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https://www.readbyqxmd.com/read/28095919/ancient-bacteria-of-the-%C3%A3-tzi-s-microbiome-a-genomic-tale-from-the-copper-age
#1
Gabriele Andrea Lugli, Christian Milani, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Sabrina Duranti, Douwe van Sinderen, Marco Ventura
BACKGROUND: Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified humans, such as the Tyrolean Iceman, has been shown to contain bacterial DNA that is suitable for population profiling of the prehistoric bacteria that colonized such ancient human hosts. RESULTS: Here, we performed a microbial cataloging of the distal gut microbiota of the Tyrolean Iceman, which highlights a predominant abundance of Clostridium and Pseudomonas species...
January 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28095329/comparing-ancient-dna-survival-and-proteome-content-in-69-archaeological-cattle-tooth-and-bone-samples-from-multiple-european-sites
#2
Caroline Wadsworth, Noemi Procopio, Cecilia Anderung, José-Miguel Carretero, Eneko Iriarte, Cristina Valdiosera, Rengert Elburg, Kirsty Penkman, Michael Buckley
No abstract text is available yet for this article.
January 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28094816/methylation-specific-targeting-of-a-chromatin-remodeling-complex-from-sponges-to-humans
#3
Jason M Cramer, Deborah Pohlmann, Fernando Gomez, Leslie Mark, Benjamin Kornegay, Chelsea Hall, Edhriz Siraliev-Perez, Ninad M Walavalkar, M Jeannette Sperlazza, Stephanie Bilinovich, Jeremy W Prokop, April L Hill, David C Williams
DNA cytosine methylation and methyl-cytosine binding domain (MBD) containing proteins are found throughout all vertebrate species studied to date. However, both the presence of DNA methylation and pattern of methylation varies among invertebrate species. Invertebrates generally have only a single MBD protein, MBD2/3, that does not always contain appropriate residues for selectively binding methylated DNA. Therefore, we sought to determine whether sponges, one of the most ancient extant metazoan lineages, possess an MBD2/3 capable of recognizing methylated DNA and recruiting the associated nucleosome remodeling and deacetylase (NuRD) complex...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28089793/eggshell-palaeogenomics-palaeognath-evolutionary-history-revealed-through-ancient-nuclear-and-mitochondrial-dna-from-madagascan-elephant-bird-aepyornis-sp-eggshell
#4
Alicia Grealy, Matthew Phillips, Gifford Miller, M Thomas P Gilbert, Jean-Marie Rouillard, David Lambert, Michael Bunce, James Haile
Palaeognaths, the sister group of all other living birds (neognaths), were once considered to be vicariant relics from the breakup of the Gondwanan supercontinent. However, recent molecular studies instead argue for dispersal of volant ancestors across marine barriers. Resolving this debate hinges upon accurately reconstructing their evolutionary relationships and dating their divergences, which often relies on phylogenetic information from extinct relatives and nuclear genomes. Mitogenomes from the extinct elephant birds of Madagascar have helped inform the palaeognath phylogeny; however, nuclear information has remained unavailable...
January 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28087320/poly-adp-ribose-polymerase-activity-and-inhibition-in-cancer
#5
REVIEW
Caleb Dulaney, Samuel Marcrom, Jennifer Stanley, Eddy S Yang
Genomic instability resultant from defective DNA repair mechanisms is a fundamental hallmark of cancer. The poly(ADP-ribose) polymerase (PARP) proteins 1, 2 and 3 catalyze the polymerization of poly(ADP-ribose) and covalent attachment to proteins in a phylogenetically ancient form of protein modification. PARPs play a role in base excision repair, homologous recombination, and non-homologous end joining. The discovery that loss of PARP activity had cytotoxic effects in cells deficient in homologous recombination has sparked a decade of translational research efforts that culminated in the FDA approval of an oral PARP inhibitor for clinical use in patients with ovarian cancer and defective homologous recombination...
January 10, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28079013/natural-product-inhibitors-of-topoisomerases-review-and-docking-study
#6
L Scotti, F J B Mendonça Júnior, F F Ribeiro, J F Tavares, M S Da Silva, J M Barbosa Filho, M T Scotti
Since ancient times, natural products have been used in treating various diseases effectively and safely. Nowadays, these natural compounds are submitted to sophisticated methodologies from isolation, computing, analytical, and even serving as pharmacophore suggestions for synthesis. The substances extracted from marine species, plants, and microorganisms present activities beneficial to our health, including protection against malignant tumors. The topoisomerase enzymes play an important role in DNA metabolism, and searching for enzyme inhibitors is an important target in the search for new anticancer drugs...
January 11, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28077774/tropical-ancient-dna-reveals-relationships-of-the-extinct-bahamian-giant-tortoise-chelonoidis-alburyorum
#7
Christian Kehlmaier, Axel Barlow, Alexander K Hastings, Melita Vamberger, Johanna L A Paijmans, David W Steadman, Nancy A Albury, Richard Franz, Michael Hofreiter, Uwe Fritz
Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1 000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island...
January 11, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28077607/anatomy-of-mdm2-and-mdm4-in-evolution
#8
REVIEW
Ban Xiong Tan, Hoe Peng Liew, Joy S Chua, Farid J Ghadessy, Yaw Sing Tan, David P Lane, Cynthia R Coffill
Mouse double minute (Mdm) genes span an evolutionary timeframe from the ancient eukaryotic placozoa Trichoplax adhaerens to Homo sapiens, implying a significant and possibly conserved cellular role throughout history. Maintenance of DNA integrity and response to DNA damage involve many key regulatory pathways, including precise control over the tumour suppressor protein p53. In most vertebrates, degradation of p53 through proteasomal targeting is primarily mediated by heterodimers of Mdm2 and the Mdm2-related protein Mdm4 (also known as MdmX)...
January 10, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/28074622/-holostei-versus-halecostomi-problem-insight-from-cytogenetics-of-ancient-nonteleost-actinopterygian-fish-bowfin-amia-calva
#9
Zuzana Majtánová, Radka Symonová, Lenin Arias-Rodriguez, Lauren Sallan, Petr Ráb
Bowfin belongs to an ancient lineage of nonteleost ray-finned fishes (actinopterygians) and is the only extant survivor of a once diverged group, the Halecomorphi or Amiiformes. Owing to the scarcity of extant nonteleost ray-finned lineages, also referred as "living fossils," their phylogenetic interrelationships have been the target of multiple hypotheses concerning their sister group relationships. Molecular and morphological data sets have produced controversial results; bowfin is considered as either the sister group to genome-duplicated teleosts (together forming the group of Halecostomi) or to gars (Lepisosteiformes; together forming the group of Holostei)...
January 11, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28072390/a-molecular-portrait-of-maternal-sepsis-from-byzantine-troy
#10
Alison M Devault, Tatum D Mortimer, Andrew Kitchen, Henrike Kiesewetter, Jacob M Enk, G Brian Golding, John Southon, Melanie Kuch, Ana T Duggan, William Aylward, Shea N Gardner, Jonathan E Allen, Andrew M King, Gerard Wright, Makoto Kuroda, Kengo Kato, Derek Eg Briggs, Gino Fornaciari, Edward C Holmes, Hendrik N Poinar, Caitlin S Pepperell
Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While excavating a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman's remains. Scanning electron microscopy of the tissue revealed 'ghost cells', resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis. Gardnerella vaginalis and Staphylococcus saprophyticus dominated the abscesses...
January 10, 2017: ELife
https://www.readbyqxmd.com/read/28063178/landscape-genetics-indicate-recently-increased-habitat-fragmentation-in-african-forest-associated-chafers
#11
Jonas Eberle, Dennis Rödder, Marc Beckett, Dirk Ahrens
Today, indigenous forests cover less than 0.6% of South Africa's land surface and are highly fragmented. Most forest relicts are very small and typically occur in fire-protected gorges along the eastern Great Escarpment. Yet, they hold a unique and valuable fauna with high endemism and ancient phylogenetic lineages, fostered by long term climatic stability and complex micro-climates. Despite numerous studies on southern African vegetation cover, the current state of knowledge about the natural extension of indigenous forests is rather fragmentary...
January 7, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28052096/sex-determination-from-fragmented-and-degenerated-dna-by-amplified-product-length-polymorphism-bidirectional-snp-analysis-of-amelogenin-and-sry-genes
#12
Kotoka Masuyama, Hideki Shojo, Hiroaki Nakanishi, Shota Inokuchi, Noboru Adachi
Sex determination is important in archeology and anthropology for the study of past societies, cultures, and human activities. Sex determination is also one of the most important components of individual identification in criminal investigations. We developed a new method of sex determination by detecting a single-nucleotide polymorphism in the amelogenin gene using amplified product-length polymorphisms in combination with sex-determining region Y analysis. We particularly focused on the most common types of postmortem DNA damage in ancient and forensic samples: fragmentation and nucleotide modification resulting from deamination...
2017: PloS One
https://www.readbyqxmd.com/read/28049632/paleogenetic-study-of-ancient-dna-suggestive-of-x-linked-acrogigantism
#13
Albert Beckers, Daniel Fernandes, Frederic Fina, Mario Novak, Angelo Abati, Liliya Rostomyan, Albert Thiry, L'Houcine Ouafik, Bertrand Pasture, Ron Pinhasi, Adrian F Daly
Extract: Dear Editor, Pituitary gigantism is caused by chronic growth hormone (GH) hypersecretion by a pituitary lesion before epiphyseal fusion. Genetic causes have been identified in nearly 50% of patients with pituitary gigantism, with germline mutations in the AIP gene being the most frequent cause (Rostomyan et al. 2015). Recently, a new form of pituitary gigantism, X-linked acrogigantism (X-LAG), was described (Trivellin et al. 2014). X-LAG is due to chromosome Xq26.3 duplication and GPR101 is the disease-associated gene (Trivellin et al...
January 3, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28039434/autophagy-wins-the-2016-nobel-prize-in-physiology-or-medicine-breakthroughs-in-baker-s-yeast-fuel-advances-in-biomedical-research
#14
Beth Levine, Daniel J Klionsky
Autophagy is an ancient pathway in which parts of eukaryotic cells are self-digested within the lysosome or vacuole. This process has been studied for the past seven decades; however, we are only beginning to gain a molecular understanding of the key steps required for autophagy. Originally characterized as a hormonal and starvation response, we now know that autophagy has a much broader role in biology, including organellar remodeling, protein and organelle quality control, prevention of genotoxic stress, tumor suppression, pathogen elimination, regulation of immunity and inflammation, maternal DNA inheritance, metabolism, and cellular survival...
December 30, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28035749/genome-compositional-organization-in-gars-shows-more-similarities-to-mammals-than-to-other-ray-finned-fish
#15
Radka Symonová, Zuzana Majtánová, Lenin Arias-Rodriguez, Libor Mořkovský, Tereza Kořínková, Lionel Cavin, Martina Johnson Pokorná, Marie Doležálková, Martin Flajšhans, Eric Normandeau, Petr Ráb, Axel Meyer, Louis Bernatchez
Genomic GC content can vary locally, and GC-rich regions are usually associated with increased DNA thermostability in thermophilic prokaryotes and warm-blooded eukaryotes. Among vertebrates, fish and amphibians appeared to possess a distinctly less heterogeneous AT/GC organization in their genomes, whereas cytogenetically detectable GC heterogeneity has so far only been documented in mammals and birds. The subject of our study is the gar, an ancient "living fossil" of a basal ray-finned fish lineage, known from the Cretaceous period...
December 30, 2016: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28034339/on-the-origin-of-iberomaurusians-new-data-based-on-ancient-mitochondrial-dna-and-phylogenetic-analysis-of-afalou-and-taforalt-populations
#16
Rym Kefi, Meriem Hechmi, Chokri Naouali, Haifa Jmel, Sana Hsouna, Eric Bouzaid, Sonia Abdelhak, Eliane Beraud-Colomb, Alain Stevanovitch
The Western North African population was characterized by the presence of Iberomaurusian civilization at the Epiplaeolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved in situ in North Africa. With the aim to contribute to a better knowledge of the settlement of North Africa we analysed the mitochondrial DNA extracted from Iberomaurusian skeletons exhumed from the archaeological site of Afalou (AFA) (15,000-11,000 YBP) in Algeria and from the archaeological site of Taforalt (TAF) (23,000-10,800 YBP) in Morocco...
December 30, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28029148/investigating-mitochondrial-dna-relationships-in-neolithic-western-europe-through-serial-coalescent-simulations
#17
Maïté Rivollat, Stéphane Rottier, Christine Couture, Marie-Hélène Pemonge, Fanny Mendisco, Mark G Thomas, Marie-France Deguilloux, Pascale Gerbault
Recent ancient DNA studies on European Neolithic human populations have provided persuasive evidence of a major migration of farmers originating from the Aegean, accompanied by sporadic hunter-gatherer admixture into early Neolithic populations, but increasing toward the Late Neolithic. In this context, ancient mitochondrial DNA data collected from the Neolithic necropolis of Gurgy (Paris Basin, France), the largest mitochondrial DNA sample obtained from a single archeological site for the Early/Middle Neolithic period, indicate little differentiation from farmers associated to both the Danubian and Mediterranean Neolithic migration routes, as well as from Western European hunter-gatherers...
December 28, 2016: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28027966/sequence-motifs-associated-with-paternal-transmission-of-mitochondrial-dna-in-the-horse-mussel-modiolus-modiolus-bivalvia-mytilidae
#18
Brent M Robicheau, Sophie Breton, Donald T Stewart
In the majority of metazoans paternal mitochondria represent evolutionary dead-ends. In many bivalves, however, this paradigm does not hold true; both maternal and paternal mitochondria are inherited. Herein, we characterize maternal and paternal mitochondrial control regions of the horse mussel, Modiolus modiolus (Bivalvia: Mytilidae). The maternal control region is 808bp long, while the paternal control region is longer at 2.3kb. We hypothesize that the size difference is due to a combination of repeated duplications within the control region of the paternal mtDNA genome, as well as an evolutionarily ancient recombination event between two sex-associated mtDNA genomes that led to the insertion of a second control region sequence in the genome that is now transmitted via males...
December 24, 2016: Gene
https://www.readbyqxmd.com/read/28025275/mirnas-in-ancient-tissue-specimens-of-the-tyrolean-iceman
#19
Andreas Keller, Stephanie Kreis, Petra Leidinger, Frank Maixner, Nicole Ludwig, Christina Backes, Valentina Galata, Gea Guerriero, Tobias Fehlmann, Andre Franke, Benjamin Meder, Albert Zink, Eckart Meese
The analysis of nucleic acids in ancient samples is largely limited to DNA. Small non-coding RNAs (microRNAs) are known to be evolutionary conserved and stable. To gain knowledge on miRNAs measured from ancient samples we profiled microRNAs in cryoconserved mummies. First, we established the approach on a World War One warrior, the "Kaiserjäger", which has been preserved for almost one century. Then, we profiled seven ancient tissue specimens including skeletal muscle, stomach mucosa, stomach content and two corpus organ tissues of the 5,300 year-old copper age mummy Iceman and compared these profiles to the presence of organ-specific miRNAs in modern tissues...
December 26, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28025001/a-molecular-phylogeny-of-dichocarpum-ranunculaceae-implications-for-eastern-asian-biogeography
#20
Kun-Li Xiang, Liang Zhao, Andrey S Erst, Sheng-Xiang Yu, Florian Jabbour, Wei Wang
East Asia is characterized by high levels of species diversity and endemism. However, the biogeographical patterns and processes underlying the distribution of biodiversity within the area are still poorly known. In this study, we used plastid (matK, trnL-F, and trnH-psbA) and nuclear (ITS) DNA sequences to investigate the historical biogeography of Dichocarpum (Ranunculaceae), an eastern Asian endemic genus throughout warm-temperate and subtropical forests of the area. Phylogenetic analyses strongly support Dichocarpum as monophyletic, which contains two major clades...
December 23, 2016: Molecular Phylogenetics and Evolution
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