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https://www.readbyqxmd.com/read/29046620/the-dental-calculus-metabolome-in-modern-and-historic-samples
#1
Irina M Velsko, Katherine A Overmyer, Camilla Speller, Lauren Klaus, Matthew J Collins, Louise Loe, Laurent A F Frantz, Krithivasan Sankaranarayanan, Cecil M Lewis, Juan Bautista Rodriguez Martinez, Eros Chaves, Joshua J Coon, Greger Larson, Christina Warinner
INTRODUCTION: Dental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/29037736/dna-barcoding-based-identification-of-hippophae-species-and-authentication-of-commercial-products-by-high-resolution-melting-analysis
#2
Yue Liu, Li Xiang, Yi Zhang, Xianrong Lai, Chao Xiong, Jingjian Li, Yanyan Su, Wei Sun, Shilin Chen
Sea buckthorn (Hippophae), an ancient crop with modern virtues, is increasingly consumed in source of foods and nutraceuticals. The growing demand leads to the adulteration of commercial sea buckthorn products, which is a common form of food fraud. Herein, a high resolution melting assay, targeting a DNA barcoding region of the internal transcribed spacer 2 (ITS2) (Bar-HRM) was developed to identify the seven native Chinese Hippophae species, and to authenticate commercial sea buckthorn products. Melting data from the HRM assay demonstrated that all Hippophae species could be clearly distinguished...
March 1, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29035021/microbial-communities-and-organic-biomarkers-in-a-proterozoic-analog-sinkhole
#3
T L Hamilton, P V Welander, H L Albrecht, J M Fulton, I Schaperdoth, L R Bird, R E Summons, K H Freeman, J L Macalady
Little Salt Spring (Sarasota County, FL, USA) is a sinkhole with groundwater vents at ~77 m depth. The entire water column experiences sulfidic (~50 μM) conditions seasonally, resulting in a system poised between oxic and sulfidic conditions. Red pinnacle mats occupy the sediment-water interface in the sunlit upper basin of the sinkhole, and yielded 16S rRNA gene clones affiliated with Cyanobacteria, Chlorobi, and sulfate-reducing clades of Deltaproteobacteria. Nine bacteriochlorophyll e homologues and isorenieratene indicate contributions from Chlorobi, and abundant chlorophyll a and pheophytin a are consistent with the presence of Cyanobacteria...
November 2017: Geobiology
https://www.readbyqxmd.com/read/29030957/mollusc-shells-as-metagenomic-archives-the-true-treasure-is-the-chest-itself
#4
Marie-Agnès Coutellec
Mollusc shells, beyond the treasure of information inherently conveyed through their morphology and chemical composition also have the capacity to preserve DNA sequences over the long term in their inner structure. This has been clearly demonstrated for the first time in the study published in this issue of Molecular Ecology Resources by Der Sarkissian et al. (). With a methodology specifically dedicated to ancient DNA and solid matrices, the authors were able to successfully extract and amplify DNA from marine shells spanning the last 7,000 years...
September 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29027988/the-history-of-tree-and-shrub-taxa-on-bol-shoy-lyakhovsky-island-new-siberian-archipelago-since-the-last-interglacial-uncovered-by-sedimentary-ancient-dna-and-pollen-data
#5
Heike H Zimmermann, Elena Raschke, Laura S Epp, Kathleen R Stoof-Leichsenring, Lutz Schirrmeister, Georg Schwamborn, Ulrike Herzschuh
Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol'shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island...
October 13, 2017: Genes
https://www.readbyqxmd.com/read/29023628/ethnic-derivation-of-the-ainu-inferred-from-ancient-mitochondrial-dna-data
#6
Noboru Adachi, Tsuneo Kakuda, Ryohei Takahashi, Hideaki Kanzawa-Kiriyama, Ken-Ichi Shinoda
OBJECTIVES: The Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern-day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large-scale immigration into Hokkaido about 150 years ago, should be examined...
October 11, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29023552/the-impact-of-male-burials-on-the-construction-of-corded-ware-identity-reconstructing-networks-of-information-in-the-3rd-millennium-bc
#7
Quentin Bourgeois, Erik Kroon
The emergence of Corded Ware Groups throughout Europe in the 3rd millennium BC is one of the most defining events in European history. From the Wolga to the Rhine communities start to speak Indo-European languages and bury their dead in an extremely similar fashion. Recent ancient DNA-analyses identify a massive migration from the Eurasian steppe as the prime cause for this event. However, there is a fundamental difference between expressing a Corded Ware identity-the sharing of world views and ideas-and having a specific DNA-profile...
2017: PloS One
https://www.readbyqxmd.com/read/29020633/erasure-of-tet-oxidized-5-methylcytosine-by-a-srap-nuclease
#8
Soo-Mi Kweon, Bing Zhu, Yibu Chen, L Aravind, Shuang-Yong Xu, Douglas E Feldman
Enzymatic oxidation of 5-methylcytosine (5mC) in DNA by the Tet dioxygenases reprograms genome function in embryogenesis and postnatal development. Tet-oxidized derivatives of 5mC such as 5-hydroxymethylcytosine (5hmC) act as transient intermediates in DNA demethylation or persist as durable marks, yet how these alternative fates are specified at individual CpGs is not understood. Here, we report that the SOS response-associated peptidase (SRAP) domain protein Srap1, the mammalian ortholog of an ancient protein superfamily associated with DNA damage response operons in bacteria, binds to Tet-oxidized forms of 5mC in DNA and catalyzes turnover of these bases to unmodified cytosine by an autopeptidase-coupled nuclease...
October 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/29019354/iron-sulfur-cluster-biosynthesis-and-trafficking-impact-on-human-disease-conditions
#9
C Wachnowsky, I Fidai, J A Cowan
Iron-sulfur clusters (Fe-S) are one of the most ancient, ubiquitous and versatile classes of metal cofactors found in nature. Proteins that contain Fe-S clusters constitute one of the largest families of proteins, with varied functions that include electron transport, regulation of gene expression, substrate binding and activation, radical generation, and, more recently discovered, DNA repair. Research during the past two decades has shown that mitochondria are central to the biogenesis of Fe-S clusters in eukaryotic cells via a conserved cluster assembly machinery (ISC assembly machinery) that also controls the synthesis of Fe-S clusters of cytosolic and nuclear proteins...
October 11, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28984839/complete-mitochondrial-genome-sequencing-of-a-burial-from-a-romano-christian-cemetery-in-the-dakhleh-oasis-egypt-preliminary-indications
#10
J Eldon Molto, Odile Loreille, Elizabeth K Mallott, Ripan S Malhi, Spence Fast, Jennifer Daniels-Higginbotham, Charla Marshall, Ryan Parr
The curse of ancient Egyptian DNA was lifted by a recent study which sequenced the mitochondrial genomes (mtGenome) of 90 ancient Egyptians from the archaeological site of Abusir el-Meleq. Surprisingly, these ancient inhabitants were more closely related to those from the Near East than to contemporary Egyptians. It has been accepted that the timeless highway of the Nile River seeded Egypt with African genetic influence, well before pre-Dynastic times. Here we report on the successful recovery and analysis of the complete mtGenome from a burial recovered from a remote Romano-Christian cemetery, Kellis 2 (K2)...
October 6, 2017: Genes
https://www.readbyqxmd.com/read/28984556/pseudomonas-tarimensis-sp-nov-an-endophytic-bacteria-isolated-from-populus-euphratica
#11
Nusratgul Anwar, Manziram Rozahon, Bolatkhan Zayadan, Hormathan Mamtimin, Mehfuzem Abdurahman, Marygul Kurban, Mihribangul Abdurusul, Tursunay Mamtimin, Muhtar Abdukerim, Erkin Rahman
An endophytic bacterium, MA-69(T), was isolated from the storage liquid in the stems of Populuseuphratica trees at the ancient Ugan River in Xinjiang, PR China. Strain MA-69(T) was found to be short rod-shaped, Gram-stain-negative, non-spore-forming, aerobic and motile by means of a monopolar flagellum. According to phylogenetic analysis based on 16S rRNA gene sequences, strain MA-69(T) was assigned to the genus Pseudomonas with highest 16S rRNA gene sequence similarity of 97.5 % to Pseudomonas azotifigens JCM 12708(T), followed by Pseudomonas matsuisoli JCM 30078(T) (97...
October 6, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28984227/leprosy-in-pre-norman-suffolk-uk-biomolecular-and-geochemical-analysis-of-the-woman-from-hoxne
#12
Sarah Inskip, G Michael Taylor, Sue Anderson, Graham Stewart
PURPOSE: A woman's skull, exhibiting features of lepromatous leprosy (LL), was recovered from a garden in Hoxne, Suffolk. The absence of post crania and lack of formal excavation meant that diagnosis and dating was uncertain. The aim of this research was to confirm the diagnosis using biomolecular means and second, to place it in context with other British leprosy cases using SNP genotyping and radiocarbon dating. METHODOLOGY: Bone from the skull was analysed by ancient DNA (aDNA) methods and subjected to radiocarbon dating...
October 6, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28981695/a-comprehensive-analysis-of-transcript-supported-de-novo-genes-in-saccharomyces-sensu-stricto-yeasts
#13
Tzu-Chiao Lu, Jun-Yi Leu, Wen-Chang Lin
Novel genes arising from random DNA sequences (de novo genes) have been suggested to be widespread in the genomes of different organisms. However, our knowledge about the origin and evolution of de novo genes is still limited. To systematically understand the general features of de novo genes, we established a robust pipeline to analyze >20,000 transcript-supported coding sequences (CDSs) from the budding yeast Saccharomyces cerevisiae. Our analysis pipeline combined phylogeny, synteny, and sequence alignment information to identify possible orthologs across 20 Saccharomycetaceae yeasts and discovered 4,340 S...
July 24, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28979290/y-str-haplogroup-diversity-in-the-jat-population-reveals-several-different-ancient-origins
#14
David G Mahal, Ianis G Matsoukas
The Jats represent a large ethnic community that has inhabited the northwest region of India and Pakistan for several thousand years. It is estimated the community has a population of over 123 million people. Many historians and academics have asserted that the Jats are descendants of Aryans, Scythians, or other ancient people that arrived and lived in northern India at one time. Essentially, the specific origin of these people has remained a matter of contention for a long time. This study demonstrated that the origins of Jats can be clarified by identifying their Y-chromosome haplogroups and tracing their genetic markers on the Y-DNA haplogroup tree...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28977014/origin-of-the-ornamented-b%C3%A3-ton-perc%C3%A3-from-the-go%C3%A5-%C3%A4-biewo-site-47-as-a-trigger-of-discussion-on-long-distance-exchange-among-early-mesolithic-communities-of-central-poland-and-northern-europe
#15
Grzegorz Osipowicz, Henryk Witas, Aleksandra Lisowska-Gaczorek, Laurie Reitsema, Krzysztof Szostek, Tomasz Płoszaj, Justyna Kuriga, Daniel Makowiecki, Krystyna Jędrychowska-Dańska, Beata Cienkosz-Stepańczak
This article describes evidence for contact and exchange among Mesolithic communities in Poland and Scandinavia, based on the interdisciplinary analysis of an ornamented bâton percé from Gołębiewo site 47 (Central Poland). Typological and chronological-cultural analyses show the artefact to be most likely produced in the North European Plain, during the Boreal period. Carbon-14 dating confirms the antiquity of the artefact. Ancient DNA analysis shows the artefact to be of Rangifer tarandus antler. Following this species designation, a dispersion analysis of Early-Holocene reindeer remains in Europe was conducted, showing this species to exist only in northern Scandinavia and north-western Russia in this period...
2017: PloS One
https://www.readbyqxmd.com/read/28962023/spatio-temporal-dynamics-of-genetic-variation-in-the-iberian-lynx-along-its-path-to-extinction-reconstructed-with-ancient-dna
#16
Mireia Casas-Marce, Elena Marmesat, Laura Soriano, Begoña Martínez-Cruz, María Lucena, Francisco Nocete, Antonio Rodríguez-Hidalgo, Antoni Canals, Jordi Nadal, Cleia Detry, Eloísa Bernáldez-Sánchez, Carlos Fernández-Rodríguez, Manuel Pérez-Ripoll, Mathias Stiller, Michael Hofreiter, Alejandro Rodríguez, Eloy Revilla, Miguel Delibes, José A Godoy
There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity amongst other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time...
August 29, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28959243/rnase-h-as-gene-modifier-driver-of-evolution-and-antiviral-defense
#17
REVIEW
Karin Moelling, Felix Broecker, Giancarlo Russo, Shinichi Sunagawa
Retroviral infections are 'mini-symbiotic' events supplying recipient cells with sequences for viral replication, including the reverse transcriptase (RT) and ribonuclease H (RNase H). These proteins and other viral or cellular sequences can provide novel cellular functions including immune defense mechanisms. Their high error rate renders RT-RNases H drivers of evolutionary innovation. Integrated retroviruses and the related transposable elements (TEs) have existed for at least 150 million years, constitute up to 80% of eukaryotic genomes and are also present in prokaryotes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28959177/ancient-permafrost-staphylococci-carry-antibiotic-resistance-genes
#18
Elena Kashuba, Alexey A Dmitriev, Shady Mansour Kamal, Ojar Melefors, Gennady Griva, Ute Römling, Ingemar Ernberg, Vladimir Kashuba, Anatoli Brouchkov
Background: Permafrost preserves a variety of viable ancient microorganisms. Some of them can be cultivated after being kept at subzero temperatures for thousands or even millions of years. Objective: To cultivate bacterial strains from permafrost. Design: We isolated and cultivated two bacterial strains from permafrost that was obtained at Mammoth Mountain in Siberia and attributed to the Middle Miocene. Bacterial genomic DNA was sequenced with 40-60× coverage and high-quality contigs were assembled. The first strain was assigned to Staphylococcus warneri species (designated MMP1) and the second one to Staphylococcus hominis species (designated MMP2), based on the classification of 16S ribosomal RNA genes and genomic sequences...
2017: Microbial Ecology in Health and Disease
https://www.readbyqxmd.com/read/28957511/inferring-past-environments-from-ancient-epigenomes
#19
David Gokhman, Anat Malul, Liran Carmel
Analyzing the conditions in which past individuals lived is key to understanding the environments and cultural transitions to which humans had to adapt. Here, we suggest a methodology to probe into past environments, using reconstructed premortem DNA methylation maps of ancient individuals. We review a large body of research showing that differential DNA methylation is associated with changes in various external and internal factors, and propose that loci whose DNA methylation level is environmentally responsive could serve as markers to infer about ancient daily life, diseases, nutrition, exposure to toxins, and more...
October 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28955047/erratum-phylogeography-of-the-tyrrhenian-red-deer-cervus-elaphus-corsicanus-resolved-using-ancient-dna-of-radiocarbon-dated-subfossils
#20
K Doan, F E Zachos, B Wilkens, J-D Vigne, N Piotrowska, A Stanković, B Jędrzejewska, K Stefaniak, M Niedziałkowska
A corarection to this Article has been published and is linked from the HTML version of this paper. The error has not been fixed in the paper.
September 27, 2017: Scientific Reports
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