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https://www.readbyqxmd.com/read/28821238/genome-wide-analysis-of-ltr-retrotransposon-diversity-and-its-impact-on-the-evolution-of-the-genus-helianthus-l
#1
Flavia Mascagni, Tommaso Giordani, Marilena Ceccarelli, Andrea Cavallini, Lucia Natali
BACKGROUND: Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels...
August 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28821184/repetitive-dna-in-the-catfish-genome-rdna-microsatellites-and-tc1-mariner-transposon-sequences-in-imparfinis-species-siluriformes-heptapteridae
#2
Juceli Gonzalez Gouveia, Ivan Rodrigo Wolf, Laurival Antonio Vilas-Boas, John Seymour Heslop-Harrison, Trude Schwarzacher, Ana Lúcia Dias
Physical mapping of repetitive DNA families in the karyotypes of fish is important to understand the organization and evolution of different orders, families, genera, or species. Fish in the genus Imparfinis show diverse karyotypes with various diploid numbers and ribosomal DNA (rDNA) locations. Here we isolated and characterized Tc1-mariner nucleotide sequences from Imparfinis schubarti, and mapped their locations together with 18S rDNA, 5S rDNA, and microsatellite probes in Imparfinis borodini and I. schubarti chromosomes...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28813779/dna-profiling-of-leuconostoc-citreum-strains-in-fermented-foods-by-repetitive-element-polymerase-chain-reaction
#3
Jasmine Kaur, Anshul Sharma, Sulhee Lee, Young-Seo Park
To identify and discriminate the bacterial species at the sub-specific level, rep-PCR method is a reliable genomic fingerprinting tool. Fourteen strains of bacteria were isolated from different food sources, identified as Leuconostoc citreum using 16S rRNA gene sequencing and amplified using rep-primers (REP, ERIC, and (GTG)5). Fingerprinting patterns generated band range in between 300-6000 bp with REP, 150-6000bp with ERIC and 200-1700 bp with (GTG)5 primers respectively. In UPGMA dendrogram analysis, 14 strains were clustered into three clades (I, II and III) with all the primers, thus differentiating them at the molecular level...
August 17, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28813547/an-experimental-and-numerical-study-of-hybrid-iii-dummy-response-to-simulated-underbody-blast-impacts
#4
Karthik Somasundaram, Anil Kalra, Don Sherman, Paul Begeman, King H Yang, John M Cavanaugh
Anthropometric test devices (ATDs) such as Hybrid III dummy have been widely used in automotive crash tests to evaluate the risks of injury at different body regions. In recent years, researchers have started using automotive ATDs to study the high-speed vertical loading response caused by underbelly blast (UBB) impacts. This study analyzed the Hybrid III dummy responses to short-duration large magnitude vertical acceleration in a laboratory setup. Two unique test conditions were investigated using a horizontal sled system to simulate the UBB loading conditions...
August 16, 2017: Journal of Biomechanical Engineering
https://www.readbyqxmd.com/read/28801912/computational-sequence-design-with-r2odna-designer
#5
James T MacDonald, Velia Siciliano
Recently developed DNA assembly methods have enabled the rapid and simultaneous assembly of multiple parts to create complex synthetic gene circuits. A number of groups have proposed the use of computationally designed orthogonal spacer sequences to guide the ordered assembly of parts using overlap-directed or homologous recombination-based methods. This approach is particularly useful for assembling multiple parts with repetitive elements. Orthogonal spacer sequences (sometimes called UNSs-unique nucleotide sequences) also have a number of other potential uses including in the design of synthetic promoters regulated by novel regulatory elements...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28800596/fungal-genome-and-mating-system-transitions-facilitated-by-chromosomal-translocations-involving-intercentromeric-recombination
#6
Sheng Sun, Vikas Yadav, R Blake Billmyre, Christina A Cuomo, Minou Nowrousian, Liuyang Wang, Jean-Luc Souciet, Teun Boekhout, Betina Porcel, Patrick Wincker, Joshua A Granek, Kaustuv Sanyal, Joseph Heitman
Species within the human pathogenic Cryptococcus species complex are major threats to public health, causing approximately 1 million infections globally annually. Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex, and it is non-pathogenic. Additionally, while pathogenic Cryptococcus species have bipolar mating systems with a single large mating type (MAT) locus that represents a derived state in Basidiomycetes, C. amylolentus has a tetrapolar mating system with 2 MAT loci (P/R and HD) located on different chromosomes...
August 11, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28794909/role-of-the-lf-sine-derived-distal-isl1-enhancer-in-patients-with-classic-bladder-exstrophy
#7
Rong Zhang, Michael Knapp, Franziska Kause, Heiko Reutter, Michael Ludwig
A genome-wide association study and meta-analysis identified ISL1 as the first genome-wide significant susceptibility gene for classic bladder exstrophy (CBE). A short interspersed repetitive element (SINE), first detected in lobe-finned fishes (LF-SINE), was shown to drive Isl1 expression in embryonic mouse genital eminence. Hence, we assumed this enhancer a conclusive target for mutations associated with CBE formation and analyzed a cohort of 200 CBE patients. Although we identified two enhancer variants in five CBE patients, their clinical significance seems unlikely, implying that sequence variants in the ISL1 LF-SINE enhancer are not frequently associated with CBE...
September 2017: Journal of Pediatric Genetics
https://www.readbyqxmd.com/read/28781414/test-suite-for-image-based-motion-estimation-of-the-brain-and-tongue
#8
Jordan Ramsey, Jerry L Prince, Arnold D Gomez
Noninvasive analysis of motion has important uses as qualitative markers for organ function and to validate biomechanical computer simulations relative to experimental observations. Tagged MRI is considered the gold standard for noninvasive tissue motion estimation in the heart, and this has inspired multiple studies focusing on other organs, including the brain under mild acceleration and the tongue during speech. As with other motion estimation approaches, using tagged MRI to measure 3D motion includes several preprocessing steps that affect the quality and accuracy of estimation...
February 11, 2017: Proceedings of SPIE
https://www.readbyqxmd.com/read/28770012/discovery-of-rare-diagnostic-aluyb8-9-elements-in-diverse-human-populations
#9
Julie Feusier, David J Witherspoon, W Scott Watkins, Clément Goubert, Thomas A Sasani, Lynn B Jorde
BACKGROUND: Polymorphic human Alu elements are excellent tools for assessing population structure, and new retrotransposition events can contribute to disease. Next-generation sequencing has greatly increased the potential to discover Alu elements in human populations, and various sequencing and bioinformatics methods have been designed to tackle the problem of detecting these highly repetitive elements. However, current techniques for Alu discovery may miss rare, polymorphic Alu elements...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28769716/a-new-morphologically-cryptic-bush-cricket-discovered-on-the-basis-of-its-song-in-the-carpathian-mountains-insecta-orthoptera-tettigoniidae
#10
Ionuţ Ştefan Iorgu, Elena Iulia Iorgu, Gergely Szövényi, Kirill Márk Orci
A new, morphologically cryptic species of phaneropterine bush-crickets is described from the grasslands of the Romanian Eastern Carpathians. Despite the morphological and acoustic similarities with the recently described Isophya nagyi Szövényi, Puskás & Orci, I. bucovinensissp. n. is characterized by a peculiar male calling song, with faster syllable repetition rate (160-220 syllables per minute, at 22-27°C) and less complex syllable structure (composed of only two elements instead of three observable in I...
2017: ZooKeys
https://www.readbyqxmd.com/read/28767325/evolutionary-relationships-and-cytotaxonomy-considerations-in-the-genus-pyrrhulina-characiformes-lebiasinidae
#11
Renata Luiza Rosa de Moraes, Luiz Antonio Carlos Bertollo, Manoela Maria Ferreira Marinho, Cassia Fernanda Yano, Terumi Hatanaka, Felipe Faix Barby, Waldo Pinheiro Troy, Marcelo de Bello Cioffi
Although fishes exhibit the greatest biodiversity among the vertebrates, a large percentage of this fauna is still underexplored on evolutionary cytogenetic questions, particularly the miniature species. The Lebiasinidae family is a particular example for such case. This study is the first one presenting differential cytogenetic methods, such as C-banding, repetitive DNAs mapping, comparative genomic hybridization (CGH), and whole chromosome painting in lebiasinid species. Pyrrhulina australis and Pyrrhulina aff...
August 2, 2017: Zebrafish
https://www.readbyqxmd.com/read/28760135/the-first-data-on-the-innervation-of-the-lophophore-in-the-rhynchonelliform-brachiopod-hemithiris-psittacea-what-is-the-ground-pattern-of-the-lophophore-in-lophophorates
#12
Elena N Temereva, Tatyana V Kuzmina
BACKGROUND: The nervous system in brachiopods has seldom been studied with modern methods. An understanding of lophophore innervation in adult brachiopods is useful for comparing the innervation of the same lophophore type among different brachiopods and can also help answer questions about the monophyly of the lophophorates. Although some brachiopods are studied with modern methods, rhynchonelliform brachiopods still require investigation. The current study used transmission electron microscopy, immunocytochemistry, and confocal laser scanning microscopy to investigate the nerve system of the lophophore and tentacles in the rhynchonelliform Hemithiris psittacea...
July 31, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28759508/metatarsal-stress-fractures
#13
Denise R Ramponi, Viki Hedderick, Susan C Maloney
Metatarsal stress fractures are also called "march fractures" or "marcher's foot." They most commonly occur in the distal second and third metatarsals. The second and third metatarsals receive the majority of stress during ambulation and are less mobile compared with the other metatarsals. The predominant risk factor is excessive overuse with repetitive motions with little recovery time such as marching activities in the military. Any element that has a detrimental effect on bone density can predispose an individual to stress fractures...
July 2017: Advanced Emergency Nursing Journal
https://www.readbyqxmd.com/read/28758383/single-organic-droplet-collision-voltammogram-via-electron-transfer-coupled-ion-transfer
#14
Cheng Liu, Pekka Peljo, Xinjian Huang, Wenxue Cheng, Lishi Wang, Haiqiang Deng
Single-emulsion toluene oil droplets (femtoliter) containing a hydrophobic redox probe that are dispersed in water stochastically collide with an ultramicroelectrode (UME). The fast-scan cyclic voltammetry (FSCV) or Fourier-transformed sinusoidal voltammetry (FTSV) is applied: the UME was scanned with a fast, repetitive triangular, or sinusoidal potential, and its current in time/frequency domains were monitored. The electron transfer at the UME/oil interface is coupled with ion transfer at the oil/water interface...
August 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28756949/expanded-satellite-repeats-amplify-a-discrete-cenp-a-nucleosome-assembly-site-on-chromosomes-that-drive-in-female-meiosis
#15
Aiko Iwata-Otsubo, Jennine M Dawicki-McKenna, Takashi Akera, Samantha J Falk, Lukáš Chmátal, Karren Yang, Beth A Sullivan, Richard M Schultz, Michael A Lampson, Ben E Black
Female meiosis provides an opportunity for selfish genetic elements to violate Mendel's law of segregation by increasing the chance of segregating to the egg [1]. Centromeres and other repetitive sequences can drive in meiosis by cheating the segregation process [2], but the underlying mechanisms are unknown. Here, we show that centromeres with more satellite repeats house more nucleosomes that confer centromere identity, containing the histone H3 variant CENP-A, and bias their segregation to the egg relative to centromeres with fewer repeats...
August 7, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28748002/high-levels-of-circulating-folate-concentrations-are-associated-with-dna-methylation-of-tumor-suppressor-and-repair-genes-p16-mlh1-and-mgmt-in-elderly-chileans
#16
Hugo Sanchez, Mohammad B Hossain, Lydia Lera, Sandra Hirsch, Cecilia Albala, Ricardo Uauy, Karin Broberg, Ana M Ronco
BACKGROUND: Changes in DNA methylation, one of the most studied epigenetic mechanisms, are considered an initial marker for early cancer detection. We evaluated how availability of dietary factors (folates and vitamin B12) involved in one-carbon metabolism may contribute to DNA methylation changes of cancer-related genes in human subjects. METHODS: We studied, by pyrosequencing, the methylation of tumor suppressor gene p16, DNA repair genes MLH1 and MGMT, and the repetitive element LINE-1 (as a surrogate for global DNA methylation), in blood of elderly individuals (n = 249) who had been exposed to folic acid (FA) through FA-fortified wheat flour during the last 12 years...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28745717/evolution-and-conservation-of-characidium-sex-chromosomes
#17
R Utsunomia, P C Scacchetti, M Hermida, R Fernández-Cebrián, X Taboada, C Fernández, M Bekaert, N J Mendes, D Robledo, J E Mank, J B Taggart, C Oliveira, F Foresti, P Martínez
Fish species exhibit substantial variation in the degree of genetic differentiation between sex chromosome pairs, and therefore offer the opportunity to study the full range of sex chromosome evolution. We used restriction-site associated DNA sequencing (RAD-seq) to study the sex chromosomes of Characidium gomesi, a species with conspicuous heteromorphic ZW/ZZ sex chromosomes. We screened 9863 single-nucleotide polymorphisms (SNPs), corresponding to ~1 marker/100 kb distributed across the genome for sex-linked variation...
July 26, 2017: Heredity
https://www.readbyqxmd.com/read/28736701/a-comparative-genome-analysis-of-cercospora-sojina-with-other-members-of-the-pathogen-genus-mycosphaerella-on-different-plant-hosts
#18
Fanchang Zeng, Xin Lian, Guirong Zhang, Xiaoman Yu, Carl A Bradley, Ray Ming
Fungi are the causal agents of many of the world's most serious plant diseases causing disastrous consequences for large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukaryotic pathogens. Here, we report the genome sequence of C. sojina, and comparative genome analysis with plant pathogen members of the genus Mycosphaerella (Zymoseptoria. tritici (synonyms M. graminicola), M. pini, M. populorum and M. fijiensis - pathogens of wheat, pine, poplar and banana, respectively)...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28734026/falling-into-a-routine-from-habits-to-situated-practices
#19
Simon Cohn, Rebecca Lynch
In line with the concept of 'nudging' people to change their behaviour, there has been increased attention on habit as a focus for psychologically-based health interventions. It is hoped that behaviours initiated by interventions not only become so regular that they are normalised into people's everyday lives, but that through repetition they may eventually become fixed and habitual. In this paper we draw on people's accounts of participating in a trial designed to encourage greater physical activity, and attend to the ways they describe their engagement with interventions within wider narratives of their everyday lives...
July 21, 2017: Sociology of Health & Illness
https://www.readbyqxmd.com/read/28730513/element-repetition-rates-encode-functionally-distinct-information-in-pied-babbler-clucks-and-purrs
#20
Sabrina Engesser, Amanda R Ridley, Simon W Townsend
Human language is a recombinant system that achieves its productivity through the combination of a limited set of sounds. Research investigating the evolutionary origin of this generative capacity has generally focused on the capacity of non-human animals to combine different types of discrete sounds to encode new meaning, with less emphasis on meaning-differentiating mechanisms achieved through potentially simpler temporal modifications within a sequence of repeated sounds. Here we show that pied babblers (Turdoides bicolor) generate two functionally distinct vocalisations composed of the same sound type, which can only be distinguished by the number of repeated elements...
July 20, 2017: Animal Cognition
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