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https://www.readbyqxmd.com/read/28160617/reinforcing-plant-evolutionary-genomics-using-ancient-dna
#1
REVIEW
Rafal M Gutaker, Hernán A Burbano
Improved understanding of ancient DNA (aDNA) biochemical properties coupled with application of next generation sequencing (NGS) methods enabled sequencing and authenticating genomes of historical samples. This advancement ignited a revolution in plant evolutionary genomics by allowing direct observations of past molecular diversity. Analyses of genomes sequenced from temporally distributed samples of Gossypium sp., Phytophthora infestans and Arabidopsis thaliana improved our understanding of the evolutionary rates and time scales at which genome remodeling takes place...
February 1, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28145542/a-spectroscopic-study-of-the-excited-state-proton-transfer-processes-of-8-bromo-7-hydroxyquinolin-2-yl-methyl-protected-phenol-in-aqueous-solutions
#2
Jinqing Huang, Adna P Muliawan, Jiani Ma, Ming De Li, Hoi Kei Chiu, Xin Lan, Davide Deodato, David Lee Phillips, Timothy M Dore
A combination of spectroscopic methods and density functional theory (DFT) computations was used to study the excited state proton transfer (ESPT) processes of (8-bromo-7-hydroxyquinolin-2-yl)methyl-protected phenol (BHQ-OPh). Characterization of the prototropic forms of BHQ-OPh in different solvent environments revealed that the neutral form predominates in acetonitrile and in 1 : 1 acetonitrile/water (pH 5.0), whereas the anionic form predominates in 1 : 1 acetonitrile/PBS (pH 7.4). Both the neutral and anionic forms were significantly populated in 1 : 1 acetonitrile/water...
February 1, 2017: Photochemical & Photobiological Sciences
https://www.readbyqxmd.com/read/28101915/early-medieval-stone-lined-graves-in-southern-germany-analysis-of-an-emerging-noble-class
#3
Andreas Rott, Nils Turner, Ulrike Scholz, Kristin von Heyking, Franziska Immler, Joris Peters, Jochen Haberstroh, Michaela Harbeck
OBJECTIVES: Stone-lined graves, which first appear in Bavarian territory during the 7(th) century AD, are assumed to be tombs of emerging nobility. While previous research on stone-lined grave goods supports their status as elite burials, an important factor defining nobility-kinship-has not been examined so far. MATERIALS AND METHODS: Morphological analysis of the commingled skeletal remains of 21 individuals from three archaeological sites was carried out. Radiocarbon dating was conducted on these individuals to gain information on usage intervals of these graves...
January 19, 2017: American Journal of Physical Anthropology
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/27994125/human-evolution-a-tale-from-ancient-genomes
#5
REVIEW
Bastien Llamas, Eske Willerslev, Ludovic Orlando
The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time...
February 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27932952/evaluating-tools-for-live-imaging-of-structural-plasticity-at-the-axon-initial-segment
#6
Adna S Dumitrescu, Mark D Evans, Matthew S Grubb
The axon initial segment (AIS) is a specialized neuronal compartment involved in the maintenance of axo-dendritic polarity and in the generation of action potentials. It is also a site of significant structural plasticity-manipulations of neuronal activity in vitro and in vivo can produce changes in AIS position and/or size that are associated with alterations in intrinsic excitability. However, to date all activity-dependent AIS changes have been observed in experiments carried out on fixed samples, offering only a snapshot, population-wide view of this form of plasticity...
2016: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/27899634/homologous-recombination-mediated-by-the-mycobacterial-adnab-helicase-without-end-resection-by-the-adnab-nucleases
#7
Richa Gupta, Mihaela-Carmen Unciuleac, Stewart Shuman, Michael S Glickman
Current models of bacterial homologous recombination (HR) posit that extensive resection of a DNA double-strand break (DSB) by a multisubunit helicase-nuclease machine (e.g. RecBCD, AddAB or AdnAB) generates the requisite 3' single-strand DNA substrate for RecA-mediated strand invasion. AdnAB, the helicase-nuclease implicated in mycobacterial HR, consists of two subunits, AdnA and AdnB, each composed of an N-terminal ATPase domain and a C-terminal nuclease domain. DSB unwinding by AdnAB in vitro is stringently dependent on the ATPase activity of the 'lead' AdnB motor translocating on the 3' ssDNA strand, but not on the putative 'lagging' AdnA ATPase...
January 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898159/interagency-partnership-to-deliver-veteran-directed-home-and-community-based-services-interviews-with-aging-and-disability-network-agency-personnel-regarding-their-experience-with-partner-department-of-veterans-affairs-medical-centers
#8
Kali S Thomas, Susan M Allen
Veteran-Directed Home and Community-Based Services (VD-HCBS) is a consumer-directed program that began in 2009 and is jointly administered in a partnership between the Veterans Health Administration and the Administration for Community Living. The objective of this article is to describe the Aging and Disability Network agency (ADNA) personnel's perceptions of the implementation of the VD-HCBS program with partner Department of Veterans Affairs medical centers (VAMCs). Qualitative interviews with 26 ADNA VD-HCBS personnel across the country were transcribed, coded, and analyzed...
2016: Journal of Rehabilitation Research and Development
https://www.readbyqxmd.com/read/27869396/-real-time-quantification-to-analyze-historical-colombian-samples-detecting-a-short-fragment-of-hypervariable-region-ii-of-mitochondrial-dna
#9
Luz Adriana Pérez, Freddy Rodríguez, Carl Henrik Langebaek, Helena Groot
Unlike other molecular biology studies, the analysis of ancient DNA (aDNA) requires special infrastructure and methodological conditions to guarantee the quality of the results. One of the main authenticity criteria is DNA quantification, where quantitative real-time PCR is often used given its sensitivity and specificity. Nevertheless, the implementation of these conditions and methodologies to fulfill authenticity criteria imply higher costs. Objective: To develop a simple and less costly method for mitochondrial DNA quantification suitable for highly degraded samples...
September 1, 2016: Biomédica: Revista del Instituto Nacional de Salud
https://www.readbyqxmd.com/read/27726818/paleopathology-of-human-infections-old-bones-antique-books-ancient-and-modern-molecules
#10
Olivier Dutour
Paleopathology studies the traces of disease on human and animal remains from ancient times. Infectious diseases have been, for over a century, one of its main fields of interest. The applications of paleogenetics methods to microbial aDNA, that started in the 90s combined to the recent development of new sequencing techniques allowing 'paleogenomics' approaches, have completely renewed the issue of the infections in the past. These advances open up new challenges in the understanding of the evolution of human-pathogen relationships, integrated in "One Health" concept...
August 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/27726782/paleomicrobiology-of-human-tuberculosis
#11
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
https://www.readbyqxmd.com/read/27643502/anti-inflammatory-anti-osteoclastogenic-and-antioxidant-effects-of-malva-sylvestris-extract-and-fractions-in-vitro-and-in-vivo-studies
#12
Bruna Benso, Marcelo Franchin, Adna Prado Massarioli, Jonas Augusto Rizzato Paschoal, Severino Matias Alencar, Gilson Cesar Nobre Franco, Pedro Luiz Rosalen
Given their medical importance, natural products represent a tremendous source of drug discovery. The aim of this study was to investigate Malva sylvestris L. extract and fractions and their pharmacological activities followed by chemical identification. The aqueous fraction (AF) was identified as the bioactive fraction in the in vitro and in vivo assays. The AF controlled the neutrophil migration to the peritoneal cavity by 66%, inhibited the antiedematogenic activity by 58.8%, and controlled IL-1β cytokine expression by 54%...
2016: PloS One
https://www.readbyqxmd.com/read/27615365/effect-of-x-ray-irradiation-on-ancient-dna-in-sub-fossil-bones-guidelines-for-safe-x-ray-imaging
#13
Alexander Immel, Adeline Le Cabec, Marion Bonazzi, Alexander Herbig, Heiko Temming, Verena J Schuenemann, Kirsten I Bos, Frauke Langbein, Katerina Harvati, Anne Bridault, Gilbert Pion, Marie-Anne Julien, Oleksandra Krotova, Nicholas J Conard, Susanne C Münzel, Dorothée G Drucker, Bence Viola, Jean-Jacques Hublin, Paul Tafforeau, Johannes Krause
Sub-fossilised remains may still contain highly degraded ancient DNA (aDNA) useful for palaeogenetic investigations. Whether X-ray computed [micro-] tomography ([μ]CT) imaging of these fossils may further damage aDNA remains debated. Although the effect of X-ray on DNA in living organisms is well documented, its impact on aDNA molecules is unexplored. Here we investigate the effects of synchrotron X-ray irradiation on aDNA from Pleistocene bones. A clear correlation appears between decreasing aDNA quantities and accumulating X-ray dose-levels above 2000 Gray (Gy)...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27606907/statistical-methods-for-analyzing-ancient-dna-from-hominins
#14
REVIEW
Montgomery Slatkin
In the past few years, the number of autosomal DNA sequences from human fossils has grown explosively and numerous partial or complete sequences are available from our closest relatives, Neanderthal and Denisovans. I review commonly used statistical methods applied to these sequences. These methods fall into three broad classes: methods for estimating levels of contamination, descriptive methods, and methods based on population genetic models. The latter two classes are largely methods developed for the analysis of present-day genomic data...
December 2016: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/27511803/radical-scavenging-activity-of-penicillin-g-ampicillin-oxacillin-and-dicloxacillin
#15
Paweł Berczyński, Aleksandra Kładna, Irena Kruk, Hassan Y Aboul-Enein
The aim of this study was to characterize the antioxidant activity of penicillin G (PG), ampicillin (AMP), oxacillin (OX) and dicloxacillin (DOX) through their reactivity towards reactive oxygen species (superoxide anion radical, O2•̅; hydroxyl radical, HO(•) ; peroxyl radical, ROO(•) ; hydrogen peroxide, H2 O2 ; DPPH(•) ) using various in vitro antioxidant assays with chemiluminescence (CL) and spectrophotometry as measurement techniques. In hydroxyl radical assays , PG, OX and AMP were found to inhibit the CL signal arising from the Fenton-like reaction in a dose-dependent manner with IC50  = 0...
August 11, 2016: Luminescence: the Journal of Biological and Chemical Luminescence
https://www.readbyqxmd.com/read/27486712/-masywne-krwawienie-z-jelita-ma%C3%A5-ego-nowa-opcja-terapeutyczna-z-lokalizacj%C3%A4-microcoil-i-laparoskopow%C3%A4-resekcj%C3%A4
#16
Andrzej Dobradin
Masywne krwawienie z przewodu pokarmowego prezentuje kompleksowy problem diagnostyczny i terapeutyczny. Dokładna identyfikacja miejsca krwawienia jest skomplikowana i chirurgiczna resekcja miejsca krwawienia jest trudne. Angiografii używanej do lokalizacji i embolizacji miejscu krwawienia w krążeniu krezkowym brakuje skuteczności ze względu na skomplikowaną sieć zespolenia naczyń krwionośnych zaopatrujących jelito cienkie. Przedoperacyjnie umieszczenie microcoil dla fluoroskopowo kierowanej laparoskopowej resekcji jelita cienkiego zostało wykorzystane w przypadku 58-letniej kobiety leczonej chemioterapią z użyciem idarubicyny i cytarabiny...
2016: Wiadomości Lekarskie: Organ Polskiego Towarzystwa Lekarskiego
https://www.readbyqxmd.com/read/27436340/toward-high-resolution-population-genomics-using-archaeological-samples
#17
REVIEW
Irina Morozova, Pavel Flegontov, Alexander S Mikheyev, Sergey Bruskin, Hosseinali Asgharian, Petr Ponomarenko, Vladimir Klyuchnikov, GaneshPrasad ArunKumar, Egor Prokhortchouk, Yuriy Gankin, Evgeny Rogaev, Yuri Nikolsky, Ancha Baranova, Eran Elhaik, Tatiana V Tatarinova
The term 'ancient DNA' (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of 'molecular paleontology'. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas...
August 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27427931/size-of-velopharyngeal-structures-after-primary-palatoplasty
#18
Ana Flavia Rodrigues da Silva, Jeniffer de Cássia Rillo Dutka, Adna Maressa Pereira do Amaral, Maíra de Souza Périco, Maria Inês Pegoraro-Krook
OBJECTIVE:  To describe and compare measures of velar length, velar thickness, and depth of the nasopharynx between two groups of patients with velopharyngeal dysfunction after primary palatoplasty: one received the modified Langenbeck procedure and the other the Furlow procedure. DESIGN:  Comparative study involving a convenience sample of videofluoroscopic films established prospectively. SETTING:  Surgeries and videofluoroscopic assessments were conducted at a craniofacial center...
July 18, 2016: Cleft Palate-craniofacial Journal
https://www.readbyqxmd.com/read/27301230/prediction-of-the-y-chromosome-haplogroups-within-a-recently-settled-turkish-population-in-sarajevo-bosnia-and-herzegovina
#19
Serkan Doğan, Gŭlşen Doğan, Adna Ašić, Larisa Besić, Biljana Klimenta, Mirsada Hukić, Yusuf Turan, Dragan Primorac, Damir Marjanović
Analysis of Y-chromosome haplogroup distribution is widely used when investigating geographical clustering of different populations, which is why it plays an important role in population genetics, human migration patterns and even in forensic investigations. Individual determination of these haplogroups is mostly based on the analysis of single nucleotide polymorphism (SNP) markers located in the non-recombining part of Y-chromosome (NRY). On the other hand, the number of forensic and anthropology studies investigating short tandem repeats on the Y-chromosome (Y-STRs) increases rapidly every year...
April 2016: Collegium Antropologicum
https://www.readbyqxmd.com/read/27289479/archaeogenetics-in-evolutionary-medicine
#20
REVIEW
Abigail Bouwman, Frank Rühli
Archaeogenetics is the study of exploration of ancient DNA (aDNA) of more than 70 years old. It is an important part of the wider studies of many different areas of our past, including animal, plant and pathogen evolution and domestication events. Hereby, we address specifically the impact of research in archaeogenetics in the broader field of evolutionary medicine. Studies on ancient hominid genomes help to understand even modern health patterns. Human genetic microevolution, e.g. related to abilities of post-weaning milk consumption, and specifically genetic adaptation in disease susceptibility, e...
September 2016: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
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