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Toshifumi Minamoto, Kimiko Uchii, Teruhiko Takahara, Takumi Kitayoshi, Tsuji Satsuki, Hiroki Yamanaka, Hideyuki Doi
The recently developed environmental DNA (eDNA) analysis has been used to estimate the distribution of aquatic vertebrates by using mitochondrial DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain drawbacks such as variable copy number and maternal inheritance. In this study, we investigated the potential of using nuclear DNA (ncDNA) as a more reliable genetic marker for eDNA analysis by using common carp (Cyprinus carpio). We measured the copy numbers of cytochrome b (CytB) gene region of mtDNA and internal transcribed spacer 1 (ITS1) region of ribosomal DNA of ncDNA in various carp tissues and then compared the detectability of these markers in eDNA samples...
August 4, 2016: Molecular Ecology Resources
Elizabeth A Raupach, Joseph A Martens, Karen M Arndt
Transcription of nonprotein-coding DNA is widespread in eukaryotes and plays important regulatory roles for many genes, including genes that are misregulated in cancer cells. Its pervasiveness presents the potential for a wealth of diverse regulatory roles for noncoding transcription. We previously showed that the act of transcribing noncoding DNA (ncDNA) across the promoter of the protein-coding SER3 gene in Saccharomyces cerevisiae positions nucleosomes over the upstream activating sequences, leading to strong repression of SER3 transcription...
2016: G3: Genes—Genomes—Genetics
Hao-Chih Kuo, Shiang-Fan Chen, Yin-Ping Fang, James A Cotton, Joe D Parker, Gábor Csorba, Burton K Lim, Judith L Eger, Chia-Hong Chen, Cheng-Han Chou, Stephen J Rossiter
Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and Murina recondita are both endemic to Taiwan and are putative sister species. To test for nonallopatric divergence and gene flow in these taxa, we generated sequences using Sanger and next-generation sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M...
December 2015: Molecular Ecology
Thomas S Bronder, Arshak Poghossian, Sabrina Scheja, Chunsheng Wu, Michael Keusgen, Dieter Mewes, Michael J Schöning
Miniaturized setup, compatibility with advanced micro- and nanotechnologies, and ability to detect biomolecules by their intrinsic molecular charge favor the semiconductor field-effect platform as one of the most attractive approaches for the development of label-free DNA chips. In this work, a capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensor covered with a layer-by-layer prepared, positively charged weak polyelectrolyte layer of PAH (poly(allylamine hydrochloride)) was used for the label-free electrical detection of DNA (deoxyribonucleic acid) immobilization and hybridization...
September 16, 2015: ACS Applied Materials & Interfaces
Sarah J Hainer, Weifeng Gu, Benjamin R Carone, Benjamin D Landry, Oliver J Rando, Craig C Mello, Thomas G Fazzio
Approximately 75% of the human genome is transcribed, the majority of which does not encode protein. However, many noncoding RNAs (ncRNAs) are rapidly degraded after transcription, and relatively few have established functions, questioning the significance of this observation. Here we show that esBAF, a SWI/SNF family nucleosome remodeling factor, suppresses transcription of ncRNAs from ∼57,000 nucleosome-depleted regions (NDRs) throughout the genome of mouse embryonic stem cells (ESCs). We show that esBAF functions to both keep NDRs nucleosome-free and promote elevated nucleosome occupancy adjacent to NDRs...
February 15, 2015: Genes & Development
Hari Manev, Svetlana Dzitoyeva
Mitochondria, intracellular organelles with their own genome, have been shown capable of interacting with epigenetic mechanisms in at least four different ways. First, epigenetic mechanisms that regulate the expression of nuclear genome influence mitochondria by modulating the expression of nuclear-encoded mitochondrial genes. Second, a cell-specific mitochondrial DNA content (copy number) and mitochondrial activity determine the methylation pattern of nuclear genes. Third, mitochondrial DNA variants influence the nuclear gene expression patterns and the nuclear DNA (ncDNA) methylation levels...
August 2013: Biomolecular Concepts
D Grant, D C Swinton, K S Chiang
Nuclear DNA (ncDNA) synthesis in Chlamydomonas reinhardtii was measured by both (32)P[or-thophosphoric acid] ((32)P) and [(14)C]adenine incorporation and found to be highly synchronous. Ca. 85% of incorporation was confined to the first 6 h of the dark period of a synchronized regime consisting of an alternating light-dark period of 12 h each. In contrast, no such synchronous incorporation pattern was found for chloroplast (cp) and mitochondrial (mt) DNAs in the same cell population. These two organellar DNAs also exhibited different (32)P-incorporation patterns in the cell cycle...
January 1978: Planta
Ganqiang Liu, John S Mattick, Ryan J Taft
It is now clear that animal genomes are predominantly non-protein-coding, and that these sequences encode a wide array of RNA transcripts and other regulatory elements that are fundamental to the development of complex life. We have previously argued that the proportion of an animal genome that is non-protein-coding DNA (ncDNA) correlates well with its apparent biological complexity. Here we extend on that work and, using data from a total of 1,627 prokaryotic and 153 eukaryotic complete and annotated genomes, show that the proportion of ncDNA per haploid genome is significantly positively correlated with a previously published proxy of biological complexity, the number of distinct cell types...
July 1, 2013: Cell Cycle
David Haughton, Félix Balado
BACKGROUND: In recent times, the application of deoxyribonucleic acid (DNA) has diversified with the emergence of fields such as DNA computing and DNA data embedding. DNA data embedding, also known as DNA watermarking or DNA steganography, aims to develop robust algorithms for encoding non-genetic information in DNA. Inherently DNA is a digital medium whereby the nucleotide bases act as digital symbols, a fact which underpins all bioinformatics techniques, and which also makes trivial information encoding using DNA straightforward...
2013: BMC Bioinformatics
Troy Ruths, Luay Nakhleh
BACKGROUND: The amount of transcription factor binding sites (TFBS) in an organism's genome positively correlates with the complexity of the regulatory network of the organism. However, the manner by which TFBS arise and accumulate in genomes and the effects of regulatory network complexity on the organism's fitness are far from being known. The availability of TFBS data from many organisms provides an opportunity to explore these issues, particularly from an evolutionary perspective...
2012: BMC Evolutionary Biology
C Wolf, D E J Linden
Because living systems depend on their environment, the evolution of environmental adaptability is inseparable from the evolution of life itself (Pross 2003). In animals and humans, environmental adaptability extends further to adaptive behavior. It has recently emerged that individual adaptability depends on the interaction of adaptation mechanisms at diverse functional levels. This interaction enables the integration of genetic, epigenetic and environmental factors for coordinated regulation of adaptations...
February 2012: Genes, Brain, and Behavior
Sarah J Hainer, Joseph A Martens
Transcription of ncDNA occurs throughout eukaryotic genomes, generating a wide array of ncRNAs. One large class of ncRNAs includes those transcribed over the promoter regions of nearby protein coding genes. Recent studies, primarily focusing on individual genes have uncovered multiple mechanisms by which promoter-associated transcriptional activity locally alters gene expression.
May 2011: Transcription
Sarah J Hainer, Joseph A Martens
Our previous studies of Saccharomyces cerevisiae described a gene repression mechanism where the transcription of intergenic noncoding DNA (ncDNA) (SRG1) assembles nucleosomes across the promoter of the adjacent SER3 gene that interfere with the binding of transcription factors. To investigate the role of histones in this mechanism, we screened a comprehensive library of histone H3 and H4 mutants for those that derepress SER3. We identified mutations altering eight histone residues (H3 residues V46, R49, V117, Q120, and K122 and H4 residues R36, I46, and S47) that strongly increase SER3 expression without reducing the transcription of the intergenic SRG1 ncDNA...
September 2011: Molecular and Cellular Biology
Sarah J Hainer, Justin A Pruneski, Rachel D Mitchell, Robin M Monteverde, Joseph A Martens
Transcription of non-protein-coding DNA (ncDNA) and its noncoding RNA (ncRNA) products are beginning to emerge as key regulators of gene expression. We previously identified a regulatory system in Saccharomyces cerevisiae whereby transcription of intergenic ncDNA (SRG1) represses transcription of an adjacent protein-coding gene (SER3) through transcription interference. We now provide evidence that SRG1 transcription causes repression of SER3 by directing a high level of nucleosomes over SRG1, which overlaps the SER3 promoter...
January 1, 2011: Genes & Development
Xiuguang Mao, Junpeng Zhang, Shuyi Zhang, Stephen J Rossiter
Instances of hybridization between mammalian taxa in the wild are rarely documented. To test for introgression between sibling species of horseshoe bat (Rhinolophus yunanensis and R. pearsoni) and two subspecies of the latter (R. p. pearsoni and R. p. chinensis), we sequenced two mtDNA and two ncDNA markers in individuals sampled from multiple localities within their overlapping ranges. The interspecific mtDNA gene tree corresponded to the expected taxonomic divisions, and coalescent-based analyses suggested divergence occurred around 4 MYA...
April 2010: Molecular Ecology
Donna Lisa de-Silva, Julia J Day, Marianne Elias, Keith Willmott, Alaine Whinnett, James Mallet
The Oleriina is one of the most speciose subtribes of the neotropical nymphalid butterfly tribe Ithomiini. They are widely distributed across the Andes and Amazonian lowlands and like other ithomiines they are involved in complex mimicry rings. This subtribe is of particular interest because it contains the most diverse ithomiine genus, Oleria, as well as two genera, Megoleria and Hyposcada, that feed on hostplants not utilized elsewhere in the tribe. Here we present the first comprehensive species-level phylogeny for the Oleriina, representing 83% of recognised species in the group, and based on 6698bp from eight mitochondrial (mt) and nuclear (nc) genes...
June 2010: Molecular Phylogenetics and Evolution
Nathan D Jackson, Christopher C Austin
Rivers can act as both islands of mesic refugia for terrestrial organisms during times of aridification and barriers to gene flow, though evidence for long-term isolation by rivers is mixed. Understanding the extent to which riverine barrier effects can be heightened for populations trapped in mesic refugia can help explain maintenance and generation of diversity in the face of Pleistocene climate change. Herein, we implement phylogenetic and population genetic approaches to investigate the phylogeographic structure and history of the ground skink, Scincella lateralis, using mtDNA and eight nuclear loci...
February 1, 2010: Evolution; International Journal of Organic Evolution
Daniel Cossíos, Mauro Lucherini, Manuel Ruiz-García, Bernard Angers
BACKGROUND: While numerous studies revealed the major role of environmental changes of the Quaternary on the evolution of biodiversity, research on the influence of that period on current South-American fauna is scarce and have usually focused on lowland regions. In this study, the genetic structure of the pampas cat (Leopardus colocolo), a widely distributed felid, was determined and linked to ancient climate fluctuations on the Andean region. RESULTS: Using both mitochondrial sequences and nuclear microsatellites, we inferred the existence of at least four groups of populations in the central Andes, while other three localities, with little sample sizes (n = 3), presented differences in only one of these markers...
2009: BMC Evolutionary Biology
Chun-Long Chen, Hui Zhou, Jian-You Liao, Liang-Hu Qu, Laurence Amar
The compact genome of the unicellular eukaryote Paramecium tetraurelia contains noncoding DNA (ncDNA) distributed into >39,000 intergenic sequences and >90,000 introns of 390 base pairs (bp) and 25 bp on average, respectively. Here we analyzed the molecular features of the ncRNA genes, introns, and intergenic sequences of this genome. We mainly used computational programs and comparative genomics possible because the P. tetraurelia genome had formed throughout whole-genome duplications (WGDs). We characterized 417 5S rRNA, snRNA, snoRNA, SRP RNA, and tRNA putative genes, 415 of which map within intergenic sequences, and two, within introns...
April 2009: RNA
Sebastian E Ahnert, Thomas M A Fink, Andrei Zinovyev
Despite tremendous advances in the field of genomics, the amount and function of the large non-coding part of the genome in higher organisms remains poorly understood. Here we report an observation, made for 37 fully sequenced eukaryotic genomes, which indicates that eukaryotes require a certain minimum amount of non-coding DNA (ncDNA). This minimum increases quadratically with the amount of DNA located in exons. Based on a simple model of the growth of regulatory networks, we derive a theoretical prediction of the required quantity of ncDNA and find it to be in excellent agreement with the data...
June 21, 2008: Journal of Theoretical Biology
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