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https://www.readbyqxmd.com/read/28817644/cheek-tooth-morphology-and-ancient-mitochondrial-dna-of-late-pleistocene-horses-from-the-western-interior-of-north-america-implications-for-the-taxonomy-of-north-american-late-pleistocene-equus
#1
Christina I Barrón-Ortiz, Antonia T Rodrigues, Jessica M Theodor, Brian P Kooyman, Dongya Y Yang, Camilla F Speller
Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to the end-Pleistocene extinction...
2017: PloS One
https://www.readbyqxmd.com/read/28817590/reconstructing-asian-faunal-introductions-to-eastern-africa-from-multi-proxy-biomolecular-and-archaeological-datasets
#2
Mary E Prendergast, Michael Buckley, Alison Crowther, Laurent Frantz, Heidi Eager, Ophélie Lebrasseur, Rainer Hutterer, Ardern Hulme-Beaman, Wim Van Neer, Katerina Douka, Margaret-Ashley Veall, Eriéndira M Quintana Morales, Verena J Schuenemann, Ella Reiter, Richard Allen, Evangelos A Dimopoulos, Richard M Helm, Ceri Shipton, Ogeto Mwebi, Christiane Denys, Mark Horton, Stephanie Wynne-Jones, Jeffrey Fleisher, Chantal Radimilahy, Henry Wright, Jeremy B Searle, Johannes Krause, Greger Larson, Nicole L Boivin
Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species...
2017: PloS One
https://www.readbyqxmd.com/read/28812610/genome-wide-interrogation-advances-resolution-of-recalcitrant-groups-in-the-tree-of-life
#3
Dahiana Arcila, Guillermo Ortí, Richard Vari, Jonathan W Armbruster, Melanie L J Stiassny, Kyung D Ko, Mark H Sabaj, John Lundberg, Liam J Revell, Ricardo Betancur-R
Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species...
January 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28803756/speciation-range-contraction-and-extinction-in-the-endemic-new-zealand-king-shag-complex
#4
Nicolas J Rawlence, Charlotte E Till, Luke J Easton, Hamish G Spencer, Rob Schuckard, David S Melville, R Paul Scofield, Alan J D Tennyson, Matt J Rayner, Jonathan M Waters, Martyn Kennedy
New Zealand's endemic King Shag (Leucocarbo carunculatus) has occupied only a narrow portion of the northeastern South Island for at least the past 240years. However, pre-human Holocene fossil and archaeological remains have suggested a far more widespread distribution of the three Leucocarbo species (King, Otago, Foveaux) on mainland New Zealand at the time of Polynesian settlement in the late 13th Century CE. We use modern and ancient DNA, and morphometric and osteological analyses, of modern King Shags and Holocene fossil Leucocarbo remains to assess the pre-human distribution and taxonomic status of the King Shag on mainland New Zealand, and the resultant conservation implications...
August 10, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28799621/ancient-dna-analysis-might-suggest-external-origin-of-individuals-from-chamber-graves-placed-in-medieval-cemetery-in-pie%C3%A5-central-poland
#5
Tomasz Płoszaj, Krystyna Jędrychowska-Dańska, Alicja Zamerska, Alicja Drozd-Lipińska, Dariusz Poliński, Andrzej Janowski, Henryk Witas
The participation of immigrants during early days in Poland of Piast's dynasty is a debated issue among archaeologists and anthropologists alike. Such hypotheses were formulated on the basis of, amongst others, the discovery of early medieval chamber graves characterized by construction features typical of the Scandinavian culture area. Archaeological and anthropological studies to date have not provided an unequivocal answer as to whether the individuals interred in those graves were autochthons who adopted a different burial rite, or perhaps immigrants from foreign lands...
August 11, 2017: Anthropologischer Anzeiger; Bericht über die Biologisch-anthropologische Literatur
https://www.readbyqxmd.com/read/28798742/preservation-and-significance-of-extracellular-dna-in-ferruginous-sediments-from-lake-towuti-indonesia
#6
Aurèle Vuillemin, Fabian Horn, Mashal Alawi, Cynthia Henny, Dirk Wagner, Sean A Crowe, Jens Kallmeyer
Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798357/origin-and-dispersal-of-early-domestic-pigs-in-northern-china
#7
Hai Xiang, Jianqiang Gao, Dawei Cai, Yunbing Luo, Baoquan Yu, Langqing Liu, Ranran Liu, Hui Zhou, Xiaoyong Chen, Weitao Dun, Xi Wang, Michael Hofreiter, Xingbo Zhao
It is widely accepted that modern pigs were domesticated independently at least twice, and Chinese native pigs are deemed as direct descendants of the first domesticated pigs in the corresponding domestication centers. By analyzing mitochondrial DNA sequences of an extensive sample set spanning 10,000 years, we find that the earliest pigs from the middle Yellow River region already carried the maternal lineages that are dominant in both younger archaeological populations and modern Chinese pigs. Our data set also supports early Neolithic pig utilization and a long-term in situ origin for northeastern Chinese pigs during 8,000-3,500 BP, suggesting a possibly independent domestication in northeast China...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28796208/palaeobiology-ensure-equal-access-to-ancient-dna
#8
Cheryl Makarewicz, Nimrod Marom, Guy Bar-Oz
No abstract text is available yet for this article.
August 9, 2017: Nature
https://www.readbyqxmd.com/read/28794033/ancient-evolution-and-dispersion-of-human-papillomavirus-type-58-variants
#9
Zigui Chen, Wendy C S Ho, Siaw Shi Boon, Priscilla T Y Law, Martin C W Chan, Rob DeSalle, Robert D Burk, Paul K S Chan
Human papillomavirus type 58 is found in 10-18% of cervical cancers in East Asia but rather uncommon elsewhere. The distribution and oncogenic potential of HPV58 variants appear to be heterogeneous since the E7 T20I/G63S variant is more prevalent in East Asia and confers 7-9 fold higher risk for cervical precancer and cancer. However, the underlying genomic mechanisms that explain the geographic and carcinogenic diversity of HPV58 variants are still poorly understood. In this study, we used a combination of phylogenetic analyses and bioinformatics to investigate the deep evolutionary history of HPV58 complete genome variants...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28771629/altitudinal-gradients-biogeographic-history-and-microhabitat-adaptation-affect-fine-scale-spatial-genetic-structure-in-african-and-neotropical-populations-of-an-ancient-tropical-tree-species
#10
Paloma Torroba-Balmori, Katharina B Budde, Katrin Heer, Santiago C González-Martínez, Sanna Olsson, Caroline Scotti-Saintagne, Maxime Casalis, Bonaventure Sonké, Christopher W Dick, Myriam Heuertz
The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs...
2017: PloS One
https://www.readbyqxmd.com/read/28766036/evaluation-of-the-antimicrobial-activities-of-ultrasonicated-spinach-leaf-extracts-using-rapd-markers-and-electron-microscopy
#11
Ammar Altemimi, Naoufal Lakhssassi, Amer Abu-Ghazaleh, David A Lightfoot
Spinach (Spinacia oleracea L.) leaves represent an important dietary source of nutrients, antioxidants and antimicrobials. As such, spinach leaves play an important role in health and have been used in the treatment of human diseases since ancient times. Here, the aims were to optimize the extraction methods for recovering antimicrobial substances of spinach leaves, determine the minimum inhibitory concentrations (MICs) of the antimicrobial substances against Escherichia coli and Staphylococcus aureus and, finally, evaluate the effects of spinach leaves' antimicrobials on bacterial DNA using central composite face-centered methods...
August 1, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28755302/per-os-infectivity-factors-a-complicated-and-evolutionarily-conserved-entry-machinery-of-baculovirus
#12
REVIEW
Xi Wang, Xiaoping Liu, George Alliwa Makalliwa, Jiang Li, Hualin Wang, Zhihong Hu, Manli Wang
Baculoviruses are a family of arthropod-specific large DNA viruses that infect insect species belonging to the orders Lepidoptera, Hymenoptera and Diptera. In nature, occlusion-derived viruses (ODVs) initiate baculovirus primary infection in the midgut epithelium of insect hosts, and this process is largely dependent on a number of ODV envelope proteins designated as per os infectivity factors (PIFs). Interestingly, PIF homologs are also present in other invertebrate large DNA viruses, which is indicative that per os infection is an ancient and phylogenetically conserved entry mechanism shared by these viruses...
July 27, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28755221/molecular-analysis-of-date-palm-genetic-diversity-using-random-amplified-polymorphic-dna-rapd-and-inter-simple-sequence-repeats-issrs
#13
Sherif F El Sharabasy, Khaled A Soliman
The date palm is an ancient domesticated plant with great diversity and has been cultivated in the Middle East and North Africa for at last 5000 years. Date palm cultivars are classified based on the fruit moisture content, as dry, semidry, and soft dates. There are a number of biochemical and molecular techniques available for characterization of the date palm variation. This chapter focuses on the DNA-based markers random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) techniques, in addition to biochemical markers based on isozyme analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28753598/genetics-new-tales-from-ancient-dna
#14
Vivien Marx
No abstract text is available yet for this article.
July 28, 2017: Nature Methods
https://www.readbyqxmd.com/read/28747494/bam35-tectivirus-intraviral-interaction-map-unveils-new-function-and-localization-of-phage-orfan-proteins
#15
Mónica Berjón-Otero, Ana Lechuga, Jitender Mehla, Peter Uetz, Margarita Salas, Modesto Redrejo-Rodríguez
Tectiviridae comprises a group of tail-less, icosahedral, membrane-containing bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria.In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology...
July 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28747476/ancient-dna-and-morphometric-analysis-reveal-extinction-and-replacement-of-new-zealand-s-unique-black-swans
#16
Nicolas J Rawlence, Afroditi Kardamaki, Luke J Easton, Alan J D Tennyson, R Paul Scofield, Jonathan M Waters
Prehistoric human impacts on megafaunal populations have dramatically reshaped ecosystems worldwide. However, the effects of human exploitation on smaller species, such as anatids (ducks, geese, and swans) are less clear. In this study we apply ancient DNA and osteological approaches to reassess the history of Australasia's iconic black swans (Cygnus atratus) including the palaeo-behaviour of prehistoric populations. Our study shows that at the time of human colonization, New Zealand housed a genetically, morphologically, and potentially ecologically distinct swan lineage (C...
July 26, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28747239/palaeoparasitology-and-palaeogenetics-review-and-perspectives-for-the-study-of-ancient-human-parasites
#17
Nathalie M-L Côté, Matthieu LE Bailly
While some species of parasites can be identified to species level from archaeological remains using microscopy (i.e. Enterobius vermicularis, Clonorchis sinensis), others can only be identified to family or genus level as different species produce eggs with similar morphology (i.e. Tænia sp. and Echinococcus sp.). Molecular and immunological approaches offer the possibility to provide more precise determination at the species level. They can also identify taxa when classic parasite markers such as eggs or cysts have been destroyed over time...
July 27, 2017: Parasitology
https://www.readbyqxmd.com/read/28746380/paleoproteomics-of-the-dental-pulp-the-plague-paradigm
#18
Rémi Barbieri, Rania Mekni, Anthony Levasseur, Eric Chabrière, Michel Signoli, Stéfan Tzortzis, Gérard Aboudharam, Michel Drancourt
Chemical decomposition and fragmentation may limit the detection of ancient host and microbial DNA while some proteins can be detected for extended periods of time. We applied paleoproteomics on 300-year-old dental pulp specimens recovered from 16 individuals in two archeological funeral sites in France, comprising one documented plague site and one documented plague-negative site. The dental pulp paleoproteome of the 16 teeth comprised 439 peptides representative of 30 proteins of human origin and 211 peptides representative of 27 proteins of non-human origin...
2017: PloS One
https://www.readbyqxmd.com/read/28745537/spatial-genetic-structure-and-body-size-divergence-in-endangered-gymnogobius-isaza-in-ancient-lake-biwa
#19
Takefumi Nakazawa, Shang-Yin Vanson Liu, Yoichiro Sakai, Kiwako S Araki, Cheng-Han Tsai, Noboru Okuda
Gymnogobius isaza is a freshwater goby endemic to ancient Lake Biwa, the largest lake in Japan. The species is now listed as 'Critically Endangered' in the Red Data Book of Japan. Nevertheless, it remains subject to fishing without any specific management strategies. Previous studies using mitochondrial DNA markers showed that this fish species has two cryptic lineages. However, little is known about spatial genetic structure and ecological differences across the broad lakescape. In this study, we collected fish samples at nine locations along the lakeshore during the breeding season and tested for the presence of spatial heterogeneity in the lineage's composition while measuring body size as the most fundamental biological trait...
July 26, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28744263/recombinant-invasive-lactococcus-lactis-carrying-a-dna-vaccine-coding-the-ag85a-antigen-increases-inf-%C3%AE-il-6-and-tnf-%C3%AE-cytokines-after-intranasal-immunization
#20
Pamela Mancha-Agresti, Camila Prosperi de Castro, Janete S C Dos Santos, Maíra A Araujo, Vanessa B Pereira, Jean G LeBlanc, Sophie Y Leclercq, Vasco Azevedo
Tuberculosis (TB) remains a major threat throughout the world and in 2015 it caused the death of 1.4 million people. The Bacillus Calmette-Guérin is the only existing vaccine against this ancient disease; however, it does not provide complete protection in adults. New vaccines against TB are eminently a global priority. The use of bacteria as vehicles for delivery of vaccine plasmids is a promising vaccination strategy. In this study, we evaluated the use of, an engineered invasive Lactococcus lactis (expressing Fibronectin-Binding Protein A from Staphylococcus aureus) for the delivery of DNA plasmid to host cells, especially to the mucosal site as a new DNA vaccine against tuberculosis...
2017: Frontiers in Microbiology
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