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ancient DNA

Vendela K Lagerholm, Edson Sandoval-Castellanos, Amélie Vaniscotte, Olga R Potapova, Teresa Tomek, Zbigniew M Bochenski, Paul Shepherd, Nick Barton, Marie-Claire Van Dyck, Rebecca Miller, Jacob Höglund, Nigel G Yoccoz, Love Dalén, John R Stewart
Global warming is predicted to cause substantial habitat rearrangements, with the most severe effects expected to occur in high-latitude biomes. However, one major uncertainty is whether species will be able to shift their ranges to keep pace with climate-driven environmental changes. Many recent studies on mammals have shown that past range contractions have been associated with local extinctions rather than survival by habitat tracking. Here, we have used an interdisciplinary approach that combines ancient DNA techniques, coalescent simulations and species distribution modelling, to investigate how two common cold-adapted bird species, willow and rock ptarmigan (Lagopus lagopus and Lagopus muta), respond to long-term climate warming...
October 20, 2016: Global Change Biology
Fátima Sánchez Barreiro, Filipe G Vieira, Michael D Martin, James Haile, M Thomas P Gilbert, Nathan Wales
Population genetic studies of non-model organisms frequently employ reduced representation library (RRL) methodologies, many of which rely on protocols in which genomic DNA is digested by one or more restriction enzymes. However, because high molecular weight DNA is recommended for these protocols, samples with degraded DNA are generally unsuitable for RRL methods. Given that ancient and historic specimens can provide key temporal perspectives to evolutionary questions, we explored how custom-designed RNA probes could enrich for RRL loci (Restriction Enzyme-Associated Loci baits, or REALbaits)...
October 19, 2016: Molecular Ecology Resources
Julien Soubrier, Graham Gower, Kefei Chen, Stephen M Richards, Bastien Llamas, Kieren J Mitchell, Simon Y W Ho, Pavel Kosintsev, Michael S Y Lee, Gennady Baryshnikov, Ruth Bollongino, Pere Bover, Joachim Burger, David Chivall, Evelyne Crégut-Bonnoure, Jared E Decker, Vladimir B Doronichev, Katerina Douka, Damien A Fordham, Federica Fontana, Carole Fritz, Jan Glimmerveen, Liubov V Golovanova, Colin Groves, Antonio Guerreschi, Wolfgang Haak, Tom Higham, Emilia Hofman-Kamińska, Alexander Immel, Marie-Anne Julien, Johannes Krause, Oleksandra Krotova, Frauke Langbein, Greger Larson, Adam Rohrlach, Amelie Scheu, Robert D Schnabel, Jeremy F Taylor, Małgorzata Tokarska, Gilles Tosello, Johannes van der Plicht, Ayla van Loenen, Jean-Denis Vigne, Oliver Wooley, Ludovic Orlando, Rafał Kowalczyk, Beth Shapiro, Alan Cooper
The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (<11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry...
October 18, 2016: Nature Communications
Mohamed M M Abdel-Latif, Mekky M Abouzied
BACKGROUND AND AIMS: Natural honey has been used as a medicine since ancient times. Honey is widely known for its antibacterial properties against H. pylori; however, the mechanisms of its antibacterial activity are not fully known. The present study was performed to examine the molecular mechanisms by which natural honey can inhibit H. pylori infection in gastric epithelial cells. METHODS: Electrophoretic mobility shift assay was used to measure NF-κB- and AP-1-DNA binding activity...
July 2016: Archives of Medical Research
Joseph Caspermeyer
No abstract text is available yet for this article.
October 15, 2016: Molecular Biology and Evolution
Martina I Gocke, Arnaud Huguet, Sylvie Derenne, Steffen Kolb, Michaela A Dippold, Guido L B Wiesenberg
Soils, paleosols and terrestrial sediments serve as archives for studying climate change, and represent important terrestrial carbon pools. Archive functioning relies on the chronological integrity of the respective units. Incorporation of younger organic matter (OM) e.g. by plant roots and associated microorganisms into deep subsoil and underlying soil parent material may reduce reliability of paleoenvironmental records and stability of buried OM. Long-term effects of sedimentary characteristics and deep rooting on deep subsoil microbial communities remain largely unknown...
October 13, 2016: Science of the Total Environment
Nadia Amanzougaghene, Kosta Y Mumcuoglu, Florence Fenollar, Shir Alfi, Gonca Yesilyurt, Didier Raoult, Oleg Mediannikov
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...
2016: PloS One
Younguk Sun, Huimin Zhang, Majid Kazemian, Joseph M Troy, Christopher Seward, Xiaochen Lu, Lisa Stubbs
Mammalian genomes contain hundreds of genes transcribed by RNA Polymerase III (Pol III), encoding noncoding RNAs and especially the tRNAs specialized to carry specific amino acids to the ribosome for protein synthesis. In addition to this well-known function, tRNAs and their genes (tDNAs) serve a variety of other critical cellular functions. For example, tRNAs and other Pol III transcripts can be cleaved to yield small RNAs with potent regulatory activities. Furthermore, from yeast to mammals, active tDNAs and related "extra-TFIIIC" (ETC) loci provide the DNA scaffolds for the most ancient known mechanism of three-dimensional chromatin architecture...
October 6, 2016: Oncotarget
Mateusz Baca, Danijela Popović, Krzysztof Stefaniak, Adrian Marciszak, Mikołaj Urbanowski, Adam Nadachowski, Paweł Mackiewicz
The cave bear (Ursus spelaeus sensu lato) is a typical representative of Pleistocene megafauna which became extinct at the end of the Last Glacial. Detailed knowledge of cave bear extinction could explain this spectacular ecological transformation. The paper provides a report on the youngest remains of the cave bear dated to 20,930 ± 140 (14)C years before present (BP). Ancient DNA analyses proved its affiliation to the Ursus ingressus haplotype. Using this record and 205 other dates, we determined, following eight approaches, the extinction time of this mammal at 26,100-24,300 cal...
December 2016: Die Naturwissenschaften
Wanlong Li, Ghana S Challa, Huilan Zhu, Wenjie Wei
Chromosomal rearrangements (CRs) play important roles in karyotype diversity and speciation. While many CR breakpoints have been characterized at the sequence level in yeast, insects and primates, little is known about the structure of evolutionary CR breakpoints in plant genomes, which are much more dynamic in genome size and sequence organization. Here, we report identification of breakpoints of a translocation between chromosome arms 4L and 5L of Triticeae, which is fixed in several species including diploid wheat and rye, by comparative mapping and comparative analysis of the draft genome and chromosome survey sequences of the Triticeae species...
October 11, 2016: G3: Genes—Genomes—Genetics
Gérard Aboudharam
The Paleomicrobiology establishes the diagnosis of ancient infectious diseases by studying ancient pathogens. This recent science also analyzes the evolution of these pathogens, virulence, and their adaptation to their habitat and their vectors. The DNA persists a long time after the death of an organism despite the chemical and enzymatic degradation. The possibility of sequencing bacterial, viral, parasitic and archaeal DNA molecules persists over time.Various sources are used for these studies: frozen tissue and particularly human tissue are a exceptional source for the analysis because at very low temperatures, all biological activity is suspended...
August 2016: Microbiology Spectrum
Didier Raoult
We have been involved in the field of paleomicrobiology since 1998, when we used dental pulp to identify Yersinia pestis as the causative agent of the great plague of Marseille (1720). We recently designed a specific technique, "suicide PCR," that can prevent contamination. A controversy arose between two teams, with one claiming that DNA must be altered to amplify it and the other group claiming that demographic data did not support the role of Y. pestis in the Black Death (i.e., the great plague of the Middle Ages)...
August 2016: Microbiology Spectrum
Abiola Olumuyiwa Olaitan, Jean-Marc Rolain
Antibiotic resistance is an ancient biological mechanism in bacteria, although its proliferation in our contemporary world has been amplified through antimicrobial therapy. Recent studies conducted on ancient environmental and human samples have uncovered numerous antibiotic-resistant bacteria and resistance genes. The resistance genes that have been reported from the analysis of ancient bacterial DNA include genes coding for several classes of antibiotics, such as glycopeptides, β-lactams, tetracyclines, and macrolides...
August 2016: Microbiology Spectrum
Catherine Thèves, Eric Crubézy, Philippe Biagini
Smallpox is considered among the most devastating of human diseases. Its spread in populations, initiated for thousands of years following a probable transmission from an animal host, was concomitant with movements of people across regions and continents, trade and wars. Literature permitted to retrace the occurrence of epidemics from ancient times to recent human history, smallpox having affected all levels of past society including famous monarchs. The disease was officially declared eradicated in 1979 following intensive vaccination campaigns...
August 2016: Microbiology Spectrum
Helen D Donoghue
Tuberculosis is a significant global disease today, so understanding its origins and history is important. It is primarily a lung infection and is transmitted by infectious aerosols from person to person, so a high population density encourages its spread. The causative organism is Mycobacterium tuberculosis, an obligate pathogen in the M. tuberculosis complex that also contains closely related species, such as Mycobacterium bovis, that primarily infect animals. Typical bone lesions occur in about 5% of untreated infections...
August 2016: Microbiology Spectrum
Jessica I Rivera-Perez, Tasha M Santiago-Rodriguez, Gary A Toranzos
Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas...
August 2016: Microbiology Spectrum
Michelle A Carmell, Gregoriy A Dokshin, Helen Skaletsky, Yueh-Chiang Hu, Josien C von Wolfswinkel, Kyomi J Igarashi, Daniel W Bellott, Michael Nefedov, Peter W Reddien, George C Enders, Vladimir N Uversky, Craig C Mello, David C Page
The advent of sexual reproduction and the evolution of a dedicated germline in multicellular organisms are critical landmarks in eukaryotic evolution. We report an ancient family of GCNA (germ cell nuclear antigen) proteins that arose in the earliest eukaryotes, and feature a rapidly evolving intrinsically disordered region (IDR). Phylogenetic analysis reveals that GCNA proteins emerged before the major eukaryotic lineages diverged; GCNA predates the origin of a dedicated germline by a billion years. Gcna gene expression is enriched in reproductive cells across eukarya - either just prior to or during meiosis in single-celled eukaryotes, and in stem cells and germ cells of diverse multicellular animals...
October 8, 2016: ELife
Sanna Olsson, Pedro Seoane Zonjic, Rocío Bautista, M Gonzalo Claros, Santiago C González-Martínez, Ivan Scotti, Caroline Scotti-Saintagne, Olivier J Hardy, Myriam Heuertz
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L. f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1...
October 8, 2016: Molecular Ecology Resources
Kaoru S Imai, Clare Hudson, Izumi Oda-Ishii, Hitoyoshi Yasuo, Yutaka Satou
Many animal embryos use nuclear β-catenin (nβ-catenin) during the segregation of endomesoderm (or endoderm) from ectoderm. This mechanism is thus likely to be evolutionarily ancient. In the ascidian embryo, nβ-catenin reiteratively drives binary fate decisions between ectoderm and endomesoderm at the 16-cell stage, and then between endoderm and margin (mesoderm and caudal neural) at the 32-cell stage. At the 16-cell stage, nβ-catenin activates endomesoderm genes in the vegetal hemisphere. At the same time, nβ-catenin suppresses the DNA-binding activity of a maternal transcription factor Gata...
October 5, 2016: Development
Alissa Mittnik, Chuan-Chao Wang, Jiří Svoboda, Johannes Krause
In the past decades ancient DNA research has brought numerous insights to archaeological research where traditional approaches were limited. The determination of sex in human skeletal remains is often challenging for physical anthropologists when dealing with incomplete, juvenile or pathological specimens. Molecular approaches allow sexing on the basis of sex-specific markers or by calculating the ratio of DNA derived from different chromosomes. Here we propose a novel approach that relies on the ratio of X chromosome-derived shotgun sequencing data to the autosomal coverage, thus establishing the probability of an XX or XY karyotype...
2016: PloS One
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