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https://www.readbyqxmd.com/read/29117125/the-small-and-the-dead-a-review-of-ancient-dna-studies-analysing-micromammal-species
#1
REVIEW
Roseina Woods, Melissa M Marr, Selina Brace, Ian Barnes
The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation...
November 8, 2017: Genes
https://www.readbyqxmd.com/read/29114402/comparative-scaffolding-and-gap-filling-of-ancient-bacterial-genomes-applied-to-two-ancient-yersinia-pestis-genomes
#2
Nina Luhmann, Daniel Doerr, Cedric Chauve
Yersinia pestis is the causative agent of the bubonic plague, a disease responsible for several dramatic historical pandemics. Progress in ancient DNA (aDNA) sequencing rendered possible the sequencing of whole genomes of important human pathogens, including the ancient Y. pestis strains responsible for outbreaks of the bubonic plague in London in the 14th century and in Marseille in the 18th century, among others. However, aDNA sequencing data are still characterized by short reads and non-uniform coverage, so assembling ancient pathogen genomes remains challenging and often prevents a detailed study of genome rearrangements...
September 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29065339/reduced-graphene-oxide-bifeo3-nanohybrids-based-signal-on-photoelectrochemical-sensing-system-for-prostate-specific-antigen-detection-coupling-with-magnetic-microfluidic-device
#3
Qian Zhou, Youxiu Lin, Kangyao Zhang, Meijin Li, Dianping Tang
A novel magnetic controlled photoelectrochemical (PEC) sensing system was designed for sensitive detection of prostate-specific antigen (PSA) using reduced graphene oxide-functionalized BiFeO3 (rGO-BiFeO3) as the photoactive material and target-triggered hybridization chain reaction (HCR) for signal amplification. Remarkably enhanced PEC performance could be obtained by using rGO-BiFeO3 as the photoelectrode material due to its accelerated charge transfer and improved the visible light absorption. Additionally, efficient and simple operation could be achieved by introducing magnetic controlled flow-through device...
October 16, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28984227/leprosy-in-pre-norman-suffolk-uk-biomolecular-and-geochemical-analysis-of-the-woman-from-hoxne
#4
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/28950041/development-of-a-multiplex-pcr-assay-for-detection-of-pseudomonas-fluorescens-with-biofilm-formation-ability
#5
Yu Xu, Wanyi Chen, Chunping You, Zhenmin Liu
Under the cold storage and processing conditions of raw milk, the psychrotrophic Pseudomonas fluorescens is usually found as predominant bacteria causing its spoilage. In this study, a multiplex PCR assay was developed for rapid and selective detection of P. fluorescens with biofilm formation ability. The target sequences were 2 genes (adnA and fliC) related to biofilm formation and flagella biosynthesis of P. fluorescens. The specificity of the mPCR assay was evaluated with 7 reference strains, isolated from raw milk, belonging to P...
October 2017: Journal of Food Science
https://www.readbyqxmd.com/read/28934125/optimized-mtdna-control-region-primer-extension-capture-analysis-for-forensically-relevant-samples-and-highly-compromised-mtdna-of-different-age-and-origin
#6
Mayra Eduardoff, Catarina Xavier, Christina Strobl, Andrea Casas-Vargas, Walther Parson
The analysis of mitochondrial DNA (mtDNA) has proven useful in forensic genetics and ancient DNA (aDNA) studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR) is commonly sequenced using established Sanger-type Sequencing (STS) protocols involving fragment sizes down to approximately 150 base pairs (bp). Recent developments include Massively Parallel Sequencing (MPS) of (multiplex) PCR-generated libraries using the same amplicon sizes...
September 21, 2017: Genes
https://www.readbyqxmd.com/read/28817590/reconstructing-asian-faunal-introductions-to-eastern-africa-from-multi-proxy-biomolecular-and-archaeological-datasets
#7
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/28813480/paleogenetic-study-on-the-17th-century-korean-mummy-with-atherosclerotic-cardiovascular-disease
#8
Dong Hoon Shin, Chang Seok Oh, Jong Ha Hong, Yusu Kim, Soong Deok Lee, Eunju Lee
While atherosclerotic cardiovascular disease (ASCVD) is known to be common among modern people exposed to various risk factors, recent paleopathological studies have shown that it affected ancient populations much more frequently than expected. In 2010, we investigated a 17th century Korean female mummy with presumptive ASCVD signs. Although the resulting report was a rare and invaluable conjecture on the disease status of an ancient East Asian population, the diagnosis had been based only on anatomical and radiological techniques, and so could not confirm the existence of ASCVD in the mummy...
2017: PloS One
https://www.readbyqxmd.com/read/28751712/activation-of-mitophagy-leads-to-decline-in-mfn2-and-loss-of-mitochondrial-mass-in-fuchs-endothelial-corneal-dystrophy
#9
Anne-Sophie Benischke, Shivakumar Vasanth, Takashi Miyai, Kishore Reddy Katikireddy, Tomas White, Yuming Chen, Adna Halilovic, Marianne Price, Francis Price, Paloma B Liton, Ula V Jurkunas
Human corneal endothelial cells (HCEnCs) are terminally differentiated cells that have limited regenerative potential. The large numbers of mitochondria in HCEnCs are critical for pump and barrier function required for corneal hydration and transparency. Fuchs Endothelial Corneal Dystrophy (FECD) is a highly prevalent late-onset oxidative stress disorder characterized by progressive loss of HCEnCs. We previously reported increased mitochondrial fragmentation and reduced ATP and mtDNA copy number in FECD. Herein, carbonyl cyanide m-chlorophenyl hydrazone (CCCP)-induced mitochondrial depolarization decreased mitochondrial mass and Mfn2 levels, which were rescued with mitophagy blocker, bafilomycin, in FECD...
July 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28737475/ancient-ascaris-dna-sequences-of-cytochrome-b-cytochrome-c-oxidase-subunit-1-nadh-dehydrogenase-subunit-1-and-internal-transcribed-spacer-1-genes-from-joseon-mummy-feces-of-korea
#10
Jong Ha Hong, Chang Seok Oh, Min Seo, Jong Yil Chai, Dong Hoon Shin
We analyzed Ascaris ancient DNA (aDNA) of cytochrome b (cyt b), cytochrome c oxidase subunit 1 (COX1), NADH dehydrogenase subunit 1 (NAD1) and internal transcribed spacer 1 (ITS1) genes extracted from the feces or precipitates of 15th to 18th century Korean mummies. After multiple Ascaris genes in ancient samples were successfully amplified by PCR, consensus sequences could be determined by the alignment of the sequences of cloned PCR products. The obtained sequences of each gene were highly similar to those of Ascaris spp...
July 24, 2017: Journal of Parasitology
https://www.readbyqxmd.com/read/28718817/time-to-spread-your-wings-a-review-of-the-avian-ancient-dna-field
#11
REVIEW
Alicia Grealy, Nicolas J Rawlence, Michael Bunce
Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of "avian ancient DNA" by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions...
July 18, 2017: Genes
https://www.readbyqxmd.com/read/28715914/leprosy-in-a-lombard-avar-cemetery-in-central-italy-campochiaro-molise-6th-8th-century-ad-ancient-dna-evidence-and-demography
#12
Mauro Rubini, Paola Zaio, Mark Spigelman, Helen D Donoghue
BACKGROUND: The study of past infectious diseases increases knowledge of the presence, impact and spread of pathogens within ancient populations. AIM: Polymerase chain reaction (PCR) was used to examine bones for the presence of Mycobacterium leprae ancient DNA (aDNA) as, even when leprosy is present, bony changes are not always pathognomonic of the disease. This study also examined the demographic profile of this population and compared it with two other populations to investigate any changes in mortality trends between different infectious diseases and between the pre-antibiotic and antibiotic eras...
July 17, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28694205/association-of-variants-in-sh2b1-and-rabep1-with-worsening-of-low-density-lipoprotein-and-glucose-parameters-in-patients-treated-with-psychotropic-drugs
#13
Aurélie Delacrétaz, Adna Zdralovic, Frederik Vandenberghe, Nuria Saigi-Morgui, Anaïs Glatard, Lina Quteineh, Mehdi Gholam-Rezaee, Wassim Raffoul, Lee Ann Applegate, Paris Jafari, Franziska Gamma, Armin von Gunten, Philippe Conus, Chin B Eap
Genetic factors associated with Body Mass Index (BMI) have been widely studied over the last decade. We examined whether genetic variants previously associated with BMI in the general population are associated with cardiometabolic parameter worsening in the psychiatric population receiving psychotropic drugs, a high-risk group for metabolic disturbances. Classification And Regression Trees (CARTs) were used as a tool capable of describing hierarchical associations, to pinpoint genetic variants best predicting worsening of cardiometabolic parameters (i...
September 10, 2017: Gene
https://www.readbyqxmd.com/read/28681914/2-000-year-old-%C3%AE-thalassemia-case-in-sardinia-suggests-malaria-was-endemic-by-the-roman-period
#14
Claudia Viganó, Cordula Haas, Frank J Rühli, Abigail Bouwman
OBJECTIVES: The island of Sardinia has one of the highest incidence rates of β-thalassemia in Europe due to its long history of endemic malaria, which, according to historical records, was introduced around 2,600 years ago by the Punics and only became endemic around the Middle Ages. In particular, the cod39 mutation is responsible for more than 95% of all β-thalassemia cases observed on the island. Debates surround the origin of the mutation. Some argue that its presence in the Western Mediterranean reflects the migration of people away from Sardinia, others that it reflects the colonization of the island by the Punics who might have carried the disease allele...
October 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28678860/multi-scale-ancient-dna-analyses-confirm-the-western-origin-of-michelsberg-farmers-and-document-probable-practices-of-human-sacrifice
#15
Alice Beau, Maïté Rivollat, Hélène Réveillas, Marie-Hélène Pemonge, Fanny Mendisco, Yohann Thomas, Philippe Lefranc, Marie-France Deguilloux
In Europe, the Middle Neolithic is characterized by an important diversification of cultures. In northeastern France, the appearance of the Michelsberg culture has been correlated with major cultural changes and interpreted as the result of the settlement of new groups originating from the Paris Basin. This cultural transition has been accompanied by the expansion of particular funerary practices involving inhumations within circular pits and individuals in "non-conventional" positions (deposited in the pits without any particular treatment)...
2017: PloS One
https://www.readbyqxmd.com/read/28643414/associating-and-dissociating-nanodimer-analysis-for-quantifying-ultrasmall-amounts-of-dna
#16
Keunsuk Kim, Jeong-Wook Oh, Young Kwang Lee, Jiwoong Son, Jwa-Min Nam
The amplification- and enzyme-free quantification of DNA at ultralow concentrations, on the order of 10-1000 targets, is highly beneficial but extremely challenging. To address this challenge, true detection signals must be reliably discriminated from false or noise signals. Herein, we describe the development of associating and dissociating nanodimer analysis (ADNA) as a method that enables a maximum number of detection signals to be collected from true target-binding events while keeping nonspecific signals at a minimum level...
June 23, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28625158/a-minimally-invasive-method-for-sampling-human-petrous-bones-from-the-cranial-base-for-ancient-dna-analysis
#17
Kendra A Sirak, Daniel M Fernandes, Olivia Cheronet, Mario Novak, Beatriz Gamarra, Tímea Balassa, Zsolt Bernert, Andrea Cséki, János Dani, József Zsolt Gallina, Gábor Kocsis-Buruzs, Ivett Kővári, Orsolya László, Ildikó Pap, Róbert Patay, Zsolt Petkes, Gergely Szenthe, Tamás Szeniczey, Tamás Hajdu, Ron Pinhasi
Ancient DNA (aDNA) research involves invasive and destructive sampling procedures that are often incompatible with anthropological, anatomical, and bioarcheological analyses requiring intact skeletal remains. The osseous labyrinth inside the petrous bone has been shown to yield higher amounts of endogenous DNA than any other skeletal element; however, accessing this labyrinth in cases of a complete or reconstructed skull involves causing major structural damage to the cranial vault or base. Here, we describe a novel cranial base drilling method (CBDM) for accessing the osseous labyrinth from the cranial base that prevents damaging the surrounding cranial features, making it highly complementary to morphological analyses...
June 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28609785/comprehensive-analysis-of-microorganisms-accompanying-human-archaeological-remains
#18
Anna Philips, Ireneusz Stolarek, Bogna Kuczkowska, Anna Juras, Luiza Handschuh, Janusz Piontek, Piotr Kozlowski, Marek Figlerowicz
Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains...
July 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28569387/synthesis-and-in-vitro-antioxidant-activity-study-of-some-new-piperazinyl-flavone-compounds
#19
Paweł Berczyński, Aleksandra Kładna, Irena Kruk, Elmas Sarı, Hatice Nehir Murat, Oya Bozdağ Dündar, Hassan Y Aboul-Enein
Flavones exhibit a variety of beneficial effects and are well known for their medicinal importance in several diseases, including cardiovascular, neurodegenerative and cancer. The inclusion of the piperazine ring to the flavone backbone is an important strategy in drug discovery but only a few studies have synthesized piperazinyl flavone compounds to test their biological activity. While there is a major focus on the antioxidant properties of drugs in therapy of several diseases of inflammatory origin, we synthesized a series of the novel piperazinyl flavone analogues bearing the phenyl ring with different substituents...
June 1, 2017: Luminescence: the Journal of Biological and Chemical Luminescence
https://www.readbyqxmd.com/read/28521913/a-6500-year-old-middle-neolithic-child-from-pollera-cave-liguria-italy-with-probable-multifocal-osteoarticular-tuberculosis
#20
Vitale S Sparacello, Charlotte A Roberts, Ammielle Kerudin, Romy Müller
Clear skeletal evidence of prehistoric tuberculosis (TB) is rare, especially in children. We describe and differentially diagnose the pathological changes displayed by a five-year-old child, Pollera 21 (PO21) dated to the Middle Neolithic of Liguria (Italy), or 5740±30 BP (Beta-409341; 6635-6453cal BP, 2σ, OxCal 4.2). PO21 shows a number of osteoarticular lesions, mainly of a lytic nature with very little bone proliferation: the vertebral column, the shoulder and pelvic girdles, and the ribcage are involved...
June 2017: International Journal of Paleopathology
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