and non-diarrheic humans

    PubMed Central

    2011-01-01

    Background Campylobacter concisus is an emerging enteric pathogen, yet it is commonly isolated from feces and the oral cavities of healthy individuals. This genetically complex species is comprised of several distinct genomospecies which may vary in pathogenic potential. Results We compared pathogenic and genotypic properties of C. concisus fecal isolates from diarrheic and healthy humans residing in the same geographic region. Analysis of amplified fragment length polymorphism (AFLP) profiles delineated two main clusters. Isolates assigned to AFLP cluster 1 belonged to genomospecies A (based on genomospecies-specific differences in the 23S rRNA gene) and were predominantly isolated from healthy individuals. This cluster also contained a reference oral strain. Isolates assigned to this cluster induced greater expression of epithelial IL-8 mRNA and more frequently contained genes coding for the zonnula occludins toxin and the S-layer RTX. Furthermore, isolates from healthy individuals induced greater apoptotic DNA fragmentation and increased metabolic activity than those from diarrheic individuals, and isolates assigned to genomospecies A (of which the majority were from healthy individuals) exhibited higher haemolytic activity compared to genomospecies B isolates. In contrast, AFLP cluster 2 was predominated by isolates belonging to genomospecies B and those from diarrheic individuals. Isolates from this cluster displayed greater mean epithelial invasion and translocation than cluster 1 isolates. Conclusion Two main genetically distinct clusters (i.e., genomospecies) were identified among C. concisus fecal isolates from healthy and diarrheic individuals. Strains within these clusters differed with respect to clinical presentation and pathogenic properties, supporting the hypothesis that pathogenic potential varies between genomospecies. ALFP cluster 2 isolates were predominantly from diarrheic patients, and exhibited higher levels of epithelial invasion and

  15. Genetic characterisation of Cryptosporidium and Giardia from dairy calves: discovery of species/genotypes consistent with those found in humans.

    PubMed

    Abeywardena, Harshanie; Jex, Aaron R; Nolan, Matthew J; Haydon, Shane R; Stevens, Melita A; McAnulty, Robin W; Gasser, Robin B

    2012-12-01

    Cryptosporidium and Giardia are important genera of parasitic protists that can cause significant diarrhoeal diseases in humans and other animals. Depending on the species/genotype of parasite, human infection may be acquired via anthroponotic or zoonotic transmission routes. Here, we undertook a molecular epidemiological investigation of these two genera of parasites in pre- and post-weaned calves from eight locations in Canterbury, New Zealand, by PCR-coupled sequencing and phylogenetic analysis of sequence data for regions in the 60 kDa glycoprotein (pgp60) gene of Cryptosporidium and/or the triose-phosphate isomerase (ptpi) gene of Giardia. The pgp60 and ptpi regions were specifically amplified from 15 (8.3%) and 11 (6.1%) of the 180 individual faecal samples, respectively. The sequences derived from all of the amplicons were aligned with homologous reference sequences and subjected to phylogenetic analysis by Bayesian inference. For Cryptosporidium, three samples contained Cryptosporidium parvum genotype IIa, subgenotypes IIaA15G3R1, IIaA19G3R1 and IIaA23G4. Twelve samples contained Cryptosporidium hominis genotype Ib, subgenotype IbA10G2R2. While subgenotypes IIaA15G3R1 and IIaA23G4 are new records, IIaA19G3R1 and IbA10G2R2 are commonly found in humans in various countries. For Giardia, two samples contained Giardia duodenalis assemblage A, also common in humans. In contrast, nine samples contained G. duodenalis assemblage E, which is the first report of this assemblage in cattle in New Zealand. Therefore, the present results indicate that dairy calves on the South Island of New Zealand harbour 'zoonotic' genotypes of Cryptosporidium and Giardia, which is likely to have significant public health implications.

  16. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics

    PubMed Central

    Campos, Paula F.; Willerslev, Eske; Sher, Andrei; Orlando, Ludovic; Axelsson, Erik; Tikhonov, Alexei; Aaris-Sørensen, Kim; Greenwood, Alex D.; Kahlke, Ralf-Dietrich; Kosintsev, Pavel; Krakhmalnaya, Tatiana; Kuznetsova, Tatyana; Lemey, Philippe; MacPhee, Ross; Norris, Christopher A.; Shepherd, Kieran; Suchard, Marc A.; Zazula, Grant D.; Shapiro, Beth; Gilbert, M. Thomas P.

    2010-01-01

    The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal that musk ox genetic diversity was much higher during the Pleistocene than at present, and has undergone several expansions and contractions over the past 60,000 years. Northeast Siberia was of key importance, as it was the geographic origin of all samples studied and held a large diverse population until local extinction at ≈45,000 radiocarbon years before present (14C YBP). Subsequently, musk ox genetic diversity reincreased at ca. 30,000 14C YBP, recontracted at ca. 18,000 14C YBP, and finally recovered in the middle Holocene. The arrival of humans into relevant areas of the musk ox range did not affect their mitochondrial diversity, and both musk ox and humans expanded into Greenland concomitantly. Thus, their population dynamics are better explained by a nonanthropogenic cause (for example, environmental change), a hypothesis supported by historic observations on the sensitivity of the species to both climatic warming and fluctuations. PMID:20212118

  17. Simple and rapid human papillomavirus genotyping method by restriction fragment length polymorphism analysis with two restriction enzymes.

    PubMed

    Chen, Linghan; Watanabe, Ken; Haruyama, Takahiro; Kobayashi, Nobuyuki

    2013-07-01

    Cervical cancer, the third most common cancer that affects women worldwide, is caused by the human papillomavirus (HPV) and is treatable when detected at an early stage. To date, more than 100 different HPV types have been described, and the development of simple, low-cost, and accurate methods to distinguish HPV genotypes is highly warranted. In this study, an HPV genotyping assay based on polymerase chain reaction (PCR) was evaluated. This method involved the use of MY09/11 primers followed by restriction fragment length polymorphism (RFLP) analysis with the restriction enzymes HpyCH4V and NlaIII. Cervical specimens preserved using CytoRich Blue fluid were collected from 1,134 female volunteers for HPV detection, and 1,111 valid samples were amplified using PCR. The PCR method was sensitive enough to detect 25 copies of HPV18, and three copies of HPV16. Out of 202 PCR-positive samples, HPV genotypes were determined in 189 samples (93.6%) by this RFLP method. Results were then evaluated further by capillary sequencing method. Concordant results between the two tests were as high as 96.0%. Thirteen samples, which tested negative with RFLP, were verified as non-specific amplifications with PCR. In conclusion, this PCR-RFLP method using restriction enzymes HpyCH4V and NlaIII is simple, non-labor intensive, and is applicable for the inexpensive determination of HPV genotypes in clinical samples.

  18. Development and Clinical Evaluation of a Highly Sensitive DNA Microarray for Detection and Genotyping of Human Papillomaviruses

    PubMed Central

    Oh, TaeJeong; Kim, ChangJin; Woo, SukKyung; Kim, TaeSeung; Jeong, DongJun; Kim, MyungSoon; Lee, Sunwoo; Cho, HyunSill; An, Sungwhan

    2004-01-01

    Human papillomavirus (HPV) has been found in cervical cancer, tonsillar cancer, and certain types of head and neck cancers. We report on a DNA microarray-based method for the simultaneous detection and typing of HPVs. The genotype spectrum discriminated by this HPV DNA microarray includes 15 high-risk HPV genotypes and 12 low-risk HPV genotypes. The HPV DNA microarray showed high degrees of specificity and reproducibility. We evaluated the performance of the HPV DNA microarray by application to three HPV-positive cell lines (HeLa, Caski, and SiHa cells) and two HPV-negative cell lines (C33A and A549 cells). The HPV DNA microarray successfully identified the known types of HPV present in the cell lines. The detection limit of the HPV DNA microarray was at least 100-fold higher than that of PCR. To assess the clinical applicability of the HPV DNA microarray, we performed the HPV genotyping assay with 73 nonmalignant and malignant samples from 39 tonsillar cancer patients. Twenty-five of the 39 (64.1%) malignant samples were positive for HPV, whereas 3 of 34 (8.8%) nonmalignant samples were positive for HPV. This result shows a preferential association of HPV with tonsillar carcinomas. The correlations of the presence of HPV with the grade of differentiation and risk factors were not significant. Our data show that the HPV DNA microarray may be useful for the diagnosis and typing of HPV in large-scale epidemiological studies. PMID:15243092

  19. Insights into epidemiology of human parvovirus B19 and detection of an unusual genotype 2 variant, Bulgaria, 2004 to 2013.

    PubMed

    Ivanova, Stefka Krumova; Mihneva, Zafira Georgieva; Toshev, Andon Krumov; Kovaleva, Valentina Pavlova; Andonova, Lubena Georgieva; Muller, Claude P; Hübschen, Judith M

    2016-01-01

    The present study aimed to determine the role of human parvovirus В19 (B19V) as an aetiological agent in measles and rubella negative fever/rash patients from Bulgaria between 2004 and 2013. A total of 1,266 sera from all over the country were tested for B19V IgM antibodies and all positives were further investigated by polymerase chain reaction (PCR). Overall, 280 sera (22%) were B19V IgM positive and 227 of these (81%) were also PCR positive. The highest number of IgM positives was found among five to nine year-old children (27%). Eight infected women gave birth to healthy children; one fetus was aborted with hydrops fetalis. Of the 55 genetic sequences obtained, 54 belonged to genotype 1a and one grouped as a genotype 2 outlier. Phylogenetic analysis of all available genotype 2 sequences covering the 994 nucleotide non-structural protein 1(NS1)/capsid viral protein 1 (VP1) unique region junction, showed that only one other sequence grouped with the outlier strain, forming a clearly distinct and well-supported cluster of genotype 2 (between-group genetic distance: 3.32%). In accordance with B19V nomenclature, this cluster may represent a new subgenotype 2b. The study showed that B19V infections may be falsely identified as rubella or measles in ca 22% of cases, emphasising the need for laboratory confirmation. PMID:26847955

  20. Uniqueness of Human Running Coordination: The Integration of Modern and Ancient Evolutionary Innovations.

    PubMed

    Kiely, John; Collins, David J

    2016-01-01

    Running is a pervasive activity across human cultures and a cornerstone of contemporary health, fitness, and sporting activities. Yet for the overwhelming predominance of human existence running was an essential prerequisite for survival. A means to hunt, and a means to escape when hunted. In a very real sense humans have evolved to run. Yet curiously, perhaps due to running's cultural ubiquity and the natural ease with which we learn to run, we rarely consider the uniqueness of human bipedal running within the animal kingdom. Our unique upright, single stance, bouncing running gait imposes a unique set of coordinative difficulties. Challenges demanding we precariously balance our fragile brains in the very position where they are most vulnerable to falling injury while simultaneously retaining stability, steering direction of travel, and powering the upcoming stride: all within the abbreviated time-frames afforded by short, violent ground contacts separated by long flight times. These running coordination challenges are solved through the tightly-integrated blending of primitive evolutionary legacies, conserved from reptilian and vertebrate lineages, and comparatively modern, more exclusively human, innovations. The integrated unification of these top-down and bottom-up control processes bestows humans with an agile control system, enabling us to readily modulate speeds, change direction, negotiate varied terrains and to instantaneously adapt to changing surface conditions. The seamless integration of these evolutionary processes is facilitated by pervasive, neural and biological, activity-dependent adaptive plasticity. Over time, and with progressive exposure, this adaptive plasticity shapes neural and biological structures to best cope with regularly imposed movement challenges. This pervasive plasticity enables the gradual construction of a robust system of distributed coordinated control, comprised of processes that are so deeply collectively entwined that

  1. Uniqueness of Human Running Coordination: The Integration of Modern and Ancient Evolutionary Innovations

    PubMed Central

    Kiely, John; Collins, David J.

    2016-01-01

    Running is a pervasive activity across human cultures and a cornerstone of contemporary health, fitness, and sporting activities. Yet for the overwhelming predominance of human existence running was an essential prerequisite for survival. A means to hunt, and a means to escape when hunted. In a very real sense humans have evolved to run. Yet curiously, perhaps due to running's cultural ubiquity and the natural ease with which we learn to run, we rarely consider the uniqueness of human bipedal running within the animal kingdom. Our unique upright, single stance, bouncing running gait imposes a unique set of coordinative difficulties. Challenges demanding we precariously balance our fragile brains in the very position where they are most vulnerable to falling injury while simultaneously retaining stability, steering direction of travel, and powering the upcoming stride: all within the abbreviated time-frames afforded by short, violent ground contacts separated by long flight times. These running coordination challenges are solved through the tightly-integrated blending of primitive evolutionary legacies, conserved from reptilian and vertebrate lineages, and comparatively modern, more exclusively human, innovations. The integrated unification of these top-down and bottom-up control processes bestows humans with an agile control system, enabling us to readily modulate speeds, change direction, negotiate varied terrains and to instantaneously adapt to changing surface conditions. The seamless integration of these evolutionary processes is facilitated by pervasive, neural and biological, activity-dependent adaptive plasticity. Over time, and with progressive exposure, this adaptive plasticity shapes neural and biological structures to best cope with regularly imposed movement challenges. This pervasive plasticity enables the gradual construction of a robust system of distributed coordinated control, comprised of processes that are so deeply collectively entwined that

  2. Oxytocin Pathway Genes: Evolutionary Ancient System Impacting on Human Affiliation, Sociality, and Psychopathology.

    PubMed

    Feldman, Ruth; Monakhov, Mikhail; Pratt, Maayan; Ebstein, Richard P

    2016-02-01

    Oxytocin (OT), a nonapeptide signaling molecule originating from an ancestral peptide, appears in different variants across all vertebrate and several invertebrate species. Throughout animal evolution, neuropeptidergic signaling has been adapted by organisms for regulating response to rapidly changing environments. The family of OT-like molecules affects both peripheral tissues implicated in reproduction, homeostasis, and energy balance, as well as neuromodulation of social behavior, stress regulation, and associative learning in species ranging from nematodes to humans. After describing the OT-signaling pathway, we review research on the three genes most extensively studied in humans: the OT receptor (OXTR), the structural gene for OT (OXT/neurophysin-I), and CD38. Consistent with the notion that sociality should be studied from the perspective of social life at the species level, we address human social functions in relation to OT-pathway genes, including parenting, empathy, and using social relationships to manage stress. We then describe associations between OT-pathway genes with psychopathologies involving social dysfunctions such as autism, depression, or schizophrenia. Human research particularly underscored the involvement of two OXTR single nucleotide polymorphisms (rs53576, rs2254298) with fewer studies focusing on other OXTR (rs7632287, rs1042778, rs2268494, rs2268490), OXT (rs2740210, rs4813627, rs4813625), and CD38 (rs3796863, rs6449197) single nucleotide polymorphisms. Overall, studies provide evidence for the involvement of OT-pathway genes in human social functions but also suggest that factors such as gender, culture, and early environment often confound attempts to replicate first findings. We conclude by discussing epigenetics, conceptual implications within an evolutionary perspective, and future directions, especially the need to refine phenotypes, carefully characterize early environments, and integrate observations of social behavior across

  3. A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years.

    PubMed

    Moorjani, Priya; Sankararaman, Sriram; Fu, Qiaomei; Przeworski, Molly; Patterson, Nick; Reich, David

    2016-05-17

    The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these studies is the reliable estimation of the age of ancient specimens. High-resolution age estimates can often be obtained using radiocarbon dating, and, while precise and powerful, this method has some biases, making it of interest to directly use genetic data to infer a date for samples that have been sequenced. Here, we report a genetic method that uses the recombination clock. The idea is that an ancient genome has evolved less than the genomes of present-day individuals and thus has experienced fewer recombination events since the common ancestor. To implement this idea, we take advantage of the insight that all non-Africans have a common heritage of Neanderthal gene flow into their ancestors. Thus, we can estimate the date since Neanderthal admixture for present-day and ancient samples simultaneously and use the difference as a direct estimate of the ancient specimen's age. We apply our method to date five Upper Paleolithic Eurasian genomes with radiocarbon dates between 12,000 and 45,000 y ago and show an excellent correlation of the genetic and (14)C dates. By considering the slope of the correlation between the genetic dates, which are in units of generations, and the (14)C dates, which are in units of years, we infer that the mean generation interval in humans over this period has been 26-30 y. Extensions of this methodology that use older shared events may be applicable for dating beyond the radiocarbon frontier.

  4. A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years.

    PubMed

    Moorjani, Priya; Sankararaman, Sriram; Fu, Qiaomei; Przeworski, Molly; Patterson, Nick; Reich, David

    2016-05-17

    The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these studies is the reliable estimation of the age of ancient specimens. High-resolution age estimates can often be obtained using radiocarbon dating, and, while precise and powerful, this method has some biases, making it of interest to directly use genetic data to infer a date for samples that have been sequenced. Here, we report a genetic method that uses the recombination clock. The idea is that an ancient genome has evolved less than the genomes of present-day individuals and thus has experienced fewer recombination events since the common ancestor. To implement this idea, we take advantage of the insight that all non-Africans have a common heritage of Neanderthal gene flow into their ancestors. Thus, we can estimate the date since Neanderthal admixture for present-day and ancient samples simultaneously and use the difference as a direct estimate of the ancient specimen's age. We apply our method to date five Upper Paleolithic Eurasian genomes with radiocarbon dates between 12,000 and 45,000 y ago and show an excellent correlation of the genetic and (14)C dates. By considering the slope of the correlation between the genetic dates, which are in units of generations, and the (14)C dates, which are in units of years, we infer that the mean generation interval in humans over this period has been 26-30 y. Extensions of this methodology that use older shared events may be applicable for dating beyond the radiocarbon frontier. PMID:27140627

  5. The human skin: a meeting ground for the ideas about macrocosm and microcosm in ancient and Medieval and Greek literature.

    PubMed

    Diamandopoulos, A A; Goudas, P; Diamandopoulos, A H

    2001-12-01

    We have been interested in the cleansing capacity of skin during the recent years. In a paper of ours (1) we presented a few references to Hippocrates' and Galen's ideas on the subject, while the main body of the article was based on the 17th-20th centuries' relative practices. In a second paper (2), we were mainly testing the ancient and Medieval Greek ideas on skin catharsis against some clinical work of ours. In this paper we now present the ideas of the pagan and Byzantine Greek authors (5th cent. BC - 10th cent. AD) on the relationship of the human body to the natural and man-made world. Special emphasis is given to the relationship between purification through the skin and world purification. Based on the similarity of the Empedokles' concept of the four elements and Hippocrates' thesis concerning the four humours, the Earth itself was personified and became a living organism that felt cold, perspired and became dry. Man started to seek a natural explanation for his diseases and alterations of his body functions. Hence, perspiration, fever, urination, headache, stroke, were explained in cosmological terms. Extracts from many medical and non-medical writers, like Empedocles, Hippocrates, Aristotle, Galen, the Fathers of the Church, Meletius latrosophista, Theophilus Protospatharius, Michael Psellus and other sources are presented, in order to show the close relationship between an abundance of diseases and an array of natural phenomena.

  6. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes.

    PubMed

    Suh, Alexander; Witt, Christopher C; Menger, Juliana; Sadanandan, Keren R; Podsiadlowski, Lars; Gerth, Michael; Weigert, Anne; McGuire, Jimmy A; Mudge, Joann; Edwards, Scott V; Rheindt, Frank E

    2016-01-01

    Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83-99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25-22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20-17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity. PMID:27097561

  7. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes

    PubMed Central

    Suh, Alexander; Witt, Christopher C.; Menger, Juliana; Sadanandan, Keren R.; Podsiadlowski, Lars; Gerth, Michael; Weigert, Anne; McGuire, Jimmy A.; Mudge, Joann; Edwards, Scott V.; Rheindt, Frank E.

    2016-01-01

    Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83–99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25–22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20–17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity. PMID:27097561

  8. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes.

    PubMed

    Suh, Alexander; Witt, Christopher C; Menger, Juliana; Sadanandan, Keren R; Podsiadlowski, Lars; Gerth, Michael; Weigert, Anne; McGuire, Jimmy A; Mudge, Joann; Edwards, Scott V; Rheindt, Frank E

    2016-04-21

    Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83-99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25-22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20-17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity.

  9. The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection

    PubMed Central

    Sams, Aaron J.; Hawks, John; Keinan, Alon

    2015-01-01

    The age of polymorphic alleles in humans is often estimated from population genetic patterns in extant human populations, such as allele frequencies, linkage disequilibrium, and rate of mutations. Ancient DNA can improve the accuracy of such estimates, as well as facilitate testing the validity of demographic models underlying many population genetic methods. Specifically, the presence of an allele in a genome derived from an ancient sample testifies that the allele is at least as old as that sample. In this study, we consider a common method for estimating allele age based on allele frequency as applied to variants from the US National Institutes of Health (NIH) Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. We view these estimates in the context of the presence or absence of each allele in the genomes of the 5300 year old Tyrolean Iceman, Ötzi, and of the 50,000 year old Altai Neandertal. Our results illuminate the accuracy of these estimates and their sensitivity to demographic events that were not included in the model underlying age estimation. Specifically, allele presence in the Iceman genome provides a good fit of allele age estimates to the expectation based on the age of that specimen. The equivalent based on the Neandertal genome leads to a poorer fit. This is likely due in part to the older age of the Neandertal and the older time of the split between modern humans and Neandertals, but also due to gene flow from Neandertals to modern humans not being considered in the underlying demographic model. Thus, the incorporation of ancient DNA can improve allele age estimation, demographic modeling, and tests of natural selection. Our results also point to the importance of considering a more diverse set of ancient samples for understanding the geographic and temporal range of individual alleles. PMID:25467111

  10. The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection.

    PubMed

    Sams, Aaron J; Hawks, John; Keinan, Alon

    2015-02-01

    The age of polymorphic alleles in humans is often estimated from population genetic patterns in extant human populations, such as allele frequencies, linkage disequilibrium, and rate of mutations. Ancient DNA can improve the accuracy of such estimates, as well as facilitate testing the validity of demographic models underlying many population genetic methods. Specifically, the presence of an allele in a genome derived from an ancient sample testifies that the allele is at least as old as that sample. In this study, we consider a common method for estimating allele age based on allele frequency as applied to variants from the US National Institutes of Health (NIH) Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. We view these estimates in the context of the presence or absence of each allele in the genomes of the 5300 year old Tyrolean Iceman, Ötzi, and of the 50,000 year old Altai Neandertal. Our results illuminate the accuracy of these estimates and their sensitivity to demographic events that were not included in the model underlying age estimation. Specifically, allele presence in the Iceman genome provides a good fit of allele age estimates to the expectation based on the age of that specimen. The equivalent based on the Neandertal genome leads to a poorer fit. This is likely due in part to the older age of the Neandertal and the older time of the split between modern humans and Neandertals, but also due to gene flow from Neandertals to modern humans not being considered in the underlying demographic model. Thus, the incorporation of ancient DNA can improve allele age estimation, demographic modeling, and tests of natural selection. Our results also point to the importance of considering a more diverse set of ancient samples for understanding the geographic and temporal range of individual alleles.

  11. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil.

    PubMed

    Malaspinas, Anna-Sapfo; Lao, Oscar; Schroeder, Hannes; Rasmussen, Morten; Raghavan, Maanasa; Moltke, Ida; Campos, Paula F; Sagredo, Francisca Santana; Rasmussen, Simon; Gonçalves, Vanessa F; Albrechtsen, Anders; Allentoft, Morten E; Johnson, Philip L F; Li, Mingkun; Reis, Silvia; Bernardo, Danilo V; DeGiorgio, Michael; Duggan, Ana T; Bastos, Murilo; Wang, Yong; Stenderup, Jesper; Moreno-Mayar, J Victor; Brunak, Søren; Sicheritz-Ponten, Thomas; Hodges, Emily; Hannon, Gregory J; Orlando, Ludovic; Price, T Douglas; Jensen, Jeffrey D; Nielsen, Rasmus; Heinemeier, Jan; Olsen, Jesper; Rodrigues-Carvalho, Claudia; Lahr, Marta Mirazón; Neves, Walter A; Kayser, Manfred; Higham, Thomas; Stoneking, Mark; Pena, Sergio D J; Willerslev, Eske

    2014-11-01

    Understanding the peopling of the Americas remains an important and challenging question. Here, we present (14)C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as 'Botocudos'. We find that their genomic ancestry is Polynesian, with no detectable Native American component. Radiocarbon analysis of the skulls shows that the individuals had died prior to the beginning of the 19th century. Our findings could either represent genomic evidence of Polynesians reaching South America during their Pacific expansion, or European-mediated transport.

  12. Sequence analyses of herpesviral enzymes suggest an ancient origin for human sexual behavior.

    PubMed Central

    Gentry, G A; Lowe, M; Alford, G; Nevins, R

    1988-01-01

    Comparison of the amino acid sequences of the deoxythymidine kinases of herpes simplex (HSV) and of marmoset herpes viruses (MHV) suggests a divergence time of 8 to 10 million years ago for HSV-1 and -2. Like MHV, HSV-1 and -2 cause local infections in their natural hosts, and direct contact between two individuals during the brief period of infectivity is needed for transmission. Because B virus, a nearer relative of HSV, depends on both oral and genital routes of transmission, we postulate that ancestral HSV (aHSV) was similar, and that for HSV-1 and -2 to diverge, genital and oral sites had to become microbiologically somewhat isolated from each other, while oral--oral and genital--genital contact had to be facilitated to maintain both aHSV strains. We propose that acquisition of continual sexual attractiveness by the ancestral human female and the adoption of close face-to-face mating, two hallmarks of human sexual behavior, provided the conditions for the divergence. PMID:3128793

  13. An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

    PubMed Central

    Wong, Vanessa K.; Baker, Stephen; Connor, Thomas R.; Pickard, Derek; Page, Andrew J.; Dave, Jayshree; Murphy, Niamh; Holliman, Richard; Sefton, Armine; Millar, Michael; Dyson, Zoe A.; Dougan, Gordon; Holt, Kathryn E.; Parkhill, Julian; Feasey, Nicholas A.; Kingsley, Robert A.; Thomson, Nicholas R.; Keane, Jacqueline A.; Weill, François- Xavier; Le Hello, Simon; Hawkey, Jane; Edwards, David J.; Harris, Simon R.; Cain, Amy K.; Hadfield, James; Hart, Peter J.; Thieu, Nga Tran Vu; Klemm, Elizabeth J.; Breiman, Robert F.; Watson, Conall H.; Edmunds, W. John; Kariuki, Samuel; Gordon, Melita A.; Heyderman, Robert S.; Okoro, Chinyere; Jacobs, Jan; Lunguya, Octavie; Msefula, Chisomo; Chabalgoity, Jose A.; Kama, Mike; Jenkins, Kylie; Dutta, Shanta; Marks, Florian; Campos, Josefina; Thompson, Corinne; Obaro, Stephen; MacLennan, Calman A.; Dolecek, Christiane; Keddy, Karen H.; Smith, Anthony M.; Parry, Christopher M.; Karkey, Abhilasha; Dongol, Sabina; Basnyat, Buddha; Arjyal, Amit; Mulholland, E. Kim; Campbell, James I.; Dufour, Muriel; Bandaranayake, Don; Toleafoa, Take N.; Singh, Shalini Pravin; Hatta, Mochammad; Newton, Paul N.; Dance, David; Davong, Viengmon; Onsare, Robert S.; Isaia, Lupeoletalalelei; Thwaites, Guy; Wijedoru, Lalith; Crump, John A.; De Pinna, Elizabeth; Nair, Satheesh; Nilles, Eric J.; Thanh, Duy Pham; Turner, Paul; Soeng, Sona; Valcanis, Mary; Powling, Joan; Dimovski, Karolina; Hogg, Geoff; Farrar, Jeremy; Mather, Alison E.; Amos, Ben

    2016-01-01

    The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations. PMID:27703135

  14. Can human papillomavirus (HPV) genotyping classify non-16/18 high-risk HPV infection by risk stratification?

    PubMed Central

    2016-01-01

    Objective Infection with high-risk genotypes of human papillomavirus (HR-HPV) is the major cause of invasive cervical cancers. HPV-16 and HPV-18 are known to be responsible for two-thirds of all invasive cervical carcinomas, followed by HPV-45, -31, and -33. Current guidelines only differentiate HPV-16/18 (+) by recommending direct colposcopy for treatment. We tried to evaluate whether there are differences in risk among 12 non-16/18 HR-HPV genotypes in this study. Methods The pathology archive database records of 1,102 consecutive gynecologic patients, who had results for cervical cytology and histology and for HPV testing, as determined by HPV 9G DNA chip, were reviewed. Results Among the 1,102 patients, 346 were non-16/18 HR-HPV (+) and 231 were HPV-16/18 (+). We calculated the odds ratios for ≥cervical intraepithelial neoplasia 2 (CIN 2) of 14 groups of each HR-HPV genotype compared with a group of HR-HPV (–) patients. Based on the odds ratio of each genotype, we divided patients with non-16/18 HR-HPV genotypes (+) into two groups: HPV-31/33/35/45/52/58 (+) and HPV-39/51/56/59/66/68 (+). The age-adjusted odds ratios for ≥CIN 2 of the HPV-31/33/35/45/52/58 (+) and HPV-39/51/56/59/66/68 (+) groups compared with a HR-HPV (–) group were 11.9 (95% CI, 7.6 to 18.8; p<0.001) and 2.4 (95% CI, 1.4 to 4.3; p<0.001), respectively, while that of the HPV-16/18 (+) group was 18.1 (95% CI, 11.6 to 28.3; p=0.003). Conclusion The 12 non-16/18 HR-HPV genotypes can be further categorized (HPV-31/33/35/45/52/58 vs. HPV-39/51/56/59/66/68) by risk stratification. The HPV-31/33/35/45/52/58 genotypes might need more aggressive action. Large scale clinical trials or cohort studies are necessary to confirm our suggestion. PMID:27550402

  15. Geochemistry Meets Anthropology: the use of Sr Isotopes as Tracers for Ancient Human Migration.

    NASA Astrophysics Data System (ADS)

    Solis, G.; Schaaf, P.; Hernandez, T.; Horn, P.; Manzanilla, L.

    2005-12-01

    Sr isotopes have increasingly become an important tool in archeology and anthropology in determining provenance of humans. By comparing isotopic signatures of human teeth and bone with the soil environment, Sr isotope ratios have been used as tracers identifying living areas. Sr isotope ratios in tooth enamel reflect the source of diet during youth, whereas ratios in dentine and bones come from the food growing in local geologies around the time of death. However, since analytical procedures vary from lab to lab we present here our new technique and how it affects results. We studied 11 teeth and 12 bone samples from the archeological site of Teotihuacan, central Mexico, as well as soil and water from the locality. Mechanical sample preparation of all teeth involved isolation of the enamel layer with the aid of an orthodontical micro-tool. For some enamel samples up to three fractions (two leachates and residue) were obtained for measurement. Thoroughly cleaned bone material underwent no leaching. As an example, 87Sr/86Sr results from a sample with ratios of 0.70477 for bone (which is identical to highland soil), 0.70530 for first leachate, 0.70590 for second leachate, and 0.70668 (mean accuracy +/- 0.00004) for enamel, clearly show enamel contamination by mobile Sr probably from soil. We thus find that repeated cleaning and particularly repeated leaching procedures, including isotopic measurement of the leachates, are critical to differentiate primary from secondary Sr isotope ratios as product of interaction of soil, sediments and water from the substrate where burials took place.

  16. Genotyping single-nucleotide polymorphisms of human genes involved in organophosphate detoxification by high-resolution melting.

    PubMed

    Kurdyukov, Ivan; Rodionov, Gennady; Radilov, Andrey; Babakov, Vladimir

    2014-08-01

    Paraoxonase-1 (PON1) and butyrylcholinesterase (BCHE) are natural bioscavengers of organophosphate acetylcholinesterase inhibitors in the human body, which can determine individual sensitivity to organophosphate toxicity. Interindividual differences in activity of PON1 (catalytic bioscavenger) and substrate specificity are strongly associated with the substitution of two amino acids: Leu/Met (L/M) at position 55 (rs854560) and Gln/Arg (Q/R) at position 192 (rs662). In the case of BCHE (stoichiometric bioscavenger) substitution, Ala/Thr (A/T) at position 539 produces the so-called "K-variant" of the enzyme (rs1803274). Threonine allele is often co-inherited with an atypical BCHE allele (rs1799807). The atypical variant of BCHE displays a lower affinity for cholinesterase inhibitors. Genotyping rs662 and rs1803274 single-nucleotide polymorphisms (SNP) by high-resolution melting (HRM) is facilitated by the nucleotide substitution A>G (G>A), which resulted in a changed number of hydrogen bonds in the PCR product and, consequently, shifted T m. In the case of rs854560, genotyping is complicated by the nucleotide substitution T>A, which has no significant effect on the T m of the PCR product. An addition of a small quantity of LL homozygote DNA into the reaction mixture before PCR discriminates the three genotypes by the melt curves due to different amounts of heteroduplexes formed in the LM and MM samples. HRM analysis can be applied for genotyping human rs854560, rs662, and rs1803274 SNPs. PMID:24705954

  17. Molecular evolution of the hypervariable region of the attachment glycoprotein gene in human respiratory syncytial virus subgroup B genotypes BA9 and BA10.

    PubMed

    Nagasawa, Koo; Hirano, Eiko; Kobayashi, Miho; Ryo, Akihide; Oishi, Kazunori; Obuchi, Masatsugu; Ishiwada, Naruhiko; Noda, Masahiro; Kuroda, Makoto; Shimojo, Naoki; Kimura, Hirokazu

    2015-12-01

    We studied the molecular evolution of the C-terminal 3rd hypervariable region in the attachment glycoprotein gene of human respiratory syncytial virus subgroup B (HRSV-B) genotypes BA9 and BA10. We performed time-scaled phylogenetic analyses using Bayesian Markov chain Monte Carlo methods. We also performed a genetic distance analysis (p-distance analysis), positive and negative selection analyses, and a Bayesian skyline plot (BSP) analysis. We found that genotype BA9 diverged from the common ancestor of genotypes BA7, BA8, and BA10, while genotype BA10 diverged from the ancestor of genotypes BA7 and BA8. Strains of both genotypes were distributed worldwide. BA9 and BA10 diverged between 1999 and 2001. Both BA9 and BA10 evolved rapidly (about 4.8×10(-3)substitutions/site/year) and formed three distinct lineages in a 10-year period. BA10 strains belonging to lineage 3 had large genetic distances (p-distance>0.07). Thus, it may be possible to classify these strains as a new genotype, BA11. No positive selection site was detected in either genotype. Phylodynamic analyses showed that the effective population size of BA10 decreased gradually since 2010 and BA9 slightly decreased since 2009. The results suggested that the recently prevalent HRSV-B genotypes BA9 and BA10 evolved uniquely, leading to epidemics of HRSV-B worldwide over a 15-year period. PMID:26408340

  18. Where are the Caribs? Ancient DNA from ceramic period human remains in the Lesser Antilles.

    PubMed

    Mendisco, F; Pemonge, M H; Leblay, E; Romon, T; Richard, G; Courtaud, P; Deguilloux, M F

    2015-01-19

    The identity and history of the indigenous groups who occupied the Lesser Antilles during the ceramic periods remain highly controversial. Although recent archaeological evidence has challenged hypotheses concerning the organization of human groups in this region, more biological data are needed to fully inform the discussion. Our study provides, to our knowledge, the first palaeogenetic data for Late Ceramic groups of the Guadeloupe archipelago, yielding crucial information concerning the identities of these groups. Despite the generally poor DNA preservation in the tested remains, we were able to retrieve Hypervariable Region 1 sequences from 11 individuals and mitochondrial single-nucleotide polymorphisms from 13 individuals. These novel data provide interesting preliminary results in favour of a common origin for all Saladoid Caribbean communities, i.e. the first ceramic groups of the region, as well as for a local continuity between the Saladoid and post-Saladoid groups. A combination of the genetic data obtained and several pieces of cultural evidence allows us to propose that two different groups inhabited the Guadeloupe archipelago during the Late Ceramic period, with the possible occupation of the La Désirade and Marie-Galante islands by groups affiliated with the Taíno communities. The working hypotheses proposed here appear consistent with recent archaeological evidence.

  19. Where are the Caribs? Ancient DNA from ceramic period human remains in the Lesser Antilles

    PubMed Central

    Mendisco, F.; Pemonge, M. H.; Leblay, E.; Romon, T.; Richard, G.; Courtaud, P.; Deguilloux, M. F.

    2015-01-01

    The identity and history of the indigenous groups who occupied the Lesser Antilles during the ceramic periods remain highly controversial. Although recent archaeological evidence has challenged hypotheses concerning the organization of human groups in this region, more biological data are needed to fully inform the discussion. Our study provides, to our knowledge, the first palaeogenetic data for Late Ceramic groups of the Guadeloupe archipelago, yielding crucial information concerning the identities of these groups. Despite the generally poor DNA preservation in the tested remains, we were able to retrieve Hypervariable Region 1 sequences from 11 individuals and mitochondrial single-nucleotide polymorphisms from 13 individuals. These novel data provide interesting preliminary results in favour of a common origin for all Saladoid Caribbean communities, i.e. the first ceramic groups of the region, as well as for a local continuity between the Saladoid and post-Saladoid groups. A combination of the genetic data obtained and several pieces of cultural evidence allows us to propose that two different groups inhabited the Guadeloupe archipelago during the Late Ceramic period, with the possible occupation of the La Désirade and Marie-Galante islands by groups affiliated with the Taíno communities. The working hypotheses proposed here appear consistent with recent archaeological evidence. PMID:25487339

  20. Giardia assemblage A: human genotype in muskoxen in the Canadian Arctic

    PubMed Central

    Kutz, Susan J; Thompson, RC Andrew; Polley, Lydden; Kandola, Kami; Nagy, John; Wielinga, Caroline M; Elkin, Brett T

    2008-01-01

    As part of an ongoing program assessing the biodiversity and impacts of parasites in Arctic ungulates we examined 72 fecal samples from muskoxen on Banks Island, Northwest Territories, Canada for Giardia and Cryptosporidium. Cryptosporidium spp. were not detected, but 21% of the samples were positive for Giardia. Sequencing of four isolates of Giardia demonstrated G. duodenalis, Assemblage A, a zoonotic genotype. PMID:18808665

  1. Validation and genotyping of multiple human polymorphic inversions mediated by inverted repeats reveals a high degree of recurrence.

    PubMed

    Aguado, Cristina; Gayà-Vidal, Magdalena; Villatoro, Sergi; Oliva, Meritxell; Izquierdo, David; Giner-Delgado, Carla; Montalvo, Víctor; García-González, Judit; Martínez-Fundichely, Alexander; Capilla, Laia; Ruiz-Herrera, Aurora; Estivill, Xavier; Puig, Marta; Cáceres, Mario

    2014-03-01

    In recent years different types of structural variants (SVs) have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we describe the results of a simple and fast inverse PCR (iPCR) protocol for high-throughput genotyping of a wide variety of inversions using a small amount of DNA. In particular, we analyzed 22 inversions predicted in humans ranging from 5.1 kb to 226 kb and mediated by inverted repeat sequences of 1.6-24 kb. First, we validated 17 of the 22 inversions in a panel of nine HapMap individuals from different populations, and we genotyped them in 68 additional individuals of European origin, with correct genetic transmission in ∼ 12 mother-father-child trios. Global inversion minor allele frequency varied between 1% and 49% and inversion genotypes were consistent with Hardy-Weinberg equilibrium. By analyzing the nucleotide variation and the haplotypes in these regions, we found that only four inversions have linked tag-SNPs and that in many cases there are multiple shared SNPs between standard and inverted chromosomes, suggesting an unexpected high degree of inversion recurrence during human evolution. iPCR was also used to check 16 of these inversions in four chimpanzees and two gorillas, and 10 showed both orientations either within or between species, providing additional support for their multiple origin. Finally, we have identified several inversions that include genes in the inverted or breakpoint regions, and at least one disrupts a potential coding gene. Thus, these results represent a significant advance in our understanding of inversion polymorphism in human populations and challenge the common view of a single origin of inversions, with important implications for inversion analysis in SNP-based studies. PMID:24651690

  2. Validation and Genotyping of Multiple Human Polymorphic Inversions Mediated by Inverted Repeats Reveals a High Degree of Recurrence

    PubMed Central

    Aguado, Cristina; Gayà-Vidal, Magdalena; Villatoro, Sergi; Oliva, Meritxell; Izquierdo, David; Giner-Delgado, Carla; Montalvo, Víctor; García-González, Judit; Martínez-Fundichely, Alexander; Capilla, Laia; Ruiz-Herrera, Aurora; Estivill, Xavier; Puig, Marta; Cáceres, Mario

    2014-01-01

    In recent years different types of structural variants (SVs) have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we describe the results of a simple and fast inverse PCR (iPCR) protocol for high-throughput genotyping of a wide variety of inversions using a small amount of DNA. In particular, we analyzed 22 inversions predicted in humans ranging from 5.1 kb to 226 kb and mediated by inverted repeat sequences of 1.6–24 kb. First, we validated 17 of the 22 inversions in a panel of nine HapMap individuals from different populations, and we genotyped them in 68 additional individuals of European origin, with correct genetic transmission in ∼12 mother-father-child trios. Global inversion minor allele frequency varied between 1% and 49% and inversion genotypes were consistent with Hardy-Weinberg equilibrium. By analyzing the nucleotide variation and the haplotypes in these regions, we found that only four inversions have linked tag-SNPs and that in many cases there are multiple shared SNPs between standard and inverted chromosomes, suggesting an unexpected high degree of inversion recurrence during human evolution. iPCR was also used to check 16 of these inversions in four chimpanzees and two gorillas, and 10 showed both orientations either within or between species, providing additional support for their multiple origin. Finally, we have identified several inversions that include genes in the inverted or breakpoint regions, and at least one disrupts a potential coding gene. Thus, these results represent a significant advance in our understanding of inversion polymorphism in human populations and challenge the common view of a single origin of inversions, with important implications for inversion analysis in SNP-based studies. PMID:24651690

  3. Population differences in the human arsenic (+3 oxidation state) methyltransferase (AS3MT) gene polymorphism detected by using genotyping method.

    PubMed

    Fujihara, Junko; Kunito, Takashi; Agusa, Tetsuro; Yasuda, Toshihiro; Iida, Reiko; Fujii, Yoshimi; Takeshita, Haruo

    2007-12-15

    Arsenic poisoning from drinking groundwater is a serious problem, particularly in developing Asian countries. Human arsenic (+3 oxidation state) methyltransferase (AS3MT) is known to catalyze the methylation of arsenite. Recently, a single nucleotide polymorphism (SNPs; rs17885947, M287T (T860C)) in the AS3MT gene was shown to be related to enzyme activity and considered to be related to genetic susceptibility to arsenic. In the present study, a useful genotyping method for M287T was developed using the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) technique. Applying this method, the genotype distribution of M287T in Ovambo (n=185), Turkish (n=191), Mongolian (n=233), Korean (n=200), and Japanese (n=370) populations were investigated. The mutation frequencies in Asian populations were relatively lower than those of African and Caucasian populations, including those from previous studies: the frequencies of mutation in the Mongolian, Korean, and Japanese populations were 0.040, 0.010, and 0.010, respectively. In the course of this study, a PCR-based genotyping method that is inexpensive and does not require specialized equipment was developed. This method could be applied to a large number of residents at risk for arsenic poisoning.

  4. Population differences in the human arsenic (+ 3 oxidation state) methyltransferase (AS3MT) gene polymorphism detected by using genotyping method

    SciTech Connect

    Fujihara, Junko; Kunito, Takashi; Agusa, Tetsuro; Yasuda, Toshihiro; Iida, Reiko; Fujii, Yoshimi; Takeshita, Haruo

    2007-12-15

    Arsenic poisoning from drinking groundwater is a serious problem, particularly in developing Asian countries. Human arsenic (+ 3 oxidation state) methyltransferase (AS3MT) is known to catalyze the methylation of arsenite. Recently, a single nucleotide polymorphism (SNPs; rs17885947, M287T (T860C)) in the AS3MT gene was shown to be related to enzyme activity and considered to be related to genetic susceptibility to arsenic. In the present study, a useful genotyping method for M287T was developed using the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) technique. Applying this method, the genotype distribution of M287T in Ovambo (n = 185), Turkish (n = 191), Mongolian (n = 233), Korean (n = 200), and Japanese (n = 370) populations were investigated. The mutation frequencies in Asian populations were relatively lower than those of African and Caucasian populations, including those from previous studies: the frequencies of mutation in the Mongolian, Korean, and Japanese populations were 0.040, 0.010, and 0.010, respectively. In the course of this study, a PCR-based genotyping method that is inexpensive and does not require specialized equipment was developed. This method could be applied to a large number of residents at risk for arsenic poisoning.

  5. Population differences in the human arsenic (+3 oxidation state) methyltransferase (AS3MT) gene polymorphism detected by using genotyping method.

    PubMed

    Fujihara, Junko; Kunito, Takashi; Agusa, Tetsuro; Yasuda, Toshihiro; Iida, Reiko; Fujii, Yoshimi; Takeshita, Haruo

    2007-12-15

    Arsenic poisoning from drinking groundwater is a serious problem, particularly in developing Asian countries. Human arsenic (+3 oxidation state) methyltransferase (AS3MT) is known to catalyze the methylation of arsenite. Recently, a single nucleotide polymorphism (SNPs; rs17885947, M287T (T860C)) in the AS3MT gene was shown to be related to enzyme activity and considered to be related to genetic susceptibility to arsenic. In the present study, a useful genotyping method for M287T was developed using the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) technique. Applying this method, the genotype distribution of M287T in Ovambo (n=185), Turkish (n=191), Mongolian (n=233), Korean (n=200), and Japanese (n=370) populations were investigated. The mutation frequencies in Asian populations were relatively lower than those of African and Caucasian populations, including those from previous studies: the frequencies of mutation in the Mongolian, Korean, and Japanese populations were 0.040, 0.010, and 0.010, respectively. In the course of this study, a PCR-based genotyping method that is inexpensive and does not require specialized equipment was developed. This method could be applied to a large number of residents at risk for arsenic poisoning. PMID:17889916

  6. A novel strategy for human papillomavirus detection and genotyping with SybrGreen and molecular beacon polymerase chain reaction.

    PubMed

    Szuhai, K; Sandhaus, E; Kolkman-Uljee, S M; Lemaître, M; Truffert, J C; Dirks, R W; Tanke, H J; Fleuren, G J; Schuuring, E; Raap, A K

    2001-11-01

    Human papillomaviruses (HPVs) play an important role in the pathogenesis of cervical cancer. For identification of the large number of different HPV types found in (pre)malignant lesions, a robust methodology is needed that combines general HPV detection with HPV genotyping. We have developed for formaldehyde-fixed samples a strategy that, in a homogeneous, real-time fluorescence polymerase chain reaction (PCR)-based assay, accomplishes general HPV detection by SybrGreen reporting of HPV-DNA amplicons, and genotyping of seven prevalent HPV types (HPV-6, -11, -16, -18, -31, -33, -45) by real-time molecular beacon PCR. The false-positive rate of the HPV SybrGreen-PCR was 4%, making it well suited as a prescreening, general HPV detection technology. The type specificity of the seven selected HPV molecular beacons was 100% and double infections were readily identified. The multiplexing capacity of the HPV molecular beacon PCR was analyzed and up to three differently labeled molecular beacons could be used in one PCR reaction without observing cross talk. The inherent quantitation capacities of real-time fluorescence PCR allowed the determination of average HPV copy number per cell. We conclude that the HPV SybrGreen-PCR in combination with the HPV molecular beacon PCR provides a robust, sensitive, and quantitative general HPV detection and genotyping methodology.

  7. Influence of the APOE genotype on hepatic stress response: Studies in APOE targeted replacement mice and human liver cells.

    PubMed

    Dose, Janina; Nebel, Almut; Piegholdt, Stefanie; Rimbach, Gerald; Huebbe, Patricia

    2016-07-01

    Apolipoprotein E (APOE) is a multifunctional plasma protein mainly acting in lipid metabolism. Human APOE is polymorphic with three major isoforms (APOE2, APOE3 and APOE4). Up to 75% of the body's APOE is produced by the liver. There is increasing evidence from studies in brain-derived cells that APOE4 affects mitochondrial function and biogenesis as well as stress and inflammatory responses - processes, whose disturbances are considered hallmarks of the ageing process. However, although the liver is the main production site of APOE, knowledge about the impact of the APOE genotype on hepatic stress response-related processes is rather limited. Therefore, we studied biomarkers of oxidative status (glutathione levels, 3-nitrotyrosine adducts, protein carbonyl concentration), ER stress (XBP1(S), BiP, DDIT3), proteasome activity, mitochondrial function (respiratory complexes, ATP levels and mitochondrial membrane potential as well as biomarkers of mitochondrial biogenesis, fission and fusion), autophagy (LC3, LAMP2A), apoptosis (BCL2, BAX, CYCS) and DNA damage in the liver of APOE targeted replacement (TR) mice and in Huh7 hepatocytes overexpressing the APOE3 and the APOE4 isoform, respectively. APOE4 mice exhibited a lower chymotrypsin-like and a higher trypsin-like proteasome activity. Levels of protein carbonyls were moderately higher in liver tissue of APOE4 vs. APOE3 mice. Other biomarkers of oxidative stress were similar between the two genotypes. Under basal conditions, the stress-response pathways investigated appeared largely unaffected by the APOE genotype. However, upon stress induction, APOE4 expressing cells showed lower levels of adenosine triphosphate (ATP) and lower mRNA levels of the ATP-generating complex V of the mitochondrial respiratory chain. Overall, our findings provide evidence for a rather low influence of the APOE genotype on the hepatic stress response processes investigated in this study. PMID:27130033

  8. Global Improvement in Genotyping of Human Papillomavirus DNA: the 2011 HPV LabNet International Proficiency Study

    PubMed Central

    Eklund, Carina; Forslund, Ola; Wallin, Keng-Ling

    2014-01-01

    Accurate and internationally comparable human papillomavirus (HPV) DNA genotyping is essential for HPV vaccine research and for HPV surveillance. The HPV Laboratory Network (LabNet) has designed international proficiency studies that can be issued regularly and in a reproducible manner. The 2011 HPV genotyping proficiency panel contained 43 coded samples composed of purified plasmids of 16 HPV types (HPV6, -11, -16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, -68a, and -68b) and 3 extraction controls. Tests that detected 50 IU of HPV16 and HPV18 and 500 genome equivalents for the other 14 HPV types in both single and multiple infections were considered proficient. Ninety-six laboratories worldwide submitted 134 data sets. Twenty-five different HPV genotyping assay methods were used, including the Linear Array, line blot/INNO-LiPA, PapilloCheck, and PCR Luminex assays. The major oncogenic HPV types, HPV16 and HPV18, were proficiently detected in 97.0% (113/116) and 87.0% (103/118) of the data sets, respectively. In 2011, 51 data sets (39%) were 100% proficient for the detection of at least one HPV type, and 37 data sets (28%) were proficient for all 16 HPV types; this was an improvement over the panel results from the 2008 and 2010 studies, when <25 data sets (23% and 19% for 2008 and 2010, respectively) were fully proficient. The improvement was also evident for the 54 laboratories that had also participated in the previous proficiency studies. In conclusion, a continuing global proficiency program has documented worldwide improvement in the comparability and reliability of HPV genotyping assay performances. PMID:24478473

  9. Human Papillomavirus Genotype-Specific Prevalence Across the Continuum of Cervical Neoplasia and Cancer

    PubMed Central

    Joste, Nancy E.; Ronnett, Brigitte M.; Hunt, William C.; Pearse, Amanda; Langsfeld, Erika; Leete, Thomas; Jaramillo, MaryAnn; Stoler, Mark H.; Castle, Philip E.; Wheeler, Cosette M.

    2014-01-01

    Background The New Mexico HPV Pap Registry was established to measure the impact of cervical cancer prevention strategies in the United States. Prior to widespread HPV vaccine implementation, we established the baseline prevalence for a broad spectrum of HPV genotypes across the continuum of cervical intraepithelial neoplasia (CIN) and cancer. Methods A population-based sample of 6,272 tissue specimens were tested for 37 HPV genotypes. The number of specimens tested within each diagnostic category was: 541 negative, 1,411 CIN grade 1 (CIN1), 2,226 CIN grade 2 (CIN2), and 2,094 CIN grade 3 (CIN3) or greater. Age-specific HPV prevalence was estimated within categories for HPV genotypes targeted by HPV vaccines. Results The combined prevalence of HPV genotypes included in the quadrivalent and nonavalent vaccines increased from 15.3% and 29.3% in CIN1 to 58.4% and 83.7% in CIN3, respectively. The prevalence of HPV types included in both vaccines tended to decrease with increasing age for CIN1, CIN2, CIN3, and squamous cell carcinoma, most notably for CIN3 and SCC. The six most common HPV types in descending order of prevalence were HPV-16, −31, −52, −58, −33, and −39 for CIN3 and HPV-16, −18, −31, −45, −52, and −33 for invasive cancers. Conclusions Health economic modeling of HPV vaccine impact should consider age-specific differences in HPV prevalence. Impact Population-based HPV prevalence in CIN is not well described but is requisite for longitudinal assessment of vaccine impact and to understand the effectiveness and performance of various cervical screening strategies in vaccinated and unvaccinated women. PMID:25363635

  10. New genotypes of Orientia tsutsugamushi isolated from humans in Eastern Taiwan.

    PubMed

    Yang, Hui-Hua; Huang, I-Tsong; Lin, Chin-Hui; Chen, Tren-Yi; Chen, Li-Kuang

    2012-01-01

    Scrub typhus, an acute febrile illness, is caused by the obligate intracellular bacterium Orientia tsutsugamushi. In our study, O. tsutsugamushi was rapidly detected and typed by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis of the 56-kDa type-specific antigen (TSA) gene. To investigate the genotypes of clinical variants of O. tsutsugamushi, we collected 3223 blood samples from eastern Taiwanese patients with suspected scrub typhus from 2002 to 2008. In total, 505 samples were found to be positive for scrub typhus infection by PCR, and bacteria were isolated from 282 of them. Four prototype genotype strains (Karp, Kato, Kawasaki and Gilliam) and eleven different Taiwanese genotype isolates (Taiwan-A, -B, -C, -D, -E, -G, -H, -J, -N, -O and -P) were identified by RPLF analysis. Taiwan-H, the major genotype in eastern Taiwan, exhibited prevalence and isolation rates of 47.3% (239/505) and 42.6% (120/282), respectively. We also assessed the genetic relatedness of the 56-kDa TSA gene among eight Taiwan-H isolates, thirteen other Taiwanese isolates and 104 DNA sequences deposited in the GenBank database using MEGA version 5.0 and PHYLIP version 3.66. We found that the Taiwan-H isolates formed into a new cluster, which was designated the Taiwan Gilliam-variant (TG-v) cluster to distinguish it from the Japanese Gilliam-variant (JG-v) cluster. According to Simplot analysis, TG-v is a new recombinant strain among Gilliam, Ikeda and Kato. Moreover, the Gilliam-Kawasaki cluster had the highest percentage of RFLP cases and was the most frequently isolated type in eastern Taiwan (50.1%, 253/505; 44.0%, 124/282). These findings shed light on the genetic evolution of O. tsutsugamushi into different strains and may be useful in vaccine development and epidemic disease control in the future.

  11. Serotypes, genotypes and antimicrobial resistance patterns of human diarrhoeagenic Escherichia coli isolates circulating in southeastern China.

    PubMed

    Chen, Y; Chen, X; Zheng, S; Yu, F; Kong, H; Yang, Q; Cui, D; Chen, N; Lou, B; Li, X; Tian, L; Yang, X; Xie, G; Dong, Y; Qin, Z; Han, D; Wang, Y; Zhang, W; Tang, Y-W; Li, L

    2014-01-01

    Diarrhoeagenic Escherichia coli (DEC) infection is a major health problem in developing countries. The prevalence and characteristics of DEC have not been thoroughly investigated in China. Consecutive faecal specimens from outpatients with acute diarrhoea in nine sentinel hospitals in southeastern China were collected from July 2009 to June 2011. Bacterial and viral pathogens were detected by culture and RT-PCR, respectively. DEC isolates were further classified into five pathotypes using multiplex PCR. The O/H serotypes, sequence types (STs) and antimicrobial susceptibility profiles of the DEC isolates were determined. A total of 2466 faecal specimens were collected, from which 347 (14.1%) DEC isolates were isolated. DEC was the dominant bacterial pathogen detected. The DEC isolates included 217 EAEC, 62 ETEC, 52 EPEC, 14 STEC, one EIEC and one EAEC/ETEC. O45 (6.6%) was the predominant serotype. Genotypic analysis revealed that the major genotype was ST complex 10 (87, 25.6%). Isolates belonging to the serogroups or genotypes of O6, O25, O159, ST48, ST218, ST94 and ST1491 were highly susceptible to the majority of antimicrobials. In contrast, isolates belonging to O45, O15, O1, O169, ST38, ST226, ST69, ST31, ST93, ST394 and ST648 were highly resistant to the majority of antimicrobials. DEC accounted for the majority of bacterial pathogens causing acute diarrhoea in southeastern China, and it is therefore necessary to test for all DEC, not only the EHEC O157:H7. Some serogroups or genotypes of DEC were highly resistant to the majority of antimicrobials. DEC surveillance should be emphasized. PMID:23521436

  12. New genotypes of Orientia tsutsugamushi isolated from humans in Eastern Taiwan.

    PubMed

    Yang, Hui-Hua; Huang, I-Tsong; Lin, Chin-Hui; Chen, Tren-Yi; Chen, Li-Kuang

    2012-01-01

    Scrub typhus, an acute febrile illness, is caused by the obligate intracellular bacterium Orientia tsutsugamushi. In our study, O. tsutsugamushi was rapidly detected and typed by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis of the 56-kDa type-specific antigen (TSA) gene. To investigate the genotypes of clinical variants of O. tsutsugamushi, we collected 3223 blood samples from eastern Taiwanese patients with suspected scrub typhus from 2002 to 2008. In total, 505 samples were found to be positive for scrub typhus infection by PCR, and bacteria were isolated from 282 of them. Four prototype genotype strains (Karp, Kato, Kawasaki and Gilliam) and eleven different Taiwanese genotype isolates (Taiwan-A, -B, -C, -D, -E, -G, -H, -J, -N, -O and -P) were identified by RPLF analysis. Taiwan-H, the major genotype in eastern Taiwan, exhibited prevalence and isolation rates of 47.3% (239/505) and 42.6% (120/282), respectively. We also assessed the genetic relatedness of the 56-kDa TSA gene among eight Taiwan-H isolates, thirteen other Taiwanese isolates and 104 DNA sequences deposited in the GenBank database using MEGA version 5.0 and PHYLIP version 3.66. We found that the Taiwan-H isolates formed into a new cluster, which was designated the Taiwan Gilliam-variant (TG-v) cluster to distinguish it from the Japanese Gilliam-variant (JG-v) cluster. According to Simplot analysis, TG-v is a new recombinant strain among Gilliam, Ikeda and Kato. Moreover, the Gilliam-Kawasaki cluster had the highest percentage of RFLP cases and was the most frequently isolated type in eastern Taiwan (50.1%, 253/505; 44.0%, 124/282). These findings shed light on the genetic evolution of O. tsutsugamushi into different strains and may be useful in vaccine development and epidemic disease control in the future. PMID:23071693

  13. Serotypes, genotypes and antimicrobial resistance patterns of human diarrhoeagenic Escherichia coli isolates circulating in southeastern China.

    PubMed

    Chen, Y; Chen, X; Zheng, S; Yu, F; Kong, H; Yang, Q; Cui, D; Chen, N; Lou, B; Li, X; Tian, L; Yang, X; Xie, G; Dong, Y; Qin, Z; Han, D; Wang, Y; Zhang, W; Tang, Y-W; Li, L

    2014-01-01

    Diarrhoeagenic Escherichia coli (DEC) infection is a major health problem in developing countries. The prevalence and characteristics of DEC have not been thoroughly investigated in China. Consecutive faecal specimens from outpatients with acute diarrhoea in nine sentinel hospitals in southeastern China were collected from July 2009 to June 2011. Bacterial and viral pathogens were detected by culture and RT-PCR, respectively. DEC isolates were further classified into five pathotypes using multiplex PCR. The O/H serotypes, sequence types (STs) and antimicrobial susceptibility profiles of the DEC isolates were determined. A total of 2466 faecal specimens were collected, from which 347 (14.1%) DEC isolates were isolated. DEC was the dominant bacterial pathogen detected. The DEC isolates included 217 EAEC, 62 ETEC, 52 EPEC, 14 STEC, one EIEC and one EAEC/ETEC. O45 (6.6%) was the predominant serotype. Genotypic analysis revealed that the major genotype was ST complex 10 (87, 25.6%). Isolates belonging to the serogroups or genotypes of O6, O25, O159, ST48, ST218, ST94 and ST1491 were highly susceptible to the majority of antimicrobials. In contrast, isolates belonging to O45, O15, O1, O169, ST38, ST226, ST69, ST31, ST93, ST394 and ST648 were highly resistant to the majority of antimicrobials. DEC accounted for the majority of bacterial pathogens causing acute diarrhoea in southeastern China, and it is therefore necessary to test for all DEC, not only the EHEC O157:H7. Some serogroups or genotypes of DEC were highly resistant to the majority of antimicrobials. DEC surveillance should be emphasized.

  14. V-shaped pits in regions of ancient Baekje kingdom paleoparasitologically confirmed as likely human-waste reservoirs.

    PubMed

    Shin, Dong Hoon; Shim, Sang-Yuck; Kim, Myeung Ju; Oh, Chang Seok; Lee, Mi-Hyun; Jung, Suk Bae; Lee, Geon Il; Chai, Jong-Yil; Seo, Min

    2014-10-01

    In a paleo-parasitological analysis of soil samples obtained from V-shaped pits dating to the ancient Baekje period in Korean history, we discovered Ascaris lumbricoides, Trichuris trichiura, and Clonorchis sinensis eggs. In light of the samples' seriously contaminated state, the V-shaped pits might have served as toilets, cesspits, or dung heaps. For a long period of time, researchers scouring archaeological sites in Korea have had difficulties locating such structures. In this context then, the present report is unique because similar kind of the ancient ruins must become an ideal resource for successful sampling in our forthcoming paleoparasitological studies. PMID:25352710

  15. V-shaped Pits in Regions of Ancient Baekje Kingdom Paleoparasitologically Confirmed as Likely Human-Waste Reservoirs

    PubMed Central

    Shin, Dong Hoon; Shim, Sang-Yuck; Kim, Myeung Ju; Oh, Chang Seok; Lee, Mi-Hyun; Jung, Suk Bae; Lee, Geon Il; Chai, Jong-Yil

    2014-01-01

    In a paleo-parasitological analysis of soil samples obtained from V-shaped pits dating to the ancient Baekje period in Korean history, we discovered Ascaris lumbricoides, Trichuris trichiura, and Clonorchis sinensis eggs. In light of the samples' seriously contaminated state, the V-shaped pits might have served as toilets, cesspits, or dung heaps. For a long period of time, researchers scouring archaeological sites in Korea have had difficulties locating such structures. In this context then, the present report is unique because similar kind of the ancient ruins must become an ideal resource for successful sampling in our forthcoming paleoparasitological studies. PMID:25352710

  16. Genotype distribution of cervical human papillomavirus DNA in women with cervical lesions in Bioko, Equatorial Guinea

    PubMed Central

    García-Espinosa, Benjamín; Nieto-Bona, Ma Paz; Rueda, Sonsoles; Silva-Sánchez, Luís Fernando; Piernas-Morales, Ma Concepción; Carro-Campos, Patricia; Cortés-Lambea, Luís; Moro-Rodríguez, Ernesto

    2009-01-01

    Background The HVP vaccine is a useful tool for preventing cervical cancer. The purpose of this study is to determine the most frequent HPV genotypes in Equatorial Guinea in order to develop future vaccination strategies to apply in this country. Methods A campaign against cervical cancer was carried out in the area on a total of 1,680 women. 26 of the women, following cytological screening, were treated surgically with a loop electrosurgical excision procedure (LEEP). Cases were studied histologically and were genotyped from paraffin blocks by applying a commercial kit that recognized 35 HPV types. Results Cytological diagnoses included 17 HSIL, 1 LSIL, 5 ASC-H and 3 AGUS. Histological diagnosis resulted in 3 cases of microinvasive squamous cell carcinoma stage IA of FIGO, 9 CIN-3, 8 CIN-2, 2 CIN-1, 3 flat condylomas and mild dysplasia of the endocervical epithelium. Fifteen of twenty-five cases genotyped were positive for HPV (60%). HPV 16 and 33 were identified in four cases each, HPV 58 in two other cases, and HPV 18, 31, 52, and 82 in one case, with one HPV 16 and 58 coinfection. Conclusion The frequency of HPV types in the African area varies in comparison to other regions, particularly in Europe and USA. Vaccination against the five most common HPV types (16, 33, 58, 18, and 31) should be considered in the geographic region of West Africa and specifically in Equatorial Guinea. PMID:19740435

  17. Unusual diversity of human rotavirus G and P genotypes in India.

    PubMed Central

    Ramachandran, M; Das, B K; Vij, A; Kumar, R; Bhambal, S S; Kesari, N; Rawat, H; Bahl, L; Thakur, S; Woods, P A; Glass, R I; Bhan, M K; Gentsch, J R

    1996-01-01

    Between April and December 1993, we determined P and G genotypes of group A rotavirus strains obtained from children admitted to diarrhea treatment centers in five Indian cities. From a total of 63 rotavirus-positive specimens, we identified 10 different strains with five different G genotypes and four distinct P types by using reverse transcription-PCR. The common worldwide strains G1P8, G2P4, G3P8, and G4P8 were underrepresented among Indian children (33%), whereas strains of P type 6 (G1P6, G2P6, G3P6, G4P6, and G9P6), which primarily infect asymptomatic newborns but are rare in children with diarrhea were common in India (43%). Of these, G9P6, a strain not previously reported to be found in children with diarrhea, was the most prevalent (22%). Eleven percent of the strains were nontypeable, and another 11% of the specimens had mixed infections. Using digoxigenin-labeled, genotype-specific hybridization probes, we confirmed all G9 strains and mixed infections tested and identified three nontypeable strains (one G9 and two P8). The epidemiological significance of G9 rotavirus strains, if confirmed in other settings, may have important implications for vaccine development. PMID:8789033

  18. Genotype distribution of human papillomavirus (HPV) and co-infections in cervical cytologic specimens from two outpatient gynecological clinics in a region of southeast Spain

    PubMed Central

    2009-01-01

    Background Human Papillomavirus (HPV) genotype distribution and co-infection occurrence was studied in cervical cytologic specimens from Murcia Region, (southeast Spain), to obtain information regarding the possible effect of the ongoing vaccination campaign against HPV16 and HPV18. Methods A total of 458 cytologic specimens were obtained from two outpatient gynecological clinics. These included 288 normal benign (N/B) specimens, 56 atypical squamous cell of undetermined significance (ASC-US), 75 low-grade squamous intraepithelial lesions (LSIL) and 39 high-grade squamous intraepithelial lesions (HSIL). HPV genotyping was performed using PCR and tube array hybridization. Results The most frequent genotype found was HPV16 (14.9% in N/B; 17.9% in ASC-US; 29.3% in LSIL and 33.3% HSIL). Distribution of other genotypes was heavily dependent on the cytologic diagnoses. Co-infections were found in 15.3% of N/B, 10.7% of ASC-US, 48% of LSIL and 25.6% of HSIL cases (significantly different at p < 0.001). Strikingly, in N/B diagnoses, genotypes from A5 species were found as coinfecting in all cases. Genotypes from A7 or A9 species appeared in co-infections in 56.5% and 54% respectively whereas genotypes from A6 species appeared in 25.1% of cases. Conclusion HPV vaccination might prevent 34.6% and 35.8% of LSIL and HSIL, respectively. Co-infection rate is dependent on both cytologic diagnosis and HPV genotype. Moreover, genotypes belonging to A5, A7 and A9 species are more often found as co-infections than genotype pertaining to A6 species. This suggests that phylogenetically related genotypes might have in common similar grades of dependency for cervical epithelium colonization. PMID:19664248

  19. Ancient deforestation revisited.

    PubMed

    Hughes, J Donald

    2011-01-01

    The image of the classical Mediterranean environment of the Greeks and Romans had a formative influence on the art, literature, and historical perception of modern Europe and America. How closely does is this image congruent with the ancient environment as it in reality existed? In particular, how forested was the ancient Mediterranean world, was there deforestation, and if so, what were its effects? The consensus of historians, geographers, and other scholars from the mid-nineteenth century through the first three quarters of the twentieth century was that human activities had depleted the forests to a major extent and caused severe erosion. My research confirmed this general picture. Since then, revisionist historians have questioned these conclusions, maintaining instead that little environmental damage was done to forests and soils in ancient Greco-Roman times. In a reconsideration of the question, this paper looks at recent scientific work providing proxy evidence for the condition of forests at various times in ancient history. I look at three scientific methodologies, namely anthracology, palynology, and computer modeling. Each of these avenues of research offers support for the concept of forest change, both in abundance and species composition, and episodes of deforestation and erosion, and confirms my earlier work.

  20. Molecular Epidemiological Analysis of Cryptosporidium spp. in the United Kingdom: Results of Genotyping Cryptosporidium spp. in 1,705 Fecal Samples from Humans and 105 Fecal Samples from Livestock Animals

    PubMed Central

    McLauchlin, J.; Amar, C.; Pedraza-Díaz, S.; Nichols, G. L.

    2000-01-01

    Cryptosporidium present in 1,705 fecal samples from humans and 105 from livestock animals were analyzed by PCR-restriction fragment length polymorphism of the Cryptosporidium oocyst wall protein. Overall, genotype 1 (human exclusive type) was detected in 37.8% of the samples from humans, genotype 2 (broad host range) was detected in 61.5%, a third genotype designated genotype 3 (Cryptosporidium meleagridis) was detected in 0.3%, and both genotypes 1 and 2 were recovered from 0.4%. All samples from livestock yielded genotype 2. Among 469 patients infected during eight drinking water-related outbreaks, five outbreaks were predominantly due to genotype 1, and three were due to genotype 2. Fifty-four samples were collected from patients involved with five swimming pool-associated outbreaks: two outbreaks were due to genotype 1, one was due to genotype 2, and the remaining two involved both genotypes 1 and 2. Among 26 family outbreaks and 1 children's nursery outbreak (2 to 3 members per group), the same genotype was recovered from the different members of each outbreak: 13 were due to genotype 1, and 14 were due to genotype 2. In eighteen patients reporting contact with animals and/or farms, genotype 1 was recovered from one patient and genotype 2 was recovered from the remaining 17. Among the sporadic cases, there were distinct geographical and temporal variations in the distribution of the genotypes. The spring peak in cases was due to genotype 2. Genotype 1 was significantly more common in patients infected during the late-summer–autumn peak and in those with a history of foreign travel. PMID:11060056

  1. The heavy metal content of skeletons from an ancient metalliferous polluted area in southern Jordan with particular reference to bioaccumulation and human health.

    PubMed

    Pyatt, F B; Pyatt, A J; Walker, C; Sheen, T; Grattan, J P

    2005-03-01

    This paper considers pollution/toxicological science in an archaeological context. Copper mining was an important activity in southern Jordan, especially during the Bronze Age, Nabatean, Roman, and Byzantine periods, and the environmental legacy of such intensive mining and smelting activities exists today in the form of massive, ancient spoil and smelting tips. The environment was heavily polluted by copper, lead, and other cations during these early periods and the effects of such pollutants continue into modern times. Samples of goat, sheep, and Bronze Age and Byzantine skeletons have been analyzed and high metal loads, from uptake by diverse processes, are reported. Emphasis is placed on the importance of sampling procedure and sample location, bioaccumulation, and the partitioning of such elements. Implications of such pollutants in terms of environmental and human health in ancient and modern times are discussed. Teeth are found to provide excellent vehicles for the monitoring of pollution in both ancient and recent times. Bronze Age skeletons exhibited chemical fingerprints different from those of the Byzantine period.

  2. Distribution and heterogeneity of hepatitis C genotypes in hepatitis patients in Cameroon.

    PubMed

    Pasquier, Christophe; Njouom, Richard; Ayouba, Ahidjo; Dubois, Martine; Sartre, Michèle Tagni; Vessière, Aurelia; Timba, Isabelle; Thonnon, Jocelyn; Izopet, Jacques; Nerrienet, Eric

    2005-11-01

    Hepatitis C virus infects humans world-wide. The virus genome varies greatly and it has several genotypes. HCV infection is highly prevalent in Central Africa and Cameroon. Initial studies on the genetic variability of HCV showed infection with HCV genotypes 1, 2, and 4. We have now sequenced the NS5b and E2 regions of 156 HCV isolates collected from patients presenting for diagnosis in Yaounde and used the data to describe the distribution of HCV genotypes and subtypes in patients with hepatitis in Cameroon. Genotype 1 was more frequent than Genotypes 4 and 2. Genotypes 1 and 4 were highly heterogeneous, containing many subtypes described previously (1b, 1c, 1e, 1h, 1l, 4f, 4t, 4p, 4k) and unsubtyped groups. There was a systematic phylogenetic concordance between NS5b and E2 sequence clustering. The Genotype 2 sequences did not vary. Neither subject age nor gender influenced HCV distribution. HCV Genotypes 1 and 4 are very heterogeneous in Cameroon, perhaps due to ancient infections. The homogeneity of HCV Genotype 2 indicates its more recent introduction from western Africa.

  3. Activity of the Novel Peptide Arminin against Multiresistant Human Pathogens Shows the Considerable Potential of Phylogenetically Ancient Organisms as Drug Sources▿

    PubMed Central

    Augustin, René; Anton-Erxleben, Friederike; Jungnickel, Stephanie; Hemmrich, Georg; Spudy, Björn; Podschun, Rainer; Bosch, Thomas C. G.

    2009-01-01

    The emergence of multidrug-resistant bacteria highlights the need for new antibacterial agents. Arminin 1a is a novel antimicrobial peptide discovered during investigations of the epithelial defense of the ancient metazoan Hydra. Following proteolytic processing, the 31-amino-acid-long positively charged C-terminal part of arminin 1a exhibits potent and broad-spectrum activity against bacteria, including multiresistant human pathogenic strains, such as methicillin-resistant Staphylococcus aureus (MRSA) strains (minimal bactericidal concentration, 0.4 μM to 0.8 μM). Ultrastructural observations indicate that bacteria are killed by disruption of the bacterial cell wall. Remarkably, the antibacterial activity of arminin 1a is not affected under the physiological salt conditions of human blood. In addition, arminin 1a is a selective antibacterial agent that does not affect human erythrocyte membranes. Arminin 1a shows no sequence homology to any known antimicrobial peptide. Because of its high level of activity against multiresistant bacterial strains pathogenic for humans, the peptide arminin 1a is a promising template for a new class of antibiotics. Our data suggest that ancient metazoan organisms such as Hydra hold promise for the detection of novel antimicrobial molecules and the treatment of infections caused by multiresistant bacteria. PMID:19770277

  4. Detection and genotyping of human papillomavirus in urine samples from unvaccinated male and female adolescents in Italy.

    PubMed

    Bianchi, Silvia; Frati, Elena Rosanna; Panatto, Donatella; Martinelli, Marianna; Amicizia, Daniela; Zotti, Carla Maria; Martinese, Morena; Bonanni, Paolo; Boccalini, Sara; Coppola, Rosa Cristina; Masia, Giuseppina; Meloni, Angelo; Castiglia, Paolo; Piana, Andrea; Gasparini, Roberto; Tanzi, Elisabetta

    2013-01-01

    The introduction of vaccination against Human Papillomavirus (HPV) in adolescent girls in 2006 has focused virological surveillance on this age group. As few studies have evaluated HPV infections in young populations, further data are needed in order to improve and extend prophylactic policy and to monitor epidemiological changes. The present study aimed at evaluating overall and type-specific HPV prevalence in both female and male adolescents in Italy. HPV DNA detection and genotyping was performed on urine samples collected from 870 unvaccinated adolescents (369 females, 501 males, 11-18 years of age) in five cities in Italy. Following DNA extraction by means of a commercial kit (NucliSENS(®)-miniMAG(®), bioMérieux), the L1 gene fragment was PCR amplified and genotyped by restriction fragment length polymorphism analysis. HPV DNA was detected in 1.5% of all samples, and in 3% and 0.4% of samples from females and males, respectively. In approximately 70% of HPV DNA positive adolescents, the infection was due to a single genotype, with 88.9% of genotypes belonging to the HR-clade. The only two HPV-positive boys (14 and 18 years old) had HPV-70 genotype. Only one of the 11 HPV-infected girls was in the 11-14 age-group. HPV prevalence was 4.2% in girls aged 15-18 years and 60% of infections were due to vaccine types HPV-16 or HPV-6/-11. This is one of the few studies, the first conducted in Italy, on HPV infection in adolescents. Urine testing is the easier way of detecting HPV infection in younger populations. Our data revealed a very low HPV prevalence, and no infections were observed in the 12-year-old vaccine target population. The majority of infections were seen in females aged 15-18 years. Overall, more than 50% and 30% of the potentially persistent HPV infections detected in this group could have been prevented by the quadrivalent and the bivalent vaccines, respectively.

  5. Detection and Genotyping of Human Papillomavirus in Urine Samples from Unvaccinated Male and Female Adolescents in Italy

    PubMed Central

    Bianchi, Silvia; Frati, Elena Rosanna; Panatto, Donatella; Martinelli, Marianna; Amicizia, Daniela; Zotti, Carla Maria; Martinese, Morena; Bonanni, Paolo; Boccalini, Sara; Coppola, Rosa Cristina; Masia, Giuseppina; Meloni, Angelo; Castiglia, Paolo; Piana, Andrea; Gasparini, Roberto; Tanzi, Elisabetta

    2013-01-01

    The introduction of vaccination against Human Papillomavirus (HPV) in adolescent girls in 2006 has focused virological surveillance on this age group. As few studies have evaluated HPV infections in young populations, further data are needed in order to improve and extend prophylactic policy and to monitor epidemiological changes. The present study aimed at evaluating overall and type-specific HPV prevalence in both female and male adolescents in Italy. HPV DNA detection and genotyping was performed on urine samples collected from 870 unvaccinated adolescents (369 females, 501 males, 11-18 years of age) in five cities in Italy. Following DNA extraction by means of a commercial kit (NucliSENS®-miniMAG®, bioMérieux), the L1 gene fragment was PCR amplified and genotyped by restriction fragment length polymorphism analysis. HPV DNA was detected in 1.5% of all samples, and in 3% and 0.4% of samples from females and males, respectively. In approximately 70% of HPV DNA positive adolescents, the infection was due to a single genotype, with 88.9% of genotypes belonging to the HR-clade. The only two HPV-positive boys (14 and 18 years old) had HPV-70 genotype. Only one of the 11 HPV-infected girls was in the 11-14 age-group. HPV prevalence was 4.2% in girls aged 15-18 years and 60% of infections were due to vaccine types HPV-16 or HPV-6/-11. This is one of the few studies, the first conducted in Italy, on HPV infection in adolescents. Urine testing is the easier way of detecting HPV infection in younger populations. Our data revealed a very low HPV prevalence, and no infections were observed in the 12-year-old vaccine target population. The majority of infections were seen in females aged 15-18 years. Overall, more than 50% and 30% of the potentially persistent HPV infections detected in this group could have been prevented by the quadrivalent and the bivalent vaccines, respectively. PMID:24255711

  6. Genotyping of human parvovirus B19 in clinical samples from Brazil and Paraguay using heteroduplex mobility assay, single-stranded conformation polymorphism and nucleotide sequencing.

    PubMed

    Mendonça, Marcos César Lima de; Ferreira, Ana Maria de Amorim; Santos, Marta Gonçalves Matos dos; Oviedo, Elva Cristina; Bello, Maria Sônia Dal; Siqueira, Marilda Mendonça; Maceira, Juan Manuel Piñeiro; von Hubinger, Maria Genoveva; Couceiro, José Nelson dos Santos Silva

    2011-06-01

    Heteroduplex mobility assay, single-stranded conformation polymorphism and nucleotide sequencing were utilised to genotype human parvovirus B19 samples from Brazil and Paraguay. Ninety-seven serum samples were collected from individuals presenting with abortion or erythema infectiosum, arthropathies, severe anaemia and transient aplastic crisis; two additional skin samples were collected by biopsy. After the procedure, all clinical samples were classified as genotype 1.

  7. Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles

    PubMed Central

    Highnam, Gareth; Franck, Christopher; Martin, Andy; Stephens, Calvin; Puthige, Ashwin; Mittelman, David

    2013-01-01

    Repetitive sequences are biologically and clinically important because they can influence traits and disease, but repeats are challenging to analyse using short-read sequencing technology. We present a tool for genotyping microsatellite repeats called RepeatSeq, which uses Bayesian model selection guided by an empirically derived error model that incorporates sequence and read properties. Next, we apply RepeatSeq to high-coverage genomes from the 1000 Genomes Project to evaluate performance and accuracy. The software uses common formats, such as VCF, for compatibility with existing genome analysis pipelines. Source code and binaries are available at http://github.com/adaptivegenome/repeatseq. PMID:23090981

  8. Autosomal short tandem repeat analysis of ancient DNA by coupled use of mini- and conventional STR kits.

    PubMed

    Oh, Chang Seok; Lee, Sang Jun; Park, Jun Bum; Lee, Soong Deok; Seo, Seung Bum; Kim, Hye Yeon; Kim, Jaehyup; Kim, Yi-Suk; Shin, Dong Hoon

    2012-05-01

    Multiplex autosomal short tandem repeat (STR) genotyping enables researchers to obtain genetic information from ancient human samples. In this study, we tested newly developed AmpFℓSTR(®) MiniFiler™ kit for autosomal STR analysis of ancient DNA (aDNA), using human femurs (n = 8) collected from medieval Korean tombs. After extracting aDNA from the bones, autosomal STR analyses were repeated for each sample using the AmpFℓSTR(®) MiniFiler™ and Identifiler™ kits. Whereas only 21.87% of larger-sized loci profiles could be obtained with the Identifiler™ kit, 75% of the same loci profiles were determined by MiniFiler™ kit analysis. This very successful amplification of large-sized STR markers from highly degraded aDNA suggests that the MiniFiler™ kit could be a useful complement to conventional STR kit analysis of ancient samples. PMID:22268568

  9. Ancient Egypt

    NASA Astrophysics Data System (ADS)

    Swamy, Ashwin Balegar

    This thesis involves development of an interactive GIS (Geographic Information System) based application, which gives information about the ancient history of Egypt. The astonishing architecture, the strange burial rituals and their civilization were some of the intriguing questions that motivated me towards developing this application. The application is a historical timeline starting from 3100 BC, leading up to 664 BC, focusing on the evolution of the Egyptian dynasties. The tool holds information regarding some of the famous monuments which were constructed during that era and also about the civilizations that co-existed. It also provides details about the religions followed by their kings. It also includes the languages spoken during those periods. The tool is developed using JAVA, a programing language and MOJO (Map Objects Java Objects) a product of ESRI (Environmental Science Research Institute) to create map objects, to provide geographic information. JAVA Swing is used for designing the user interface. HTML (Hyper Text Markup Language) pages are created to provide the user with more information related to the historic period. CSS (Cascade Style Sheets) and JAVA Scripts are used with HTML5 to achieve creative display of content. The tool is kept simple and easy for the user to interact with. The tool also includes pictures and videos for the user to get a feel of the historic period. The application is built to motivate people to know more about one of the prominent and ancient civilization of the Mediterranean world.

  10. Hepatitis E Virus (HEV) Genotype 3 Infection of Human Liver Chimeric Mice as a Model for Chronic HEV Infection

    PubMed Central

    Pas, Suzan D.; van der Net, Guido; de Man, Robert A.; Osterhaus, Albert D. M. E.; Haagmans, Bart L.; Boonstra, Andre

    2016-01-01

    ABSTRACT Genotype 3 (gt3) hepatitis E virus (HEV) infections are emerging in Western countries. Immunosuppressed patients are at risk of chronic HEV infection and progressive liver damage, but no adequate model system currently mimics this disease course. Here we explore the possibilities of in vivo HEV studies in a human liver chimeric mouse model (uPA+/+Nod-SCID-IL2Rγ−/−) next to the A549 cell culture system, using HEV RNA-positive EDTA-plasma, feces, or liver biopsy specimens from 8 immunocompromised patients with chronic gt3 HEV. HEV from feces- or liver-derived inocula showed clear virus propagation within 2 weeks after inoculation onto A549 cells, compared to slow or no HEV propagation of HEV RNA-positive, EDTA-plasma samples. These in vitro HEV infectivity differences were mirrored in human-liver chimeric mice after intravenous (i.v.) inoculation of selected samples. HEV RNA levels of up to 8 log IU HEV RNA/gram were consistently present in 100% of chimeric mouse livers from week 2 to week 14 after inoculation with human feces- or liver-derived HEV. Feces and bile of infected mice contained moderate to large amounts of HEV RNA, while HEV viremia was low and inconsistently detected. Mouse-passaged HEV could subsequently be propagated for up to 100 days in vitro. In contrast, cell culture-derived or seronegative EDTA-plasma-derived HEV was not infectious in inoculated animals. In conclusion, the infectivity of feces-derived human HEV is higher than that of EDTA-plasma-derived HEV both in vitro and in vivo. Persistent HEV gt3 infections in chimeric mice show preferential viral shedding toward mouse bile and feces, paralleling the course of infection in humans. IMPORTANCE Hepatitis E virus (HEV) genotype 3 infections are emerging in Western countries and are of great concern for immunosuppressed patients at risk for developing chronic HEV infection. Lack of adequate model systems for chronic HEV infection hampers studies on HEV infectivity and transmission

  11. HPV Direct Flow CHIP: a new human papillomavirus genotyping method based on direct PCR from crude-cell extracts.

    PubMed

    Herraez-Hernandez, Elsa; Alvarez-Perez, Martina; Navarro-Bustos, Gloria; Esquivias, Javier; Alonso, Sonia; Aneiros-Fernandez, Jose; Lacruz-Pelea, Cesar; Sanchez-Aguera, Magdalena; Santamaria, Javier Saenz; de Antonio, Jesus Chacon; Rodriguez-Peralto, Jose Luis

    2013-10-01

    HPV Direct Flow CHIP is a newly developed test for identifying 18 high-risk and 18 low-risk human papillomavirus (HPV) genotypes. It is based on direct PCR from crude-cell extracts, automatic flow-through hybridization, and colorimetric detection. The aim of this study was to evaluate the performance of HPV Direct Flow CHIP in the analysis of 947 samples from routine cervical screening or the follow-up of abnormal Pap smears. The specimens were dry swab samples, liquid-based cytology samples, or formalin-fixed paraffin-embedded tissues. The genotype distribution was in agreement with known epidemiological data for the Spanish population. Three different subgroups of the samples were also tested by Linear Array (LA) HPV Genotyping Test (n=108), CLART HPV2 (n=82), or Digene Hybrid Capture 2 (HC2) HPV DNA Test (n=101). HPV positivity was 73.6% by HPV Direct Flow CHIP versus 67% by LA, 65.9% by HPV Direct Flow CHIP versus 59.8% by CLART, and 62.4% by HPV Direct Flow CHIP versus 42.6% by HC2. HPV Direct Flow CHIP showed a positive agreement of 88.6% with LA (k=0.798), 87.3% with CLART (k=0.818), and 68.2% with HC2 (k=0.618). In conclusion, HPV Direct Flow CHIP results were comparable with those of the other methods tested. Although further investigation is needed to compare the performance of this new test with a gold-standard reference method, these preliminary findings evidence the potential value of HPV Direct Flow CHIP in HPV vaccinology and epidemiology studies.

  12. Genotype and Phenotype Patterns of Human Immunodeficiency Virus Type 1 Resistance to Enfuvirtide during Long-Term Treatment

    PubMed Central

    Menzo, Stefano; Castagna, Antonella; Monachetti, Alessia; Hasson, Hamid; Danise, Anna; Carini, Elisabetta; Bagnarelli, Patrizia; Lazzarin, Adriano; Clementi, Massimo

    2004-01-01

    The human immunodeficiency virus type 1 (HIV-1) fusion inhibitor enfuvirtide has recently been introduced into clinical practice and has exhibited efficient anti-HIV-1 activity in combination with other antiretroviral agents. In the present study, we addressed the effect of long-term treatment with enfuvirtide on the intrahost evolution of HIV-1. The genotype and phenotype patterns and the relative replication capacity (rRC) of enfuvirtide-resistant HIV-1 mutants were evaluated in samples from 11 subjects (7 virological nonresponders and 4 responders) who received the compound for more than 1 year in combination with different regimens. Selection of one or more mutations clustering in a sequence (amino acids 36 to 45) of the gp41 N-terminal heptad repeat was observed in samples from the seven virological nonresponders but not in those from responders. In two subjects who discontinued enfuvirtide, reversion of the resistant genotype was detected within 3 months. Recombinant clones bearing mutated gp41 sequences displayed reduced susceptibilities to enfuvirtide, with the 50% inhibitory concentrations (IC50s) ranging from 0.6 to 12.8 μg/ml, whereas the IC50 for isolates with baseline sequences was 0.013 ± 0.010 μg/ml. Interestingly, long-term monitoring of resistant variants provided evidence that ongoing adaptation to the drug is paralleled by phenotypic changes. A limited drop in the rRC in the absence of drug was observed for clones from four of the seven nonresponders bearing mutations associated with resistance. Overall, the data indicate that the different genotype patterns associated with a detectable degree of HIV-1 resistance to enfuvirtide generated during long-term treatments are characterized by a substantially low genetic barrier, possible ongoing adaptation with increased degrees of resistance, and limited influence on the viral rRC. PMID:15328081

  13. Prevalence of human papillomavirus and its genotype among 1336 invasive cervical cancer patients in Hunan province, central south China.

    PubMed

    Wang, Linqian; Wu, Baiping; Li, Junjun; Chen, Liyu

    2015-03-01

    Existing data on the genotype distribution of human papillomavirus (HPV) are limited in Hunan province, central south China. To evaluate the prevalence of HPV infection and its genotype among women with invasive cervical cancer in Hunan, a total of 1,336 patients were included in this study between July 2012 and June 2013. Eighteen high-risk and eight low-risk genotypes of HPV were detected by Luminex xMAP technology. The results show that HPV prevalence in invasive cervical cancer in Hunan was 75.7%. A single HPV infection was found in 82.3% of the HPV-positive samples, and 91.8% of the cases had high-risk HPV infection. The most common HPV type was HPV 16 (50.6%), followed by HPV 58 (12.4%), HPV 52 (10.9%), HPV 18 (7.3%), HPV 33 (5.5%), HPV 59 (4.2%), HPV 39 (4.0%), HPV 61 (3.4%), HPV 31 (3.3%), and HPV 56 (3.2%). A single infection with HPV 16 was detected in 42.5% of the samples, which was significantly more frequent than any other HPV type in this population. Dual-infection with HPV 16 and HPV 52 were relatively common. The available vaccines for HPV 16 and 18 are therefore expected to have a substantial impact on reducing the burden of cervical cancer in China, even though HPV 18 showed a lower frequency. In addition to HPV 16 and 18, other HPV types including 58, 52, and 33, should be targeted in the next generation HPV vaccines.

  14. Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX

    PubMed Central

    Brotherton, Paul; Sanchez, Juan J.; Cooper, Alan; Endicott, Phillip

    2010-01-01

    The analysis of targeted genetic loci from ancient, forensic and clinical samples is usually built upon polymerase chain reaction (PCR)-generated sequence data. However, many studies have shown that PCR amplification from poor-quality DNA templates can create sequence artefacts at significant levels. With hominin (human and other hominid) samples, the pervasive presence of highly PCR-amplifiable human DNA contaminants in the vast majority of samples can lead to the creation of recombinant hybrids and other non-authentic artefacts. The resulting PCR-generated sequences can then be difficult, if not impossible, to authenticate. In contrast, single primer extension (SPEX)-based approaches can genotype single nucleotide polymorphisms from ancient fragments of DNA as accurately as modern DNA. A single SPEX-type assay can amplify just one of the duplex DNA strands at target loci and generate a multi-fold depth-of-coverage, with non-authentic recombinant hybrids reduced to undetectable levels. Crucially, SPEX-type approaches can preferentially access genetic information from damaged and degraded endogenous ancient DNA templates over modern human DNA contaminants. The development of SPEX-type assays offers the potential for highly accurate, quantitative genotyping from ancient hominin samples. PMID:19864251

  15. Complex evolutionary patterns of two rare human G3P[9] rotavirus strains possessing a feline/canine-like H6 genotype on an AU-1-like genotype constellation.

    PubMed

    Wang, Yuan-Hong; Pang, Bei-Bei; Zhou, Xuan; Ghosh, Souvik; Tang, Wei-Feng; Peng, Jin-Song; Hu, Quan; Zhou, Dun-Jin; Kobayashi, Nobumichi

    2013-06-01

    The group A rotavirus (RVA) G3P[9] is a rare VP7-VP4 genotype combination, detected occasionally in humans and cats. Other than the prototype G3P[9] strain, RVA/Human- tc/JPN/AU-l/1982/G3P3[9], the whole genomes of only two human G3P[9] RVA strains and two feline G3P[9] RVA strains have been analyzed so far, revealing complex evolutionary patterns, distinct from that of AU-1. We report here the whole genomic analyses of two human G3P[9] RVA strains, RVA/Human-tc/CHN/L621/2006/G3P[9] and RVA/Human-wt/CHN/E2451/2011/G3P[9], detected in patients with diarrhea in China. Strains L621 and E2451 possessed a H6 NSP5 genotype on an AU-1-like genotype constellation, not reported previously. However, not all the genes of L621 and E2451 were closely related to those of AU-1, or to each other, revealing different evolutionary patterns among the AU-1-like RVAs. The VP7, VP4, VP6 and NSP4 genes of E2451 and L621 were found to cluster together with human G3P[9] RVA strains believed to be of possible feline/canine origin, and feline or raccoon dog RVA strains. The VP1, VP3, NSP2 and NSP5 genes of E2451 and L621 formed distinct clusters in genotypes typically found in feline/canine RVA strains or RVA strains from other host species which are believed to be of feline/canine RVA origin. The VP2 genes of E2451 and L621, and NSP3 gene of L621 clustered among RVA strains from different host species which are believed to have a complete or partial feline/canine RVA origin. The NSP1 genes of E2451 and L621, and NSP3 gene of E2451 clustered with AU-1 and several other strains possessing a complete or partial feline RVA strain BA222-05-like genotype constellation. Taken together, these observations suggest that nearly all the eleven gene segments of G3P[9] RVA strains L621 and E2451 might have originated from feline/canine RVAs, and that reassortments may have occurred among these feline/canine RVA strains, before being transmitted to humans.

  16. Complex evolutionary patterns of two rare human G3P[9] rotavirus strains possessing a feline/canine-like H6 genotype on an AU-1-like genotype constellation.

    PubMed

    Wang, Yuan-Hong; Pang, Bei-Bei; Zhou, Xuan; Ghosh, Souvik; Tang, Wei-Feng; Peng, Jin-Song; Hu, Quan; Zhou, Dun-Jin; Kobayashi, Nobumichi

    2013-06-01

    The group A rotavirus (RVA) G3P[9] is a rare VP7-VP4 genotype combination, detected occasionally in humans and cats. Other than the prototype G3P[9] strain, RVA/Human- tc/JPN/AU-l/1982/G3P3[9], the whole genomes of only two human G3P[9] RVA strains and two feline G3P[9] RVA strains have been analyzed so far, revealing complex evolutionary patterns, distinct from that of AU-1. We report here the whole genomic analyses of two human G3P[9] RVA strains, RVA/Human-tc/CHN/L621/2006/G3P[9] and RVA/Human-wt/CHN/E2451/2011/G3P[9], detected in patients with diarrhea in China. Strains L621 and E2451 possessed a H6 NSP5 genotype on an AU-1-like genotype constellation, not reported previously. However, not all the genes of L621 and E2451 were closely related to those of AU-1, or to each other, revealing different evolutionary patterns among the AU-1-like RVAs. The VP7, VP4, VP6 and NSP4 genes of E2451 and L621 were found to cluster together with human G3P[9] RVA strains believed to be of possible feline/canine origin, and feline or raccoon dog RVA strains. The VP1, VP3, NSP2 and NSP5 genes of E2451 and L621 formed distinct clusters in genotypes typically found in feline/canine RVA strains or RVA strains from other host species which are believed to be of feline/canine RVA origin. The VP2 genes of E2451 and L621, and NSP3 gene of L621 clustered among RVA strains from different host species which are believed to have a complete or partial feline/canine RVA origin. The NSP1 genes of E2451 and L621, and NSP3 gene of E2451 clustered with AU-1 and several other strains possessing a complete or partial feline RVA strain BA222-05-like genotype constellation. Taken together, these observations suggest that nearly all the eleven gene segments of G3P[9] RVA strains L621 and E2451 might have originated from feline/canine RVAs, and that reassortments may have occurred among these feline/canine RVA strains, before being transmitted to humans. PMID:23403096

  17. Re-investigation of the concordance of human NAT2 phenotypes and genotypes.

    PubMed

    Bolt, Hermann M; Selinski, Silvia; Dannappel, Doris; Blaszkewicz, Meinolf; Golka, Klaus

    2005-04-01

    A comparative study of N-acetyltransferase 2 (NAT2) genotyping and phenotyping (caffeine test method) was performed on 211 persons to elucidate apparent discrepancies in the assignment of NAT2*12 and NAT2*13 alleles which occur in the literature. The study used the standard procedures of genotyping (two PCR runs and application of seven restriction enzymes) and phenotyping (determination of the two caffeine metabolites 5-acetylamino-6-formylamino-3-methyluracil (AFMU) and 1-methylxanthine (1X)), as documented in detail and validated by the Deutsche Forschungsgemeinschaft. The data were consistent with an AFMU/1X molar ratio of 0.85 as cut-off point (antimode) between phenotypically slow and rapid acetylators. Under this provision, several R/S allele combinations did not comply, either fully or partly, with their associated phenotypes. In particular, there was a wide phenotypic overlap of the alleged rapid allele combination groups (i) NAT2*12A/*5A; NAT2*12C/*5D; NAT2*4/*5B, (ii) NAT2*13/*6B; NAT2*4/*6A, and (iii) NAT2*13/*7A; NAT2*4/*7B. These groups obviously contained both phenotypically rapid and slow acetylators. If one assumes that the presence of one "wild type" allele NAT2*4 defines a rapid acetylator the assignment of the alleles NAT2*12A, NAT2*12C, and NAT*13 as determinants of a rapid acetylator phenotype must be questioned. This refers in particular to the nucleotide changes A803G (NAT2*12A, NAT2*12C) and C282T (NAT2*13). Based on discussions in the literature and the data presented here, there is accumulating evidence that current assignments of the NAT2*12 and NAT2*13 alleles as determinants of a rapid acetylator state should be reconsidered.

  18. Ancient autophagy

    PubMed Central

    Klionsky, Daniel J.

    2013-01-01

    These days, when we talk about the origin of a protein, or even a pathway, we are typically referring to evolutionary lineages based on nucleotide sequences. For example, is a particular protein’s function conserved? How far back did it first appear? Are there homologs in higher eukaryotes? However, a simpler question (or perhaps I should say, a non-molecular biology question) is when was the process first detected in the paleontological record? Of course I assumed that macroautophagy was ancient, but a new finding (see p. 632 in this issue of the journal) provides an unexpected—and exciting—piece of information for our field. For the first time, scientists have discovered fossil evidence for an actual subcellular pathway—and it looks like it might actually be autophagy (I admit I am biased, but you can decide for yourself). PMID:23388466

  19. Magnetic nanowires for rapid and ultrasensitive isolation of DNA from cervical specimens for the detection of multiple human papillomaviruses genotypes.

    PubMed

    Lee, HyungJae; Hwang, Na Rae; Hwang, Sang-Hyun; Cho, Youngnam

    2016-12-15

    Detecting human papillomavirus (HPV) is central in diagnosing and monitoring HPV-related disease. However, limited sensitivity and the wide variability of the HPV genome pose challenges in the identification of HPV genes, particularly high-risk types. This study reports the development of polyethyleneimine-conjugated magnetic nanowires (PEI-MNWs) and their use in the isolation, identification, and analysis of multiple genotypes of HPV DNA from cervical cancer specimens. The nanowires are electrochemically doped with a high density of magnetic nanoparticles and biotin moieties during potentiostatic deposition, thereby allowing conjugating cationic branched polymers to direct the attachment of negatively charged DNA molecules with strong magnetic response. For proof of concept, the rapid and ultrasensitive isolation of HPV DNA is performed at concentrations as low as 10pg/mL with an efficiency of >95%. For clinical optimization, the analytical and clinical sensitivity of PEI-MNWs is compared with that of the Roche Cobas 4800 HPV Test and demonstrates excellent correlation for multiple HPV DNA genotypes with superior threshold cycle values. The high sensitivity, specificity, and good reproducibility of PEI-MNWs are particularly well suited for the recovery of DNA and provide significant and clinically meaningful evidence for the early detection and treatment of HPV-associated cancers.

  20. Magnetic nanowires for rapid and ultrasensitive isolation of DNA from cervical specimens for the detection of multiple human papillomaviruses genotypes.

    PubMed

    Lee, HyungJae; Hwang, Na Rae; Hwang, Sang-Hyun; Cho, Youngnam

    2016-12-15

    Detecting human papillomavirus (HPV) is central in diagnosing and monitoring HPV-related disease. However, limited sensitivity and the wide variability of the HPV genome pose challenges in the identification of HPV genes, particularly high-risk types. This study reports the development of polyethyleneimine-conjugated magnetic nanowires (PEI-MNWs) and their use in the isolation, identification, and analysis of multiple genotypes of HPV DNA from cervical cancer specimens. The nanowires are electrochemically doped with a high density of magnetic nanoparticles and biotin moieties during potentiostatic deposition, thereby allowing conjugating cationic branched polymers to direct the attachment of negatively charged DNA molecules with strong magnetic response. For proof of concept, the rapid and ultrasensitive isolation of HPV DNA is performed at concentrations as low as 10pg/mL with an efficiency of >95%. For clinical optimization, the analytical and clinical sensitivity of PEI-MNWs is compared with that of the Roche Cobas 4800 HPV Test and demonstrates excellent correlation for multiple HPV DNA genotypes with superior threshold cycle values. The high sensitivity, specificity, and good reproducibility of PEI-MNWs are particularly well suited for the recovery of DNA and provide significant and clinically meaningful evidence for the early detection and treatment of HPV-associated cancers. PMID:27494810

  1. Genotyping for Human Papillomavirus (HPV) 16/18/52/58 Has a Higher Performance than HPV16/18 Genotyping in Triaging Women with Positive High-risk HPV Test in Northern Thailand

    PubMed Central

    Khunamornpong, Surapan; Settakorn, Jongkolnee; Sukpan, Kornkanok; Suprasert, Prapaporn; Srisomboon, Jatupol; Intaraphet, Suthida; Siriaunkgul, Sumalee

    2016-01-01

    Background Testing for high-risk human papillomavirus DNA (HPV test) has gained increasing acceptance as an alternative method to cytology in cervical cancer screening. Compared to cytology, HPV test has a higher sensitivity for the detection of histologic high-grade squamous intraepithelial lesion or worse (HSIL+), but this could lead to a large colposcopy burden. Genotyping for HPV16/18 has been recommended in triaging HPV-positive women. This study was aimed to evaluate the screening performance of HPV testing and the role of genotyping triage in Northern Thailand. Methods A population-based cervical screening program was performed in Chiang Mai (Northern Thailand) using cytology (conventional Pap test) and HPV test (Hybrid Capture 2). Women who had abnormal cytology or were HPV-positive were referred for colposcopy. Cervical samples from these women were genotyped using the Linear Array assay. Results Of 5,456 women, 2.0% had abnormal Pap test results and 6.5% tested positive with Hybrid Capture 2. Of 5,433 women eligible for analysis, 355 with any positive test had histologic confirmation and 57 of these had histologic HSIL+. The sensitivity for histologic HSIL+ detection was 64.9% for Pap test and 100% for Hybrid Capture 2, but the ratio of colposcopy per detection of each HSIL+ was more than two-fold higher with Hybrid Capture 2 than Pap test (5.9 versus 2.8). Genotyping results were available in 316 samples. HPV52, HPV16, and HPV58 were the three most common genotypes among women with histologic HSIL+. Performance of genotyping triage using HPV16/18/52/58 was superior to that of HPV16/18, with a higher sensitivity (85.7% versus 28.6%) and negative predictive value (94.2% versus 83.9%). Conclusions In Northern Thailand, HPV testing with genotyping triage shows better screening performance than cervical cytology alone. In this region, the addition of genotyping for HPV52/58 to HPV16/18 is deemed necessary in triaging women with positive HPV test. PMID

  2. Antigenic analysis of divergent genotypes human Enterovirus 71 viruses by a panel of neutralizing monoclonal antibodies: current genotyping of EV71 does not reflect their antigenicity.

    PubMed

    Chen, Yixin; Li, Chuan; He, Delei; Cheng, Tong; Ge, Shengxiang; Shih, James Wai-Kuo; Zhao, Qinjian; Chen, Pei-Jer; Zhang, Jun; Xia, Ningshao

    2013-01-01

    In recent year, Enterovirus 71 (EV71)-associated hand, foot and mouth disease (HFMD) has become an important public health issue in China. EV71 has been classified into genotypes A, B1-B5 and C1-C5. With such genetic diversity, whether the convalescent or recovery antibody responses can cross-protect infections from other genotypes remains a question. Understanding of the antigenicity of such diverse genetic EV71 isolates is crucial for the EV71 vaccine development. Here, a total of 186 clones anti-EV71 MAbs was generated and characterized with Western blot and cell-based neutralization assay. Forty neutralizing anti-EV71 MAbs were further used to analyze the antigenic properties of 18 recent EV71 isolates representing seven genotypes in neutralization assay. We found that most neutralizing anti-EV71 MAbs are specific to conformational epitopes. We also classified the 40 neutralizing anti-EV71 MAbs into two classes according to their reactivity patterns with 18 EV71 isolates. Class I MAb can neutralize all isolates, suggesting conserved epitopes are present among EV71. Class II MAb includes four subclasses (IIa-IId) and neutralizes only subgroups of EV71 strains. Conversely, 18 EV71 strains were grouped into antigenic types 1 and four antigenic subtypes (2.1-2.4). These results suggest that the current genotyping of EV71 does not reflect their antigenicity which may be important in the selection of EV71 vaccine strains. This panel of neutralizing anti-EV71 MAbs may be useful for the recognition of emerging antigenic variants of EV71 and vaccine development.

  3. Advances in alloimmune thrombocytopenia: perspectives on current concepts of human platelet antigens, antibody detection strategies, and genotyping

    PubMed Central

    Hayashi, Tomoya; Hirayama, Fumiya

    2015-01-01

    Alloimmunisation to platelets leads to the production of antibodies against platelet antigens and consequently to thrombocytopenia. Numerous molecules located on the platelet surface are antigenic and induce immune-mediated platelet destruction with symptoms that can be serious. Human platelet antigens (HPA) cause thrombocytopenias, such as neonatal alloimmune thrombocytopenia, post-transfusion purpura, and platelet transfusion refractoriness. Thirty-four HPA are classified into 28 systems. Assays to identify HPA and anti-HPA antibodies are critically important for preventing and treating thrombocytopenia caused by anti-HPA antibodies. Significant progress in furthering our understanding of HPA has been made in the last decade: new HPA have been discovered, antibody-detection methods have improved, and new genotyping methods have been developed. We review these advances and discuss issues that remain to be resolved as well as future prospects for preventing and treating immune thrombocytopenia. PMID:26057488

  4. Genotyping of ABO blood group system by PCR and RFLP on mummies discovered at Taklamakan desert in 1912.

    PubMed

    Lin, Z; Kondo, T; Minamino, T; Sun, E; Liu, G; Ohshima, T

    1996-10-01

    ABO genotyping was carried out using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) method on the dried remains of nine human mummies which had been discovered at Taklamakan desert in 1912. In all the nine mummies, ABO genotype could be determined as BO type, and ABO phenotype of the eight mummies with hair specimen could be revealed as B type using absorption-elution method. These results mean that ABO phenotype estimated from its genotype by PCR-RFLP was consistent with that by absorption-elution method in all of the eight cases examined. And in the other one child mummy, ABO phenotype could not be examined because of no hair specimen. Although it is impossible to assess the allele frequency of ABO blood group system in the populations having lived in Gao Chang at that time, the present study shows a possibility of ABO genotyping from ancient human remains.

  5. FADS2 genotype regulates delta-6 desaturase activity and inflammation in human adipose tissue.

    PubMed

    Vaittinen, Maija; Walle, Paula; Kuosmanen, Emmi; Männistö, Ville; Käkelä, Pirjo; Ågren, Jyrki; Schwab, Ursula; Pihlajamäki, Jussi

    2016-01-01

    Obesity is associated with disturbed lipid metabolism and low-grade inflammation in tissues. The aim of this study was to investigate the association between FA metabolism and adipose tissue (AT) inflammation in the Kuopio Obesity Surgery study. We investigated the association of surgery-induced weight loss and FA desaturase (FADS)1/2 genotypes with serum and AT FA profile and with AT inflammation, measured as interleukin (IL)-1β and NFκB pathway gene expression, in order to find potential gene-environment interactions. We demonstrated an association between serum levels of saturated and polyunsaturated n-6 FAs, and estimated enzyme activities of FADS1/2 genes with IL-1β expression in AT both at baseline and at follow-up. Variation in the FADS1/2 genes associated with IL-1β and NFκB pathway gene expression in SAT after weight reduction, but not at baseline. In addition, the FA composition in subcutaneous and visceral fat correlated with serum FAs, and the associations between serum PUFAs and estimated D6D enzyme activity with AT inflammation were also replicated with corresponding AT FAs and AT inflammation. We conclude that the polymorphism in FADS1/2 genes associates with FA metabolism and AT inflammation, leading to an interaction between weight loss and FADS1/2 genes in the regulation of AT inflammation.

  6. Analysis of Ancient DNA in Microbial Ecology.

    PubMed

    Gorgé, Olivier; Bennett, E Andrew; Massilani, Diyendo; Daligault, Julien; Pruvost, Melanie; Geigl, Eva-Maria; Grange, Thierry

    2016-01-01

    The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples and identifying ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota. PMID:26791510

  7. Analysis of Ancient DNA in Microbial Ecology.

    PubMed

    Gorgé, Olivier; Bennett, E Andrew; Massilani, Diyendo; Daligault, Julien; Pruvost, Melanie; Geigl, Eva-Maria; Grange, Thierry

    2016-01-01

    The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples and identifying ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.

  8. Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics.

    PubMed

    Ottoni, Claudio; Flink, Linus Girdland; Evin, Allowen; Geörg, Christina; De Cupere, Bea; Van Neer, Wim; Bartosiewicz, László; Linderholm, Anna; Barnett, Ross; Peters, Joris; Decorte, Ronny; Waelkens, Marc; Vanderheyden, Nancy; Ricaut, François-Xavier; Cakirlar, Canan; Cevik, Ozlem; Hoelzel, A Rus; Mashkour, Marjan; Karimlu, Azadeh Fatemeh Mohaseb; Seno, Shiva Sheikhi; Daujat, Julie; Brock, Fiona; Pinhasi, Ron; Hongo, Hitomi; Perez-Enciso, Miguel; Rasmussen, Morten; Frantz, Laurent; Megens, Hendrik-Jan; Crooijmans, Richard; Groenen, Martien; Arbuckle, Benjamin; Benecke, Nobert; Vidarsdottir, Una Strand; Burger, Joachim; Cucchi, Thomas; Dobney, Keith; Larson, Greger

    2013-04-01

    Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ~8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages.

  9. Tracheostomy in ancient Egypt.

    PubMed

    Blomstedt, Patric

    2014-08-01

    It has often been reported that the ancient Egyptians performed tracheostomies. An analysis of this claim demonstrates it to be founded on only two depictions from the Protodynastic period (thirty-first century bc). These depictions are difficult to reconcile with tracheostomy from an anatomical point of view and can more easily be explained as human sacrifices. Considering that Egyptian surgery included only minor procedures even at its zenith during later dynastic periods, it is difficult to imagine that they would have developed such an advanced procedure at such an early date.

  10. Serotypic and genotypic characterization of human serotype 10 rotaviruses from asymptomatic neonates.

    PubMed Central

    Dunn, S J; Greenberg, H B; Ward, R L; Nakagomi, O; Burns, J W; Vo, P T; Pax, K A; Das, M; Gowda, K; Rao, C D

    1993-01-01

    Human rotaviruses were isolated from asymptomatic neonates at various hospitals and clinics in the city of Bangalore, India, and were found to be subgroup I specific and possess long RNA patterns (M. Sukumaran, K. Gowda, P. P. Maiya, T. P. Srinivas, M. S. Kumar, S. Aijaz, R. R. Reddy, L. Padilla, H. B. Greenberg, and C. D. Rao, Arch. Virol. 126:239-251, 1992). Three of these strains were adapted to tissue culture and found by serotype analysis and neutralization assays to be of serotype 10, a serotype commonly found in cattle but infrequently found in humans and not previously identified in neonates. By RNA-RNA hybridization, a high level of relatedness to a serotype 10 bovine rotavirus strain and a low-to-medium level of relatedness to a human rotavirus strain were observed. Since this human isolate shares a genogroup with bovine rotavirus, it is likely that it originated by interspecies transmission. A human rotavirus strain isolated from asymptomatic neonates and similar to bovine rotavirus might represent a good vaccine candidate. Images PMID:8380181

  11. Genetic Characterization of Human-Derived Hydatid Cysts of Echinococcus granulosus Sensu Lato in Heilongjiang Province and the First Report of G7 Genotype of E. canadensis in Humans in China

    PubMed Central

    Zeng, Zhaolin; Zhao, Wei; Liu, Aiqin; Piao, Daxun; Jiang, Tao; Cao, Jianping; Shen, Yujuan; Liu, Hua; Zhang, Weizhe

    2014-01-01

    Cystic echinococcosis (CE) caused by the larval stage of Echinococcus granulosus sensu lato (s.l.) is one of the most important zoonotic parasitic diseases worldwide and 10 genotypes (G1–G10) have been reported. In China, almost all the epidemiological and genotyping studies of E. granulosus s.l. are from the west and northwest pasturing areas. However, in Heilongjiang Province of northeastern China, no molecular information is available on E. granulosus s.l. To understand and to speculate on possible transmission patterns of E. granulosus s.l., we molecularly identified and genotyped 10 hydatid cysts from hepatic CE patients in Heilongjiang Province based on mitochondrial cytochrome c oxidase subunit I (cox1), cytochrome b (cytb) and NADH dehydrogenase subunit 1 (nad1) genes. Two genotypes were identified, G1 genotype (n = 6) and G7 genotype (n = 4). All the six G1 genotype isolates were identical to each other at the cox1 locus; three and two different sequences were obtained at the cytb and nad1 loci, respectively, with two cytb gene sequences not being described previously. G7 genotype isolates were identical to each other at the cox1, cytb and nad1 loci; however, the cytb gene sequence was not described previously. This is the first report of G7 genotype in humans in China. Three new cytb gene sequences from G1 and G7 genotypes might reflect endemic genetic characterizations. Pigs might be the main intermediate hosts of G7 genotype in our investigated area by homology analysis. The results will aid in making more effective control strategies for the prevention of transmission of E. granulosus s.l. PMID:25329820

  12. Genetic characterization of human-derived hydatid cysts of Echinococcus granulosus sensu lato in Heilongjiang Province and the first report of G7 genotype of E. canadensis in humans in China.

    PubMed

    Zhang, Tiemin; Yang, Dong; Zeng, Zhaolin; Zhao, Wei; Liu, Aiqin; Piao, Daxun; Jiang, Tao; Cao, Jianping; Shen, Yujuan; Liu, Hua; Zhang, Weizhe

    2014-01-01

    Cystic echinococcosis (CE) caused by the larval stage of Echinococcus granulosus sensu lato (s.l.) is one of the most important zoonotic parasitic diseases worldwide and 10 genotypes (G1-G10) have been reported. In China, almost all the epidemiological and genotyping studies of E. granulosus s.l. are from the west and northwest pasturing areas. However, in Heilongjiang Province of northeastern China, no molecular information is available on E. granulosus s.l. To understand and to speculate on possible transmission patterns of E. granulosus s.l., we molecularly identified and genotyped 10 hydatid cysts from hepatic CE patients in Heilongjiang Province based on mitochondrial cytochrome c oxidase subunit I (cox1), cytochrome b (cytb) and NADH dehydrogenase subunit 1 (nad1) genes. Two genotypes were identified, G1 genotype (n = 6) and G7 genotype (n = 4). All the six G1 genotype isolates were identical to each other at the cox1 locus; three and two different sequences were obtained at the cytb and nad1 loci, respectively, with two cytb gene sequences not being described previously. G7 genotype isolates were identical to each other at the cox1, cytb and nad1 loci; however, the cytb gene sequence was not described previously. This is the first report of G7 genotype in humans in China. Three new cytb gene sequences from G1 and G7 genotypes might reflect endemic genetic characterizations. Pigs might be the main intermediate hosts of G7 genotype in our investigated area by homology analysis. The results will aid in making more effective control strategies for the prevention of transmission of E. granulosus s.l.

  13. Widespread presence of human-pathogenic Enterocytozoon bieneusi genotype D in farmed foxes (Vulpes vulpes) and raccoon dogs (Nyctereutes procyonoides) in China: first identification and zoonotic concern.

    PubMed

    Yang, Yuqi; Lin, Yongchao; Li, Qiao; Zhang, Siwen; Tao, Wei; Wan, Qiang; Jiang, Yanxue; Li, Wei

    2015-11-01

    Enterocytozoon bieneusi is a well-known causative agent of microsporidial infections in a variety of mammal hosts including humans in China, whereas there were no epidemiological data on wild animals bred in captivity, and the role of the neglected hosts in transmission of zoonotic microsporidiasis remains unknown. Herein, we investigated feces from 191 farmed foxes (Vulpes vulpes) and 162 farmed raccoon dogs (Nyctereutes procyonoides) for the prevalence and genotypic characteristics of E. bieneusi in Harbin City, northeast China. Polymerase chain reaction (PCR) targeting the internal transcribed spacer (ITS) of the rRNA gene enabled the identification of 53 (27.7%) and 17 (10.5%) positives from fox and raccoon dog specimens, respectively. There was only minor difference in prevalence between juvenile and adult foxes. Adult raccoon dogs have an infection rate significantly higher than juveniles. The most common human-pathogenic E. bieneusi, genotype D, is widespread among foxes and raccoon dogs of various ages by sequence analysis of the ITS locus. Genotypes CHN-DC1 and mixed CHN-DC1/WildBoar3 were detected in one adult raccoon dog each. Here is the first report describing the presence of zoonotic E. bieneusi genotypes in farmed foxes and raccoon dogs. The widespread existence of genotype D in surveyed animals is of great concern for public health. PMID:26341801

  14. Widespread presence of human-pathogenic Enterocytozoon bieneusi genotype D in farmed foxes (Vulpes vulpes) and raccoon dogs (Nyctereutes procyonoides) in China: first identification and zoonotic concern.

    PubMed

    Yang, Yuqi; Lin, Yongchao; Li, Qiao; Zhang, Siwen; Tao, Wei; Wan, Qiang; Jiang, Yanxue; Li, Wei

    2015-11-01

    Enterocytozoon bieneusi is a well-known causative agent of microsporidial infections in a variety of mammal hosts including humans in China, whereas there were no epidemiological data on wild animals bred in captivity, and the role of the neglected hosts in transmission of zoonotic microsporidiasis remains unknown. Herein, we investigated feces from 191 farmed foxes (Vulpes vulpes) and 162 farmed raccoon dogs (Nyctereutes procyonoides) for the prevalence and genotypic characteristics of E. bieneusi in Harbin City, northeast China. Polymerase chain reaction (PCR) targeting the internal transcribed spacer (ITS) of the rRNA gene enabled the identification of 53 (27.7%) and 17 (10.5%) positives from fox and raccoon dog specimens, respectively. There was only minor difference in prevalence between juvenile and adult foxes. Adult raccoon dogs have an infection rate significantly higher than juveniles. The most common human-pathogenic E. bieneusi, genotype D, is widespread among foxes and raccoon dogs of various ages by sequence analysis of the ITS locus. Genotypes CHN-DC1 and mixed CHN-DC1/WildBoar3 were detected in one adult raccoon dog each. Here is the first report describing the presence of zoonotic E. bieneusi genotypes in farmed foxes and raccoon dogs. The widespread existence of genotype D in surveyed animals is of great concern for public health.

  15. The prevalence and genotypic analysis of Toxoplasma gondii in human sera and brain tissue from individuals in Scotland between 2006 - 2012.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Up to date information about the prevalence of Toxoplasma gondii in humans is lacking for the UK population, with even less information available about the prevalence of the parasite in people in Scotland. To address this, two different study groups were used to determine the prevalence and genotyp...

  16. Complete genome sequencing of a multidrug-resistant and human-invasive Salmonella enterica serovar Typhimurium strain of the emerging sequence type 213 genotype

    DOE PAGESBeta

    Calva, Edmundo; Silva, Claudia; Zaidi, Mussaret B.; Sanchez-Flores, Alejandro; Estrada, Karel; Silva, Genivaldo G. Z.; Soto-Jiménez, Luz M.; Wiesner, Magdalena; Fernández-Mora, Marcos; Edwards, Robert A.; et al

    2015-06-18

    Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the state of Yucatán, Mexico, from a human systemic infection. The YU39 strain is representative of the multidrug-resistant emergent sequence type 213 (ST213) genotype. The YU39 complete genome is composed of a chromosome and seven plasmids.

  17. Discordances between Interpretation Algorithms for Genotypic Resistance to Protease and Reverse Transcriptase Inhibitors of Human Immunodeficiency Virus Are Subtype Dependent

    PubMed Central

    Snoeck, Joke; Kantor, Rami; Shafer, Robert W.; Van Laethem, Kristel; Deforche, Koen; Carvalho, Ana Patricia; Wynhoven, Brian; Soares, Marcelo A.; Cane, Patricia; Clarke, John; Pillay, Candice; Sirivichayakul, Sunee; Ariyoshi, Koya; Holguin, Africa; Rudich, Hagit; Rodrigues, Rosangela; Bouzas, Maria Belen; Brun-Vézinet, Françoise; Reid, Caroline; Cahn, Pedro; Brigido, Luis Fernando; Grossman, Zehava; Soriano, Vincent; Sugiura, Wataru; Phanuphak, Praphan; Morris, Lynn; Weber, Jonathan; Pillay, Deenan; Tanuri, Amilcar; Harrigan, Richard P.; Camacho, Ricardo; Schapiro, Jonathan M.; Katzenstein, David; Vandamme, Anne-Mieke

    2006-01-01

    The major limitation of drug resistance genotyping for human immunodeficiency virus remains the interpretation of the results. We evaluated the concordance in predicting therapy response between four different interpretation algorithms (Rega 6.3, HIVDB-08/04, ANRS [07/04], and VGI 8.0). Sequences were gathered through a worldwide effort to establish a database of non-B subtype sequences, and demographic and clinical information about the patients was gathered. The most concordant results were found for nonnucleoside reverse transcriptase (RT) inhibitors (93%), followed by protease inhibitors (84%) and nucleoside RT inhibitor (NRTIs) (76%). For therapy-naive patients, for nelfinavir, especially for subtypes C and G, the discordances were driven mainly by the protease (PRO) mutational pattern 82I/V + 63P + 36I/V for subtype C and 82I + 63P + 36I + 20I for subtype G. Subtype F displayed more discordances for ritonavir in untreated patients due to the combined presence of PRO 20R and 10I/V. In therapy-experienced patients, subtype G displayed a lot of discordances for saquinavir and indinavir due to mutational patterns involving PRO 90 M and 82I. Subtype F had more discordance for nelfinavir attributable to the presence of PRO 88S and 82A + 54V. For the NRTIs lamivudine and emtricitabine, CRF01_AE had more discordances than subtype B due to the presence of RT mutational patterns 65R + 115 M and 118I + 215Y, respectively. Overall, the different algorithms agreed well on the level of resistance scored, but some of the discordances could be attributed to specific (subtype-dependent) combinations of mutations. It is not yet known whether therapy response is subtype dependent, but the advice given to clinicians based on a genotypic interpretation algorithm differs according to the subtype. PMID:16436728

  18. Human Immunodeficiency Virus Replication and Genotypic Resistance in Blood and Lymph Nodes after a Year of Potent Antiretroviral Therapy

    PubMed Central

    Günthard, Huldrych F.; Wong, Joseph K.; Ignacio, Caroline C.; Guatelli, John C.; Riggs, Nanette L.; Havlir, Diane V.; Richman, Douglas D.

    1998-01-01

    Potent antiretroviral therapy can reduce human immunodeficiency virus (HIV) in plasma to levels below the limit of detection for up to 2 years, but the extent to which viral replication is suppressed is unknown. To search for ongoing viral replication in 10 patients on combination antiretroviral therapy for up to 1 year, the emergence of genotypic drug resistance across different compartments was studied and correlated with plasma viral RNA levels. In addition, lymph node (LN) mononuclear cells were assayed for the presence of multiply spliced RNA. Population sequencing of HIV-1 pol was done on plasma RNA, peripheral blood mononuclear cell (PBMC) RNA, PBMC DNA, LN RNA, LN DNA, and RNA from virus isolated from PBMCs or LNs. A special effort was made to obtain sequences from patients with undetectable plasma RNA, emphasizing the rapidly emerging lamivudine-associated M184V mutation. Furthermore, concordance of drug resistance mutations across compartments was investigated. No evidence for viral replication was found in patients with plasma HIV RNA levels of <20 copies/ml. In contrast, evolving genotypic drug resistance or the presence of multiply spliced RNA provided evidence for low-level replication in subjects with plasma HIV RNA levels between 20 and 400 copies/ml. All patients failing therapy showed multiple drug resistance mutations in different compartments, and multiply spliced RNA was present upon examination. Concordance of nucleotide sequences from different tissue compartments obtained concurrently from individual patients was high: 98% in the protease and 94% in the reverse transcriptase regions. These findings argue that HIV replication differs significantly between patients on potent antiretroviral therapy with low but detectable viral loads and those with undetectable viral loads. PMID:9499103

  19. Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba.

    PubMed

    Alemán, Yoan; Vinken, Lore; Kourí, Vivian; Pérez, Lissette; Álvarez, Alina; Abrahantes, Yeissel; Fonseca, Carlos; Pérez, Jorge; Correa, Consuelo; Soto, Yudira; Schrooten, Yoeri; Vandamme, Anne-Mieke; Van Laethem, Kristel

    2015-01-01

    As commercial human immunodeficiency virus type 1 drug resistance assays are expensive, they are not commonly used in resource-limited settings. Hence, a more affordable in-house procedure was set up taking into account the specific epidemiological and economic circumstances of Cuba. The performance characteristics of the in-house assay were evaluated using clinical samples with various subtypes and resistance patterns. The lower limit of amplification was determined on dilutions series of 20 clinical isolates and ranged from 84 to 529 RNA copies/mL. For the assessment of trueness, 14 clinical samples were analyzed and the ViroSeq HIV-1 Genotyping System v2.0 was used as the reference standard. The mean nucleotide sequence identity between the two assays was 98.7% ± 1.0. Additionally, 99.0% of the amino acids at drug resistance positions were identical. The sensitivity and specificity in detecting drug resistance mutations was respectively 94.1% and 99.5%. Only few discordances in drug resistance interpretation patterns were observed. The repeatability and reproducibility were evaluated using 10 clinical samples with 3 replicates per sample. The in-house test was very precise as nucleotide sequence identity among paired nucleotide sequences ranged from 98.7% to 99.9%. The acceptance criteria were met by the in-house test for all performance characteristics, demonstrating a high degree of accuracy. Subsequently, the applicability in routine clinical practice was evaluated on 380 plasma samples. The amplification success rate was 91% and good quality consensus sequences encoding the entire protease and the first 335 codons in reverse transcriptase could be obtained for 99% of the successful amplicons. The reagent cost per sample using the in-house procedure was around € 80 per genotyping attempt. Overall, the in-house assay provided good results, was feasible with equipment and reagents available in Cuba and was half as expensive as commercial assays.

  20. Comparison of real-time multiplex human papillomavirus (HPV) PCR assays with INNO-LiPA HPV genotyping extra assay.

    PubMed

    Else, Elizabeth A; Swoyer, Ryan; Zhang, Yuhua; Taddeo, Frank J; Bryan, Janine T; Lawson, John; Van Hyfte, Inez; Roberts, Christine C

    2011-05-01

    Real-time type-specific multiplex human papillomavirus (HPV) PCR assays were developed to detect HPV DNA in samples collected for the efficacy determination of the quadrivalent HPV (type 6, 11, 16, and 18) L1 virus-like particle (VLP) vaccine (Gardasil). Additional multiplex (L1, E6, and E7 open reading frame [ORF]) or duplex (E6 and E7 ORF) HPV PCR assays were developed to detect high-risk HPV types, including HPV type 31 (HPV31), HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV56, HPV58, and HPV59. Here, we evaluated clinical specimen concordance and compared the limits of detection (LODs) between multiplex HPV PCR assays and the INNO-LiPA HPV Genotyping Extra assay, which detects 28 types, for the 14 HPV types common to both of these methods. Overall HPV detection agreement rates were >90% for swabs and >95% for thin sections. Statistically significant differences in detection were observed for HPV6, HPV16, HPV18, HPV35, HPV39, HPV45, HPV56, HPV58, and HPV59 in swabs and for HPV45, HPV58, and HPV59 in thin sections. Where P was <0.05, discordance was due to detection of more HPV-positive samples by the multiplex HPV PCR assays. LODs were similar for eight HPV types, significantly lower in multiplex assays for five HPV types, and lower in INNO-LiPA for HPV6 only. LODs were under 50 copies for all HPV types, with the exception of HPV39, HPV58, and HPV59 in the INNO-LiPA assay. The overall percent agreement for detection of 14 HPV types between the type-specific multiplex HPV PCR and INNO-LiPA genotyping assays was good. The differences in positive sample detection favored multiplex HPV PCR, suggesting increased sensitivity of HPV DNA detection by type-specific multiplex HPV PCR assays.

  1. Expression Quantitative Trait Loci Analysis Identifies Associations Between Genotype and Gene Expression in Human Intestine

    PubMed Central

    KABAKCHIEV, BOYKO; SILVERBERG, MARK S.

    2013-01-01

    . CONCLUSIONS eQTL analysis of intestinal tissue supports findings that some eQTL remain stable across cell types, whereas others are specific to the sampled location. Our findings confirm and expand the number of known genotypes associated with expression and could help elucidate mechanisms of intestinal disease. PMID:23474282

  2. Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping.

    PubMed

    Light, Nicholas; Adoue, Véronique; Ge, Bing; Chen, Shu-Huang; Kwan, Tony; Pastinen, Tomi

    2014-09-01

    Allele-specific (AS) assessment of chromatin has the potential to elucidate specific cis-regulatory mechanisms, which are predicted to underlie the majority of the known genetic associations to complex disease. However, development of chromatin landscapes at allelic resolution has been challenging since sites of variable signal strength require substantial read depths not commonly applied in sequencing based approaches. In this study, we addressed this by performing parallel analyses of input DNA and chromatin immunoprecipitates (ChIP) on high-density Illumina genotyping arrays. Allele-specificity for the histone modifications H3K4me1, H3K4me3, H3K27ac, H3K27me3, and H3K36me3 was assessed using ChIP samples generated from 14 lymphoblast and 6 fibroblast cell lines. AS-ChIP SNPs were combined into domains and validated using high-confidence ChIP-seq sites. We observed characteristic patterns of allelic-imbalance for each histone-modification around allele-specifically expressed transcripts. Notably, we found H3K4me1 to be significantly anti-correlated with allelic expression (AE) at transcription start sites, indicating H3K4me1 allelic imbalance as a marker of AE. We also found that allelic chromatin domains exhibit population and cell-type specificity as well as heritability within trios. Finally, we observed that a subset of allelic chromatin domains is regulated by DNase I-sensitive quantitative trait loci and that these domains are significantly enriched for genome-wide association studies hits, with autoimmune disease associated SNPs specifically enriched in lymphoblasts. This study provides the first genome-wide maps of allelic-imbalance for five histone marks. Our results provide new insights into the role of chromatin in cis-regulation and highlight the need for high-depth sequencing in ChIP-seq studies along with the need to improve allele-specificity of ChIP-enrichment.

  3. Phenotypic and genotypic characterization of Salmonella enterica serovar Dublin isolates from cattle and humans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Introduction: Antimicrobial resistance (AR), particularly multi-drug resistance (MDR), is of global concern. Salmonella causes approximately 93.8 million human infections worldwide/year including 1.2 million cases in the US. An increase in both AR and MDR among some serotypes has been observed. Sa...

  4. Prevalence and genotypic characteristics of Clostridium difficle in a closed and integrated human and swine population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recently, increases in cases of community-acquired Clostridium difficile have led researchers to explore additional sources of infection. The objective of this study was to compare C. difficile isolated from a closed population of both humans and swine to investigate possible food safety and occupa...

  5. MtDNA Haplogroup A10 Lineages in Bronze Age Samples Suggest That Ancient Autochthonous Human Groups Contributed to the Specificity of the Indigenous West Siberian Population

    PubMed Central

    Pilipenko, Aleksandr S.; Trapezov, Rostislav O.; Zhuravlev, Anton A.; Molodin, Vyacheslav I.; Romaschenko, Aida G.

    2015-01-01

    Background The craniometric specificity of the indigenous West Siberian human populations cannot be completely explained by the genetic interactions of the western and eastern Eurasian groups recorded in the archaeology of the area from the beginning of the 2nd millennium BC. Anthropologists have proposed another probable explanation: contribution to the genetic structure of West Siberian indigenous populations by ancient human groups, which separated from western and eastern Eurasian populations before the final formation of their phenotypic and genetic features and evolved independently in the region over a long period of time. This hypothesis remains untested. From the genetic point of view, it could be confirmed by the presence in the gene pool of indigenous populations of autochthonous components that evolved in the region over long time periods. The detection of such components, particularly in the mtDNA gene pool, is crucial for further clarification of early regional genetic history. Results and Conclusion We present the results of analysis of mtDNA samples (n = 10) belonging to the A10 haplogroup, from Bronze Age populations of West Siberian forest-steppe (V—I millennium BC), that were identified in a screening study of a large diachronic sample (n = 96). A10 lineages, which are very rare in modern Eurasian populations, were found in all the Bronze Age groups under study. Data on the A10 lineages’ phylogeny and phylogeography in ancient West Siberian and modern Eurasian populations suggest that A10 haplogroup underwent a long-term evolution in West Siberia or arose there autochthonously; thus, the presence of A10 lineages indicates the possible contribution of early autochthonous human groups to the genetic specificity of modern populations, in addition to contributions of later interactions of western and eastern Eurasian populations. PMID:25950581

  6. High Ancient Genetic Diversity of Human Lice, Pediculus humanus, from Israel Reveals New Insights into the Origin of Clade B Lice

    PubMed Central

    Amanzougaghene, Nadia; Mumcuoglu, Kosta Y.; Fenollar, Florence; Alfi, Shir; Yesilyurt, Gonca; Raoult, Didier; Mediannikov, Oleg

    2016-01-01

    The human head louse, Pediculus humanus capitis, is subdivided into several significantly divergent mitochondrial haplogroups, each with particular geographical distributions. Historically, they are among the oldest human parasites, representing an excellent marker for tracking older events in human evolutionary history. In this study, ancient DNA analysis using real-time polymerase chain reaction (qPCR), combined with conventional PCR, was applied to the remains of twenty-four ancient head lice and their eggs from the Roman period which were recovered from Israel. The lice and eggs were found in three combs, one of which was recovered from archaeological excavations in the Hatzeva area of the Judean desert, and two of which found in Moa, in the Arava region, close to the Dead Sea. Results show that the head lice remains dating approximately to 2,000 years old have a cytb haplogroup A, which is worldwide in distribution, and haplogroup B, which has thus far only been found in contemporary lice from America, Europe, Australia and, most recently, Africa. More specifically, this haplogroup B has a B36 haplotype, the most common among B haplogroups, and has been present in America for at least 4,000 years. The present findings confirm that clade B lice existed, at least in the Middle East, prior to contacts between Native Americans and Europeans. These results support a Middle Eastern origin for clade B followed by its introduction into the New World with the early peoples. Lastly, the presence of Acinetobacter baumannii DNA was demonstrated by qPCR and sequencing in four head lice remains belonging to clade A. PMID:27741281

  7. How ancient are ancient asexuals?

    PubMed

    Martens, Koen; Rossetti, Giampaolo; Horne, David J

    2003-04-01

    Ancient asexual animal groups, such as bdelloid rotifers and darwinuloid ostracods, are excellent model organisms to study the effects of long-term asexuality. However, the absolute length of time that these groups have been fully asexual is mostly ignored. In the case of the darwinuloid ostracods, the fossil record shows that sexual reproduction disappeared almost completely after the end of Permian mass extinction (ca. 245 Myr ago), although several putative records of males from the Mesozoic obscure the exact time-frame of obligate asexuality in darwinuloids. Here, we re-examine the Mesozoic darwinuloid records, with regard to the reproductive mode of the assemblages. Three criteria to distinguish males in fossil populations (lack of brood pouch, position of muscle scars and size dimorphism) are used here to test for the presence of males in darwinuloid assemblages. A large, well-preserved assemblage of Darwinula leguminella (Forbes 1885) from the latest Jurassic (ca. 145 Myr ago) of England is found to be markedly variable in size and shape, but nevertheless turns out to be an all female assemblage. The exceptional preservation of the material also allows the re-assignment of this species to the extant darwinuloid genus Alicenula. All other putative dimorphic darwinuloid records from the Mesozoic are re-examined using the same criteria. The hypothesis that these assemblages represent bisexual populations is rejected for all post-Triassic (ca. 208 Myr ago) records. PMID:12713746

  8. Geographic Divergence of Bovine and Human Shiga Toxin–Producing Escherichia coli O157:H7 Genotypes, New Zealand1

    PubMed Central

    Cookson, Adrian L.; Campbell, Donald M.; Duncan, Gail E.; Prattley, Deborah; Carter, Philip; Besser, Thomas E.; Shringi, Smriti; Hathaway, Steve; Marshall, Jonathan C.; French, Nigel P.

    2014-01-01

    Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a zoonotic pathogen of public health concern worldwide. To compare the local and large-scale geographic distributions of genotypes of STEC O157:H7 isolates obtained from various bovine and human sources during 2008–2011, we used pulsed-field gel electrophoresis and Shiga toxin–encoding bacteriophage insertion (SBI) typing. Using multivariate methods, we compared isolates from the North and South Islands of New Zealand with isolates from Australia and the United States. The STEC O157:H7 population structure differed substantially between the 2 islands and showed evidence of finer scale spatial structuring, which is consistent with highly localized transmission rather than disseminated foodborne outbreaks. The distribution of SBI types differed markedly among isolates from New Zealand, Australia, and the United States. Our findings also provide evidence for the historic introduction into New Zealand of a subset of globally circulating STEC O157:H7 strains that have continued to evolve and be transmitted locally between cattle and humans. PMID:25568924

  9. Human G3P[9] rotavirus strains possessing an identical genotype constellation to AU-1 isolated at high prevalence in Brazil, 1997-1999.

    PubMed

    Tsugawa, Takeshi; Rainwater-Lovett, Kaitlin; Tsutsumi, Hiroyuki

    2015-03-01

    Rotavirus (RV) A is a very common cause of acute diarrhoea in infants and young children worldwide. Most human strains are classified into two major Wa-like and DS-1-like genotype constellations, whilst a minor third strain, AU-1, was described in 1989 among human RV isolates from Japan. AU-1 demonstrates a high degree of homology to a feline RV, FRV-1, which suggests interspecies transmission of feline RV. However, there has been no subsequent report of RVs possessing the AU-1 genotype throughout all 11 genes of the genome. Between March 1997 and December 1999, 157 RV-positive stool samples were collected from Brazilian children, and 16 of the RVs (10.2 %) were P[9] genotype. We analysed eight strains by almost full-genome sequencing. These eight strains were divided into two groups: five AU-1-like and three Wa-like strains. Four of the five AU-1-like strains had the AU-1-like genotype constellation throughout the 11 genes. The remaining AU-1-like strain was considered to be a reassortant strain comprosed of nine, two and one genes from the AU-1-like, Wa-like and G9 strains, respectively. The three Wa-like strains were considered to be reassortants comprising seven to eight genes and three to four genes from Wa-like and non-Wa-like strains, respectively. This report of human G3P[9] RV strains possessing the AU-1 genotype constellation throughout all genes demonstrates the stability and infectivity of the AU-1-like strain with its original genotype over distance and time.

  10. Human G3P[9] rotavirus strains possessing an identical genotype constellation to AU-1 isolated at high prevalence in Brazil, 1997–1999

    PubMed Central

    Rainwater-Lovett, Kaitlin; Tsutsumi, Hiroyuki

    2015-01-01

    Rotavirus (RV) A is a very common cause of acute diarrhoea in infants and young children worldwide. Most human strains are classified into two major Wa-like and DS-1-like genotype constellations, whilst a minor third strain, AU-1, was described in 1989 among human RV isolates from Japan. AU-1 demonstrates a high degree of homology to a feline RV, FRV-1, which suggests interspecies transmission of feline RV. However, there has been no subsequent report of RVs possessing the AU-1 genotype throughout all 11 genes of the genome. Between March 1997 and December 1999, 157 RV-positive stool samples were collected from Brazilian children, and 16 of the RVs (10.2 %) were P[9] genotype. We analysed eight strains by almost full-genome sequencing. These eight strains were divided into two groups: five AU-1-like and three Wa-like strains. Four of the five AU-1-like strains had the AU-1-like genotype constellation throughout the 11 genes. The remaining AU-1-like strain was considered to be a reassortant strain comprosed of nine, two and one genes from the AU-1-like, Wa-like and G9 strains, respectively. The three Wa-like strains were considered to be reassortants comprising seven to eight genes and three to four genes from Wa-like and non-Wa-like strains, respectively. This report of human G3P[9] RV strains possessing the AU-1 genotype constellation throughout all genes demonstrates the stability and infectivity of the AU-1-like strain with its original genotype over distance and time. PMID:25467218

  11. Prevalence of High-Risk Human Papillomavirus (HR-HPV) Genotypes and Multiple Infections in Cervical Abnormalities from Northern Xinjiang, China

    PubMed Central

    Du, Jingyun; Jiang, Jianjun; Jia, Xuesong; Chen, Chuangfu; Wang, Yuanzhi

    2016-01-01

    Multiple human papillomavirus (HPV) genotypes often coexist within the cervical epithelia and are frequently detected together in various grades of the cervical neoplasia. To date, only a few reports exist on multiple HPV infections of HPV in Xinjiang Uygur Autonomous Region (XUAR). In the present study, we investigated the prevalence of High-Risk HPV (HR-HPV) genotypes and multiple infections. Cervical cytology samples were collected from 428 women who presented cervical abnormalities. Genotyping of HPV was performed by polymerase chain reaction–sequencing based typing (PCR-SBT) using consensus primers and specific primers. Of them, 166 samples were positive for HPV according to PCR results using the consensus primers. These samples contained cervical abnormalities enriched with inflammation (n = 107), cervical intraepithelial neoplasia (CIN) I (n = 19), CINII-III (n = 9) and cervical cancer (n = 31). Of the 166 HPV positive samples as determined by PCR analysis, 151 were further typed by PCR-SBT using 19 pairs of genotype-specific primers. Using this method, 17 different HR-HPV genotypes were identified. The most frequently observed HPV genotypes were HPV16 (44.0%, 73/166), 53 (28.9%, 48/166), 52 (25.3%, 42/166), 58 (22.3%, 37/166) and 35 (17.5%, 29/166). The proportions of single and multiple infections in the HPV-positive specimens were 34.9% and 65.1%, respectively. Multiple HPV types were most prevalent in the inflammatory state (63.0%), followed by cervical cancer (24.1%), CINI (11.1%), and CINII-III (1.9%). The results of our data analyses suggested that i) multiple HPV infection is not necessarily correlated with the severity of cervical abnormalities; and ii) among the multiple HPV infections, double infections combined with HPV16 is the most common. In addition, L1 full-length sequences of the top five high-risk HPV genotypes were amplified and sequenced. According to the L1 sequence of the epidemic genotypes that were amplified, we found that these

  12. Suicide in ancient Greece.

    PubMed

    Laios, K; Tsoukalas, G; Kontaxaki, M-I; Karamanou, M; Androutsos, G

    2014-01-01

    The theme of suicide appears several times in ancient Greek literature. However, each such reference acquires special significance depending on the field from which it originates. Most of the information found in mythology, but the suicide in a mythological tale, although in terms of motivation and mental situation of heroes may be in imitation of similar incidents of real life, in fact is linked with the principles of the ancient Greek religion. In ancient drama and mainly in tragedies suicide conduces to the tragic hypostasis of the heroes and to the evolution of the plot and also is a tool in order to be presented the ideas of poets for the relations of the gods, the relation among gods and men and the relation among the men. In ancient Greek philosophy there were the deniers of suicide, who were more concerned about the impact of suicide on society and also these who accepted it, recognizing the right of the individual to put an end to his life, in order to avoid personal misfortunes. Real suicides will be found mostly from historical sources, but most of them concern leading figures of the ancient world. Closer to the problem of suicide in the everyday life of antiquity are ancient Greek medicines, who studied the phenomenon more general without references to specific incidents. Doctors did not approve in principal the suicide and dealt with it as insane behavior in the development of the mental diseases, of melancholia and mania. They considered that the discrepancy of humors in the organ of logic in the human body will cause malfunction, which will lead to the absurdity and consequently to suicide, either due to excessive concentration of black bile in melancholia or due to yellow bile in mania. They believed that greater risk to commit suicide had women, young people and the elderly. As therapy they used the drugs of their time with the intention to induce calm and repression in the ill person, therefore they mainly used mandragora. In general, we would say

  13. Suicide in ancient Greece.

    PubMed

    Laios, K; Tsoukalas, G; Kontaxaki, M-I; Karamanou, M; Androutsos, G

    2014-01-01

    The theme of suicide appears several times in ancient Greek literature. However, each such reference acquires special significance depending on the field from which it originates. Most of the information found in mythology, but the suicide in a mythological tale, although in terms of motivation and mental situation of heroes may be in imitation of similar incidents of real life, in fact is linked with the principles of the ancient Greek religion. In ancient drama and mainly in tragedies suicide conduces to the tragic hypostasis of the heroes and to the evolution of the plot and also is a tool in order to be presented the ideas of poets for the relations of the gods, the relation among gods and men and the relation among the men. In ancient Greek philosophy there were the deniers of suicide, who were more concerned about the impact of suicide on society and also these who accepted it, recognizing the right of the individual to put an end to his life, in order to avoid personal misfortunes. Real suicides will be found mostly from historical sources, but most of them concern leading figures of the ancient world. Closer to the problem of suicide in the everyday life of antiquity are ancient Greek medicines, who studied the phenomenon more general without references to specific incidents. Doctors did not approve in principal the suicide and dealt with it as insane behavior in the development of the mental diseases, of melancholia and mania. They considered that the discrepancy of humors in the organ of logic in the human body will cause malfunction, which will lead to the absurdity and consequently to suicide, either due to excessive concentration of black bile in melancholia or due to yellow bile in mania. They believed that greater risk to commit suicide had women, young people and the elderly. As therapy they used the drugs of their time with the intention to induce calm and repression in the ill person, therefore they mainly used mandragora. In general, we would say

  14. Epigenetics of Ancient DNA

    PubMed Central

    Zhenilo, S. V.; Sokolov, A.S.; Prokhortchouk, E. B.

    2016-01-01

    Initially, the study of DNA isolated from ancient specimens had been based on the analysis of the primary nucleotide sequence. This approach has allowed researchers to study the evolutionary changes that occur in different populations and determine the influence of the environment on genetic selection. However, the improvement of methodological approaches to genome-wide analysis has opened up new possibilities in the search for the epigenetic mechanisms involved in the regulation of gene expression. It was discovered recently that the methylation status of the regulatory elements of the HOXD cluster and MEIS1 gene changed during human evolution. Epigenetic changes in these genes played a key role in the evolution of the limbs of modern humans. Recent works have demonstrated that it is possible to determine the transcriptional activity of genes in ancient DNA samples by combining information on DNA methylation and the DNAaseI hypersensitive sequences located at the transcription start sites of genes. In the nearest future, if a preserved fossils brain is found, it will be possible to identify the evolutionary changes in the higher nervous system associated with epigenetic differences. PMID:27795845

  15. Genotype analyses of human commensal scalp fungi, Malassezia globosa, and Malassezia restricta on the scalps of patients with dandruff and healthy subjects.

    PubMed

    Hiruma, Midori; Cho, Otomi; Hiruma, Masataro; Kurakado, Sanae; Sugita, Takashi; Ikeda, Shigaku

    2014-06-01

    Dandruff and seborrheic dermatitis are common afflictions of the human scalp caused by commensal scalp fungi belonging to the genus Malassezia. Malassezia globosa and Malassezia restricta are the predominant species found on the scalp. The intergenic spacer regions of these species' rRNA genes contain short sequence repeats (SSR): (GT)n and (CT)n in M. globosa and (CT)n and (AT)n in M. restricta. In the present study, we compared the genotypes (SSR) of M. globosa and M. restricta colonizing the scalps of patients with dandruff and healthy individuals. For M. globosa, the genotype (GT)10:(CT)8 (40.3 %, 25/62) was predominant followed by (GT)9:(CT)8 (14.5 %, 9/62) and (GT)11:(CT)8 (14.5 %, 9/62) in patients with dandruff, whereas the genotypes in healthy subjects were diverse. For M. restricta, the genotype (CT)6:(AT)6 (59.7 %, 37/62) was predominant followed by (CT)6:(AT)8 (24.2 %, 15/62) in patients with dandruff, while four genotypes, (CT)6:(AT)6 (10.5 %, 6/57), (CT)6:(AT)7 (22.8 %, 13/57), (CT)6:(AT)8 (17.5 %, 10/57), and (CT)6:(AT)10 (21.1 %, 12/57), accounted for 71.9 % of all combinations in healthy subjects. The results of this study suggest that the M. globosa genotype (GT)10:(CT)8 and the M. restricta genotype (CT)6:(AT)6 may be involved in the development of dandruff. PMID:24792417

  16. Detection and Genotyping of Human Papillomavirus DNA in Formalin-Fixed Paraffin-Embedded Specimens with the HPV Direct Flow CHIP System

    PubMed Central

    Herraez-Hernandez, Elsa; Preda, Ovidiu; Alonso, Sonia; Pardo, Rosario Serrano; Olmo, Asuncion

    2013-01-01

    The novel HPV Direct Flow CHIP commercial system for Human Papillomavirus (HPV) genotyping is based on rapid PCR and automatic reverse dot blot hybridization to genotype-specific probes, allowing the detection of 36 HPV genotypes. This study examined the performance of HPV Direct Flow CHIP in formalin-fixed paraffin-embedded (FFPE) samples (n= 99). Each sample was analyzed both by Direct PCR, using crude cell extracts without DNA purification, and by conventional PCR, using purified DNA. Pair-wise analysis of the results demonstrated strong concordance between the results obtained with the two protocols, although a slightly higher rate of multiple infections was detected by conventional PCR. In summary, HPV Direct Flow CHIP achieves effective HPV detection from FFPE samples with both Direct PCR and Conventional PCR protocols. PMID:24222806

  17. Pregnancy - associated human listeriosis: Virulence and genotypic analysis of Listeria monocytogenes from clinical samples.

    PubMed

    Soni, Dharmendra Kumar; Singh, Durg Vijai; Dubey, Suresh Kumar

    2015-09-01

    Listeria monocytogenes, a life-threatening pathogen, poses severe risk during pregnancy, may cause abortion, fetal death or neonatal morbidity in terms of septicemia and meningitis. The present study aimed at characterizing L. monocytogenes isolated from pregnant women based on serotyping, antibiotic susceptibility, virulence genes, in vivo pathogenicity test and ERIC- and REP-PCR fingerprint analyses. The results revealed that out of 3700 human clinical samples, a total of 30 (0.81%) isolates [12 (0.80%) from placental bit (1500), 18 (0.81%) from vaginal swab (2200)] were positive for L. monocytogenes. All the isolates belonged to serogroup 4b, and were + ve for virulence genes tested i.e. inlA, inlC, inlJ, plcA, prfA, actA, hlyA, and iap. Based on the mice inoculation tests, 20 isolates showed 100% and 4 isolates 60% relative virulence while 6 isolates were non-pathogenic. Moreover, 2 and 10 isolates were resistant to ciprofloxacin and cefoxitin, respectively, while the rest susceptible to other antibiotics used in this study. ERIC- and REP-PCR collectively depicted that the isolates from placental bit and vaginal swab had distinct PCR fingerprints except a few isolates with identical patterns. This study demonstrates prevalence of pathogenic strains mostly resistant to cefoxitin and/or ciprofloxacin. The results indicate the importance of isolating and characterizing the pathogen from human clinical samples as the pre-requisite for accurate epidemiological investigations. PMID:26231373

  18. Human Papillomavirus Genotyping After Denaturation of Specimens for Hybrid Capture 2 Testing: Feasibility Study for the HPV Persistence and Progression Cohort†

    PubMed Central

    LaMere, Brandon J.; Kornegay, Janet; Fetterman, Barbara; Sadorra, Mark; Shieh, Jen; Castle, Philip E.

    2009-01-01

    Human papillomavirus (HPV) genotyping could be clinically useful, depending on the results of large, prospective studies like the HPV Persistence and Progression cohort. The cohort is based on genotyping and follow-up of Hybrid Capture-positive women at Kaiser Permanente, Northern California. HPV DNA testing by Hybrid Capture 2 requires denaturation with alkali, possibly damaging the DNA for optimal PCR-based genotyping. A feasibility study was conducted on paired aliquots of anonymized specimens from 100 women with low-grade intraepithelial lesion cytology. Test aliquots were left in denaturant for 10 or 18 hours at 4°C and then neutralized; comparison aliquots were not denatured but diluted to match the timing, temperature, concentration and salt conditions of the treated specimens. The masked aliquots were tested using a commercialized PCR-based assay that detects of 37 HPV genotypes. There was no overall effect of treatment on test positivity or number of types. HPV16 was marginally more likely to be detected in untreated versus treated aliquots (P = 0.09) but HPV45 was marginally more likely to be detected in treated than untreated aliquots (P = 0.07), suggesting that these differences represented chance (intra-test variability). It can be concluded that residual Hybrid Capture-positive specimens can be accurately genotyped by PCR after Hybrid Capture 2 processing. PMID:17673302

  19. Detection of Common, Emerging and Uncommon VP4, and VP7 Human Group A Rotavirus Genotypes from Urban Sewage Samples in Uruguay.

    PubMed

    Tort, Luis Fernando Lopez; Victoria, Matías; Lizasoain, Andrés; García, Mariana; Berois, Mabel; Cristina, Juan; Leite, José Paulo Gagliardi; Gómez, Mariela Martínez; Miagostovich, Marize Pereira; Colina, Rodney

    2015-12-01

    Environmental approach has proven to be a useful tool for epidemiological studies demonstrating through environmental studies the diversity of viruses circulating in a given population. The aim of this study was to perform a phylogenetic characterization of the group A rotavirus (RVA) glycoprotein (G)- and protease-sensitive (P)-genotypes obtained from sewage samples (n = 116) collected in six cities of Uruguay during March 2011 to April 2013. A worldwide standardized semi-nested multiplex RT-PCR (SNM RT-PCR) protocol directed against VP4 and VP7 genes were conducted for RVA detection and consensual DNA fragments were submitted to nucleotide sequencing. P and/or G genotype was successfully determined by phylogenetic analysis in 61% (n = 37) of the positive samples obtained by SNM RT-PCR (n = 61). The RVA genotypes were as follow: G1 (n = 2), G2 (n = 14), G3 (n = 5), G12 (n = 2), P[4] (n = 4), P[8] (n = 16), and P[3] (n = 2). Interestingly, through phylogenetic analysis, emerging, and uncommon human genotypes could be detected. Results obtained from the comparison of RVA genotypes detected in the current study and Uruguayan RVA strains previously described for contemporary clinical pediatric cases showed that monitoring sewage may be a good screening option for a rapid and economical overview of the circulating genotypes in the surrounding human population and a useful approximation to study RVA epidemiology in a future vaccine monitoring program. The present study represents the first report in Uruguay that describes the phylogenetic diversity of RVA from urban sewage samples.

  20. Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases

    PubMed Central

    Allen, Mariet; Carrasquillo, Minerva M.; Funk, Cory; Heavner, Benjamin D.; Zou, Fanggeng; Younkin, Curtis S.; Burgess, Jeremy D.; Chai, High-Seng; Crook, Julia; Eddy, James A.; Li, Hongdong; Logsdon, Ben; Peters, Mette A.; Dang, Kristen K.; Wang, Xue; Serie, Daniel; Wang, Chen; Nguyen, Thuy; Lincoln, Sarah; Malphrus, Kimberly; Bisceglio, Gina; Li, Ma; Golde, Todd E.; Mangravite, Lara M.; Asmann, Yan; Price, Nathan D.; Petersen, Ronald C.; Graff-Radford, Neill R.; Dickson, Dennis W.; Younkin, Steven G.; Ertekin-Taner, Nilüfer

    2016-01-01

    Previous genome-wide association studies (GWAS), conducted by our group and others, have identified loci that harbor risk variants for neurodegenerative diseases, including Alzheimer's disease (AD). Human disease variants are enriched for polymorphisms that affect gene expression, including some that are known to associate with expression changes in the brain. Postulating that many variants confer risk to neurodegenerative disease via transcriptional regulatory mechanisms, we have analyzed gene expression levels in the brain tissue of subjects with AD and related diseases. Herein, we describe our collective datasets comprised of GWAS data from 2,099 subjects; microarray gene expression data from 773 brain samples, 186 of which also have RNAseq; and an independent cohort of 556 brain samples with RNAseq. We expect that these datasets, which are available to all qualified researchers, will enable investigators to explore and identify transcriptional mechanisms contributing to neurodegenerative diseases. PMID:27727239

  1. Genotypic diversity and virulent factors of Staphylococcus epidermidis isolated from human breast milk.

    PubMed

    Begović, Jelena; Jovčić, Branko; Papić-Obradović, Milena; Veljović, Katarina; Lukić, Jovanka; Kojić, Milan; Topisirović, Ljubiša

    2013-02-22

    Staphylococcus epidermidis strains were isolated from the expressed human breast milk (EHM) of 14 healthy donor mothers. Genetic diversity was evaluated using RAPD-PCR REP-PCR and pulse-field gel electrophoresis (PFGE). PFGE allowed the best discrimination of the isolates, since it provided for the greatest diversity of the analyzed genomes. Among the S. epidermidis strains, resistance to gentamicin, tetracycline, erythromycin, clindamycin or vancomycin was detected, whilst four isolates were multiresistant. The results from our study demonstrate that staphylococci from EHM could be reservoirs of resistance genes, since we showed that tetK could be transferred from EHM staphylococci to Gram-negative Escherichia coli. Most of the staphylococcal strains displayed excellent proteolytic and lipolytic activities. Additionally, the presence of ica genes, which was related to their ability to form a biofilm on tissue culture plates, and the presence of virulence factors including autolysin/adhesin AtLE, point to their pathogenic potential.

  2. New cryptosporidium genotypes in HIV-infected persons.

    PubMed Central

    Pieniazek, N. J.; Bornay-Llinares, F. J.; Slemenda, S. B.; da Silva, A. J.; Moura, I. N.; Arrowood, M. J.; Ditrich, O.; Addiss, D. G.

    1999-01-01

    Using DNA sequencing and phylogenetic analysis, we identified four distinct Cryptosporidium genotypes in HIV-infected patients: genotype 1 (human), genotype 2 (bovine) Cryptosporidium parvum, a genotype identical to C. felis, and one identical to a Cryptosporidium sp. isolate from a dog. This is the first identification of human infection with the latter two genotypes. PMID:10341184

  3. Complete genotype constellation of human rotavirus group A circulating in Thailand, 2008-2011.

    PubMed

    Theamboonlers, A; Maiklang, O; Thongmee, T; Chieochansin, T; Vuthitanachot, V; Poovorawan, Y

    2014-01-01

    This study has identified diverse and re-assorted group A rotavirus (RVA) strains by sequence and phylogenetic analysis of the 11 genomic segments. The 22 cases investigated in this study were collected from children with diarrhea between 2008 and 2011. The RVA genomic constellations identified in this study were identified as G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 22.7% (5/22); G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 27.3% (6/22); G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 18.2% (4/22); G3-P[9]-I3-R3-C3-M3-A3-N3-T3-E3-H6 4.6% (1/22); G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 9.1% (2/22); G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 4.6% (1/22) and G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 13.6% (3/22). Two RVA strains, possessing a complete AU-1-like genomic backbone, showed re-assortment for genes 3 and 11, revealing possible zoonotic re-assortment events between human and canine strains. In addition, one of the analyzed strains revealed a G12 specificity for VP7 in combination with a porcine-like P[6] VP4 and a complete Wa-like constellation. Continuous surveillance of rotavirus strains and their evolution may be useful for understanding the emergence of novel strains through interspecies genome re-assortment between human and animal viruses.

  4. Detection of Anaplasma phagocytophilum genotypes that are potentially virulent for human in wild ruminants and Ixodes ricinus in Central Italy.

    PubMed

    Di Domenico, M; Pascucci, I; Curini, V; Cocco, A; Dall'Acqua, F; Pompilii, C; Cammà, C

    2016-07-01

    Human granulocytic anaplasmosis (HGA) is an emerging tick-borne zoonosis worldwide. As is the case for many tick-borne diseases, the epidemiological cycle is associated to the environmental conditions, including the presence of wild vertebrate reservoir hosts, vectors, climate and vegetation. In this study a total number of 87 spleen samples of wild ruminants carcasses from Central Italy, and 77 Ixodes ricinus collected from the same dead animals were screened for Anaplasma phagocytophilum by using Real Time PCR. A. phagocytophilum DNA was detected in 75%, 66.7% and 54.2% of the spleen samples from red deer (Cervus elaphus), Apennine chamois (Rupicapra pyrenaica ornata) and roe deer (Capreolus capreolus) respectively, whereas it was detected in the 31.2% of I. ricinus. A total of 27 positive samples were characterized by sequencing a portion of the groEL gene. Two A. phagocytophilum lineages could clearly be delineated from the phylogenetic tree. Four sequences from red deer, 2 from I. ricinus and 1 from Apennine chamois clustered into lineage I together with those previously described as virulent genotypes related to HGA. The presence of A. phagocytophilum DNA in the Apennine chamois represents the first report for this Italian endemic subspecies. PMID:27020736

  5. High-risk human papilloma virus genotypes in cervical carcinoma of Serbian women: Distribution and association with pathohistological findings.

    PubMed

    Stamenković, Miodrag; Knežević, Aleksandra; Knežević, Ivana; Kuzmanović, Igor; Karalić, Danijela; Milenković, Sanja; Jovanović, Tanja

    2016-09-01

    A significant role of high-risk Human papilloma viruses (HR HPV) in the development of cervical carcinoma is well known. HR HPV 16 and 18 account for approximately 70% of all cases of cervical cancer worldwide. The incidence of cervical cancer in Serbia, is one of the highest in Europe. The aim of our study was to investigate the distribution of HR HPV types in cervical carcinoma of Serbian women, as well as association between the HPV types and pathohistological findings. The study included 80 archival cervical cancer tissues from the same number of patients. The presence of HPV DNA was determined using MY09/MY11 primers for L1 gene and GP1/GP2 primers for E1 gene. HPV was detected in 78.75% tissues. HR HPV genotypes found in the decreasing order of frequency were: HPV16 (80.39%), HPV33 (7.84%), HPV58 (5.88%), HPV18 (1.96%), HPV45 (1.96%) and HPV53 (1.96%). The examined tissues were 91.25% squamous cell carcinomas and 8.75% adenocarcinoma. The high frequency of HPV 16 was observed in both types of carcinoma (80.8% and 75%, respectively) while the prevalence of HPV18 was low. These results may contribute to the implementation of cervical carcinoma prevention program in Serbia, including the selection of the most appropriate vaccine and immunization program. PMID:27461126

  6. Innate immune responses in human hepatocyte-derived cell lines alter genotype 1 hepatitis E virus replication efficiencies

    PubMed Central

    Devhare, Pradip B.; Desai, Swapnil; Lole, Kavita S.

    2016-01-01

    Hepatitis E virus (HEV) is a significant health problem in developing countries causing sporadic and epidemic forms of acute viral hepatitis. Hepatitis E is a self-limiting disease; however, chronic HEV infections are being reported in immunocompromised individuals. The disease severity is more during pregnancy with high mortality (20–25%), especially in third trimester. Early cellular responses after HEV infection are not completely understood. We analyzed innate immune responses associated with genotype-I HEV replication in human hepatoma cell lines (Huh7, Huh7.5 and HepG2/C3A) using HEV replicon system. These cells supported HEV replication with different efficiencies due to the cell type specific innate immune responses. HepG2/C3A cells were less supportive to HEV replication as compared to Huh7.5 and S10-3 cells. Reconstitution of the defective RIG-I and TLR3 signaling in Huh7.5 cells enabled them to induce higher level antiviral responses and restrict HEV replication, suggesting the involvement of both RIG-I and TLR3 in sensing HEV RNA and downstream activation of interferon regulatory factor 3 (IRF3) to generate antiviral responses. Inhibition of IRF3 mediated downstream responses in HepG2/C3A cells by pharmacological inhibitor BX795 significantly improved HEV replication efficiency implying the importance of this study in establishing a better cell culture system for future HEV studies. PMID:27230536

  7. Genetic determinants of antithyroid drug-induced agranulocytosis by human leukocyte antigen genotyping and genome-wide association study

    PubMed Central

    Chen, Pei-Lung; Shih, Shyang-Rong; Wang, Pei-Wen; Lin, Ying-Chao; Chu, Chen-Chung; Lin, Jung-Hsin; Chen, Szu-Chi; Chang, Ching-Chung; Huang, Tien-Shang; Tsai, Keh Sung; Tseng, Fen-Yu; Wang, Chih-Yuan; Lu, Jin-Ying; Chiu, Wei-Yih; Chang, Chien-Ching; Chen, Yu-Hsuan; Chen, Yuan-Tsong; Fann, Cathy Shen-Jang; Yang, Wei-Shiung; Chang, Tien-Chun

    2015-01-01

    Graves' disease is the leading cause of hyperthyroidism affecting 1.0–1.6% of the population. Antithyroid drugs are the treatment cornerstone, but may cause life-threatening agranulocytosis. Here we conduct a two-stage association study on two separate subject sets (in total 42 agranulocytosis cases and 1,208 Graves' disease controls), using direct human leukocyte antigen genotyping and SNP-based genome-wide association study. We demonstrate HLA-B*38:02 (Armitage trend Pcombined=6.75 × 10−32) and HLA-DRB1*08:03 (Pcombined=1.83 × 10−9) as independent susceptibility loci. The genome-wide association study identifies the same signals. Estimated odds ratios for these two loci comparing effective allele carriers to non-carriers are 21.48 (95% confidence interval=11.13–41.48) and 6.13 (95% confidence interval=3.28–11.46), respectively. Carrying both HLA-B*38:02 and HLA-DRB1*08:03 increases odds ratio to 48.41 (Pcombined=3.32 × 10−21, 95% confidence interval=21.66–108.22). Our results could be useful for antithyroid-induced agranulocytosis and potentially for agranulocytosis caused by other chemicals. PMID:26151496

  8. Characterization of a human isolate of Tritrichomonas foetus (cattle/swine genotype) infected by a zoonotic opportunistic infection

    PubMed Central

    SUZUKI, Jun; KOBAYASHI, Seiki; OSUKA, Hanako; KAWAHATA, Daisuke; OISHI, Tsuyoshi; SEKIGUCHI, Koji; HAMADA, Atsuo; IWATA, Satoshi

    2015-01-01

    Tritrichomonas species flagellates (IMC strain) were isolated from the biliary tract of an individual who had developed cholecystitis as a complication of acquired agammaglobulinemia. Sequence analysis of Tritrichomonas sp. (IMC clone 2 (cl2)) was performed for several genetic regions including the ITS1-5.8S rDNA-ITS2 region, the cysteine protease (CP)-1, CP-2 and CP-4 to CP-9 genes, and the cytosolic malate dehydrogenase 1 gene. In addition to comparison of the variable-length DNA repeats in the isolate clone with those in T. foetus (Inui cl2) and the T. mobilensis (U.S.A.: M776 cl2) reference strains, this analysis showed that the Tritrichomonas sp. (IMC cl2) was T. foetus (cattle/swine genotype). Injection of T. foetus (IMC cl2) directly into the livers of CBA mice resulted in liver abscess formation on Day 7. Moreover, inoculation via orogastric intubation caused infection in the cecum on Day 5 in CBA mice co-infected with Entamoeba histolytica (HM-1: IMSS cl6). T. foetus (IMC cl2) was able to grow in YI-S medium for over 20 days, even at 5°C. These results indicate that the T. foetus isolate is able to survive in the feces and edible organ meat of the definitive host for a prolonged period of time, and it is possible that the parasite could infect humans. PMID:26685985

  9. A Schisandra-Derived Compound Schizandronic Acid Inhibits Entry of Pan-HCV Genotypes into Human Hepatocytes

    PubMed Central

    Qian, Xi-Jing; Zhang, Xiao-Lian; Zhao, Ping; Jin, Yong-Sheng; Chen, Hai-Sheng; Xu, Qing-Qiang; Ren, Hao; Zhu, Shi-Ying; Tang, Hai-Lin; Zhu, Yong-Zhe; Qi, Zhong-Tian

    2016-01-01

    Despite recent progress in the development of hepatitis C virus (HCV) inhibitors, cost-effective antiviral drugs, especially among the patients receiving liver transplantations, are still awaited. Schisandra is a traditional medicinal herb used to treat a range of liver disorders including hepatitis for thousands of years in China. To isolate the bioactive compounds of schisandra for the treatment of HCV infection, we screened a schisandra-extracts library and identified a tetracyclic triterpenoid, schizandronic acid (SZA), as a novel HCV entry inhibitor. Our findings suggested that SZA potently inhibited pan-HCV genotype entry into hepatoma cells and primary human hepatocytes without interfering virus binding on cell surface or internalization. However, virion-cell fusion process was impaired in the presence of SZA, along with the increased host membrane fluidity. We also found that SZA inhibited the spread of HCV to the neighboring cells, and combinations of SZA with interferon or telaprevir resulted in additive synergistic effect against HCV. Additionally, SZA diminished the establishment of HCV infection in vivo. The SZA target is different from conventional direct-acting antiviral agents, therefore, SZA is a potential therapeutic compound for the development of effective HCV entry inhibitors, especially for patients who need to prevent HCV reinfection during the course of liver transplantations. PMID:27252043

  10. A Schisandra-Derived Compound Schizandronic Acid Inhibits Entry of Pan-HCV Genotypes into Human Hepatocytes.

    PubMed

    Qian, Xi-Jing; Zhang, Xiao-Lian; Zhao, Ping; Jin, Yong-Sheng; Chen, Hai-Sheng; Xu, Qing-Qiang; Ren, Hao; Zhu, Shi-Ying; Tang, Hai-Lin; Zhu, Yong-Zhe; Qi, Zhong-Tian

    2016-01-01

    Despite recent progress in the development of hepatitis C virus (HCV) inhibitors, cost-effective antiviral drugs, especially among the patients receiving liver transplantations, are still awaited. Schisandra is a traditional medicinal herb used to treat a range of liver disorders including hepatitis for thousands of years in China. To isolate the bioactive compounds of schisandra for the treatment of HCV infection, we screened a schisandra-extracts library and identified a tetracyclic triterpenoid, schizandronic acid (SZA), as a novel HCV entry inhibitor. Our findings suggested that SZA potently inhibited pan-HCV genotype entry into hepatoma cells and primary human hepatocytes without interfering virus binding on cell surface or internalization. However, virion-cell fusion process was impaired in the presence of SZA, along with the increased host membrane fluidity. We also found that SZA inhibited the spread of HCV to the neighboring cells, and combinations of SZA with interferon or telaprevir resulted in additive synergistic effect against HCV. Additionally, SZA diminished the establishment of HCV infection in vivo. The SZA target is different from conventional direct-acting antiviral agents, therefore, SZA is a potential therapeutic compound for the development of effective HCV entry inhibitors, especially for patients who need to prevent HCV reinfection during the course of liver transplantations. PMID:27252043

  11. Genome-wide genotype and sequence-based reconstruction of the 140,000 year history of modern human ancestry.

    PubMed

    Shriner, Daniel; Tekola-Ayele, Fasil; Adeyemo, Adebowale; Rotimi, Charles N

    2014-01-01

    We investigated ancestry of 3,528 modern humans from 163 samples. We identified 19 ancestral components, with 94.4% of individuals showing mixed ancestry. After using whole genome sequences to correct for ascertainment biases in genome-wide genotype data, we dated the oldest divergence event to 140,000 years ago. We detected an Out-of-Africa migration 100,000-87,000 years ago, leading to peoples of the Americas, east and north Asia, and Oceania, followed by another migration 61,000-44,000 years ago, leading to peoples of the Caucasus, Europe, the Middle East, and south Asia. We dated eight divergence events to 33,000-20,000 years ago, coincident with the Last Glacial Maximum. We refined understanding of the ancestry of several ethno-linguistic groups, including African Americans, Ethiopians, the Kalash, Latin Americans, Mozabites, Pygmies, and Uygurs, as well as the CEU sample. Ubiquity of mixed ancestry emphasizes the importance of accounting for ancestry in history, forensics, and health. PMID:25116736

  12. Genome-wide genotype and sequence-based reconstruction of the 140,000 year history of modern human ancestry

    PubMed Central

    Shriner, Daniel; Tekola-Ayele, Fasil; Adeyemo, Adebowale; Rotimi, Charles N.

    2014-01-01

    We investigated ancestry of 3,528 modern humans from 163 samples. We identified 19 ancestral components, with 94.4% of individuals showing mixed ancestry. After using whole genome sequences to correct for ascertainment biases in genome-wide genotype data, we dated the oldest divergence event to 140,000 years ago. We detected an Out-of-Africa migration 100,000–87,000 years ago, leading to peoples of the Americas, east and north Asia, and Oceania, followed by another migration 61,000–44,000 years ago, leading to peoples of the Caucasus, Europe, the Middle East, and south Asia. We dated eight divergence events to 33,000–20,000 years ago, coincident with the Last Glacial Maximum. We refined understanding of the ancestry of several ethno-linguistic groups, including African Americans, Ethiopians, the Kalash, Latin Americans, Mozabites, Pygmies, and Uygurs, as well as the CEU sample. Ubiquity of mixed ancestry emphasizes the importance of accounting for ancestry in history, forensics, and health. PMID:25116736

  13. A sociability gene? Meta-analysis of oxytocin receptor genotype effects in humans.

    PubMed

    Bakermans-Kranenburg, Marian J; van Ijzendoorn, Marinus H

    2014-04-01

    Variation in the oxytocin receptor (OXTR) gene may partly explain individual differences in oxytocin-related social behavior. Two single nucleotide polymorphisms (SNPs) have been suggested as promising candidates: rs53576 and rs2254298, although the results of studies were not consistent. We carried out meta-analyses for these two SNPs, covering five domains of outcomes: (a) biology, (b) personality, (c) social behavior, (d) psychopathology, and (e) autism, on the basis of 82 pertinent effect sizes, 48 for OXTR rs53576 (N=17 559) and 34 for OXTR rs2254298 (N=13 547). Combined effect sizes did not differ from zero in any of the domains, nor for all domains combined. Clinical status, age, and sex did not moderate the effect sizes. Minor allele frequency was related to ethnicity, with significantly lower minor allele frequencies in samples with predominantly Caucasian participants. The domain of biological functioning seemed most promising, but comprised few studies. We conclude that so far two of the most intensively studied OXTR SNPs (rs53576 and rs2254298) failed to explain a significant part of human social behavior.

  14. Giardia duodenalis in Damascus, Syria: Identification of Giardia genotypes in a sample of human fecal isolates using polymerase chain reaction and restriction fragment length polymorphism analyzing method.

    PubMed

    Skhal, Dania; Aboualchamat, Ghalia; Al Nahhas, Samar

    2016-02-01

    Giardia duodenalis is a common gastrointestinal parasite that infects humans and many other mammals. It is most prevalent in many developing and industrialized countries. G. duodenalis is considered to be a complex species. While no morphological distinction among different assemblages exist, it can be genetically differentiated into eight major assemblages: A to H. The aim of this study was to determine the genetic heterogeneity of G. duodenalis in human isolates (a study conducted for the first time in Syria). 40 fecal samples were collected from three different hospitals during the hot summer season of 2014. Extraction of genomic DNA from all Giardia positive samples (based on a microscopic examination) was performed using QIAamp DNA Stool Mini Kit. β-giardin gene was used to differentiate between different Giardia assemblages. The 514 bp fragment was amplified using the Polymerase Chain Reaction method, followed by digestion in HaeIII restriction enzyme. Our result showed that genotype A was more frequent than genotype B, 27/40 (67.5%); 4/40 (10%) respectively. A mixed genotype of A+B was only detected in 9 isolates (22.5%). This is the first molecular study performed on G. duodenalis isolates in Syria in order to discriminate among the different genotypes. Further expanded studies using more genes are needed to detect and identify the Giardia parasite at the level of assemblage and sub-assemblage.

  15. Distribution of human papillomavirus genotypes among cervical intraepithelial neoplasia and invasive cancers in Macao.

    PubMed

    Hlaing, Thazin; Yip, Yuk-Ching; Ngai, Karry L K; Vong, Heong-Ting; Wong, Sio-In; Ho, Wendy C S; Batalha, Sellma L S C; Chan, Paul K S

    2010-09-01

    Macao is a densely populated city situated in East Asia where a relatively high prevalence of human papillomavirus (HPV) types 52 and 58 has been reported in women with invasive cervical cancer. To provide data for a population-specific estimation on the impact of HPV vaccines, paraffin-embedded tissues collected from women with invasive cervical cancer or cervical intrapeitheilal neoplasia grade 2 or 3 confirmed histologically were examined for HPV using the INNO-LiPa kit. Of the 35 HPV-positive patients with invasive cancer, one HPV type was detected in 68.6%, and 31.4% were co-infected with more than one HPV type. Overall, HPV 16, HPV 18, HPV 52, and HPV 54 were the most common types found respectively in 57.1%, 17%, 11.4%, and 8.5% of patients with invasive cervical cancer. Among the 59 HPV-positive patients with cervical intraepithelial neoplasia grade 2/3, 55.9% hardbored one HPV type, and 44.1% had co-infections. The common HPV types found included HPV 16 (52.5%), HPV 52 (23.7%), HPV 58 (18.7%), and HPV 33 (17%). Although HPV 11 (a low-risk type) was also found commonly in invasive cervical cancers (14.3%) and cervical intraepithelial neoplasia grade 2/3 (15.3%), the fact that they all existed as co-infections with another high-risk type suggested HPV 11 was not the cause of the lesion. The current vaccines targeting HPV 16/18 are expected to cover 62.9-74.3% of invasive cervical cancers and 32.2-55.9% of cervical intraepithelial neoplasia 2/3 in Macao. Widespread HPV vaccination is expected to reduce substantially the disease burden associated with cervical neoplasia in Macao.

  16. Reconstructing the dynamics of ancient human populations from radiocarbon dates: 10 000 years of population growth in Australia.

    PubMed

    Johnson, Christopher N; Brook, Barry W

    2011-12-22

    Measuring trends in the size of prehistoric populations is fundamental to our understanding of the demography of ancient people and their responses to environmental change. Archaeologists commonly use the temporal distribution of radiocarbon dates to reconstruct population trends, but this can give a false picture of population growth because of the loss of evidence from older sites. We demonstrate a method for quantifying this bias, and we use it to test for population growth through the Holocene of Australia. We used model simulations to show how turnover of site occupation across an archaeological landscape, interacting with erasure of evidence at abandoned sites, can create an increase in apparent site occupation towards the present when occupation density is actually constant. By estimating the probabilities of abandonment and erasure from archaeological data, we then used the model to show that this effect does not account for the observed increase in occupation through the Holocene in Australia. This is best explained by population growth, which was low for the first part of the Holocene but accelerated about 5000 years ago. Our results provide new evidence for the dynamism of non-agricultural populations through the Holocene.

  17. Genotyping and Molecular Characterization of Hepatitis B Virus from Human Immunodeficiency Virus-Infected Individuals in Southern Africa

    PubMed Central

    Makondo, Euphodia; Bell, Trevor G.; Kramvis, Anna

    2012-01-01

    Hepatitis B virus (HBV) and human immunodeficiency virus (HIV) are hyperendemic in sub-Saharan Africa. The HBV genotypes prevailing in HIV-infected Africans are unknown. Our aim was to determine the HBV genotypes in HIV-infected participants and to identify clinically significant HBV mutations. From 71 HBV DNA+ve HIV-infected participants, 49 basic core promoter/precore (BCP/PC) and 29 complete S regions were successfully sequenced. Following phylogenetic analysis of 29 specimens in the complete S region, 28 belonged to subgenotype A1 and one to D3. Mutations affecting HBeAg expression at the transcriptional (1762T1764A), translational (Kozak 1809–1812, initiation 1814–1816, G1896A with C1858T), or post translational levels (G1862T), were responsible for the high HBeAg-negativity observed. The G1862T mutation occurred only in subgenotype A1 isolates, which were found in one third (7/21) of HBsAg−ve participants, but in none of the 18 HBsAg+ve participants (p<0.05). Pre-S deletion mutants were detected in four HBsAg+ve and one HBsAg−ve participant/s. The following mutations occurred significantly more frequently in HBV isolated in this study than in strains of the same cluster of the phylogenetic tree: ps1F25L, ps1V88L/A; ps2Q10R, ps2 R48K/T, ps2A53V and sQ129R/H, sQ164A/V/G/D, sV168A and sS174N (p<0.05). ps1I48V/T occurred more frequently in females than males (p<0.05). Isolates with sV168A occurred more frequently in participants with viral loads >200 IU per ml (p<0.05) and only sS174N occurred more frequently in HBsAg−ve than in HBsAg+ve individuals (p<0.05). Prior to initiation of ART, ten percent, 3 of 29 isolates sequenced, had drug resistance mutations rtV173L, rtL180M+rtM204V and rtV214A, respectively. This study has provided important information on the molecular characteristics of HBV in HIV-infected southern Africans prior to ART initiation, which has important clinical relevance in the management of HBV/HIV co-infection in our unique setting

  18. Prevalence, Genotype Distribution and Risk Factors for Cervical Human Papillomavirus Infection in the Grand Tunis Region, Tunisia

    PubMed Central

    Ennaifer, Emna; Letaief, Hajer; Salsabil, Rejaibi; Lassili, Thalja; Chahed, Karim; Bougatef, Souha; Bahrini, Asma; El Fehri, Emna; Ouerhani, Kaouther; Paez Jimenez, Adela; Guizani, Ikram; Boubaker, Med Samir; Ben Alaya, Nissaf Bouafif ép

    2016-01-01

    Implementation of Human Papillomavirus (HPV) vaccination should be considered a key cervical cancer prevention strategy in Tunisia, where Pap smear screening is not efficient. This study aims to estimate the prevalence and to identify risk factors associated with HPV infection among women from Grand Tunis, Tunisia. We conducted a cross-sectional study, between December 2012 and May 2013. Eligible women for this study were those aged 18–65 years, sexually active, who sought medical attention at their primary health care centre or clinic in Grand Tunis, Tunisia and who gave written consent. A liquid-based Pap smear sample was obtained from all women using a cervical brush. Only women with betaglobin positive test were further analysed for HPV detection and typing. A nested-PCR of the L1 region was performed followed by reverse line blot hybridization to facilitate the specific detection of 31 HPV genotypes. Multiple logistic regression modeling was used for the analysis of associations between variables with some considered possible confounders after checking for interactions. A total of 391 women were enrolled in this study and 325 out of the 391 cervical samples were positive for the betaglobin test. Overall HPV prevalence was 13.2% [9.8%−17.5%], with the following most prevalent HPV genotypes: HPV6 (40%), HPV40 (14%), HPV16 (12%), HPV52 (9%), HPV31 and HPV59 (7%), followed by HPV68 (4%). Mean age of HPV positive women was 40.7±0.92 years. Independently associated risk factors of HPV infection were smoking (OR:2.8 [0.8–9.6]), low income (OR:9.6 [1.4–63.4), bad housing type (OR:2.5 [1–6.8]), partner with multiple sexual relationship (OR:4.5 [0.9–22.9]) and single women (widowed, divorced, separated, never married) (OR:6.9 [1.1–42.2]). This study provides the first national-based estimate of HPV prevalence in Tunisia. Our findings contribute to the evidence on the current burden of HPV infection, the critical role of sexual behaviour and socioeconomic

  19. Prevalence, Genotype Distribution and Risk Factors for Cervical Human Papillomavirus Infection in the Grand Tunis Region, Tunisia.

    PubMed

    Ardhaoui, Monia; Ennaifer, Emna; Letaief, Hajer; Salsabil, Rejaibi; Lassili, Thalja; Chahed, Karim; Bougatef, Souha; Bahrini, Asma; El Fehri, Emna; Ouerhani, Kaouther; Paez Jimenez, Adela; Guizani, Ikram; Boubaker, Med Samir; Ben Alaya, Nissaf Bouafif Ép

    2016-01-01

    Implementation of Human Papillomavirus (HPV) vaccination should be considered a key cervical cancer prevention strategy in Tunisia, where Pap smear screening is not efficient. This study aims to estimate the prevalence and to identify risk factors associated with HPV infection among women from Grand Tunis, Tunisia. We conducted a cross-sectional study, between December 2012 and May 2013. Eligible women for this study were those aged 18-65 years, sexually active, who sought medical attention at their primary health care centre or clinic in Grand Tunis, Tunisia and who gave written consent. A liquid-based Pap smear sample was obtained from all women using a cervical brush. Only women with betaglobin positive test were further analysed for HPV detection and typing. A nested-PCR of the L1 region was performed followed by reverse line blot hybridization to facilitate the specific detection of 31 HPV genotypes. Multiple logistic regression modeling was used for the analysis of associations between variables with some considered possible confounders after checking for interactions. A total of 391 women were enrolled in this study and 325 out of the 391 cervical samples were positive for the betaglobin test. Overall HPV prevalence was 13.2% [9.8%-17.5%], with the following most prevalent HPV genotypes: HPV6 (40%), HPV40 (14%), HPV16 (12%), HPV52 (9%), HPV31 and HPV59 (7%), followed by HPV68 (4%). Mean age of HPV positive women was 40.7±0.92 years. Independently associated risk factors of HPV infection were smoking (OR:2.8 [0.8-9.6]), low income (OR:9.6 [1.4-63.4), bad housing type (OR:2.5 [1-6.8]), partner with multiple sexual relationship (OR:4.5 [0.9-22.9]) and single women (widowed, divorced, separated, never married) (OR:6.9 [1.1-42.2]). This study provides the first national-based estimate of HPV prevalence in Tunisia. Our findings contribute to the evidence on the current burden of HPV infection, the critical role of sexual behaviour and socioeconomic status and

  20. Apps for Ancient Civilizations

    ERIC Educational Resources Information Center

    Thompson, Stephanie

    2011-01-01

    This project incorporates technology and a historical emphasis on science drawn from ancient civilizations to promote a greater understanding of conceptual science. In the Apps for Ancient Civilizations project, students investigate an ancient culture to discover how people might have used science and math smartphone apps to make their lives…

  1. MLVA genotyping of Brucella melitensis and Brucella abortus isolates from different animal species and humans and identification of Brucella suis vaccine strain S2 from cattle in China.

    PubMed

    Jiang, Hai; Wang, Heng; Xu, Liqing; Hu, Guiying; Ma, Junying; Xiao, Pei; Fan, Weixing; Di, Dongdong; Tian, Guozhong; Fan, Mengguang; Mi, Jingchuan; Yu, Ruiping; Song, Litao; Zhao, Hongyan; Piao, Dongri; Cui, Buyun

    2013-01-01

    In China, brucellosis is an endemic disease and the main sources of brucellosis in animals and humans are infected sheep, cattle and swine. Brucella melitensis (biovars 1 and 3) is the predominant species, associated with sporadic cases and outbreak in humans. Isolates of B. abortus, primarily biovars 1 and 3, and B. suis biovars 1 and 3 are also associated with sporadic human brucellosis. In this study, the genetic profiles of B. melitensis and B. abortus isolates from humans and animals were analyzed and compared by multi-locus variable-number tandem-repeat analysis (MLVA). Among the B. melitensis isolates, the majority (74/82) belonged to MLVA8 genotype 42, clustering in the 'East Mediterranean' group. Two B. melitensis biovar 1 genotype 47 isolates, belonging to the 'Americas' group, were recovered; both were from the Himalayan blue sheep (Pseudois nayaur, a wild animal). The majority of B. abortus isolates (51/70) were biovar 3, genotype 36. Ten B. suis biovar 1 field isolates, including seven outbreak isolates recovered from a cattle farm in Inner Mongolia, were genetically indistinguishable from the vaccine strain S2, based on MLVA cluster analysis. MLVA analysis provided important information for epidemiological trace-back. To the best of our knowledge, this is the first report to associate Brucella cross-infection with the vaccine strain S2 based on molecular comparison of recovered isolates to the vaccine strain. MLVA typing could be an essential assay to improve brucellosis surveillance and control programs.

  2. Type-specific detection of human papillomaviruses in Kazakh esophageal squamous cell carcinoma by genotyping both E6 and L1 genes with MALDI-TOF mass spectrometry

    PubMed Central

    Dong, Hong-Chao; Cui, Xiao-Bin; Wang, Liang-Hai; Li, Man; Shen, Yao-Yuan; Zhu, Jian-Bo; Li, Cheng-Fang; Hu, Jian-Ming; Li, Shu-Gang; Yang, Lei; Zhang, Wen-Jie; Chen, Yun-Zhao; Li, Feng

    2015-01-01

    Background: Many studies have suggested a relationship between human papillomavirus (HPV) infection and the risk of esophageal squamous cell carcinoma (ESCC). However, findings are inconclusive, potentially because of geographic heterogeneity and variations in detection methods. Objectives: We sought to further investigate the prevalence of HPV with a new detection method, the MassARRAY Sequenom technique, in esophageal squamous cell carcinomas occurring in patients belonging to Kazakh populations in Xinjiang, China. Study design: In the present study, a novel genotyping method for detecting 30 HPV genotypes, specifically by genotyping both the HPV E6 and L1 genes with multiplex PCR using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (PCR-MS) was first adopted to evaluate HPV genotypes in 89 esophageal cancer samples and 49 matched adjacent normal esophageal tissues. Results: Six HPV genotypes (HPV6, HPV16, HPV33, HPV39, HPV51, and HPV82) were present in at least 51.7% of the esophageal carcinoma tissues, which was significantly greater than 28.6% prevalence among controls (P < 0.05). HPV16 was the most common of all the genotypes investigated (HPV16 prevalence in carcinoma tissue: 49.4%; odds ratio 3.02, 95% confidence interval 1.39-6.53). HPV-positive ESCC patients were generally younger than HPV-negative patients (P = 0.04). In addition, HPV infection was more common in cases of well-differentiated and shallower invasive depth. Conclusions: Based on this new detection method, our findings reiterate the possibility that HPV infection (especially HPV16) may be involved in the etiology of esophageal carcinoma in the Kazakh populations and that HPV E6 gene positivity may be associated with prognosis of patients. PMID:26722514

  3. Whole genotype constellation of prototype feline rotavirus strains FRV-1 and FRV64 and their phylogenetic relationships with feline-like human rotavirus strains.

    PubMed

    Gauchan, Punita; Sasaki, Eriko; Nakagomi, Toyoko; Do, Loan Phuong; Doan, Yen Hai; Mochizuki, Masami; Nakagomi, Osamu

    2015-02-01

    Feline rotaviruses, members of the species Rotavirus A, are an infrequent source of zoonotic infections, and were previously shown by RNA-RNA hybridization assays to possess two distinct genomic RNA constellations, represented by strains FRV-1 and FRV64. Due to the lack of whole genome sequence information for FRV-1, human rotavirus strain AU-1 has been used as a surrogate for the genotype constellation of feline rotaviruses. The aim of this study was to determine the whole genome sequence of FRV-1 and FRV64 to help understand the genetic relationships among existing feline rotaviruses from the evolutionary perspective. The genotype constellations of FRV-1 and FRV64 were G3-P[9]-I3-R3-C3-M3-A3-N3-T3-E3-H3 and G3-P[3]-I3-R3-C2-M3-A9-N2-T3-E3-H6, respectively. FRV-1 has a genotype constellation identical to that of the AU-1 strain. Although for individual genes they shared lineages, with the exception of genes encoding VP2, VP6 and VP7, the sequence identity between FRV-1 and AU-1 was considered to be sufficiently high for the AU-1 to be regarded as an example of the direct transmission of a feline rotavirus to a child. On the other hand, the FRV64 strain was not only similar in all the 11 genome segments to another feline rotavirus strain, Cat97, but also to canine rotavirus strains (K9 and CU-1) and feline/canine-like human rotavirus strains (Ro1845 and HCR3A). In conclusion, this study revealed intermingled sharing of genotypes and lineages among feline rotaviruses, suggesting the occurrence of frequent reassortment events over the course of evolution to emerge in four genotype constellations represented by FRV-1, FRV64/Cat97, Cat2 and BA222 strains.

  4. Whole genotype constellation of prototype feline rotavirus strains FRV-1 and FRV64 and their phylogenetic relationships with feline-like human rotavirus strains.

    PubMed

    Gauchan, Punita; Sasaki, Eriko; Nakagomi, Toyoko; Do, Loan Phuong; Doan, Yen Hai; Mochizuki, Masami; Nakagomi, Osamu

    2015-02-01

    Feline rotaviruses, members of the species Rotavirus A, are an infrequent source of zoonotic infections, and were previously shown by RNA-RNA hybridization assays to possess two distinct genomic RNA constellations, represented by strains FRV-1 and FRV64. Due to the lack of whole genome sequence information for FRV-1, human rotavirus strain AU-1 has been used as a surrogate for the genotype constellation of feline rotaviruses. The aim of this study was to determine the whole genome sequence of FRV-1 and FRV64 to help understand the genetic relationships among existing feline rotaviruses from the evolutionary perspective. The genotype constellations of FRV-1 and FRV64 were G3-P[9]-I3-R3-C3-M3-A3-N3-T3-E3-H3 and G3-P[3]-I3-R3-C2-M3-A9-N2-T3-E3-H6, respectively. FRV-1 has a genotype constellation identical to that of the AU-1 strain. Although for individual genes they shared lineages, with the exception of genes encoding VP2, VP6 and VP7, the sequence identity between FRV-1 and AU-1 was considered to be sufficiently high for the AU-1 to be regarded as an example of the direct transmission of a feline rotavirus to a child. On the other hand, the FRV64 strain was not only similar in all the 11 genome segments to another feline rotavirus strain, Cat97, but also to canine rotavirus strains (K9 and CU-1) and feline/canine-like human rotavirus strains (Ro1845 and HCR3A). In conclusion, this study revealed intermingled sharing of genotypes and lineages among feline rotaviruses, suggesting the occurrence of frequent reassortment events over the course of evolution to emerge in four genotype constellations represented by FRV-1, FRV64/Cat97, Cat2 and BA222 strains. PMID:25351516

  5. VP4 and VP7 genotyping by reverse transcription-PCR of human rotavirus in mexican children with acute diarrhea.

    PubMed

    Rodríguez Castillo, A; Villa, A V; Ramírez González, J E; Mayén Pimentel, E; Melo Munguía, M; Díaz De Jesús, B; Olivera Díaz, H; García Lozano, H

    2000-10-01

    Dual typing (VP4 and VP7) of rotavirus obtained from 257 Mexican children during three epidemiological seasons was performed by reverse transcription-PCR. The P1G1 genotype was the most prevalent (40%), followed by P1G3 (19%) and P2G2 (16%). Thirty-one specimens (12%) presented mixed infections, while some genotypes were not found. This is the first dual typing of isolates from diarrhea cases in Mexico.

  6. Human cytomegalovirus UL55, UL144, and US28 genotype distribution in infants infected congenitally or postnatally.

    PubMed

    Paradowska, Edyta; Studzińska, Mirosława; Suski, Patrycja; Kasztelewicz, Beata; Wiśniewska-Ligier, Małgorzata; Zawilińska, Barbara; Gaj, Zuzanna; Nowakowska, Dorota

    2015-10-01

    Cytomegalovirus (CMV) is the most common cause of congenital infection. This pathogen exhibits extensive genetic variability in the genes that encode structural envelope glycoproteins, regulatory proteins, and proteins that contribute to immune evasion. However, the role of specific viral strains in the outcome of congenital CMV infection is unclear. Variation in the UL55 gene encoding glycoprotein B (gB), the UL144 gene encoding TNF α-like receptor, and the US28 gene encoding β-chemokine receptor was determined in 60 newborn infants with congenital CMV infection and 90 infants with postnatal or undefined CMV infection. CMV polymorphisms were studied in relation to disease outcome and viral load. Genotyping was performed by a sequencing analysis of PCR-amplified fragments, and the viral load was measured by quantitative real-time PCR. The results demonstrated that (1) the UL55 and US28 genotype distributions were similar among the group of congenital and postnatal CMV infection; (2) the UL144 B1 genotype was more prevalent in congenital than in postnatal infection and was detected in 70% of newborns with asymptomatic congenital infection; and (3) none of the examined genotype was significantly linked with symptomatic CMV infection. No relationship was observed between genotype and viral load. The results revealed that UL55, UL144, and US28 polymorphisms are not associated with the outcome of CMV infection in infants, but the presence of UL144 B1 genotype might be virological marker of asymptomatic infection at birth.

  7. Human cytomegalovirus UL55, UL144, and US28 genotype distribution in infants infected congenitally or postnatally.

    PubMed

    Paradowska, Edyta; Studzińska, Mirosława; Suski, Patrycja; Kasztelewicz, Beata; Wiśniewska-Ligier, Małgorzata; Zawilińska, Barbara; Gaj, Zuzanna; Nowakowska, Dorota

    2015-10-01

    Cytomegalovirus (CMV) is the most common cause of congenital infection. This pathogen exhibits extensive genetic variability in the genes that encode structural envelope glycoproteins, regulatory proteins, and proteins that contribute to immune evasion. However, the role of specific viral strains in the outcome of congenital CMV infection is unclear. Variation in the UL55 gene encoding glycoprotein B (gB), the UL144 gene encoding TNF α-like receptor, and the US28 gene encoding β-chemokine receptor was determined in 60 newborn infants with congenital CMV infection and 90 infants with postnatal or undefined CMV infection. CMV polymorphisms were studied in relation to disease outcome and viral load. Genotyping was performed by a sequencing analysis of PCR-amplified fragments, and the viral load was measured by quantitative real-time PCR. The results demonstrated that (1) the UL55 and US28 genotype distributions were similar among the group of congenital and postnatal CMV infection; (2) the UL144 B1 genotype was more prevalent in congenital than in postnatal infection and was detected in 70% of newborns with asymptomatic congenital infection; and (3) none of the examined genotype was significantly linked with symptomatic CMV infection. No relationship was observed between genotype and viral load. The results revealed that UL55, UL144, and US28 polymorphisms are not associated with the outcome of CMV infection in infants, but the presence of UL144 B1 genotype might be virological marker of asymptomatic infection at birth. PMID:25926093

  8. Complete genome sequencing of a multidrug-resistant and human-invasive Salmonella enterica serovar Typhimurium strain of the emerging sequence type 213 genotype

    SciTech Connect

    Calva, Edmundo; Silva, Claudia; Zaidi, Mussaret B.; Sanchez-Flores, Alejandro; Estrada, Karel; Silva, Genivaldo G. Z.; Soto-Jiménez, Luz M.; Wiesner, Magdalena; Fernández-Mora, Marcos; Edwards, Robert A.; Vinuesa, Pablo

    2015-06-18

    Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the state of Yucatán, Mexico, from a human systemic infection. The YU39 strain is representative of the multidrug-resistant emergent sequence type 213 (ST213) genotype. The YU39 complete genome is composed of a chromosome and seven plasmids.

  9. Cervical infections by multiple human papillomavirus (HPV) genotypes: Prevalence and impact on the risk of precancerous epithelial lesions.

    PubMed

    Bello, Barbara Dal; Spinillo, Arsenio; Alberizzi, Paola; Cesari, Stefania; Gardella, Barbara; D'Ambrosio, Gioacchino; Roccio, Marianna; Silini, Enrico Maria

    2009-04-01

    A large proportion of human papillomavirus (HPV) infections is sustained by multiple genotypes. The effect of multiple infections on the risk of cervical intraepithelial neoplasia (CIN) and the potential efficacy of vaccine on these infections are controversial. We performed viral typing by SFP(10)-LIPA on a consecutive series of 1,323 women undergoing colposcopy, 69% of whom had cervical biopsy, and correlated CIN severity with the type and number of HPVs. Overall prevalence of HPV-DNA was 68.9%, 97.3% in CIN1, and 98.1% in CIN>/=2. HPV positivity correlated with younger age (35.9 vs. 37.3 years, P = 0.026) and history of CIN (P < 0.001). Multiple types were detected in 44.2% of cases, including 63.1% CIN1 and 80.8% CIN>/=2. Twenty-three different types were detected, HPV-16, 31 and 52 being the most frequent. Infections by HPV-6, 11, 16, or 18 occurred in 59.4% of CIN1 and 71.3% of CIN>/=2. Number of viral types and class of oncogenic risk were linearly correlated with CIN severity (P < 0.0001) by univariate and multivariate analyses controlling for age and history of CIN. The effect of the number of HPV types was maintained after exclusion from the model of infections by HPV-6, 11, 16, and 18. Frequency, distribution, and clinical correlates of multiple HPV infections highlight the importance of assessing individual types in the management and the prediction of outcome of women with abnormal baseline cytology and point to potential limitations in current vaccine strategies.

  10. Drug-drug Interaction between Losartan and Paclitaxel in Human Liver Microsomes with Different CYP2C8 Genotypes.

    PubMed

    Mukai, Yuji; Senda, Asuna; Toda, Takaki; Hayakawa, Toru; Eliasson, Erik; Rane, Anders; Inotsume, Nobuo

    2015-06-01

    The cytochrome P450 (CYP) 2C8*3 allele is associated with reduced metabolic activity of paclitaxel. This study was aimed to investigate the inhibitory effect of losartan on paclitaxel metabolism in human liver microsomes (HLMs) and to determine the impact of the CYP2C8*3 polymorphism. HLMs that contained the CYP2C8*1 homozygote (HL60) or CYP2C8*3 heterozygote (HL54) genotype were used for the inhibition study. Losartan, at a concentration of 50 μmol/L, significantly inhibited paclitaxel metabolism by 29% and 57% in the HL60 (p < 0.001) and HL54 (p < 0.01), respectively. When using HL60, losartan and the CYP3A4-selective inhibitors, erythromycin and ketoconazole, caused a greater inhibition of the paclitaxel metabolism than quercetin, a CYP2C8-selective inhibitor. This demonstrated that the paclitaxel metabolism was mainly catalysed by CYP3A4 in HL60. There were no significant differences found for the inhibitory effects caused by the four inhibitors of the paclitaxel metabolism in HL54, indicating that both CYP2C8 and CYP3A4 play important roles in paclitaxel metabolism in HL54. These findings suggest that 50 μmol/L of losartan inhibits both CYP2C8 and CYP3A4 in HLMs. In summary, losartan inhibited paclitaxel metabolism, with concentrations over 50 μmol/L in HLMs. The CYP2C8*3 allele carriers are likely susceptible to the interactions of losartan and CYP3A4 inhibitors to paclitaxel metabolism.

  11. Ten years of global evolution of the human respiratory syncytial virus BA genotype with a 60-nucleotide duplication in the G protein gene.

    PubMed

    Trento, Alfonsina; Casas, Inmaculada; Calderón, Ana; Garcia-Garcia, Maria L; Calvo, Cristina; Perez-Breña, Pilar; Melero, José A

    2010-08-01

    The emergence of natural isolates of human respiratory syncytial virus group B (HRSV-B) with a 60-nucleotide (nt) duplication in the G protein gene in Buenos Aires, Argentina, in 1999 (A. Trento et al., J. Gen. Virol. 84:3115-3120, 2003) and their dissemination worldwide allowed us to use the duplicated segment as a natural tag to examine in detail the evolution of HRSV during propagation in its natural host. Viruses with the duplicated segment were all clustered in a new genotype, named BA (A. Trento et al., J. Virol. 80:975-984, 2006). To obtain information about the prevalence of these viruses in Spain, we tested for the presence of the duplicated segment in positive HRSV-B clinical samples collected at the Severo Ochoa Hospital (Madrid) during 12 consecutive epidemics (1996-1997 to 2007-2008). Viruses with the 60-nt duplication were found in 61 samples, with a high prevalence relative to the rest of B genotypes in the most recent seasons. Global phylogenetic and demographic analysis of all G sequences containing the duplication, collected across five continents up until April 2009, revealed that the prevalence of the BA genotype increased gradually until 2004-2005, despite its rapid dissemination worldwide. After that date and coinciding with a bottleneck effect on the population size, a relatively new BA lineage (BA-IV) replaced all other group B viruses, suggesting further adaptation of the BA genotype to its natural host.

  12. Giardia duodenalis genotypes and Cryptosporidium species in humans and domestic animals in Côte d'Ivoire: occurrence and evidence for environmental contamination.

    PubMed

    Berrilli, Federica; D'Alfonso, Rossella; Giangaspero, Annunziata; Marangi, Marianna; Brandonisio, Olga; Kaboré, Yolande; Glé, Christoph; Cianfanelli, Cristina; Lauro, Renato; Di Cave, David

    2012-03-01

    Giardia duodenalis genotypes and Cryptosporidium species were studied in humans and free-ranging animals living in closed enclaves in Côte d'Ivoire. Three hundred and seven stool samples were tested from humans, and 47 from freely roaming domestic animals (dogs, goats, ducks, chickens). Molecular characterization of the isolates was performed by sequence analysis of a portion of the SSU-rDNA for Giardia and the COWP gene for Cryptosporidium, and a β-giardin SYBR-green real-time PCR was also used to confirm the assignment of Giardia isolates to Assemblages. In humans, genotyping of Giardia assigned many of the sequences (43/56 by the SSU-rDNA gene, and 36/61 by the β-giardin gene) to Assemblage B. The animal species harboured only zoonotic Assemblages A and B, except for dogs, in which host specific Assemblages C and D were also detected. Cryptosporidium meleagridis, C. parvum and C. hominis were detected in humans, while among the animals only chickens were found positive for oocysts, identified as C. meleagridis and C. parvum. The results provide further evidence about the role of free-ranging domestic animals living closely with humans in the environmental dissemination and potential transmission of these anthropozoonotic pathogens to humans.

  13. Ancient medicine--a review.

    PubMed

    Zuskin, Eugenija; Lipozencić, Jasna; Pucarin-Cvetković, Jasna; Mustajbegović, Jadranka; Schachter, Neil; Mucić-Pucić, Branka; Neralić-Meniga, Inja

    2008-01-01

    Different aspects of medicine and/or healing in several societies are presented. In the ancient times as well as today medicine has been closely related to magic, science and religion. Various ancient societies and cultures had developed different views of medicine. It was believed that a human being has two bodies: a visible body that belongs to the earth and an invisible body of heaven. In the earliest prehistoric days, a different kind of medicine was practiced in countries such as Egypt, Greece, Rome, Mesopotamia, India, Tibet, China, and others. In those countries, "medicine people" practiced medicine from the magic to modern physical practices. Medicine was magical and mythological, and diseases were attributed mostly to the supernatural forces. The foundation of modern medicine can be traced back to ancient Greeks. Tibetan culture, for instance, even today, combines spiritual and practical medicine. Chinese medicine developed as a concept of yin and yang, acupuncture and acupressure, and it has even been used in the modern medicine. During medieval Europe, major universities and medical schools were established. In the ancient time, before hospitals had developed, patients were treated mostly in temples.

  14. Ancient medicine--a review.

    PubMed

    Zuskin, Eugenija; Lipozencić, Jasna; Pucarin-Cvetković, Jasna; Mustajbegović, Jadranka; Schachter, Neil; Mucić-Pucić, Branka; Neralić-Meniga, Inja

    2008-01-01

    Different aspects of medicine and/or healing in several societies are presented. In the ancient times as well as today medicine has been closely related to magic, science and religion. Various ancient societies and cultures had developed different views of medicine. It was believed that a human being has two bodies: a visible body that belongs to the earth and an invisible body of heaven. In the earliest prehistoric days, a different kind of medicine was practiced in countries such as Egypt, Greece, Rome, Mesopotamia, India, Tibet, China, and others. In those countries, "medicine people" practiced medicine from the magic to modern physical practices. Medicine was magical and mythological, and diseases were attributed mostly to the supernatural forces. The foundation of modern medicine can be traced back to ancient Greeks. Tibetan culture, for instance, even today, combines spiritual and practical medicine. Chinese medicine developed as a concept of yin and yang, acupuncture and acupressure, and it has even been used in the modern medicine. During medieval Europe, major universities and medical schools were established. In the ancient time, before hospitals had developed, patients were treated mostly in temples. PMID:18812066

  15. MIRU-VNTR genotype diversity and indications of homoplasy in M. avium strains isolated from humans and slaughter pigs in Latvia.

    PubMed

    Kalvisa, Adrija; Tsirogiannis, Constantinos; Silamikelis, Ivars; Skenders, Girts; Broka, Lonija; Zirnitis, Agris; Jansone, Inta; Ranka, Renate

    2016-09-01

    Diseases which are caused by non-tuberculous mycobacteria (NTM) are an increasing problem in the developed countries. In Latvia, one of the most clinically important members of NTM is Mycobacterium avium (M. avium), an opportunistic pathogen which has been isolated from several lung disease patients and tissue samples of slaughter pigs. This study was designed to characterize the genetic diversity of the M. avium isolates in Latvia and to compare the distribution of genotypic patterns among humans and pigs. Eleven (Hall and Salipante, 2010) clinical M. avium samples, isolated from patients of Center of Tuberculosis and Lung Diseases (years 2003-2010), and 32 isolates from pig necrotic mesenterial lymph nodes in different regions (years 2003-2007) were analyzed. The majority (42 of 43) of samples were identified as M. avium subsp. hominissuis; one porcine isolate belonged to M. avium subsp. avium. MIRU-VNTR genotyping revealed 13 distinct genotypes, among which nine genotype patterns, including M. avium subsp. avium isolate, were newly identified. IS1245 RFLP fingerprinting of 25 M. avium subsp. hominissuis samples yielded 17 different IS1245 RFLP patterns, allowing an efficient discrimination of isolates. Clusters of identical RFLP profiles were observed within host species, geographical locations and time frame of several years. Additional in silico analysis on simulated MIRU-VNTR genotype population datasets showed that the MIRU-VNTR pattern similarity could partly arise due to probabilistic increase of acquiring homoplasy among subpopulations, thus the similar MIRU-VNTR profiles of M. avium strains even in close geographical proximity should be interpreted with caution. PMID:27178993

  16. Human Papillomavirus Virus (HPV) Genotype- and Age-Specific Analyses of External Genital Lesions Among Men in the HPV Infection in Men (HIM) Study

    PubMed Central

    Ingles, Donna J.; Pierce Campbell, Christine M.; Messina, Jane A.; Stoler, Mark H.; Lin, Hui-Yi; Fulp, William J.; Abrahamsen, Martha; Sirak, Bradley A.; O'Keefe, Michael T.; Papenfuss, Mary; Gage, Christine; Carvalho da Silva, Roberto; Gonzalez Sosa, Rossana; Rojas Juarez, Oscar; Villa, Luisa L.; Lazcano Ponce, Eduardo; Giuliano, Anna R.

    2015-01-01

    Background. Human papillomavirus (HPV) causes external genital lesions (EGLs) in men, including condyloma and penile intraepithelial neoplasia (PeIN). We sought to determine the incidence of pathologically confirmed EGLs, by lesion type, among men in different age groups and to evaluate the HPV types that were associated with EGL development. Methods. HPV Infection in Men (HIM) study participants who contributed ≥2 visits from 2009–2013 were included in the biopsy cohort. Genotyping by an HPV line-probe assay was performed on all pathologically confirmed EGLs. Age-specific analyses were conducted for incident EGLs, with Kaplan–Meier estimation of cumulative incidence. Results. This biopsy cohort included 2754 men (median follow-up duration, 12.4 months [interquartile range, 6.9–19.2 months]). EGLs (n = 377) were pathologically confirmed in 228 men, 198 of whom had incident EGLs. The cumulative incidence of any EGL was highest among men <45 years old and, for condyloma, decreased significantly over time with age. The genotype-specific incidence of EGL varied by pathological diagnoses, with high- and low-risk genotypes found in 15.6% and 73.2% of EGLs, respectively. Condyloma primarily contained HPV 6 or 11. While PeIN lesions primarily contained HPV 16, 1 PeIN III lesion was positive for HPV 6 only. Conclusion. Low- and high-risk HPV genotypes contribute to the EGL burden. Men remain susceptible to HPV-related EGLs throughout the life span, making it necessary to ensure the longevity of immune protection against the most common causative HPV genotypes. PMID:25344518

  17. The Kalash genetic isolate: ancient divergence, drift, and selection.

    PubMed

    Ayub, Qasim; Mezzavilla, Massimo; Pagani, Luca; Haber, Marc; Mohyuddin, Aisha; Khaliq, Shagufta; Mehdi, Syed Qasim; Tyler-Smith, Chris

    2015-05-01

    The Kalash represent an enigmatic isolated population of Indo-European speakers who have been living for centuries in the Hindu Kush mountain ranges of present-day Pakistan. Previous Y chromosome and mitochondrial DNA markers provided no support for their claimed Greek descent following Alexander III of Macedon's invasion of this region, and analysis of autosomal loci provided evidence of a strong genetic bottleneck. To understand their origins and demography further, we genotyped 23 unrelated Kalash samples on the Illumina HumanOmni2.5M-8 BeadChip and sequenced one male individual at high coverage on an Illumina HiSeq 2000. Comparison with published data from ancient hunter-gatherers and European farmers showed that the Kalash share genetic drift with the Paleolithic Siberian hunter-gatherers and might represent an extremely drifted ancient northern Eurasian population that also contributed to European and Near Eastern ancestry. Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319-2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600-12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia. PMID:25937445

  18. The Kalash genetic isolate: ancient divergence, drift, and selection.

    PubMed

    Ayub, Qasim; Mezzavilla, Massimo; Pagani, Luca; Haber, Marc; Mohyuddin, Aisha; Khaliq, Shagufta; Mehdi, Syed Qasim; Tyler-Smith, Chris

    2015-05-01

    The Kalash represent an enigmatic isolated population of Indo-European speakers who have been living for centuries in the Hindu Kush mountain ranges of present-day Pakistan. Previous Y chromosome and mitochondrial DNA markers provided no support for their claimed Greek descent following Alexander III of Macedon's invasion of this region, and analysis of autosomal loci provided evidence of a strong genetic bottleneck. To understand their origins and demography further, we genotyped 23 unrelated Kalash samples on the Illumina HumanOmni2.5M-8 BeadChip and sequenced one male individual at high coverage on an Illumina HiSeq 2000. Comparison with published data from ancient hunter-gatherers and European farmers showed that the Kalash share genetic drift with the Paleolithic Siberian hunter-gatherers and might represent an extremely drifted ancient northern Eurasian population that also contributed to European and Near Eastern ancestry. Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319-2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600-12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia.

  19. Diversification of four human HOX gene clusters by step-wise evolution rather than ancient whole-genome duplications.

    PubMed

    Abbasi, Amir Ali

    2015-11-01

    HOX genes encode transcriptional factors that play a pivotal role in specifying regional identity in nearly every bilateral animal. The birth of HOX gene cluster and its subsequent evolution, either in regulation or function, underlie the evolution of many bilaterian features and hence to the evolutionary radiation of this group. Despite of this importance, evolution of HOX cluster in vertebrates remains largely obscure because the phylogenetic history of these genes is poorly resolved. This has led to the controversy about whether four HOX clusters in human originated through two rounds (2R) of whole-genome duplications or instead evolved by small-scale events early in vertebrate evolution. Recently, the large-scale phylogenetic analysis of triplicate and quadruplicate paralogous regions residing on human HOX-bearing chromosomes provided an unprecedented insight into events that shaped vertebrate genome early in their history. Based on these data and comparative genomic analysis of fruit fly, red floor beetle, and human, this study infers the genic content of minimal HOX locus in the Urbilaterian and reconstructs its duplication history. It appears that four HOX clusters of humans are not remnants of polyploidy events in vertebrate ancestry. Rather, current evidence suggests that one-to-four transition in HOX cluster number occurred by three-step sequential process involving regional duplication events. Therefore, it is concluded that the evolutionary origin of vertebrate novelties, including the complexity of their body, is the consequence of small-scale genetic changes at widely different times over their history.

  20. Medicine among the ancient Maya.

    PubMed

    Garcia-Kutzbach, A

    1976-07-01

    Medicine among the ancient Mayas was a blend of religion and science. It was practiced by priests who inherited their position and received extensive education. The Mayas sutured wounds with human hair, reduced fractures, and used casts. They were skillful dental surgeons and made prostheses from jade and turquoise and filled teeth with iron pyrite. Three clinical diseases, pinta, leishmaniasis, and yellow fever, and several psychiatric syndromes were described.

  1. Molecular epidemiology of human papillomavirus genotype in women with high-grade squamous intraepithelial lesion and cervical cancer: will a quadrivalent vaccine be necessary in Thailand?

    PubMed

    Sukasem, Chonlaphat; Pairoj, Wantanich; Saekang, Nipa; Pombubpha, Hiranyaratsami; Srichunrasami, Chutatip; Pongtippan, Atcharaporn; Junyangdikul, Pairoj; Chantratita, Wasun

    2011-01-01

    This study was designed to investigate the distribution of human papillomavirus (HPV) genotypes among a group of patients with high-grade squamous intraepithelial lesion (HSIL) or worse cytology. Consequently, the genotype-specific HPV infection in a group of HSIL and invasive cervical cancer (ICC) samples was described. Specimens were collected prospectively from 132 women referred for colposcopic examination. All the women underwent Papanicolaou (Pap) smears and colposcopies and some also underwent cervical excision procedure biopsy. The HPV genotype was determined using the INNO-LiPA assay. Among the 132 genotyped samples, 90.91% (120/132) were diagnosed HSIL, whereas 9.09% (12/132) were ICC. From the overall prevalence of HPV in the patients, 77.27% (102/132) and 22.72% (30/132) of cases had single and multiple genotype infections, respectively. The most common cases with statistical significance were high-risk HPV (HR-HPV) infections in 128 samples (96.97%), whereas, four individuals (3.03%) barely were low-risk HPV (LR-HPV) infected, P < 0.0001, χ(2). The most prevalent genotypes were frequently HPV-16 (65/167; 38.92%, followed by HPV-58 (25/167; 14.97%), HPV-18 (18/167; 10.78%), HPV-33 (13/167; 7.19%), and HPV-68 (11/167; 6.59%). In addition, HPV-11 (2/132; 1.51%) and HPV-6 (1/132; 0.76%) also were observed in this study, which confirmed the high distribution of HR-HPV among women with HSIL and ICC. HPV-58; a unique high-risk HPV, is prevalent in a group of HSIL and ICC cases. These data also contribute evidence that HPV-16, -18, -58, -33, and -68 genotypes are high-risk and high distribution among women with HSIL and ICC. Therefore, HPV-58, HPV-33, and HPV-68 should be considered for development of the next vaccine generation in Thailand.

  2. Improving ancient DNA read mapping against modern reference genomes

    PubMed Central

    2012-01-01

    Background Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA. Results In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%. Conclusions We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important

  3. Simple methodology to directly genotype Trypanosoma cruzi discrete typing units in single and mixed infections from human blood samples.

    PubMed

    Bontempi, Iván A; Bizai, María L; Ortiz, Sylvia; Manattini, Silvia; Fabbro, Diana; Solari, Aldo; Diez, Cristina

    2016-09-01

    Different DNA markers to genotype Trypanosoma cruzi are now available. However, due to the low quantity of parasites present in biological samples, DNA markers with high copy number like kinetoplast minicircles are needed. The aim of this study was to complete a DNA assay called minicircle lineage specific-PCR (MLS-PCR) previously developed to genotype the T. cruzi DTUs TcV and TcVI, in order to genotype DTUs TcI and TcII and to improve TcVI detection. We screened kinetoplast minicircle hypervariable sequences from cloned PCR products from reference strains belonging to the mentioned DTUs using specific kDNA probes. With the four highly specific sequences selected, we designed primers to be used in the MLS-PCR to directly genotype T. cruzi from biological samples. High specificity and sensitivity were obtained when we evaluated the new approach for TcI, TcII, TcV and TcVI genotyping in twenty two T. cruzi reference strains. Afterward, we compared it with hybridization tests using specific kDNA probes in 32 blood samples from chronic chagasic patients from North Eastern Argentina. With both tests we were able to genotype 94% of the samples and the concordance between them was very good (kappa=0.855). The most frequent T. cruzi DTUs detected were TcV and TcVI, followed by TcII and much lower TcI. A unique T. cruzi DTU was detected in 18 samples meantime more than one in the remaining; being TcV and TcVI the most frequent association. A high percentage of mixed detections were obtained with both assays and its impact was discussed.

  4. An investigation into the ancient abortion laws: comparing ancient Persia with ancient Greece and Rome.

    PubMed

    Yarmohammadi, Hassan; Zargaran, Arman; Vatanpour, Azadeh; Abedini, Ehsan; Adhami, Siamak

    2013-01-01

    Since the dawn of medicine, medical rights and ethics have always been one of mankind's concerns. In any civilisation, attention paid to medical laws and ethics depends on the progress of human values and the advancement of medical science. The history of various civilisations teaches that each had its own views on medical ethics, but most had something in common. Ancient civilisations such as Greece, Rome, or Assyria did not consider the foetus to be alive and therefore to have human rights. In contrast, ancient Persians valued the foetus as a living person equal to others. Accordingly, they brought laws against abortion, even in cases of sexual abuse. Furthermore, abortion was considered to be a murder and punishments were meted out to the mother, father, and the person performing it. PMID:24304111

  5. An investigation into the ancient abortion laws: comparing ancient Persia with ancient Greece and Rome.

    PubMed

    Yarmohammadi, Hassan; Zargaran, Arman; Vatanpour, Azadeh; Abedini, Ehsan; Adhami, Siamak

    2013-01-01

    Since the dawn of medicine, medical rights and ethics have always been one of mankind's concerns. In any civilisation, attention paid to medical laws and ethics depends on the progress of human values and the advancement of medical science. The history of various civilisations teaches that each had its own views on medical ethics, but most had something in common. Ancient civilisations such as Greece, Rome, or Assyria did not consider the foetus to be alive and therefore to have human rights. In contrast, ancient Persians valued the foetus as a living person equal to others. Accordingly, they brought laws against abortion, even in cases of sexual abuse. Furthermore, abortion was considered to be a murder and punishments were meted out to the mother, father, and the person performing it.

  6. Human-Environment Interactions during the Last 8000 Years in the Environs of the Ancient City of Ephesus, Western Turkey

    NASA Astrophysics Data System (ADS)

    Stock, F.; Knipping, M.; Pint, A.; Brückner, H.

    2014-12-01

    About 6 millennia ago the maximum Holocene transgression reached c. 20 km inland. Thereafter, the coastline has continuously shifted westwards due to the progradation of the Küçük Menderes delta and its tributaries. Consequently, settlement and harbour sites were established following the retreating coastline. Our interdisciplinary geoarchaeological research focuses on (i) the detection of spatial and temporal shifts in the coastline during the past millennia and the human response to these changes; (ii) the human impact on the landscape, especially in the environs of the Roman Harbour and the harbour canal; (iii) the reconstruction of the vegetation history of the Ephesia. More than 200 drill cores were retrieved from geo-bioarchives. For a better understanding of the depositional environments, we carried out geochemical, sedimentological, microfaunal, palynological and parasitological analyses in Ephesus' harbours and in the environs of two Neolithic settlement sites. Diagnostic ceramic finds, AMS-14C age estimates and a tephra layer were used for the chronological framework.The results reveal human impact in sediments: early agricultural use in the Neolithic period; several meters of sediment with a high concentration of fig and grape seeds in the Koressos harbour during the 6th-3rd centuries BC; an accelerated sedimentation rate up to the factor of ten in Hellenistic and Roman times. Heavy metal pollution, sugar melon and fruit tree pollen, as well as eggs of intestinal parasites occur in the Roman harbour and its canal during the prosperity period of the city. Pollen analysis revealed the dominance of deciduous oak, in a landscape with human impact, already since the 6th millennium BC. From Hellenistic times onwards, fruit trees appear next to crop and pasture farming. After the decline of the city in the 7th century AD, pine trees became dominant, presumably on abandoned land. In the Belevi swamp to the northeast of Ephesus, the ash from the Minoan

  7. Resolving the bulk δ 15N values of ancient human and animal bone collagen via compound-specific nitrogen isotope analysis of constituent amino acids

    NASA Astrophysics Data System (ADS)

    Styring, Amy K.; Sealy, Judith C.; Evershed, Richard P.

    2010-01-01

    Stable nitrogen isotope analysis is a fundamental tool in assessing dietary preferences and trophic positions within contemporary and ancient ecosystems. In order to assess more fully the dietary contributions to human tissue isotope values, a greater understanding of the complex biochemical and physiological factors which underpin bulk collagen δ 15N values is necessary. Determinations of δ 15N values of the individual amino acids which constitute bone collagen are necessary to unravel these relationships, since different amino acids display different δ 15N values according to their biosynthetic origins. A range of collagen isolates from archaeological faunal and human bone ( n = 12 and 11, respectively), representing a spectrum of terrestrial and marine protein origins and diets, were selected from coastal and near-coastal sites at the south-western tip of Africa. The collagens were hydrolysed and δ 15N values of their constituent amino acids determined as N-acetylmethyl esters (NACME) via gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). The analytical approach employed accounts for 56% of bone collagen nitrogen. Reconstruction of bulk bone collagen δ 15N values reveals a 2‰ offset from bulk collagen δ 15N values which is attributable to the δ 15N value of the amino acids which cannot currently be determined by GC-C-IRMS, notably arginine which comprises 53% of the nitrogen unaccounted for (23% of the total nitrogen). The δ 15N values of individual amino acids provide insights into both the contributions of various amino acids to the bulk δ 15N value of collagen and the factors influencing trophic position and the nitrogen source at the base of the food web. The similarity in the δ 15N values of alanine, glutamate, proline and hydroxyproline reflects the common origin of their amino groups from glutamate. The depletion in the δ 15N value of threonine with increasing trophic level indicates a fundamental difference between

  8. Evolutionary diversity of bile salts in reptiles and mammals, including analysis of ancient human and extinct giant ground sloth coprolites

    PubMed Central

    2010-01-01

    Background Bile salts are the major end-metabolites of cholesterol and are also important in lipid and protein digestion and in influencing the intestinal microflora. We greatly extend prior surveys of bile salt diversity in both reptiles and mammals, including analysis of 8,000 year old human coprolites and coprolites from the extinct Shasta ground sloth (Nothrotherium shastense). Results While there is significant variation of bile salts across species, bile salt profiles are generally stable within families and often within orders of reptiles and mammals, and do not directly correlate with differences in diet. The variation of bile salts generally accords with current molecular phylogenies of reptiles and mammals, including more recent groupings of squamate reptiles. For mammals, the most unusual finding was that the Paenungulates (elephants, manatees, and the rock hyrax) have a very different bile salt profile from the Rufous sengi and South American aardvark, two other mammals classified with Paenungulates in the cohort Afrotheria in molecular phylogenies. Analyses of the approximately 8,000 year old human coprolites yielded a bile salt profile very similar to that found in modern human feces. Analysis of the Shasta ground sloth coprolites (approximately 12,000 years old) showed the predominant presence of glycine-conjugated bile acids, similar to analyses of bile and feces of living sloths, in addition to a complex mixture of plant sterols and stanols expected from an herbivorous diet. Conclusions The bile salt synthetic pathway has become longer and more complex throughout vertebrate evolution, with some bile salt modifications only found within single groups such as marsupials. Analysis of the evolution of bile salt structures in different species provides a potentially rich model system for the evolution of a complex biochemical pathway in vertebrates. Our results also demonstrate the stability of bile salts in coprolites preserved in arid climates

  9. Development of a Laboratory Project to Determine Human ABO Genotypes--Limitations Lead to Further Student Explorations

    ERIC Educational Resources Information Center

    Salerno, Theresa A.

    2009-01-01

    A multiplex allele-specific PCR analysis was developed to identify six "common" genotypes: AA, AO, BB, BO, OO, and AB. This project included a pre-laboratory exercise that provided active learning experiences and developed critical thinking skills. This laboratory resulted in many successful analyses, which were verified by student knowledge of…

  10. The glutathione-S-transferase Mu 1 null genotype modulates ozone-induced airway inflammation in humans*

    EPA Science Inventory

    Background: The Glutathione-S-Transferase Mu 1 null genotype has been reported to be a risk factor for acute respiratory disease associated with increases in ambient air ozone. Ozone is known to cause an immediate decrease in lung function and increased airway inflammation. Howev...

  11. MLVA Genotyping of Brucella melitensis and Brucella abortus Isolates from Different Animal Species and Humans and Identification of Brucella suis Vaccine Strain S2 from Cattle in China

    PubMed Central

    Xu, Liqing; Hu, Guiying; Ma, Junying; Xiao, Pei; Fan, Weixing; Di, Dongdong; Tian, Guozhong; Fan, Mengguang; Mi, Jingchuan; Yu, Ruiping; Song, Litao; Zhao, Hongyan; Piao, Dongri; Cui, Buyun

    2013-01-01

    In China, brucellosis is an endemic disease and the main sources of brucellosis in animals and humans are infected sheep, cattle and swine. Brucella melitensis (biovars 1 and 3) is the predominant species, associated with sporadic cases and outbreak in humans. Isolates of B. abortus, primarily biovars 1 and 3, and B. suis biovars 1 and 3 are also associated with sporadic human brucellosis. In this study, the genetic profiles of B. melitensis and B. abortus isolates from humans and animals were analyzed and compared by multi-locus variable-number tandem-repeat analysis (MLVA). Among the B. melitensis isolates, the majority (74/82) belonged to MLVA8 genotype 42, clustering in the ‘East Mediterranean’ group. Two B. melitensis biovar 1 genotype 47 isolates, belonging to the ‘Americas’ group, were recovered; both were from the Himalayan blue sheep (Pseudois nayaur, a wild animal). The majority of B. abortus isolates (51/70) were biovar 3, genotype 36. Ten B. suis biovar 1 field isolates, including seven outbreak isolates recovered from a cattle farm in Inner Mongolia, were genetically indistinguishable from the vaccine strain S2, based on MLVA cluster analysis. MLVA analysis provided important information for epidemiological trace-back. To the best of our knowledge, this is the first report to associate Brucella cross-infection with the vaccine strain S2 based on molecular comparison of recovered isolates to the vaccine strain. MLVA typing could be an essential assay to improve brucellosis surveillance and control programs. PMID:24124546

  12. Laser capture microdissection as a tool to evaluate human papillomavirus genotyping and methylation as biomarkers of persistence and progression of anal lesions

    PubMed Central

    Cornall, Alyssa M; Roberts, Jennifer M; Molano, Monica; Machalek, Dorothy A; Phillips, Samuel; Hillman, Richard J; Grulich, Andrew E; Jin, Fengyi; Poynten, I Mary; Templeton, David J; Garland, Suzanne M; Tabrizi, Sepehr N

    2015-01-01

    Introduction Anal squamous cell carcinoma is preceded by persistent infection with high-risk human papillomavirus (HPV) and the cancer precursor, high-grade squamous intraepithelial lesion (HSIL). Detection of specific HPV genotypes and HPV-related biomarkers may be an option for primary anal screening. However, more data on the natural history of HPV-related anal lesions are required. The outcomes from this study will enhance our understanding of the clinical and biological behaviour of HPV-related anal lesions and inform the development of future HPV genotype and/or biomarker screening tests. Methods and analysis HIV-negative and HIV-positive men who have sex with men, aged 35 years and over, recruited from community-based settings in Sydney, Australia, attend 6 clinic visits over 3 years. At the first 5 visits, participants undergo a digital anorectal examination, an anal swab for HPV genotyping and anal cytology, and high-resolution anoscopy with directed biopsy of any visible abnormalities that are suggestive of any abnormality suspicious of SIL. Tissue sections from participants diagnosed with histologically confirmed HSIL at the baseline clinic visit will undergo laser capture microdissection, HPV detection and genotyping, and quantitation of CpG methylation in baseline and follow-up biopsies. Histological and cytological findings in combination with HPV genotyping data will be used to identify persistent HSIL. HSIL will be stratified as non-persistent and persistent based on their status at 12 months. The performance of HPV genotype and methylation status in predicting disease persistence at 12 months will be assessed, along with associations with HIV status and other covariates such as age. Ethics and dissemination The St Vincent's Hospital Ethics Committee granted ethics approval for the study. Written informed consent is obtained from all individuals before any study-specific procedures are performed. Findings from this study will be disseminated

  13. Ancient Astronomy in Armenia

    NASA Astrophysics Data System (ADS)

    Parsamian, Elma S.

    2007-08-01

    The most important discovery, which enriched our knowledge of ancient astronomy in Armenia, was the complex of platforms for astronomical observations on the Small Hill of Metzamor, which may be called an ancient “observatory”. Investigations on that Hill show that the ancient inhabitants of the Armenian Highlands have left us not only pictures of celestial bodies, but a very ancient complex of platforms for observing the sky. Among the ancient monuments in Armenia there is a megalithic monument, probably, being connected with astronomy. 250km South-East of Yerevan there is a structure Zorats Kar (Karahunge) dating back to II millennium B.C. Vertical megaliths many of which are more than two meters high form stone rings resembling ancient stone monuments - henges in Great Britain and Brittany. Medieval observations of comets and novas by data in ancient Armenian manuscripts are found. In the collection of ancient Armenian manuscripts (Matenadaran) in Yerevan there are many manuscripts with information about observations of astronomical events as: solar and lunar eclipses, comets and novas, bolides and meteorites etc. in medieval Armenia.

  14. Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey.

    PubMed

    Ottoni, Claudio; Rasteiro, Rita; Willet, Rinse; Claeys, Johan; Talloen, Peter; Van de Vijver, Katrien; Chikhi, Lounès; Poblome, Jeroen; Decorte, Ronny

    2016-02-01

    More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine) and a modern sample from the nearby town of Ağlasun. Our analyses revealed no genetic discontinuity across two millennia in the region and Bayesian coalescence-based simulations indicated that a major population decline in the area coincided with the final abandonment of Sagalassos, rather than with the Plague of Justinian or the mentioned earthquake. PMID:26998313

  15. Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey

    PubMed Central

    Ottoni, Claudio; Willet, Rinse; Claeys, Johan; Talloen, Peter; Van de Vijver, Katrien; Chikhi, Lounès; Poblome, Jeroen; Decorte, Ronny

    2016-01-01

    More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine) and a modern sample from the nearby town of Ağlasun. Our analyses revealed no genetic discontinuity across two millennia in the region and Bayesian coalescence-based simulations indicated that a major population decline in the area coincided with the final abandonment of Sagalassos, rather than with the Plague of Justinian or the mentioned earthquake. PMID:26998313

  16. Comparing human papillomavirus prevalences in women with normal cytology or invasive cervical cancer to rank genotypes according to their oncogenic potential: a meta-analysis of observational studies

    PubMed Central

    2013-01-01

    Background Mucosal human papillomavirus (HPV) infection is a necessary cause of cervical cancer. Vaccine and non-vaccine genotype prevalences may change after vaccine introduction. Therefore, it appears essential to rank HPV genotypes according to their oncogenic potential for invasive cervical cancer, independently of their respective prevalences. Methods We performed meta-analyses of published observational studies and estimated pooled odds ratios with random-effects models for 32 HPV genotypes, using HPV-16 as the reference. Results Twenty-seven studies yielded 9,252 HPV-infected women: 2,902 diagnosed with invasive cervical cancer and 6,350 with normal cytology. Expressed as (odds ratio [95% confidence interval]), HPV-18 (0.63 [0.51, 0.78]) ranked closest to HPV-16, while other genotypes showed continuously decreasing relative oncogenic potentials: HPV-45 (0.35 [0.22, 0.55]), HPV-69 (0.28 [0.09, 0.92]), HPV-58 (0.24 [0.15, 0.38]), HPV-31 (0.22 [0.14, 0.35]), HPV-33 (0.22 [0.12, 0.38]), HPV-34 (0.21 [0.06, 0.80]), HPV-67 (0.21 [0.06, 0.67]), HPV-39 (0.17 [0.09, 0.30]), HPV-59 (0.17 [0.09, 0.31]), HPV-73 (0.16 [0.06, 0.41]), and HPV-52 (0.16 [0.11, 0.23]). Conclusions Our results support the markedly higher oncogenic potentials of HPV-16 and -18, followed by HPV-31, -33, -39, -45, -52, -58 and -59, and highlight the need for further investigation of HPV-34, -67, -69 and -73. Overall, these findings could have important implications for the prevention of cervical cancer. PMID:23941096

  17. Anal Human Papillomavirus Genotype Distribution in HIV-Infected Men Who Have Sex with Men by Geographical Origin, Age, and Cytological Status in a Spanish Cohort

    PubMed Central

    Torres, Montserrat; González, Cristina; del Romero, Jorge; Viciana, Pompeyo; Ocampo, Antonio; Rodríguez-Fortúnez, Patricia; Masiá, Mar; Blanco, José Ramón; Portilla, Joaquín; Rodríguez, Carmen; Hernández-Novoa, Beatriz; del Amo, Julia

    2013-01-01

    Knowledge of human papillomavirus (HPV) type distribution in populations at risk for anal cancer is needed. Here, we describe the anal HPV genotype distribution in a large Spanish cohort (Cohort of the Spanish HIV Research Network HPV [CoRIS-HPV]) of HIV-positive men who have sex with men (MSM) according to geographical origin, age, and cytological status. A cross-sectional analysis of baseline data from 1,439 HIV-infected MSM (2007 to 2012) was performed. Anal HPV genotyping was performed using the Linear Array HPV genotyping test. Descriptive analyses of subject characteristics, prevalences, and 95% confidence intervals (CI) were performed. The global prevalences of HPV, high-risk HPV (HR-HPV), and low-risk HPV (LR-HPV) types were 95.8%, 83.0%, and 72.7%, respectively. Among the HR-HPV types, HPV16 was the most common, followed by HPV59, -39, -51, -18, and -52. The prevalence of multiple HR-HPV infections was 58.5%. There were no differences in the crude analyses between Spanish and Latin-American MSM for most HPV types, and a peak in prevalence for most HPV types was seen in patients in their late thirties. Globally and by specific HPV groups, men with abnormal anal cytologies had a higher prevalence of infection than those with normal cytologies. This study has the largest number of HIV-positive MSM with HPV genotype data analyzed according to cytological status as far as we know. The information gained from this study can help with the design of anal cancer prevention strategies in HIV-positive patients. PMID:23966501