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Sample records for satellite dna family

  1. A new family of satellite DNA sequences as a major component of centromeric heterochromatin in owls (Strigiformes).

    Science.gov (United States)

    Yamada, Kazuhiko; Nishida-Umehara, Chizuko; Matsuda, Yoichi

    2004-03-01

    We isolated a new family of satellite DNA sequences from HaeIII- and EcoRI-digested genomic DNA of the Blakiston's fish owl ( Ketupa blakistoni). The repetitive sequences were organized in tandem arrays of the 174 bp element, and localized to the centromeric regions of all macrochromosomes, including the Z and W chromosomes, and microchromosomes. This hybridization pattern was consistent with the distribution of C-band-positive centromeric heterochromatin, and the satellite DNA sequences occupied 10% of the total genome as a major component of centromeric heterochromatin. The sequences were homogenized between macro- and microchromosomes in this species, and therefore intraspecific divergence of the nucleotide sequences was low. The 174 bp element cross-hybridized to the genomic DNA of six other Strigidae species, but not to that of the Tytonidae, suggesting that the satellite DNA sequences are conserved in the same family but fairly divergent between the different families in the Strigiformes. Secondly, the centromeric satellite DNAs were cloned from eight Strigidae species, and the nucleotide sequences of 41 monomer fragments were compared within and between species. Molecular phylogenetic relationships of the nucleotide sequences were highly correlated with both the taxonomy based on morphological traits and the phylogenetic tree constructed by DNA-DNA hybridization. These results suggest that the satellite DNA sequence has evolved by concerted evolution in the Strigidae and that it is a good taxonomic and phylogenetic marker to examine genetic diversity between Strigiformes species.

  2. Amplification, contraction and genomic spread of a satellite DNA family (E180) in Medicago (Fabaceae) and allied genera.

    Science.gov (United States)

    Rosato, Marcela; Galián, José A; Rosselló, Josep A

    2012-03-01

    Satellite DNA is a genomic component present in virtually all eukaryotic organisms. The turnover of highly repetitive satellite DNA is an important element in genome organization and evolution in plants. Here we assess the presence and physical distribution of the repetitive DNA E180 family in Medicago and allied genera. Our goals were to gain insight into the karyotype evolution of Medicago using satellite DNA markers, and to evaluate the taxonomic and phylogenetic signal of a satellite DNA family in a genus hypothesized to have a complex evolutionary history. Seventy accessions from Medicago, Trigonella, Melilotus and Trifolium were analysed by PCR to assess the presence of the repetitive E180 family, and fluorescence in situ hybridization (FISH) was used for physical mapping in somatic chromosomes. The E180 repeat unit was PCR-amplified in 37 of 40 taxa in Medicago, eight of 12 species of Trigonella, six of seven species of Melilotus and in two of 11 Trifolium species. Examination of the mitotic chromosomes revealed that only 13 Medicago and two Trigonella species showed FISH signals using the E180 probe. Stronger hybridization signals were observed in subtelomeric and interstitial loci than in the pericentromeric loci, suggesting this satellite family has a preferential genomic location. Not all 13 Medicago species that showed FISH localization of the E180 repeat were phylogenetically related. However, nine of these species belong to the phylogenetically derived clade including the M. sativa and M. arborea complexes. The use of the E180 family as a phylogenetic marker in Medicago should be viewed with caution. Its amplification appears to have been produced through recurrent and independent evolutionary episodes in both annual and perennial Medicago species as well as in basal and derived clades.

  3. Satellite DNA: An Evolving Topic

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    Manuel A. Garrido-Ramos

    2017-09-01

    Full Text Available Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS, together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.

  4. Satellite DNA: An Evolving Topic.

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    Garrido-Ramos, Manuel A

    2017-09-18

    Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.

  5. Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae).

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    Martinsen, Lene; Johnsen, Arild; Venanzetti, Federica; Bachmann, Lutz

    2010-01-04

    The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH) ribozyme structure and activity embedded within each repeat. We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH) region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species. The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

  6. Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae

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    Venanzetti Federica

    2010-01-01

    Full Text Available Abstract Background The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH ribozyme structure and activity embedded within each repeat. Results We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species. Conclusions The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

  7. Organization and molecular evolution of CENP-A--associated satellite DNA families in a basal primate genome

    National Research Council Canada - National Science Library

    Lee, Hye-Ran; Hayden, Karen E; Willard, Huntington F

    2011-01-01

    ... satellite is found in old and new world monkey genomes, little is known about the organization, function, and evolution of centromeric sequences in more distant primates, including lemurs. Aye-Aye...

  8. Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies

    Czech Academy of Sciences Publication Activity Database

    Ambrožová, K.; Mandáková, T.; Bureš, P.; Neumann, Pavel; Leitch, I. J.; Koblížková, Andrea; Macas, Jiří; Lysák, M.

    2011-01-01

    Roč. 107, č. 2 (2011), s. 255-268 ISSN 0305-7364 R&D Projects: GA ČR GA521/07/0284; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50510513 Keywords : Fritillaria * Liliaceae * repetitive DNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.030, year: 2011

  9. Diversity and distribution of alpha satellite DNA in the genome of an Old World monkey: Cercopithecus solatus.

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    Cacheux, Lauriane; Ponger, Loïc; Gerbault-Seureau, Michèle; Richard, Florence Anne; Escudé, Christophe

    2016-11-14

    Alpha satellite is the major repeated DNA element of primate centromeres. Evolution of these tandemly repeated sequences has led to the existence of numerous families of monomers exhibiting specific organizational patterns. The limited amount of information available in non-human primates is a restriction to the understanding of the evolutionary dynamics of alpha satellite DNA. We carried out the targeted high-throughput sequencing of alpha satellite monomers and dimers from the Cercopithecus solatus genome, an Old World monkey from the Cercopithecini tribe. Computational approaches were used to infer the existence of sequence families and to study how these families are organized with respect to each other. While previous studies had suggested that alpha satellites in Old World monkeys were poorly diversified, our analysis provides evidence for the existence of at least four distinct families of sequences within the studied species and of higher order organizational patterns. Fluorescence in situ hybridization using oligonucleotide probes that are able to target each family in a specific way showed that the different families had distinct distributions on chromosomes and were not homogeneously distributed between chromosomes. Our new approach provides an unprecedented and comprehensive view of the diversity and organization of alpha satellites in a species outside the hominoid group. We consider these data with respect to previously known alpha satellite families and to potential mechanisms for satellite DNA evolution. Applying this approach to other species will open new perspectives regarding the integration of satellite DNA into comparative genomic and cytogenetic studies.

  10. Satellite DNA Sequences in Canidae and Their Chromosome Distribution in Dog and Red Fox.

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    Vozdova, Miluse; Kubickova, Svatava; Cernohorska, Halina; Fröhlich, Jan; Rubes, Jiri

    2016-01-01

    Satellite DNA is a characteristic component of mammalian centromeric heterochromatin, and a comparative analysis of its evolutionary dynamics can be used for phylogenetic studies. We analysed satellite and satellite-like DNA sequences available in NCBI for 4 species of the family Canidae (red fox, Vulpes vulpes, VVU; domestic dog, Canis familiaris, CFA; arctic fox, Vulpes lagopus, VLA; raccoon dog, Nyctereutes procyonoides procyonoides, NPR) by comparative sequence analysis, which revealed 86-90% intraspecies and 76-79% interspecies similarity. Comparative fluorescence in situ hybridisation in the red fox and dog showed signals of the red fox satellite probe in canine and vulpine autosomal centromeres, on VVUY, B chromosomes, and in the distal parts of VVU9q and VVU10p which were shown to contain nucleolus organiser regions. The CFA satellite probe stained autosomal centromeres only in the dog. The CFA satellite-like DNA did not show any significant sequence similarity with the satellite DNA of any species analysed and was localised to the centromeres of 9 canine chromosome pairs. No significant heterochromatin block was detected on the B chromosomes of the red fox. Our results show extensive heterogeneity of satellite sequences among Canidae and prove close evolutionary relationships between the red and arctic fox. © 2017 S. Karger AG, Basel.

  11. Comparative study of satellite DNA in ants of the Messor genus.

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    Lorite, Pedro; Carrillo, José A; Tinaut, Alberto; Palomeque, Teresa

    2002-09-04

    The satellite DNA of ants Messor barbarus and Messor bouvieri is analysed. The results are compared with the satellite DNA data from Messor structor previously reported and with new data obtained from the genome of geographically distinct M. structor population, which have shown that this satellite DNA is highly conserved within the species. The satellite DNA is organized as tandemly repeated 79 bp monomers in all species. The sampled sequences of the three species show a high similarity and all belong to the same family of satellite DNA. Sequence comparisons suggested the occurrence of highly effective homogenization mechanism acting upon the ant genomes. In accordance with this hypothesis, putative gene conversion tracts are identified when the different monomers of the same species are compared. The highest sequence conservation in all species corresponds to a single region with inverted repeats. A CENP-B-like motif was found in this region. The possibility that it may be involved in the homogenization of satellite DNA is discussed.

  12. New satellite DNA in Lacerta s. str. lizards (Sauria: Lacertidae): evolutionary pathways and phylogenetic impact.

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    Ciobanu, Doina; Grechko, Vernata V; Darevsky, Ilya S; Kramerov, Dmitri A

    2004-11-15

    A new tandemly repeated (satellite) DNA family namely Agi160, from Lacerta agilis and Lacerta strigata (Lacerta sensu stricto (s. str.), Linnaeus 1758) have been cloned and sequenced. Agi160 is found in the above two species, as well as two other representatives of the same genus, L. viridis and L. media. DNA hybridization did not reveal it in Darevskia, Podarcis, Zootoca, Eremias, Ophisops, and Gallotia - the other genera of the family Lacertidae. The results suggest that Agi160 is a Lacerta s. str. specific family of tandem DNA repeats. However, a comparison between sequences of Agi160 and CLsat repeat units revealed 60 bp regions 62-74% identical. The latter is a satellite DNA family typical for Darevskia (syn. "L. saxicola complex") (Grechko et al., Molecular-genetic classification and phylogenetic relatedness of some species of Lacertidae lizards by taxonoprint data. Mol Biol 32:172-183, 1988.). Both Agi160 and CLsat tandem repeats share several common features (e.g., the same AT content and distribution of multiple short A-T runs, internal structure of repeated units, the presence of conservative regions). These data are indicative of their common origin and a possibly strong selective pressure upon conserving both satellites. A comparative analysis of structure, organization, and abundance of these two families of satDNA reveals evolutionary pathways that led to their formation and divergence. The data are consistent with the hypotheses of the concerted evolution of satellite DNA families. The possibility of use of Agi160 as a phylogenetic tool, defining relationships within Lacerta s. str., as well as within the whole family of Lacertidae is discussed. Copyright 2004 Wiley-Liss, Inc.

  13. Evaluation of intra- and interspecific divergence of satellite DNA sequences by nucleotide frequency calculation and pairwise sequence comparison

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    Kato Mikio

    2003-01-01

    Full Text Available Satellite DNA sequences are known to be highly variable and to have been subjected to concerted evolution that homogenizes member sequences within species. We have analyzed the mode of evolution of satellite DNA sequences in four fishes from the genus Diplodus by calculating the nucleotide frequency of the sequence array and the phylogenetic distances between member sequences. Calculation of nucleotide frequency and pairwise sequence comparison enabled us to characterize the divergence among member sequences in this satellite DNA family. The results suggest that the evolutionary rate of satellite DNA in D. bellottii is about two-fold greater than the average of the other three fishes, and that the sequence homogenization event occurred in D. puntazzo more recently than in the others. The procedures described here are effective to characterize mode of evolution of satellite DNA.

  14. Evolutionary dynamics of satellite DNA repeats from Phaseolus beans.

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    Ribeiro, Tiago; Dos Santos, Karla G B; Richard, Manon M S; Sévignac, Mireille; Thareau, Vincent; Geffroy, Valérie; Pedrosa-Harand, Andrea

    2017-03-01

    Common bean (Phaseolus vulgaris) subtelomeres are highly enriched for khipu, the main satellite DNA identified so far in this genome. Here, we comparatively investigate khipu genomic organization in Phaseolus species from different clades. Additionally, we identified and characterized another satellite repeat, named jumper, associated to khipu. A mixture of P. vulgaris khipu clones hybridized in situ confirmed the presence of khipu-like sequences on subterminal chromosome regions in all Phaseolus species, with differences in the number and intensity of signals between species and when species-specific clones were used. Khipu is present as multimers of ∼500 bp and sequence analyses of cloned fragments revealed close relationship among khipu repeats. The new repeat, named jumper, is a 170-bp satellite sequence present in all Phaseolus species and inserted into the nontranscribed spacer (NTS) of the 5S rDNA in the P. vulgaris genome. Nevertheless, jumper was found as a high-copy repeat at subtelomeres and/or pericentromeres in the Phaseolus microcarpus lineage only. Our data argue for khipu as an important subtelomeric satellite DNA in the genus and for a complex satellite repeat composition of P. microcarpus subtelomeres, which also contain jumper. Furthermore, the differential amplification of these repeats in subtelomeres or pericentromeres reinforces the presence of a dynamic satellite DNA library in Phaseolus.

  15. Characterisation of a GC-rich telomeric satellite DNA in Eumeces schneideri Daudin (Reptilia, Scincidae).

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    Giovannotti, M; Nisi Cerioni, P; Caputo, V; Olmo, E

    2009-01-01

    A hitherto undescribed satellite DNA family (AvaII satDNA) has been isolated and characterised in Eumeces schneideri, a squamate reptile belonging to the family Scincidae. AvaII satDNA is characterised by a monomer length of 208 bp, a GC content of 59% and exhibits a certain degree of CpG methylation. FISH experiments with AvaII satDNA probe produced bright signals (i) at the end of the short arms of all subtelocentric chromosomes except for pair 14, in which the signal was at the end of the long arms, (ii) at the ends of both arms of the small metacentric chromosomes 12, and (iii) in a terminal position on the acrocentric chromosomes 11 and 13. AvaII satDNA repeats were not found in the metacentric pair 3, whereas only a weak interstitial signal occurred in the metacentric pairs 1 and 2. C-banding showed that this satellite represents most of the constitutive heterochromatin in the genome of this skink, and chromomycin A(3) staining produced a clear signal overlapping with the satellite, except for NOR-associated heterochromatin. In addition, quantitative dot blot analysis showed that these repetitive sequences constitute about 3% of the genomic DNA of this lizard. AvaII satDNA sequence analysis revealed the occurrence of short guanine residue stretches for which a function in structural stability of these sequences and a role in recombination with telomeric sequences can be hypothesised. Fibre FISH experiments showed that on some chromatin fibres telomeric sequences and AvaII satellite DNA repeats are intermingled or overlapping. (c) 2009 S. Karger AG, Basel.

  16. Properties of CENP-B and its target sequence in a satellite DNA

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    Masumoto, H.; Yoda, K.; Ikeno, M.; Kitagawa, K.; Muro, Y.; Okazaki, T. [Nagoya Univ. (Japan)

    1993-12-31

    The centromere plays an essential role in the proper segregation of eukaryotic chromosomes at mitosis and meiosis. The centromere is the multifunctional domain of chromosome responsible for sister chromatid association at the inner site and for microtubule attachment at the outer surface. It also acts as a mechanochemical motor for chromosome movement. These multiple centromere functions must, in some way, be directed by a cis-acting DNA sequence located in the centromere region. Indeed, specific centromere DNA sequences (CEN-DNA) were identified in two yeast species. In Saccharomyces cerevisiae, CEN-DNA consists of roughly 125 bp sequence composed of three conserved elements. In contrast, the centromere sequence of S. pombe is quite different from S. cerevisiae in length and sequence organization. The molecular bases for understanding the structure and function of the centromere/kinetochore domain have not been elucidated in higher eukaryotes. In mammalian cells, satellite DNA`s are localized in the centromeric heterochromatin or heterochromatic arm. In all human chromosomes, the alpha satellite or alphoid DNA family, a highly repetitive DNA composed of about 170 bp fundamental monomer repeating units, is found at the primary constriction. Its function, however, has not been established.

  17. Is radon emission in caves causing deletions in satellite DNA sequences of cave-dwelling crickets?

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    Allegrucci, Giuliana; Sbordoni, Valerio; Cesaroni, Donatella

    2015-01-01

    The most stable isotope of radon, 222Rn, represents the major source of natural radioactivity in confined environments such as mines, caves and houses. In this study, we explored the possible radon-related effects on the genome of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae) sampled in caves with different concentrations of radon. We analyzed specimens from ten populations belonging to two genetically closely related species, D. geniculata and D. laetitiae, and explored the possible association between the radioactivity dose and the level of genetic polymorphism in a specific family of satellite DNA (pDo500 satDNA). Radon concentration in the analyzed caves ranged from 221 to 26,000 Bq/m3. Specimens coming from caves with the highest radon concentration showed also the highest variability estimates in both species, and the increased sequence heterogeneity at pDo500 satDNA level can be explained as an effect of the mutation pressure induced by radon in cave. We discovered a specific category of nuclear DNA, the highly repetitive satellite DNA, where the effects of the exposure at high levels of radon-related ionizing radiation are detectable, suggesting that the satDNA sequences might be a valuable tool to disclose harmful effects also in other organisms exposed to high levels of radon concentration.

  18. Characterization of Non-coding DNA Satellites Associated with Sweepoviruses (Genus Begomovirus, Geminiviridae) - Definition of a Distinct Class of Begomovirus-Associated Satellites.

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    Lozano, Gloria; Trenado, Helena P; Fiallo-Olivé, Elvira; Chirinos, Dorys; Geraud-Pouey, Francis; Briddon, Rob W; Navas-Castillo, Jesús

    2016-01-01

    Begomoviruses (family Geminiviridae) are whitefly-transmitted, plant-infecting single-stranded DNA viruses that cause crop losses throughout the warmer parts of the World. Sweepoviruses are a phylogenetically distinct group of begomoviruses that infect plants of the family Convolvulaceae, including sweet potato (Ipomoea batatas). Two classes of subviral molecules are often associated with begomoviruses, particularly in the Old World; the betasatellites and the alphasatellites. An analysis of sweet potato and Ipomoea indica samples from Spain and Merremia dissecta samples from Venezuela identified small non-coding subviral molecules in association with several distinct sweepoviruses. The sequences of 18 clones were obtained and found to be structurally similar to tomato leaf curl virus-satellite (ToLCV-sat, the first DNA satellite identified in association with a begomovirus), with a region with significant sequence identity to the conserved region of betasatellites, an A-rich sequence, a predicted stem-loop structure containing the nonanucleotide TAATATTAC, and a second predicted stem-loop. These sweepovirus-associated satellites join an increasing number of ToLCV-sat-like non-coding satellites identified recently. Although sharing some features with betasatellites, evidence is provided to suggest that the ToLCV-sat-like satellites are distinct from betasatellites and should be considered a separate class of satellites, for which the collective name deltasatellites is proposed.

  19. Characterization of non-coding DNA satellites associated with sweepoviruses (genus Begomovirus, Geminiviridae - definition of a distinct class of begomovirus-associated satellites

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    Gloria eLozano

    2016-02-01

    Full Text Available Begomoviruses (family Geminiviridae are whitefly-transmitted, plant-infecting single-stranded DNA viruses that cause crop losses throughout the warmer parts of the World. Sweepoviruses are a phylogenetically distinct group of begomoviruses that infect plants of the family Convolvulaceae, including sweet potato (Ipomoea batatas. Two classes of subviral molecules are often associated with begomoviruses, particularly in the Old World; the betasatellites and the alphasatellites. An analysis of sweet potato and Ipomoea indica samples from Spain and Merremia dissecta samples from Venezuela identified small non-coding subviral molecules in association with several distinct sweepoviruses. The sequences of 18 clones were obtained and found to be structurally similar to tomato leaf curl virus–satellite (ToLCV-sat, the first DNA satellite identified in association with a begomovirus, with a region with significant sequence identity to the conserved region of betasatellites, an A-rich sequence, a predicted stem-loop structure containing the nonanucleotide TAATATTAC, and a second predicted stem-loop. These sweepovirus-associated satellites join an increasing number of ToLCV-sat-like non-coding satellites identified recently. Although sharing some features with betasatellites, evidence is provided to suggest that the ToLCV-sat-like satellites are distinct from betasatellites and should be considered a separate class of satellites, for which the collective name deltasatellites is proposed.

  20. Evaluating the relative clinical efficiency of family medicine satellite clinics.

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    Rohrer, James E; Bernard, Matthew; Adamson, Steve; Naessens, James; Furst, Joseph; Angstman, Kurt

    2007-01-01

    A study was conducted to evaluate the impact of decentralization in family medicine clinic services by comparing utilization of services in 3 satellite clinics to utilization patterns of patients served at the hub clinic. It was expected that a hub clinic would be more efficient than satellite clinics because of tighter administrative control and economies of scale. Stable chronically ill patients were used as a homogeneous tracer condition in a secondary analysis of 12 months of archival data. Three types of service use were analyzed: laboratory visits, x-ray visits, and visits to specialists. Among 1,410 stable chronically ill family medicine patients, 303 (21.5%) had 10 more laboratory visits, 222 (15.7%) had 2 or more x-ray visits, and 617 (43.8 %) had 2 or more visits to a specialist. Patients at one of the satellite clinics had greater odds of receiving 2 or more x-rays but lower odds of receiving 10 or more laboratory visits, in comparison with the hub clinic. Patients at the other 2 satellite clinics did not differ from hub patients for any type of service use. Overall, stable chronically ill patients were treated with approximately equal clinical efficiency in our satellite clinics. Some differences in efficiency may occur in some clinics, but these appear to be idiosyncratic rather than due to clinic size or distance from central control.

  1. Evolutionary Story of a Satellite DNA from Phodopus sungorus (Rodentia, Cricetidae)

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    Paço, Ana; Adega, Filomena; Meštrović, Nevenka; Plohl, Miroslav; Chaves, Raquel

    2014-01-01

    With the goal to contribute for the understanding of satellite DNA evolution and its genomic involvement, in this work it was isolated and characterized the first satellite DNA (PSUcentSat) from Phodopus sungorus (Cricetidae). Physical mapping of this sequence in P. sungorus showed large PSUcentSat arrays located at the heterochromatic (peri)centromeric region of five autosomal pairs and Y-chromosome. The presence of orthologous PSUcentSat sequences in the genomes of other Cricetidae and Muridae rodents was also verified, presenting however, an interspersed chromosomal distribution. This distribution pattern suggests a PSUcentSat-scattered location in an ancestor of Muridae/Cricetidae families, that assumed afterwards, in the descendant genome of P. sungorus a restricted localization to few chromosomes in the (peri)centromeric region. We believe that after the divergence of the studied species, PSUcentSat was most probably highly amplified in the (peri)centromeric region of some chromosome pairs of this hamster by recombinational mechanisms. The bouquet chromosome configuration (prophase I) possibly displays an important role in this selective amplification, providing physical proximity of centromeric regions between chromosomes with similar size and/or morphology. This seems particularly evident for the acrocentric chromosomes of P. sungorus (including the Y-chromosome), all presenting large PSUcentSat arrays at the (peri)centromeric region. The conservation of this sequence in the studied genomes and its (peri)centromeric amplification in P. sungorus strongly suggests functional significance, possibly displaying this satellite family different functions in the different genomes. The verification of PSUcentSat transcriptional activity in normal proliferative cells suggests that its transcription is not stage-limited, as described for some other satellites. PMID:25336681

  2. Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing.

    Science.gov (United States)

    Kim, Jung-Hyun; Ebersole, Thomas; Kouprina, Natalay; Noskov, Vladimir N; Ohzeki, Jun-Ichirou; Masumoto, Hiroshi; Mravinac, Brankica; Sullivan, Beth A; Pavlicek, Adam; Dovat, Sinisa; Pack, Svetlana D; Kwon, Yoo-Wook; Flanagan, Patrick T; Loukinov, Dmitri; Lobanenkov, Victor; Larionov, Vladimir

    2009-04-01

    The role of repetitive DNA sequences in pericentromeric regions with respect to kinetochore/heterochromatin structure and function is poorly understood. Here, we use a mouse erythroleukemia cell (MEL) system for studying how repetitive DNA assumes or is assembled into different chromatin structures. We show that human gamma-satellite DNA arrays allow a transcriptionally permissive chromatin conformation in an adjacent transgene and efficiently protect it from epigenetic silencing. These arrays contain CTCF and Ikaros binding sites. In MEL cells, this gamma-satellite DNA activity depends on binding of Ikaros proteins involved in differentiation along the hematopoietic pathway. Given our discovery of gamma-satellite DNA in pericentromeric regions of most human chromosomes and a dynamic chromatin state of gamma-satellite arrays in their natural location, we suggest that gamma-satellite DNA represents a unique region of the functional centromere with a possible role in preventing heterochromatin spreading beyond the pericentromeric region.

  3. Characterization of RUSI, a telomere-associated satellite DNA, in the genus Rumex (Polygonaceae).

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    Navajas-Pérez, R; Schwarzacher, T; Ruiz Rejón, M; Garrido-Ramos, M A

    2009-01-01

    A satellite-DNA family (RUSI) has been isolated and characterized in Rumexinduratus Boiss and Reuter (Polygonaceae), an Iberian endemic polygamous sorrel. The RUSI repeats are 170 bp in length and approximately 68% AT-rich containing different variants of degenerate telomere motifs--(TT)(n)AN(GG)(n) -, a typical feature of subtelomeric DNA repeats adjacent to telomeres, which have been referred to as telomere-associated sequences or TASs. In fact, fluorescent in situhybridization showed that this satellite DNA is located in subtelomeric positions of most of the chromosomes of R. induratus, with some centromeric loci. PCR and Southern-blot hybridization assays for sequence conservation in the genus Rumex, indicated that the RUSI sequences are restricted to the genomes of R. induratus and R. scutatus, both species of the section Scutati, suggesting that they are recently evolved. Sequence variation within the two species is high (mean value of sequence differences between repeats of 15% for R. induratus and 7.5% for R. scutatus) and the degree of sequence differentiation between species is low with no species-specific variants, postulated to be due to slowed rates of spreading of sequence variants by molecular homogenizing mechanisms. Characteristics of RUSI sequences are discussed in the light of their chromosomal location and analyzed for their evolutionary and phylogenetic implications. Copyright 2009 S. Karger AG, Basel.

  4. Evolutionary Origin of Higher-Order Repeat Structure in Alpha-Satellite DNA of Primate Centromeres

    Science.gov (United States)

    Koga, Akihiko; Hirai, Yuriko; Terada, Shoko; Jahan, Israt; Baicharoen, Sudarath; Arsaithamkul, Visit; Hirai, Hirohisa

    2014-01-01

    Alpha-satellite DNA (AS) is a main DNA component of primate centromeres, consisting of tandemly repeated units of ∼170 bp. The AS of humans contains sequences organized into higher-order repeat (HOR) structures, in which a block of multiple repeat units forms a larger repeat unit and the larger units are repeated tandemly. The presence of HOR in AS is widely thought to be unique to hominids (family Hominidae; humans and great apes). Recently, we have identified an HOR-containing AS in the siamang, which is a small ape species belonging to the genus Symphalangus in the family Hylobatidae. This result supports the view that HOR in AS is an attribute of hominoids (superfamily Hominoidea) rather than hominids. A single example is, however, not sufficient for discussion of the evolutionary origin of HOR-containing AS. In the present study, we developed an efficient method for detecting signs of large-scale HOR and demonstrated HOR of AS in all the three other genera. Thus, AS organized into HOR occurs widely in hominoids. Our results indicate that (i) HOR-containing AS was present in the last common ancestor of hominoids or (ii) HOR-containing AS emerged independently in most or all basal branches of hominoids. We have also confirmed HOR occurrence in centromeric AS in the Hylobatidae family, which remained unclear in our previous study because of the existence of AS in subtelomeric regions, in addition to centromeres, of siamang chromosomes. PMID:24585002

  5. Molecular analysis and genomic organization of major DNA satellites in banana (Musa spp..

    Directory of Open Access Journals (Sweden)

    Jana Čížková

    Full Text Available Satellite DNA sequences consist of tandemly arranged repetitive units up to thousands nucleotides long in head-to-tail orientation. The evolutionary processes by which satellites arise and evolve include unequal crossing over, gene conversion, transposition and extra chromosomal circular DNA formation. Large blocks of satellite DNA are often observed in heterochromatic regions of chromosomes and are a typical component of centromeric and telomeric regions. Satellite-rich loci may show specific banding patterns and facilitate chromosome identification and analysis of structural chromosome changes. Unlike many other genomes, nuclear genomes of banana (Musa spp. are poor in satellite DNA and the information on this class of DNA remains limited. The banana cultivars are seed sterile clones originating mostly from natural intra-specific crosses within M. acuminata (A genome and inter-specific crosses between M. acuminata and M. balbisiana (B genome. Previous studies revealed the closely related nature of the A and B genomes, including similarities in repetitive DNA. In this study we focused on two main banana DNA satellites, which were previously identified in silico. Their genomic organization and molecular diversity was analyzed in a set of nineteen Musa accessions, including representatives of A, B and S (M. schizocarpa genomes and their inter-specific hybrids. The two DNA satellites showed a high level of sequence conservation within, and a high homology between Musa species. FISH with probes for the satellite DNA sequences, rRNA genes and a single-copy BAC clone 2G17 resulted in characteristic chromosome banding patterns in M. acuminata and M. balbisiana which may aid in determining genomic constitution in interspecific hybrids. In addition to improving the knowledge on Musa satellite DNA, our study increases the number of cytogenetic markers and the number of individual chromosomes, which can be identified in Musa.

  6. Molecular analysis and genomic organization of major DNA satellites in banana (Musa spp.).

    Science.gov (United States)

    Čížková, Jana; Hřibová, Eva; Humplíková, Lenka; Christelová, Pavla; Suchánková, Pavla; Doležel, Jaroslav

    2013-01-01

    Satellite DNA sequences consist of tandemly arranged repetitive units up to thousands nucleotides long in head-to-tail orientation. The evolutionary processes by which satellites arise and evolve include unequal crossing over, gene conversion, transposition and extra chromosomal circular DNA formation. Large blocks of satellite DNA are often observed in heterochromatic regions of chromosomes and are a typical component of centromeric and telomeric regions. Satellite-rich loci may show specific banding patterns and facilitate chromosome identification and analysis of structural chromosome changes. Unlike many other genomes, nuclear genomes of banana (Musa spp.) are poor in satellite DNA and the information on this class of DNA remains limited. The banana cultivars are seed sterile clones originating mostly from natural intra-specific crosses within M. acuminata (A genome) and inter-specific crosses between M. acuminata and M. balbisiana (B genome). Previous studies revealed the closely related nature of the A and B genomes, including similarities in repetitive DNA. In this study we focused on two main banana DNA satellites, which were previously identified in silico. Their genomic organization and molecular diversity was analyzed in a set of nineteen Musa accessions, including representatives of A, B and S (M. schizocarpa) genomes and their inter-specific hybrids. The two DNA satellites showed a high level of sequence conservation within, and a high homology between Musa species. FISH with probes for the satellite DNA sequences, rRNA genes and a single-copy BAC clone 2G17 resulted in characteristic chromosome banding patterns in M. acuminata and M. balbisiana which may aid in determining genomic constitution in interspecific hybrids. In addition to improving the knowledge on Musa satellite DNA, our study increases the number of cytogenetic markers and the number of individual chromosomes, which can be identified in Musa.

  7. Centromeric alpha satellite DNA amplification and translocation in an unusually large chromosome 14p+ variant.

    Science.gov (United States)

    Dale, S; Earle, E; Voullaire, L; Rogers, J; Choo, K H

    1989-05-01

    We report cytogenetic and molecular studies on a family that carries, in the father, an unusually large chromosome 14p+ variant [WSi-var(14)(p+)] and, in one of his children, a translocation [DSi-der(14)] involving the variant chromosome. Increase in the size of WSi-var(14)(p+) was estimated to be approximately 35% that of a normal chromosome 14. Presence of extra chromosomal material in this variant chromosome was demonstrated by G-banding using trypsin and staining with Leishman, G-banding using bromodeoxyuridine (BrdU) and Giemsa, and R-banding using BrdU and Giemsa. This material was positive using C-banding with BaOH and staining with Giemsa and negative in DAPI/distamycin staining, suggesting that it contained repetitive DNA but probably not of the types found in the heterochromatic regions of chromosomes 1, 9, 15, 16, and Y. Staining of the nucleolus organiser region (NOR) with AgNO3 indicated the retention of the NOR in WSi-var(14)(p+) but not in DSi-der(14). In situ hybridisation of metaphase cells with an alpha satellite DNA probe specific for human acrocentric chromosomes demonstrated a significantly increased amount of centromeric alpha sequences in WSi-var(14)(p+). Most or all of the extra alpha sequences were retained in DSi-der(14), indicating translocation near the very distal end of the enlarged region. The extra alpha satellite DNA material may have originated through amplification of some centromeric segments. The possible role of the amplified DNA in chromosomal translocations is discussed.

  8. Unraveling the sequence dynamics of the formation of genus-specific satellite DNAs in the family solanaceae.

    Science.gov (United States)

    Jo, S-H; Park, H-M; Kim, S-M; Kim, H H; Hur, C-G; Choi, D

    2011-05-01

    Tandemly repeated DNAs, referred to as satellite DNAs, often occur in a genome in a genus-specific manner. However, the mechanisms for generation and evolution for these sequences are largely unknown because of the uncertain origins of the satellite DNAs. We found highly divergent genus-specific satellite DNAs that showed sequence similarity with genus-specific intergenic spacers (IGSs) in the family Solanaceae, which includes the genera Nicotiana, Solanum and Capsicum. The conserved position of the IGS between 25S and 18S rDNA facilitates comparison of IGS sequences across genera, even in the presence of very low sequence similarity. Sequence comparison of IGS may elucidate the procedure of the genesis of complex monomer units of the satellite DNAs. Within the IGS of Capsicum species, base substitutions and copy number variation of subrepeat monomers were causes of monomer divergence in IGS sequences. At the level of inter-generic IGS sequences of the family Solanaceae, however, genus-specific motif selection, motif shuffling between subrepeats and differential amplification among motifs were involved in formation of genus-specific IGS. Therefore, the genus-specific satellite DNAs in Solanaceae plants can be generated from differentially organized repeat monomers of the IGS rather than by accumulation of mutations from pre-existent satellite DNAs.

  9. Uncoupling of satellite DNA and centromeric function in the genus Equus.

    Directory of Open Access Journals (Sweden)

    Francesca M Piras

    2010-02-01

    Full Text Available In a previous study, we showed that centromere repositioning, that is the shift along the chromosome of the centromeric function without DNA sequence rearrangement, has occurred frequently during the evolution of the genus Equus. In this work, the analysis of the chromosomal distribution of satellite tandem repeats in Equus caballus, E. asinus, E. grevyi, and E. burchelli highlighted two atypical features: 1 several centromeres, including the previously described evolutionary new centromeres (ENCs, seem to be devoid of satellite DNA, and 2 satellite repeats are often present at non-centromeric termini, probably corresponding to relics of ancestral now inactive centromeres. Immuno-FISH experiments using satellite DNA and antibodies against the kinetochore protein CENP-A demonstrated that satellite-less primary constrictions are actually endowed with centromeric function. The phylogenetic reconstruction of centromere repositioning events demonstrates that the acquisition of satellite DNA occurs after the formation of the centromere during evolution and that centromeres can function over millions of years and many generations without detectable satellite DNA. The rapidly evolving Equus species gave us the opportunity to identify different intermediate steps along the full maturation of ENCs.

  10. Uncoupling of Satellite DNA and Centromeric Function in the Genus Equus

    Science.gov (United States)

    Magnani, Elisa; Bertoni, Livia; Attolini, Carmen; Khoriauli, Lela; Raimondi, Elena; Giulotto, Elena

    2010-01-01

    In a previous study, we showed that centromere repositioning, that is the shift along the chromosome of the centromeric function without DNA sequence rearrangement, has occurred frequently during the evolution of the genus Equus. In this work, the analysis of the chromosomal distribution of satellite tandem repeats in Equus caballus, E. asinus, E. grevyi, and E. burchelli highlighted two atypical features: 1) several centromeres, including the previously described evolutionary new centromeres (ENCs), seem to be devoid of satellite DNA, and 2) satellite repeats are often present at non-centromeric termini, probably corresponding to relics of ancestral now inactive centromeres. Immuno-FISH experiments using satellite DNA and antibodies against the kinetochore protein CENP-A demonstrated that satellite-less primary constrictions are actually endowed with centromeric function. The phylogenetic reconstruction of centromere repositioning events demonstrates that the acquisition of satellite DNA occurs after the formation of the centromere during evolution and that centromeres can function over millions of years and many generations without detectable satellite DNA. The rapidly evolving Equus species gave us the opportunity to identify different intermediate steps along the full maturation of ENCs. PMID:20169180

  11. Cloning and characterization of a tandemly repeated DNA sequence in the crane family (Gruidae).

    Science.gov (United States)

    Chen, Z Q; Lin, C C; Hodgetts, R B

    1989-08-01

    A tandemly repeated DNA sequence possessing a unique PstI site has been characterized in several species of the crane family. The "Pst family" comprises at least 8800 monomer units 187 base pairs (bp) in length and constitutes 0.14% of the genome of the sarus crane (Grus antigone). The array is located in the centromeric heterochromatin of chromosome 2 in the two species where in situ hybridizations of a cloned monomer to metaphase chromosome spreads were carried out. DNA sequence comparisons between five monomer units from G. antigone revealed a high degree of homology between four of the individual repeats, while the fifth was somewhat divergent. The G + C content deduced from the DNA sequence makes it likely that the Pst family constitutes part of a density satellite seen in profiles of crane DNA centrifuged to equilibrium in CsCl. The common occurrence of tandem arrays such as the Pst family, with repeat lengths close to 200 bp, leads us to an hypothesis implicating nucleosomes in the evolution of such families.

  12. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.

    Science.gov (United States)

    Novák, Petr; Ávila Robledillo, Laura; Koblížková, Andrea; Vrbová, Iva; Neumann, Pavel; Macas, Jirí

    2017-07-07

    Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent k-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. GlaI digestion of mouse γ-satellite DNA: study of primary structure and ACGT sites methylation

    Directory of Open Access Journals (Sweden)

    Gonchar Danila A

    2009-07-01

    Full Text Available Abstract Background Patterns of mouse DNA hydrolysis with restriction enzymes are coincided with calculated diagrams of genomic DNA digestion in silico, except presence of additional bright bands, which correspond to monomer and dimer of γ-satellite DNA. Only small portion of mouse γ-satellite DNA sequences are presented in databases. Methyl-directed endonuclease GlaI cleaves mouse DNA and may be useful for a detailed study of primary structure and CG dinucleotides methylation in γ-satellite DNA. Results We have constructed a physical map and produced experimental patterns of mouse γ-satellite DNA hydrolysis with unique site-specific methyl-directed endonuclease GlaI and several restriction endonucleases. Fifty two DNA fragments of γ-satellite DNA have been cloned and sequenced. We have not observed any mutations of CG dinucleotide in position 208 of monomeric γ-satellite DNA and confirmed 50% methylation of this CG dinucleoitide. A comparison of consensus sequences of arrayed γ-satellite DNA and small blocks of satellite DNA (140 monomers and less has shown a higher level of mutations and an absence of conserved CG dinucleotide in last ones. A replacement of CG dinucleotide by CA-dinucleotide in positions 178 and 17 in chromosomes 9 and 3, respectively, has been observed in blocks of monomers. Conclusion Arrayed γ-satellite DNA from mouse has at least one conservative CG-dinucleotide. Consensus sequences of this DNA and γ-satellite DNA in small blocks of monomers are differing. The last one displays a higher level of CG dinucleotides mutations and an absence of conservative CG-dinucleotide. Presence of conservative and half-methylated CG-dinucleotide supports an idea of importance of this CG dinucleotide methylation/demethylation in arrayed γ-satellite DNA functioning.

  14. Cloning, characterization and chromosomal location of a satellite DNA from the Pacific oyster, Crassostrea gigas

    Digital Repository Service at National Institute of Oceanography (India)

    Clabby, C.; Goswami, U.; Flavin, F.; Wilkins, N.P.; Houghton, J.A.; Powell, R.

    Elsevier Science B.V. All rights reserved. 0378-1119/96/$15.00 205 GENE 09452 Cloning, characterization and chromosomal location of a satellite DNA from the Pacific oyster, Crassostrea gigas (HaelII and FokI repeated DNA; tandem repetition; genomic...: 16 October 1995 SUMMARY We report the cloning and characterization of a high-copy-number, tandem-repeat satellite DNA sequence from the genome of the Pacific oyster, Crassostrea gigas (Cg). The monomeric unit was found to be 166 (_+ 2) bp in length...

  15. Comparative Analysis of Satellite DNA in the Drosophila melanogaster Species Complex

    Directory of Open Access Journals (Sweden)

    Madhav Jagannathan

    2017-02-01

    Full Text Available Satellite DNAs are highly repetitive sequences that account for the majority of constitutive heterochromatin in many eukaryotic genomes. It is widely recognized that sequences and locations of satellite DNAs are highly divergent even in closely related species, contributing to the hypothesis that satellite DNA differences may underlie speciation. However, due to its repetitive nature, the mapping of satellite DNAs has been mostly left out of recent genomics analyses, hampering the use of molecular genetics techniques to better understand their role in speciation and evolution. Satellite DNAs are most extensively and comprehensively mapped in Drosophila melanogaster, a species that is also an excellent model system with which to study speciation. Yet the lack of comprehensive knowledge regarding satellite DNA identity and location in its sibling species (D. simulans, D. mauritiana, and D. sechellia has prevented the full utilization of D. melanogaster in studying speciation. To overcome this problem, we initiated the mapping of satellite DNAs on the genomes of the D. melanogaster species complex (D. melanogaster, D. simulans, D. mauritiana, and D. sechellia using multi-color fluorescent in situ hybridization (FISH probes. Our study confirms a striking divergence of satellite DNAs in the D. melanogaster species complex, even among the closely related species of the D. simulans clade (D. simulans, D. mauritiana, and D. sechellia, and suggests the presence of unidentified satellite sequences in these species.

  16. Comparative Analysis of Satellite DNA in the Drosophila melanogaster Species Complex.

    Science.gov (United States)

    Jagannathan, Madhav; Warsinger-Pepe, Natalie; Watase, George J; Yamashita, Yukiko M

    2017-02-09

    Satellite DNAs are highly repetitive sequences that account for the majority of constitutive heterochromatin in many eukaryotic genomes. It is widely recognized that sequences and locations of satellite DNAs are highly divergent even in closely related species, contributing to the hypothesis that satellite DNA differences may underlie speciation. However, due to its repetitive nature, the mapping of satellite DNAs has been mostly left out of recent genomics analyses, hampering the use of molecular genetics techniques to better understand their role in speciation and evolution. Satellite DNAs are most extensively and comprehensively mapped in Drosophila melanogaster, a species that is also an excellent model system with which to study speciation. Yet the lack of comprehensive knowledge regarding satellite DNA identity and location in its sibling species (D. simulans, D. mauritiana, and D. sechellia) has prevented the full utilization of D. melanogaster in studying speciation. To overcome this problem, we initiated the mapping of satellite DNAs on the genomes of the D. melanogaster species complex (D. melanogaster, D. simulans, D. mauritiana, and D. sechellia) using multi-color fluorescent in situ hybridization (FISH) probes. Our study confirms a striking divergence of satellite DNAs in the D. melanogaster species complex, even among the closely related species of the D. simulans clade (D. simulans, D. mauritiana, and D. sechellia), and suggests the presence of unidentified satellite sequences in these species. Copyright © 2017 Jagannathan et al.

  17. Forensic utilization of familial searches in DNA databases.

    Science.gov (United States)

    Gershaw, Cassandra J; Schweighardt, Andrew J; Rourke, Linda C; Wallace, Margaret M

    2011-01-01

    DNA evidence is widely recognized as an invaluable tool in the process of investigation and identification, as well as one of the most sought after types of evidence for presentation to a jury. In the United States, the development of state and federal DNA databases has greatly impacted the forensic community by creating an efficient, searchable system that can be used to eliminate or include suspects in an investigation based on matching DNA profiles - the profile already in the database to the profile of the unknown sample in evidence. Recent changes in legislation have begun to allow for the possibility to expand the parameters of DNA database searches, taking into account the possibility of familial searches. This article discusses prospective positive outcomes of utilizing familial DNA searches and acknowledges potential negative outcomes, thereby presenting both sides of this very complicated, rapidly evolving situation. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  18. Distribution and sequence homogeneity of an abundant satellite DNA in the beetle, Tenebrio molitor.

    Science.gov (United States)

    Davis, C A; Wyatt, G R

    1989-01-01

    The mealworm beetle, Tenebrio molitor, contains an unusually abundant and homogeneous satellite DNA which constitutes up to 60% of its genome. The satellite DNA is shown to be present in all of the chromosomes by in situ hybridization. 18 dimers of the repeat unit were cloned and sequenced. The consensus sequence is 142 nt long and lacks any internal repeat structure. Monomers of the sequence are very similar, showing on average a 2% divergence from the calculated consensus. Variant nucleotides are scattered randomly throughout the sequence although some variants are more common than others. Neighboring repeat units are no more alike than randomly chosen ones. The results suggest that some mechanism, perhaps gene conversion, is acting to maintain the homogeneity of the satellite DNA despite its abundance and distribution on all of the chromosomes. Images PMID:2762148

  19. On DNA codes from a family of chain rings

    Directory of Open Access Journals (Sweden)

    Elif Segah Oztas

    2017-01-01

    Full Text Available In this work, we focus on reversible cyclic codes which correspond to reversible DNA codes or reversible-complement DNA codes over a family of finite chain rings, in an effort to extend what was done by Yildiz and Siap in [20]. The ring family that we have considered are of size $2^{2^k}$, $k=1,2, \\cdots$ and we match each ring element with a DNA $2^{k-1}$-mer. We use the so-called $u^2$-adic digit system to solve the reversibility problem and we characterize cyclic codes that correspond to reversible-complement DNA-codes. We then conclude our study with some examples.

  20. Hairpin structures formed by alpha satellite DNA of human centromeres are cleaved by human topoisomerase IIα

    Science.gov (United States)

    Jonstrup, Anette Thyssen; Thomsen, Tina; Wang, Yong; Knudsen, Birgitta R.; Koch, Jørn; Andersen, Anni H.

    2008-01-01

    Although centromere function has been conserved through evolution, apparently no interspecies consensus DNA sequence exists. Instead, centromere DNA may be interconnected through the formation of certain DNA structures creating topological binding sites for centromeric proteins. DNA topoisomerase II is a protein, which is located at centromeres, and enzymatic topoisomerase II activity correlates with centromere activity in human cells. It is therefore possible that topoisomerase II recognizes and interacts with the alpha satellite DNA of human centromeres through an interaction with potential DNA structures formed solely at active centromeres. In the present study, human topoisomerase IIα-mediated cleavage at centromeric DNA sequences was examined in vitro. The investigation has revealed that the enzyme recognizes and cleaves a specific hairpin structure formed by alpha satellite DNA. The topoisomerase introduces a single-stranded break at the hairpin loop in a reaction, where DNA ligation is partly uncoupled from the cleavage reaction. A mutational analysis has revealed, which features of the hairpin are required for topoisomerease IIα-mediated cleavage. Based on this a model is discussed, where topoisomerase II interacts with two hairpins as a mediator of centromere cohesion. PMID:18824478

  1. Population variation in the A chromosome distribution of satellite DNA and ribosomal DNA in the grasshopper Eyprepocnemis plorans.

    Science.gov (United States)

    Cabrero, J; Perfectti, F; Gómez, R; Camacho, J P M; López-León, M D

    2003-01-01

    The double FISH analysis of two repetitive DNAs (a satellite DNA and ribosomal DNA) in 12 natural populations of the grasshopper Eyprepocnemis plorans collected at the south (Granada and Málaga provinces) and south-east (Albacete and Murcia provinces) of the Iberian Peninsula has shown their wide-spread presence throughout the whole genome as well as extensive variation among populations. Both DNAs are found in most A chromosomes. Regularly, both DNAs occurred in the S11 and X chromosomes, rDNA in the S10 and satDNA in the L2 and M3. No correlation was found between the number of satDNA and rDNA clusters in the A genomes of the 12 populations analysed, and both figures were independent of the presence of B chromosomes. The genomic distribution of both DNAs showed no association with the geographical localization of the populations analysed. Finally, we provide evidence that the supernumerary chromosome segment proximally located on the S11 chromosome is, in most cases, the result of satDNA amplification but, in some cases, it might also derive from amplification of both satDNA and rDNA.

  2. Sequence-specific physical properties of African green monkey alpha-satellite DNA contribute to centromeric heterochromatin formation

    NARCIS (Netherlands)

    Bussiek, M.; Hoischen, Christian; Diekmann, Stephan; Bennink, Martin L.

    2009-01-01

    Satellite DNA, a major component of eukaryotic centromeric heterochromatin, is potentially associated with the processes ensuring the faithful segregation of the genetic material during cell division. Structural properties of alpha-satellite DNA (AS) from African green monkey (AGM) were studied.

  3. A neocentromere on human chromosome 3 without detectable alpha-satellite DNA forms morphologically normal kinetochores

    DEFF Research Database (Denmark)

    Wandall, A; Tranebjaerg, L; Tommerup, Niels

    1998-01-01

    A neocentromere at 3q26 was observed in a father and his daughter on a chromosome 3 with deleted centromeric region. No alpha-satellite DNA was detectable at the 3q26 neocentromere, but it was weakly positive with anticentromere (CREST) antibodies. Electron microscopy showed that the neocentromere...

  4. Factors influencing the yield of satellite DNA in extractions from Drosophila virilis and Drosophila melanogaster adults and embryos.

    Science.gov (United States)

    Rae, P M; Barnett, T R; Babbitt, D G

    1976-05-03

    The application of different DNA extraction methods to identical batches of Drosophila virilis and Drosophila melanogaster flies or embryos has revealed that the ionic strength of a homogenization medium is of critical importance if chloroform extractions are performed. The low yield of satellite DNA after homogenization in low salt buffers is less severe if EDTA is included in the buffer. Phenol extraction procedures result in no such differential behavior of satellite and main band DNA, but under certain circumstances a particular satellite fraction of Drosophila virilis DNA may be lost.

  5. Locational diversity of alpha satellite DNA and intergeneric hybridization aspects in the Nomascus and Hylobates genera of small apes.

    Directory of Open Access Journals (Sweden)

    Sudarath Baicharoen

    Full Text Available Recently, we discovered that alpha satellite DNA has unique and genus-specific localizations on the chromosomes of small apes. This study describes the details of alpha satellite localization in the genera Nomascus and Hylobates and explores their usefulness in distinguishing parental genome sets in hybrids between these genera. Fluorescence in situ hybridization was used to establish diagnostic criteria of alpha satellite DNA markers in discriminating small ape genomes. In particular we established the genus specificity of alpha satellite distribution in three species of light-cheeked gibbons (Nomascus leucogenys, N. siki, and N. gabriellae in comparison to that of Hylobates lar. Then we determined the localization of alpha satellite DNA in a hybrid individual which resulted from a cross between these two genera. In Nomascus the alpha satellite DNA blocks were located at the centromere, telomere, and four interstitial regions. In Hylobates detectable amounts of alpha satellite DNA were seen only at centromeric regions. The differences in alpha satellite DNA locations between Nomascus and Hylobates allowed us to easily distinguish the parental chromosomal sets in the genome of intergeneric hybrid individuals found in Thai and Japanese zoos. Our study illustrates how molecular cytogenetic markers can serve as diagnostic tools to identify the origin of individuals. These molecular tools can aid zoos, captive breeding programs and conservation efforts in managing small apes species. Discovering more information on alpha satellite distribution is also an opportunity to examine phylogenetic and evolutionary questions that are still controversial in small apes.

  6. Satellite DNA Modulates Gene Expression in the Beetle Tribolium castaneum after Heat Stress.

    Directory of Open Access Journals (Sweden)

    Isidoro Feliciello

    2015-08-01

    Full Text Available Non-coding repetitive DNAs have been proposed to perform a gene regulatory role, however for tandemly repeated satellite DNA no such role was defined until now. Here we provide the first evidence for a role of satellite DNA in the modulation of gene expression under specific environmental conditions. The major satellite DNA TCAST1 in the beetle Tribolium castaneum is preferentially located within pericentromeric heterochromatin but is also dispersed as single repeats or short arrays in the vicinity of protein-coding genes within euchromatin. Our results show enhanced suppression of activity of TCAST1-associated genes and slower recovery of their activity after long-term heat stress relative to the same genes without associated TCAST1 satellite DNA elements. The level of gene suppression is not influenced by the distance of TCAST1 elements from the associated genes up to 40 kb from the genes' transcription start sites, but it does depend on the copy number of TCAST1 repeats within an element, being stronger for the higher number of copies. The enhanced gene suppression correlates with the enrichment of the repressive histone marks H3K9me2/3 at dispersed TCAST1 elements and their flanking regions as well as with increased expression of TCAST1 satellite DNA. The results reveal transient, RNAi based heterochromatin formation at dispersed TCAST1 repeats and their proximal regions as a mechanism responsible for enhanced silencing of TCAST1-associated genes. Differences in the pattern of distribution of TCAST1 elements contribute to gene expression diversity among T. castaneum strains after long-term heat stress and might have an impact on adaptation to different environmental conditions.

  7. Consent process for US-based family reference DNA samples.

    Science.gov (United States)

    Katsanis, Sara H; Snyder, Lindsey; Arnholt, Kelly; Mundorff, Amy Z

    2018-01-01

    DNA collection from family members of the missing is a tenet for missing persons' and mass fatality investigations. Procedures for consenting family members are disparate, depending on the context supporting the reason for sample collection. While guidelines and best practices have been developed for handling mass fatalities and for identification of the missing, these guidelines do not address standard consent practices for living family members of potential victims. We examined the relevant U.S. laws, international guidelines and best practices, sampled consent forms currently used for DNA collection of family members, and drafted model language for a consent form to communicate the required and recommended information. We modeled the consent form on biobank consenting practices and tested the consent language among students and the general population for constructive feedback and readability. We also asked respondents to consider the options for DNA collection and either hypothetically agree or disagree. The model language presented here highlights information important to relay in consent processes and can serve as a foundation for future consent practices in mass fatalities and missing persons' investigations. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. RNA Pol II promotes transcription of centromeric satellite DNA in beetles.

    Directory of Open Access Journals (Sweden)

    Zeljka Pezer

    Full Text Available Transcripts of centromeric satellite DNAs are known to play a role in heterochromatin formation as well as in establishment of the kinetochore. However, little is known about basic mechanisms of satellite DNA expression within constitutive heterochromatin and its regulation. Here we present comprehensive analysis of transcription of abundant centromeric satellite DNA, PRAT from beetle Palorus ratzeburgii (Coleoptera. This satellite is characterized by preservation and extreme sequence conservation among evolutionarily distant insect species. PRAT is expressed in all three developmental stages: larvae, pupae and adults at similar level. Transcripts are abundant comprising 0.033% of total RNA and are heterogeneous in size ranging from 0.5 kb up to more than 5 kb. Transcription proceeds from both strands but with 10 fold different expression intensity and transcripts are not processed into siRNAs. Most of the transcripts (80% are not polyadenylated and remain in the nucleus while a small portion is exported to the cytoplasm. Multiple, irregularly distributed transcription initiation sites as well as termination sites have been mapped within the PRAT sequence using primer extension and RLM-RACE. The presence of cap structure as well as poly(A tails in a portion of the transcripts indicate RNA polymerase II-dependent transcription and a putative polymerase II promoter site overlaps the most conserved part of the PRAT sequence. The treatment of larvae with alpha-amanitin decreases the level of PRAT transcripts at concentrations that selectively inhibit pol II activity. In conclusion, stable, RNA polymerase II dependant transcripts of abundant centromeric satellite DNA, not regulated by RNAi, have been identified and characterized. This study offers a basic understanding of expression of highly abundant heterochromatic DNA which in beetle species constitutes up to 50% of the genome.

  9. Amplification of satellite III DNA in an unusually large chromosome 14p+ variant.

    Science.gov (United States)

    Earle, E; Dale, S; Choo, K H

    1989-05-01

    A phenotypically normal male (WSm) was found to have an unusually large short arm of chromosome 14. Increase in the size of this variant chromosome [Wsm-var(14)] was estimated to be approximately 30% that of a normal chromosome 14 by G-banding using trypsin and staining with Leishman. The extra chromosomal material was positive in CBG staining (C-banding using BaOH and staining with Giemsa), suggesting the presence of repetitive DNA. In situ hybridisation using repetitive probes demonstrated this material to be strongly positive for satellite III DNA, and negative for Y-specific heterochromatic DNA. Hybridisation with an alpha DNA probe specific for human acrocentric chromosomes indicated the retention of the centromere, and the absence of alpha DNA in the extra chromosomal material. We propose the origin of the extra chromosomal material in WSm-var(14) to be a result of amplification of contiguous satellite III DNA that is normally present in the short arm of chromosome 14. This variant chromosome does not appear to be associated with the abnormal phenotype in WSm's daughter who is mentally retarded and carries a t(1;?)(q41;?) translocation of chromosome 1.

  10. Maternal inheritance and mitochondrial DNA variants in familial Parkinson's disease

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    Pfeiffer Ronald F

    2010-04-01

    Full Text Available Abstract Background Mitochondrial function is impaired in Parkinson's disease (PD and may contribute to the pathogenesis of PD, but the causes of mitochondrial impairment in PD are unknown. Mitochondrial dysfunction is recapitulated in cell lines expressing mitochondrial DNA (mtDNA from PD patients, implicating mtDNA variants or mutations, though the role of mtDNA variants or mutations in PD risk remains unclear. We investigated the potential contribution of mtDNA variants or mutations to the risk of PD. Methods We examined the possibility of a maternal inheritance bias as well as the association between mitochondrial haplogroups and maternal inheritance and disease risk in a case-control study of 168 multiplex PD families in which the proband and one parent were diagnosed with PD. 2-tailed Fisher Exact Tests and McNemar's tests were used to compare allele frequencies, and a t-test to compare ages of onset. Results The frequency of affected mothers of the proband with PD (83/167, 49.4% was not significantly different from the frequency of affected females of the proband generation (115/259, 44.4% (Odds Ratio 1.22; 95%CI 0.83 - 1.81. After correcting for multiple tests, there were no significant differences in the frequencies of mitochondrial haplogroups or of the 10398G complex I gene polymorphism in PD patients compared to controls, and no significant associations with age of onset of PD. Mitochondrial haplogroup and 10398G polymorphism frequencies were similar in probands having an affected father as compared to probands having an affected mother. Conclusions These data fail to demonstrate a bias towards maternal inheritance in familial PD. Consistent with this, we find no association of common haplogroup-defining mtDNA variants or for the 10398G variant with the risk of PD. However, these data do not exclude a role for mtDNA variants in other populations, and it remains possible that other inherited mitochondrial DNA variants, or somatic mDNA

  11. A homologous subfamily of satellite III DNA on human chromosomes 14 and 22.

    OpenAIRE

    Choo, K H; Earle, E; McQuillan, C.

    1990-01-01

    We describe a new subfamily of human satellite III DNA that is represented on two different acrocentric chromosomes. This DNA is composed of a tandemly repeated array of diverged 5-base-pair monomer units of the sequence GGAAT or GGAGT. These monomers are organised into a 1.37-kilobase higher-order structure that is itself tandemly reiterated. Using a panel of somatic cell hybrids containing specific human chromosomes, this higher-order structure is demonstrated on chromosomes 14 and 22, but ...

  12. Hybridization of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP and microsatellites.

    Science.gov (United States)

    Nijman, I J; Otsen, M; Verkaar, E L C; de Ruijter, C; Hanekamp, E; Ochieng, J W; Shamshad, S; Rege, J E O; Hanotte, O; Barwegen, M W; Sulawati, T; Lenstra, J A

    2003-01-01

    Hybridization between wild and domestic bovine species occurs worldwide either spontaneously or by organized crossing. We have analysed hybridization of banteng (Bos javanicus) and zebu (Bos indicus) in south-east Asian cattle using mitochondrial DNA (PCR-RFLP and sequencing), AFLP, satellite fragment length polymorphisms (SFLP or PCR-RFLP of satellite DNA) and microsatellite genotyping. The Indonesian Madura zebu breed is reputed to be of hybrid zebu-banteng origin, but this has never been documented and Bali cattle are considered to be a domesticated form of banteng. The banteng mitochondrial type was found in all animals sampled on the isle of Bali, Indonesia, but only in 35% of the animals from a Malaysian Bali-cattle population. The Madura animals also carried mitochondrial DNA of either zebu and banteng origin. In both populations, zebu introgression was confirmed by AFLP and SFLP. Microsatellite analysis of the Malaysian Bali population revealed for 12 out of 15 loci screened, Bali-cattle-specific alleles, several of which were also found in wild banteng animals. The tools we have described are suitable for the detection of species in introgression studies, which are essential for the genetic description of local breeds and the preservation of their economic and cultural value.

  13. Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata).

    Science.gov (United States)

    Prakhongcheep, Ornjira; Thapana, Watcharaporn; Suntronpong, Aorarat; Singchat, Worapong; Pattanatanang, Khampee; Phatcharakullawarawat, Rattanin; Muangmai, Narongrit; Peyachoknagul, Surin; Matsubara, Kazumi; Ezaz, Tariq; Srikulnath, Kornsorn

    2017-08-16

    Satellite DNAs (stDNAs) are highly repeated sequences that constitute large portions of any genome. The evolutionary dynamics of stDNA (e.g. copy number, nucleotide sequence, location) can, therefore, provide an insight into genome organization and evolution. We investigated the evolutionary origin of VSAREP stDNA in 17 monitor lizards (seven Asian, five Australian, and five African) at molecular and cytogenetic level. Results revealed that VSAREP is conserved in the genome of Asian and Australian varanids, but not in African varanids, suggesting that these sequences are either differentiated or lost in the African varanids. Phylogenetic and arrangement network analyses revealed the existence of at least four VSAREP subfamilies. The similarity of each sequence unit within the same VSAREP subfamily from different species was higher than those of other VSAREP subfamilies belonging to the same species. Additionally, all VSAREP subfamilies isolated from the three Australian species (Varanus rosenbergi, V. gouldii, and V. acanthurus) were co-localized near the centromeric or pericentromeric regions of the macrochromosomes, except for chromosomes 3 and 4 in each Australian varanid. However, their chromosomal arrangements were different among species. The VSAREP stDNA family lack homogenized species-specific nucleotide positions in varanid lineage. Most VSAREP sequences were shared among varanids within the four VSAREP subfamilies. This suggests that nucleotide substitutions in each varanid species accumulated more slowly than homogenization rates in each VSAREP subfamily, resulting in non-species-specific evolution of stDNA profiles. Moreover, changes in location of VSAREP stDNA in each Australian varanid suggests a correlation with chromosomal rearrangements, leading to karyotypic differences among these species.

  14. Replication of alpha-satellite DNA arrays in endogenous human centromeric regions and in human artificial chromosome.

    Science.gov (United States)

    Erliandri, Indri; Fu, Haiqing; Nakano, Megumi; Kim, Jung-Hyun; Miga, Karen H; Liskovykh, Mikhail; Earnshaw, William C; Masumoto, Hiroshi; Kouprina, Natalay; Aladjem, Mirit I; Larionov, Vladimir

    2014-10-01

    In human chromosomes, centromeric regions comprise megabase-size arrays of 171 bp alpha-satellite DNA monomers. The large distances spanned by these arrays preclude their replication from external sites and imply that the repetitive monomers contain replication origins. However, replication within these arrays has not previously been profiled and the role of alpha-satellite DNA in initiation of DNA replication has not yet been demonstrated. Here, replication of alpha-satellite DNA in endogenous human centromeric regions and in de novo formed Human Artificial Chromosome (HAC) was analyzed. We showed that alpha-satellite monomers could function as origins of DNA replication and that replication of alphoid arrays organized into centrochromatin occurred earlier than those organized into heterochromatin. The distribution of inter-origin distances within centromeric alphoid arrays was comparable to the distribution of inter-origin distances on randomly selected non-centromeric chromosomal regions. Depletion of CENP-B, a kinetochore protein that binds directly to a 17 bp CENP-B box motif common to alpha-satellite DNA, resulted in enrichment of alpha-satellite sequences for proteins of the ORC complex, suggesting that CENP-B may have a role in regulating the replication of centromeric regions. Mapping of replication initiation sites in the HAC revealed that replication preferentially initiated in transcriptionally active regions. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  15. DnaJ/Hsp40 Family and Parkinson's Disease

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    Takafumi Hasegawa

    2018-01-01

    Full Text Available Parkinson's disease (PD is the second most common devastating neurodegenerative disorder after Alzheimer's disease. The precise molecular and cellular basis underlying PD still remains uncertain; however, accumulating evidence suggests that neuronal cell death is caused by a combination of environmental and genetic factors. Over the previous two decades, more than 20 genes have been identified as the cause of and/or risk for PD. Because sporadic and familial forms of PD have many similarities in clinical and neuropathological features, common molecular pathways, such as aberrant mitochondrial and protein homeostasis, are likely to exist in both conditions. Of the various genes and proteins involved in PD, the versatile DnaJ/Hsp40 co-chaperones have attracted particular attention since several genes encoding this protein family have been successively identified as the cause of the familial forms of PD/Parkinsonism. In this review, we will introduce the current knowledge regarding the integratory and modulatory effect of DnaJ/Hsp40 in various cellular functions and argue how the failure of these proteins may initiate and/or facilitate of the disease.

  16. DNA barcoding of the Lemnaceae, a family of aquatic monocots

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    Wang Wenqin

    2010-09-01

    Full Text Available Abstract Background Members of the aquatic monocot family Lemnaceae (commonly called duckweeds represent the smallest and fastest growing flowering plants. Their highly reduced morphology and infrequent flowering result in a dearth of characters for distinguishing between the nearly 38 species that exhibit these tiny, closely-related and often morphologically similar features within the same family of plants. Results We developed a simple and rapid DNA-based molecular identification system for the Lemnaceae based on sequence polymorphisms. We compared the barcoding potential of the seven plastid-markers proposed by the CBOL (Consortium for the Barcode of Life plant-working group to discriminate species within the land plants in 97 accessions representing 31 species from the family of Lemnaceae. A Lemnaceae-specific set of PCR and sequencing primers were designed for four plastid coding genes (rpoB, rpoC1, rbcL and matK and three noncoding spacers (atpF-atpH, psbK-psbI and trnH-psbA based on the Lemna minor chloroplast genome sequence. We assessed the ease of amplification and sequencing for these markers, examined the extent of the barcoding gap between intra- and inter-specific variation by pairwise distances, evaluated successful identifications based on direct sequence comparison of the "best close match" and the construction of a phylogenetic tree. Conclusions Based on its reliable amplification, straightforward sequence alignment, and rates of DNA variation between species and within species, we propose that the atpF-atpH noncoding spacer could serve as a universal DNA barcoding marker for species-level identification of duckweeds.

  17. [Frequency of various mini- and micro-satellite sequences in DNA of human chromosome 13].

    Science.gov (United States)

    Ryskov, A P; Kupriianova, N S; Kapanadze, B I; Nechvolodov, K K; Pozmogova, G E; Prosniak, M I; Iankovskiĭ, N K

    1993-10-01

    The frequency of specific mini- and micro-satellites known also as short tandem repeated sequences (STR) in the human 13 chromosome was estimated by hybridization of STR core oligonucleotides to recombinant cosmid clones transferred to a grid from a human 13 chromosome specific cosmid library ICRF Lawrist 4 C108 (DN L4/HS 13). Oligonucleotides: M13 and Jeffreys minisatellite core sequences and micro-satellite core sequences (TCC)5, (CAC)5, and (GACA)4 were [gamma-32P] end labeled and hybridized to membrane filters carrying good ordered cosmid clones. It was shown that great number of all these mini- and micro-satellite copies (besides of Jeffreys minisatellite) are spread independently along the 13th chromosome. It was also estimated that two or more (GACA)n blocks present in the same cosmid (i.e. on the stretch of 40-50 kb) forming similar groups of clustered micro-satellites. The interesting peculiarity has been recorded that some (GACA)n+ cosmids are also hybridizable to conservative 28SrDNA 3'-fragment that indicates that (GACA)n localization in the nucleoli area. As the result of it we began the creation of a new highly polymorphic markers collections for these chromosome.

  18. A homologous subfamily of satellite III DNA on human chromosomes 14 and 22.

    Science.gov (United States)

    Choo, K H; Earle, E; McQuillan, C

    1990-10-11

    We describe a new subfamily of human satellite III DNA that is represented on two different acrocentric chromosomes. This DNA is composed of a tandemly repeated array of diverged 5-base-pair monomer units of the sequence GGAAT or GGAGT. These monomers are organised into a 1.37-kilobase higher-order structure that is itself tandemly reiterated. Using a panel of somatic cell hybrids containing specific human chromosomes, this higher-order structure is demonstrated on chromosomes 14 and 22, but not on the remaining acrocentric chromosomes. In situ hybridisation studies have localised the sequence to the proximal p-arm region of these chromosomes. Analysis by pulsed-field gel electrophoresis (PFGE) reveals that 70-110 copies of the higher-order structure are tandemly organised on a chromosome into a major domain which appears to be flanked on both sides by non-tandemly repeated genomic DNA. In addition, some of the satellite III sequences are interspersed over a number of other PFGE fragments. This study provides fundamental knowledge on the structure and evolution of the acrocentric chromosomes, and should extend our understanding of the complex process of interchromosomal interaction which may be responsible for Robertsonian translocation and meiotic nondisjunction involving these chromosomes.

  19. FA-SAT Is an Old Satellite DNA Frozen in Several Bilateria Genomes

    Science.gov (United States)

    Ferreira, Daniela; Mendes-da-Silva, Ana; Meles, Susana; Adega, Filomena

    2017-01-01

    Abstract In recent years, a growing body of evidence has recognized the tandem repeat sequences, and specifically satellite DNA, as a functional class of sequences in the genomic “dark matter.” Using an original, complementary, and thus an eclectic experimental design, we show that the cat archetypal satellite DNA sequence, FA-SAT, is “frozen” conservatively in several Bilateria genomes. We found different genomic FA-SAT architectures, and the interspersion pattern was conserved. In Carnivora genomes, the FA-SAT-related sequences are also amplified, with the predominance of a specific FA-SAT variant, at the heterochromatic regions. We inspected the cat genome project to locate FA-SAT array flanking regions and revealed an intensive intermingling with transposable elements. Our results also show that FA-SAT-related sequences are transcribed and that the most abundant FA-SAT variant is not always the most transcribed. We thus conclude that the DNA sequences of FA-SAT and their transcripts are “frozen” in these genomes. Future work is needed to disclose any putative function that these sequences may play in these genomes.

  20. Evolutionary dynamics of an at-rich satellite DNA and its contribution to karyotype differentiation in wild diploid Arachis species.

    Science.gov (United States)

    Samoluk, Sergio Sebastián; Robledo, Germán; Bertioli, David; Seijo, José Guillermo

    2017-04-01

    Satellite DNA (satDNA) is a major component of the heterochromatic regions of eukaryote genomes and usually shows a high evolutionary dynamic, even among closely related species. Section Arachis (genus Arachis) is composed of species belonging to six different genomes (A, B, D, F, G and K). The most distinguishing features among these genomes are the amount and distribution of the heterochromatin in the karyotypes. With the objective of gaining insight into the sequence composition and evolutionary dynamics of the heterochromatin fraction in Arachis, we investigated here the sequence diversity, genomic abundance, and chromosomal distribution of a satDNA family (ATR-2) among seven diploid species of section Arachis. All of the isolated sequences were AT-rich and highly conserved at both intraspecific and interspecific levels, without any species-specific polymorphism. Pairwise comparisons of isolated ATR-2 monomers revealed that most of the nucleotide sites were in the first two transitional stages of Strachan's model. However, the abundance of ATR-2 was significantly different among genomes according to the 'library hypothesis'. Fluorescent in situ hybridization revealed that ATR-2 is a main component of the DAPI + centromeric heterochromatin of the A, F, and K genomes. Thus, the evolution of the different heterochromatin patterns observed in Arachis genomes can be explained, at least in part, by the differential representation of ATR-2 among the different species or even among the chromosomes of the same complement. These findings are the first to demonstrate the participation of satDNA sequences in the karyotype diversification of wild diploid Arachis species.

  1. 5-bp Classical Satellite DNA Loci from Chromosome-1 Instability in Cervical Neoplasia Detected by DNA Breakage Detection/Fluorescence in Situ Hybridization (DBD-FISH

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    Jaime Gosálvez

    2013-02-01

    Full Text Available We aimed to evaluate the association between the progressive stages of cervical neoplasia and DNA damage in 5-bp classical satellite DNA sequences from chromosome-1 in cervical epithelium and in peripheral blood lymphocytes using DNA breakage detection/fluorescence in situ hybridization (DBD-FISH. A hospital-based unmatched case-control study was conducted in 2011 with a sample of 30 women grouped according to disease stage and selected according to histological diagnosis; 10 with low-grade squamous intraepithelial lesions (LG-SIL, 10 with high-grade SIL (HG-SIL, and 10 with no cervical lesions, from the Unidad Medica de Alta Especialidad of The Mexican Social Security Institute, IMSS, Mexico. Specific chromosome damage levels in 5-bp classical satellite DNA sequences from chromosome-1 were evaluated in cervical epithelium and peripheral blood lymphocytes using the DBD-FISH technique. Whole-genome DNA hybridization was used as a reference for the level of damage. Results of Kruskal-Wallis test showed a significant increase according to neoplastic development in both tissues. The instability of 5-bp classical satellite DNA sequences from chromosome-1 was evidenced using chromosome-orientation FISH. In conclusion, we suggest that the progression to malignant transformation involves an increase in the instability of 5-bp classical satellite DNA sequences from chromosome-1.

  2. 5-bp Classical Satellite DNA Loci from Chromosome-1 Instability in Cervical Neoplasia Detected by DNA Breakage Detection/Fluorescence in Situ Hybridization (DBD-FISH)

    Science.gov (United States)

    Cortés-Gutiérrez, Elva I.; Ortíz-Hernández, Brenda L.; Dávila-Rodríguez, Martha I.; Cerda-Flores, Ricardo M; Fernández, José Luis; López-Fernández, Carmen; Gosálvez, Jaime

    2013-01-01

    We aimed to evaluate the association between the progressive stages of cervical neoplasia and DNA damage in 5-bp classical satellite DNA sequences from chromosome-1 in cervical epithelium and in peripheral blood lymphocytes using DNA breakage detection/fluorescence in situ hybridization (DBD-FISH). A hospital-based unmatched case-control study was conducted in 2011 with a sample of 30 women grouped according to disease stage and selected according to histological diagnosis; 10 with low-grade squamous intraepithelial lesions (LG-SIL), 10 with high-grade SIL (HG-SIL), and 10 with no cervical lesions, from the Unidad Medica de Alta Especialidad of The Mexican Social Security Institute, IMSS, Mexico. Specific chromosome damage levels in 5-bp classical satellite DNA sequences from chromosome-1 were evaluated in cervical epithelium and peripheral blood lymphocytes using the DBD-FISH technique. Whole-genome DNA hybridization was used as a reference for the level of damage. Results of Kruskal-Wallis test showed a significant increase according to neoplastic development in both tissues. The instability of 5-bp classical satellite DNA sequences from chromosome-1 was evidenced using chromosome-orientation FISH. In conclusion, we suggest that the progression to malignant transformation involves an increase in the instability of 5-bp classical satellite DNA sequences from chromosome-1. PMID:23429197

  3. Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM Surveys Using Whiteflies (Aleyrodidae

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    Karyna Rosario

    2016-02-01

    Full Text Available Monopartite begomoviruses (Geminiviridae, which are whitefly-transmitted single-stranded DNA viruses known for causing devastating crop diseases, are often associated with satellite DNAs. Since begomovirus acquisition or exchange of satellite DNAs may lead to adaptation to new plant hosts and emergence of new disease complexes, it is important to investigate the diversity and distribution of these molecules. This study reports begomovirus-associated satellite DNAs identified during a vector-enabled metagenomic (VEM survey of begomoviruses using whiteflies collected in various locations (California (USA, Guatemala, Israel, Puerto Rico, and Spain. Protein-encoding satellite DNAs, including alphasatellites and betasatellites, were identified in Israel, Puerto Rico, and Guatemala. Novel alphasatellites were detected in samples from Guatemala and Puerto Rico, resulting in the description of a phylogenetic clade (DNA-3-type alphasatellites dominated by New World sequences. In addition, a diversity of small (~640–750 nucleotides satellite DNAs similar to satellites associated with begomoviruses infecting Ipomoea spp. were detected in Puerto Rico and Spain. A third class of satellite molecules, named gammasatellites, is proposed to encompass the increasing number of reported small (<1 kilobase, non-coding begomovirus-associated satellite DNAs. This VEM-based survey indicates that, although recently recovered begomovirus genomes are variations of known genetic themes, satellite DNAs hold unexplored genetic diversity.

  4. Interplay of selective pressure and stochastic events directs evolution of the MEL172 satellite DNA library in root-knot nematodes.

    Science.gov (United States)

    Mestrović, Nevenka; Castagnone-Sereno, Philippe; Plohl, Miroslav

    2006-12-01

    According to the library model, related species can have in common satellite DNA (satDNA) families amplified in differing abundances, but reasons for persistence of particular sequences in the library during long periods of time are poorly understood. In this paper, we characterize 3 related satDNAs coexisting in the form of a library in mitotic parthenogenetic root-knot nematodes of the genus Meloidogyne. Due to sequence similarity and conserved monomer length of 172 bp, this group of satDNAs is named MEL172. Analysis of sequence variability patterns among monomers of the 3 MEL172 satellites revealed 2 low-variable (LV) domains highly reluctant to sequence changes, 2 moderately variable (MV) domains characterized by limited number of mutations, and 1 highly variable (HV) domain. The latter domain is prone to rapid spread and homogenization of changes. Comparison of the 3 MEL172 consensus sequences shows that the LV domains have 6% changed nucleotide positions, the MV domains have 48%, whereas 78% divergence is concentrated in the HV domain. Conserved distribution of intersatellite variability might indicate a complex pattern of interactions in heterochromatin, which limits the range and phasing of allowed changes, implying a possible selection imposed on monomer sequences. The lack of fixed species-diagnostic mutations in each of the examined MEL172 satellites suggests that they existed in unaltered form in a common ancestor of extant species. Consequently, the evolution of these satellites seems to be driven by interplay of selective constraints and stochastic events. We propose that new satellites were derived from an ancestral progenitor sequence by nonrandom accumulation of mutations due to selective pressure on particular sequence segments. In the library of particular taxa, established satellites might be subject to differential amplification at chance due to stochastic mechanisms of concerted evolution.

  5. Rapid shift in genotype of human mitochondrial DNA in a family with Leber's hereditary optic neuropathy

    NARCIS (Netherlands)

    Bolhuis, P. A.; Bleeker-Wagemakers, E. M.; Ponne, N. J.; van Schooneveld, M. J.; Westerveld, A.; van den Bogert, C.; Tabak, H. F.

    1990-01-01

    Mitochondrial DNA isolated from white blood cells was investigated in families suffering from Leber's hereditary optic neuropathy. A recently described mutation at nucleotide position 11778 was present in 5 out of 12 families and heteroplasmic mitochondrial DNA was observed in 2 of these 5 families.

  6. S1 satellite DNA repetitive units display identical structure and overall variability in all Anatolian brown frog taxa.

    Science.gov (United States)

    Picariello, Orfeo; Feliciello, Isidoro; Chinali, Gianni

    2016-02-01

    S1 satellite DNA from Palearctic brown frogs has a species-specific structure in all European species. We characterized S1 satellite DNA from the Anatolian brown frogs Rana macrocnemis, R. camerani, and R. holtzi in order to define their taxonomic rank and the structure of this satellite in this frog lineage. Southern blots of genomic DNA digested with KpnI, EcoRV, NdeI, NheI, or StuI produced the same pattern of satellite DNA bands. Moreover, quantitative dot blots showed that this satellite DNA accounts for 0.1 % of the genome in all taxa. Analysis of the overall genomic variability of the S1a repeat sequence in specimens from various populations demonstrated that this repetitive unit also has the same size (476 bp), the same most common sequence (MCS) and the same overall variability in all three taxa, and also in R. macrocnemis tavasensis. The S1a repetitive unit presents three deletions of 9, 8 and 1 bp compared to the 494-bp S1a repeat from European frogs. The S1a MCS has three variable positions (sequence WWTK in positions 183-186), due to the presence of two repeat subpopulations with motifs AATG and WWTT in all taxa. Unlike previously analyzed mitochondrial and nuclear sequences that show considerable variations among these taxa, no difference could be detected in the structure and variability of the S1 satellite repetitive units. This suggests that these taxa should belong to a single species. Our results indicate that this satellite DNA variety probably formed when the Anatolian lineage radiated from common ancestor about 4 mya, and since then has maintained its structure in all four taxa examined.

  7. Dissecting the Satellite DNA Landscape in Three Cactophilic Drosophila Sequenced Genomes

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    Leonardo G. de Lima

    2017-08-01

    Full Text Available Eukaryote genomes are replete with repetitive DNAs. This class includes tandemly repeated satellite DNAs (satDNA which are among the most abundant, fast evolving (yet poorly studied genomic components. Here, we used high-throughput sequencing data from three cactophilic Drosophila species, D. buzzatii, D. seriema, and D. mojavensis, to access and study their whole satDNA landscape. In total, the RepeatExplorer software identified five satDNAs, three previously described (pBuM, DBC-150 and CDSTR198 and two novel ones (CDSTR138 and CDSTR130. Only pBuM is shared among all three species. The satDNA repeat length falls within only two classes, between 130 and 200 bp or between 340 and 390 bp. FISH on metaphase and polytene chromosomes revealed the presence of satDNA arrays in at least one of the following genomic compartments: centromeric, telomeric, subtelomeric, or dispersed along euchromatin. The chromosomal distribution ranges from a single chromosome to almost all chromosomes of the complement. Fiber-FISH and sequence analysis of contigs revealed interspersion between pBuM and CDSTR130 in the microchromosomes of D. mojavensis. Phylogenetic analyses showed that the pBuM satDNA underwent concerted evolution at both interspecific and intraspecific levels. Based on RNA-seq data, we found transcription activity for pBuM (in D. mojavensis and CDSTR198 (in D. buzzatii in all five analyzed developmental stages, most notably in pupae and adult males. Our data revealed that cactophilic Drosophila present the lowest amount of satDNAs (1.9–2.9% within the Drosophila genus reported so far. We discuss how our findings on the satDNA location, abundance, organization, and transcription activity may be related to functional aspects.

  8. Obesity-induced sperm DNA methylation changes at satellite repeats are reprogrammed in rat offspring

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    Neil A Youngson

    2016-01-01

    Full Text Available There is now strong evidence that the paternal contribution to offspring phenotype at fertilisation is more than just DNA. However, the identity and mechanisms of this nongenetic inheritance are poorly understood. One of the more important questions in this research area is: do changes in sperm DNA methylation have phenotypic consequences for offspring? We have previously reported that offspring of obese male rats have altered glucose metabolism compared with controls and that this effect was inherited through nongenetic means. Here, we describe investigations into sperm DNA methylation in a new cohort using the same protocol. Male rats on a high-fat diet were 30% heavier than control-fed males at the time of mating (16-19 weeks old, n = 14/14. A small (0.25% increase in total 5-methyl-2Ͳ-deoxycytidine was detected in obese rat spermatozoa by liquid chromatography tandem mass spectrometry. Examination of the repetitive fraction of the genome with methyl-CpG binding domain protein-enriched genome sequencing (MBD-Seq and pyrosequencing revealed that retrotransposon DNA methylation states in spermatozoa were not affected by obesity, but methylation at satellite repeats throughout the genome was increased. However, examination of muscle, liver, and spermatozoa from male 27-week-old offspring from obese and control fathers (both groups from n = 8 fathers revealed that normal DNA methylation levels were restored during offspring development. Furthermore, no changes were found in three genomic imprints in obese rat spermatozoa. Our findings have implications for transgenerational epigenetic reprogramming. They suggest that postfertilization mechanisms exist for normalising some environmentally-induced DNA methylation changes in sperm cells.

  9. The family of Quasi-satellite periodic orbits in the co-planar RTBP

    Science.gov (United States)

    Pousse, Alexandre; Robutel, Philippe; Vienne, Alain

    2015-05-01

    In the framework of the Restricted Three-body Problem (RTBP), we consider a primary whose mass is equal to one, a secondary on circular or eccentric motion with a mass ɛ and a massless third body. The three bodies are in coplanar motion and in co-orbital resonance.We actually know three classes of regular co-orbital motions: in rotating frame with the secondary, the tadpole orbits (TP) librate around Lagrangian equilibria L4 or L5 the horseshoe orbits (HS) encompass the three equilibrium points L3, L4 and L5 the quasi-satellite orbits (QS) are remote retrograde satellite around the secondary, but outside of its Hill sphere.Contrarily to TP orbits which emerge from a fixed point in rotating frame, QS orbits emanate from a one-parameter family of periodic orbits, denoted family-f by Henon (1969). In the averaged problem, this family can be understood as a family of fixed points. However, the eccentricity of these orbits can reach high values. Consequently a development in eccentricity will not be efficient.Using the method developed by Nesvorný et al. (2002) which is valid for every values of eccentricity, we study the QS periodic orbits family with a numerical averaging.In the circular case, I will present the validity domain of the average approximation and a particular orbit. Then, I will highlight an unexpected result for very high eccentricity on families of periodic orbits that originate from L3, L4 and L5. Finally, I will sketch out an analytic method adapted to QS motion and exhibit associated results in the eccentric case.

  10. Coorbital motion in the co-planar RTBP: family of Quasi-satellite periodic orbits

    Science.gov (United States)

    Pousse, A.; Robutel, P.; Vienne, A.

    2015-10-01

    In the framework of the Restricted Three-body Problem (RTBP), we consider a primary whose mass is equal to one, a secondary on circular or eccentric motion with a mass # and a massless third body. The three bodies are in coplanar motion and in co-orbital resonance. We actually know three classes of regular coorbital motions: in rotating frame with the secondary, the tadpole orbits (TP) librate around Lagrangian equilibria L4 or L5; the horseshoe orbits (HS) encompass the three equilibrium points L3, L4 and L5; the quasi-satellite orbits (QS) are remote retrograde satellite around the secondary, but outside of its Hill sphere. Contrarily to TP orbits which emerge from a fixed point in rotating frame, QS orbits emanate from a oneparameter family of periodic orbits, denoted family-f by Henon (1969). In the averaged problem, this family can be understood as a family of fixed points. However, the eccentricity of these orbits can reach high values. Consequently a development in eccentricity will not be efficient. Using the method developed by Nesvorny et al. (2002) which is valid for every values of eccentricity, we study the QS periodic orbits family with a numerical averaging. In the circular case, I will present the validity domain of the average approximation and a particular orbit. Then, I will highlight an unexpected result for very high eccentricity on families of periodic orbits that originate from L3, L4 and L5. Finally, I will sketch out an analytic method adapted to QS motion and exhibit associated results in the eccentric case.

  11. Poxvirus uracil-DNA glycosylase-An unusual member of the family I uracil-DNA glycosylases: Poxvirus Uracil-DNA Glycosylase

    Energy Technology Data Exchange (ETDEWEB)

    Schormann, Norbert [Department of Medicine, University of Alabama at Birmingham, Birmingham Alabama 35294; Zhukovskaya, Natalia [Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia Pennsylvania 19104; Bedwell, Gregory [Department of Microbiology, University of Alabama at Birmingham, Birmingham Alabama 35294; Nuth, Manunya [Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia Pennsylvania 19104; Gillilan, Richard [MacCHESS (Macromolecular Diffraction Facility at CHESS) Cornell University, Ithaca New York 14853; Prevelige, Peter E. [Department of Microbiology, University of Alabama at Birmingham, Birmingham Alabama 35294; Ricciardi, Robert P. [Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia Pennsylvania 19104; Abramson Cancer Center, School of Medicine, University of Pennsylvania, Philadelphia Pennsylvania 19104; Banerjee, Surajit [Department of Chemistry and Chemical Biology, Cornell University, and NE-CAT Argonne Illinois 60439; Chattopadhyay, Debasish [Department of Medicine, University of Alabama at Birmingham, Birmingham Alabama 35294

    2016-11-02

    We report that uracil-DNA glycosylases are ubiquitous enzymes, which play a key role repairing damages in DNA and in maintaining genomic integrity by catalyzing the first step in the base excision repair pathway. Within the superfamily of uracil-DNA glycosylases family I enzymes or UNGs are specific for recognizing and removing uracil from DNA. These enzymes feature conserved structural folds, active site residues and use common motifs for DNA binding, uracil recognition and catalysis. Within this family the enzymes of poxviruses are unique and most remarkable in terms of amino acid sequences, characteristic motifs and more importantly for their novel non-enzymatic function in DNA replication. UNG of vaccinia virus, also known as D4, is the most extensively characterized UNG of the poxvirus family. D4 forms an unusual heterodimeric processivity factor by attaching to a poxvirus-specific protein A20, which also binds to the DNA polymerase E9 and recruits other proteins necessary for replication. D4 is thus integrated in the DNA polymerase complex, and its DNA-binding and DNA scanning abilities couple DNA processivity and DNA base excision repair at the replication fork. In conclusion, the adaptations necessary for taking on the new function are reflected in the amino acid sequence and the three-dimensional structure of D4. We provide an overview of the current state of the knowledge on the structure-function relationship of D4.

  12. De novo generation of satellite DNA-based artificial chromosomes by induced large-scale amplification.

    Science.gov (United States)

    Csonka, Erika

    2011-01-01

    Mammalian artificial chromosomes (MACs) are engineered chromosomes with defined genetic content that can function as non-integrating vectors with large carrying capacity and stability. The large carrying capacity allows the engineering of MACs with multiple copies of the same transgene, gene complexes, and to include regulatory elements necessary for the regulated expression of transgene(s). In recent years, different approaches have been explored to generate MACs (Vos Curr Opin Genet Dev 8:351-359, 1998; Danielle et al. Trends Biotech 23:573-583, 2005; Duncan and Hadlaczky Curr Opin Biotech 18:420-424, 2007): (1) the de novo formation by centromere seeding, the "bottom-up" approach, (2) the truncation of natural chromosomes or the modification of naturally occurring minichromosomes, the "top-down" approach, and (3) the in vivo "inductive" approach. Satellite DNA-based artificial chromosomes (SATACs) generated by the in vivo "inductive" method have the potential to become an efficient tool in diverse gene technology applications such as cellular protein manufacturing (Kennard et al. BioPharm Int 20:52-59, 2007; Kennard et al. Biotechnol Bioeng 104:526-539, 2009; Kennard et al. Biotechnol Bioeng 104:540-553, 2009), transgenic animal production (Telenius et al. Chromosome Res 7:3-7, 1999; Co et al. Chromosome Res 8:183-191, 2000; Monteith et al. Methods Mol Biol 240:227-242, 2003), and ultimately a safe vector for gene therapy (Vanderbyl et al. Stem Cells 22:324-333, 2004; Vanderbyl et al. Exp Hematol 33:1470-1476, 2005; Katona et al. Cell. Mol. Life Sci 65:3830-3838, 2008). A detailed protocol for the de novo generation of satellite DNA-based artificial chromosomes (SATACs) via induced large-scale amplification is presented.

  13. Mitochondrial DNA mutation in an Italian family with Leber hereditary optic neuropathy.

    Science.gov (United States)

    Carducci, C; Leuzzi, V; Scuderi, M; De Negri, A M; Gabrieli, C B; Antonozzi, I; Pontecorvi, A

    1991-10-01

    Mitochondrial (mt) DNA from a Southern Italian family with Leber hereditary optic neuropathy was analyzed for the presence of the reported mutation at position 11778 of the ND4 subunit gene. The point mutation was found in mt DNA extracted from peripheral blood in all members of the family with the exclusion of the father, and was present in a homoplasmic fashion, despite the phenotypic heterogeneity of disease presentation among family members.

  14. De novo formed satellite DNA-based mammalian artificial chromosomes and their possible applications.

    Science.gov (United States)

    Katona, Robert L

    2015-02-01

    Mammalian artificial chromosomes (MACs) are non-integrating, autonomously replicating natural chromosome-based vectors that may carry a vast amount of genetic material, which in turn enable potentially prolonged, safe, and regulated therapeutic transgene expression and render MACs as attractive genetic vectors for "gene replacement" or for controlling differentiation pathways in target cells. Satellite-DNA-based artificial chromosomes (SATACs) can be made by induced de novo chromosome formation in cells of different mammalian and plant species. These artificially generated accessory chromosomes are composed of predictable DNA sequences, and they contain defined genetic information. SATACs have already passed a number of obstacles crucial to their further development as gene therapy vectors, including large-scale purification, transfer of purified artificial chromosomes into different cells and embryos, generation of transgenic animals and germline transmission with purified SATACs, and the tissue-specific expression of a therapeutic gene from an artificial chromosome in the milk of transgenic animals. SATACs could be used in cell therapy protocols. For these methods, the most versatile target cell would be one that was pluripotent and self-renewing to address multiple disease target cell types, thus making multilineage stem cells, such as adult derived early progenitor cells and embryonic stem cells, as attractive universal host cells.

  15. Molecular characterization of the first satellite DNA with CENP-B and CDEIII motifs in the bat Pipistrellus kuhli.

    Science.gov (United States)

    Fantaccione, Stefania; Pontecorvo, Giovanni; Zampella, Vincenzo

    2005-04-25

    The centromere is an essential structure in the chromosomes of all eukariotes and is central to the mechanism that ensures proper segregation during mitosis and meiosis. The comparison of DNA sequence motifs, organization and kinetocore components from yeast to man is beginning to indicate that, although centromeres are highly variable DNA elements, a conserved pattern of sequence arrangement and function is emerging. We have identified and characterized the first satellite DNA (P.k.SAT) from microbat species Pipistrellus kuhli. The presence of mammalian CENP-B box and yeast CDEIII box could indicate the participation of P.k.SAT in centromere organization.

  16. [Variability of satellite DNA II and IV in cattle, various representatives of the subfamily Bovinae and their hybrids].

    Science.gov (United States)

    Smirnov, A F; Pavlova, V A; Sleptsov, M K; Steklenev, E P

    1996-09-01

    Polymorphism of satellite DNA II and IV was studied in Bos taurus by means of Southern blotting and dot hybridization. Of primary interest is the absence of restriction fragment length polymorphism at the individual and interbreed levels. Differences in the content of satellite II in the genome are demonstrated for animals of the Kholmogorskaya and Yakutian breeds. The specific features of satellite IV organization in the bison, banteng and yak are revealed, allowing the use of the satellite as a specific genetic marker. Superposition of parental organizational types of this class of repeats is detected for the interspecies hybrids yak x cattle, banteng x cattle, and bison x cattle. At the same time, several cases of deviation from classic inheritance of such parental types in the interspecies hybrids were found.

  17. Heterogeneous dynamics in DNA site discrimination by the structurally homologous DNA-binding domains of ETS-family transcription factors

    Science.gov (United States)

    He, Gaofei; Tolic, Ana; Bashkin, James K.; Poon, Gregory M. K.

    2015-01-01

    The ETS family of transcription factors exemplifies current uncertainty in how eukaryotic genetic regulators with overlapping DNA sequence preferences achieve target site specificity. PU.1 and Ets-1 represent archetypes for studying site discrimination by ETS proteins because their DNA-binding domains are the most divergent in sequence, yet they share remarkably superimposable DNA-bound structures. To gain insight into the contrasting thermodynamics and kinetics of DNA recognition by these two proteins, we investigated the structure and dynamics of site discrimination by their DNA-binding domains. Electrophoretic mobilities of complexes formed by the two homologs with circularly permuted binding sites showed significant dynamic differences only for DNA complexes of PU.1. Free solution measurements by dynamic light scattering showed PU.1 to be more dynamic than Ets-1; moreover, dynamic changes are strongly coupled to site discrimination by PU.1, but not Ets-1. Interrogation of the protein/DNA interface by DNA footprinting showed similar accessibility to dimethyl sulfate for PU.1/DNA and Ets-1/DNA complexes, indicating that the dynamics of PU.1/DNA complexes reside primarily outside that interface. An information-based analysis of the two homologs’ binding motifs suggests a role for dynamic coupling in PU.1's ability to enforce a more stringent sequence preference than Ets-1 and its proximal sequence homologs. PMID:25824951

  18. Molecular characterization of begomoviruses and DNA satellites associated with okra leaf curl disease in Cameroon.

    Science.gov (United States)

    Leke, Walter N; Sattar, Muhammad N; Ngane, Emilia B; Ngeve, Jacob M; Kvarnheden, Anders; Brown, Judith K

    2013-06-01

    Okra leaf curl disease (OLCD) is the most important viral disease of okra in West Africa. In this study, a complex of begomoviruses and associated DNA satellites were identified in symptomatic okra plants from southwestern Cameroon. Sequence analyses showed that two of the plants (Lik1 and Njo5) were infected with a begomovirus being a recombinant of cotton leaf curl Gezira virus (CLCuGeV) and okra yellow crinkle virus (OYCrV). The recombinant genome shared highest nucleotide identity with isolates of CLCuGeV at 87.8% and is therefore considered to be member of a new begomovirus species, Okra leaf curl Cameroon virus (OLCuCMV). One plant (Mue5) was infected by a begomovirus with 95.8% nucleotide identy to CLCuGeV, while in the plants Lik1, Mue1 and Njo5, a begomovirus was identified showing highest nucleotide identity at 93.7% with OYCrV. The nucleotide comparisons and phylogenetic analyses suggest that these isolates represent new Cameroonian strains of CLCuGeV and OYCrV (CLCuGeV-CM and OYCrV-CM). Mixed infection of OLCuCMV and OYCrV-CM was found in two of the plants. A betasatellite and two divergent alphasatellites were also associated with the begomoviruses. The betasatellite was identified as cotton leaf curl Gezira betasatellite (CLCuGeB) with the highest nucleotide identity at 93.3% to other African isolates of CLCuGeB. The alphasatellites, herein named Alpha-1 and Alpha-2, shared 97.3% and 95.2% identity, respectively, with cotton leaf curl Gezira alphasatellite (CLCuGeA) and okra leaf curl Burkina Faso alphasatellite (OLCuBFA). These collective results emphasize the extent of diversity among okra-infecting begomovirus-satellite complexes in western Africa. Copyright © 2013 Elsevier B.V. All rights reserved.

  19. De novo evolution of satellite DNA on the rye B chromosome.

    Science.gov (United States)

    Langdon, T; Seago, C; Jones, R N; Ougham, H; Thomas, H; Forster, J W; Jenkins, G

    2000-02-01

    The most distinctive region of the rye B chromosome is a subtelomeric domain that contains an exceptional concentration of B-chromosome-specific sequences. At metaphase this domain appears to be the physical counterpart of the subtelomeric heterochromatic regions present on standard rye chromosomes, but its conformation at interphase is less condensed. In this report we show that the two sequence families that have been previously found to make up the bulk of the domain have been assembled from fragments of a variety of sequence elements, giving rise to their ostensibly foreign origin. A single mechanism, probably based on synthesis-dependent strand annealing (SDSA), is responsible for their assembly. We provide evidence for sequential evolution of one family on the B chromosome itself. The extent of these rearrangements and the complexity of the higher-order organization of the B-chromosome-specific families indicate that instability is a property of the domain itself, rather than of any single sequence. Indirect evidence suggests that particular fragments may have been selected to confer different properties on the domain and that rearrangements are frequently selected for their effect on DNA structure. The current organization appears to represent a transient stage in the evolution of a conventional heterochromatic region from complex sequences.

  20. A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases

    Directory of Open Access Journals (Sweden)

    Aravind L

    2008-10-01

    Full Text Available Abstract Using sequence profile methods and structural comparisons we characterize a previously unknown family of nucleic acid polymerases in a group of mobile elements from genomes of diverse bacteria, an algal plastid and certain DNA viruses, including the recently reported Sputnik virus. Using contextual information from domain architectures and gene-neighborhoods we present evidence that they are likely to possess both primase and DNA polymerase activity, comparable to the previously reported prim-pol proteins. These newly identified polymerases help in defining the minimal functional core of superfamily A DNA polymerases and related RNA polymerases. Thus, they provide a framework to understand the emergence of both DNA and RNA polymerization activity in this class of enzymes. They also provide evidence that enigmatic DNA viruses, such as Sputnik, might have emerged from mobile elements coding these polymerases. Reviewers This article was reviewed by Eugene Koonin and Mark Ragan.

  1. Molecular cloning and characterization of satellite DNA sequences from constitutive heterochromatin of the habu snake (Protobothrops flavoviridis, Viperidae) and the Burmese python (Python bivittatus, Pythonidae).

    Science.gov (United States)

    Matsubara, Kazumi; Uno, Yoshinobu; Srikulnath, Kornsorn; Seki, Risako; Nishida, Chizuko; Matsuda, Yoichi

    2015-12-01

    Highly repetitive DNA sequences of the centromeric heterochromatin provide valuable molecular cytogenetic markers for the investigation of genomic compartmentalization in the macrochromosomes and microchromosomes of sauropsids. Here, the relationship between centromeric heterochromatin and karyotype evolution was examined using cloned repetitive DNA sequences from two snake species, the habu snake (Protobothrops flavoviridis, Crotalinae, Viperidae) and Burmese python (Python bivittatus, Pythonidae). Three satellite DNA (stDNA) families were isolated from the heterochromatin of these snakes: 168-bp PFL-MspI from P. flavoviridis and 196-bp PBI-DdeI and 174-bp PBI-MspI from P. bivittatus. The PFL-MspI and PBI-DdeI sequences were localized to the centromeric regions of most chromosomes in the respective species, suggesting that the two sequences were the major components of the centromeric heterochromatin in these organisms. The PBI-MspI sequence was localized to the pericentromeric region of four chromosome pairs. The PFL-MspI and the PBI-DdeI sequences were conserved only in the genome of closely related species, Gloydius blomhoffii (Crotalinae) and Python molurus, respectively, although their locations on the chromosomes were slightly different. In contrast, the PBI-MspI sequence was also in the genomes of P. molurus and Boa constrictor (Boidae), and additionally localized to the centromeric regions of eight chromosome pairs in B. constrictor, suggesting that this sequence originated in the genome of a common ancestor of Pythonidae and Boidae, approximately 86 million years ago. The three stDNA sequences showed no genomic compartmentalization between the macrochromosomes and microchromosomes, suggesting that homogenization of the centromeric and/or pericentromeric stDNA sequences occurred in the macrochromosomes and microchromosomes of these snakes.

  2. Association of pKi-67 with satellite DNA of the human genome in early G1 cells.

    Science.gov (United States)

    Bridger, J M; Kill, I R; Lichter, P

    1998-01-01

    pKi-67 is a nucleolar antigen that provides a specific marker for proliferating cells. It has been shown previously that pKi-67's distribution varies in a cell cycle-dependent manner: it coats all chromosomes during mitosis, accumulates in nuclear foci during G1 phase (type I distribution) and localizes within nucleoli in late G1 S and G2 phase (type II distribution). Although no function has as yet been ascribed to pKi-67, it has been found associated with centromeres in G1. In the present study the distribution pattern of pKi-67 during G1 in human dermal fibroblasts (HDFs) was analysed in more detail. Synchronization experiments show that in very early G1 cells pKi-67 coincides with virtually all satellite regions analysed, i.e. with centromeric (alpha-satellite), telomeric (minisatellite) and heterochromatic blocks (satellite III) on chromosomes 1 and Y (type Ia distribution). In contrast, later in the G1 phase, a smaller fraction of satellite DNA regions are found collocalized with pKi-67 foci (type Ib distribution). When all pKi-67 becomes localized within nucleoli, even fewer satellite regions remain associated with the pKi-67 staining. However, all centromeric and short arm regions of the acrocentric chromosomes, which are in very close proximity to or even contain the rRNA genes, are collocalized with anti-pKi-67 staining throughout the remaining interphase of the cell cycle. Thus, our data demonstrate that during post-mitotic reformation and nucleogenesis there is a progressive decline in the fraction of specific satellite regions of DNA that remain associated with pKi-67. This may be relevant to nucleolar reformation following mitosis.

  3. Molecular Characterization of Begomoviruses and DNA Satellites Associated with a New Host Spanish Flag (Lantana camara) in India

    OpenAIRE

    Marwal, Avinash; Kumar Sahu, Anurag; Gaur, Rajarshi Kumar

    2013-01-01

    In the year 2010 yellowing of leaf vein disease was observed on Spanish Flag (Lantana camara) in Sirsa, Haryana province, India. There was no earlier report of association of begomovirus and DNA satellites with Lantana camara. Therefore, molecular characterization and understanding of the genomic analysis of begomovirus infecting Lantana camara is imperative for the pathogen diagnosis and disease management. This is the first report and molecular characterization of a begomovirus associated w...

  4. Primer-Independent DNA Synthesis by a Family B DNA Polymerase from Self-Replicating Mobile Genetic Elements

    Directory of Open Access Journals (Sweden)

    Modesto Redrejo-Rodríguez

    2017-11-01

    Full Text Available Family B DNA polymerases (PolBs play a central role during replication of viral and cellular chromosomes. Here, we report the discovery of a third major group of PolBs, which we denote primer-independent PolB (piPolB, that might be a link between the previously known protein-primed and RNA/DNA-primed PolBs. PiPolBs are encoded by highly diverse mobile genetic elements, pipolins, integrated in the genomes of diverse bacteria and also present as circular plasmids in mitochondria. Biochemical characterization showed that piPolB displays efficient DNA polymerization activity that can use undamaged and damaged templates and is endowed with proofreading and strand displacement capacities. Remarkably, the protein is also capable of template-dependent de novo DNA synthesis, i.e., DNA-priming activity, thereby breaking the long-standing dogma that replicative DNA polymerases require a pre-existing primer for DNA synthesis. We suggest that piPolBs are involved in self-replication of pipolins and may also contribute to bacterial DNA damage tolerance.

  5. Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly

    Directory of Open Access Journals (Sweden)

    V.A. Shepelev

    2015-09-01

    Full Text Available Centromeric alpha satellite (AS is composed of highly identical higher-order DNA repetitive sequences, which make the standard assembly process impossible. Because of this the AS repeats were severely underrepresented in previous versions of the human genome assembly showing large centromeric gaps. The latest hg38 assembly (GCA_000001405.15 employed a novel method of approximate representation of these sequences using AS reference models to fill the gaps. Therefore, a lot more of assembled AS became available for genomic analysis. We used the PERCON program previously described by us to annotate various suprachromosomal families (SFs of AS in the hg38 assembly and presented the results of our primary analysis as an easy-to-read track for the UCSC Genome Browser. The monomeric classes, characteristic of the five known SFs, were color-coded, which allowed quick visual assessment of AS composition in whole multi-megabase centromeres down to each individual AS monomer. Such comprehensive annotation of AS in the human genome assembly was performed for the first time. It showed the expected prevalence of the known major types of AS organization characteristic of the five established SFs. Also, some less common types of AS arrays were identified, such as pure R2 domains in SF5, apparent J/R and D/R mixes in SF1 and SF2, and several different SF4 higher-order repeats among reference models and in regular contigs. No new SFs or large unclassed AS domains were discovered. The dataset reveals the architecture of human centromeres and allows classification of AS sequence reads by alignment to the annotated hg38 assembly. The data were deposited here: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgt.customText=https://dl.dropboxusercontent.com/u/22994534/AS-tracks/human-GRC-hg38-M1SFs.bed.bz2.

  6. Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly.

    Science.gov (United States)

    Shepelev, V A; Uralsky, L I; Alexandrov, A A; Yurov, Y B; Rogaev, E I; Alexandrov, I A

    2015-09-01

    Centromeric alpha satellite (AS) is composed of highly identical higher-order DNA repetitive sequences, which make the standard assembly process impossible. Because of this the AS repeats were severely underrepresented in previous versions of the human genome assembly showing large centromeric gaps. The latest hg38 assembly (GCA_000001405.15) employed a novel method of approximate representation of these sequences using AS reference models to fill the gaps. Therefore, a lot more of assembled AS became available for genomic analysis. We used the PERCON program previously described by us to annotate various suprachromosomal families (SFs) of AS in the hg38 assembly and presented the results of our primary analysis as an easy-to-read track for the UCSC Genome Browser. The monomeric classes, characteristic of the five known SFs, were color-coded, which allowed quick visual assessment of AS composition in whole multi-megabase centromeres down to each individual AS monomer. Such comprehensive annotation of AS in the human genome assembly was performed for the first time. It showed the expected prevalence of the known major types of AS organization characteristic of the five established SFs. Also, some less common types of AS arrays were identified, such as pure R2 domains in SF5, apparent J/R and D/R mixes in SF1 and SF2, and several different SF4 higher-order repeats among reference models and in regular contigs. No new SFs or large unclassed AS domains were discovered. The dataset reveals the architecture of human centromeres and allows classification of AS sequence reads by alignment to the annotated hg38 assembly. The data were deposited here: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgt.customText=https://dl.dropboxusercontent.com/u/22994534/AS-tracks/human-GRC-hg38-M1SFs.bed.bz2.

  7. How a Small Family of Yeast IDPs Control Complicated Processes Related to DNA Replication

    DEFF Research Database (Denmark)

    Marabini, Riccardo

    Ribonucleotide reductase (RNR) and proliferating cell nuclear antigen (PCNA) are two essential proteins involved in DNA replication. RNR catalyzes the last and rate limiting step of the deoxyribonucleotide biosynthetic pathway. The dysregulation of RNR has been related to higher mutation rate...... and the onset of cancer. PCNA is part of the DNA sliding clamp family, and it is a processivity factor that enhances the activity of DNA polymerases both in DNA replication and repair. In the last two decades, a family of five small intrinsically disordered proteins (IDP) has been identified and genetically...... characterized in budding and fission yeast. Within this protein family Dif1 (from S. cerevisiae) and Spd1 (from S. pombe) were analyzed in this study. These proteins were previously found to interact with and regulate the activity of RNR and Spd1 was also linked to PCNA dependent signaling for degradation...

  8. Two Family B DNA Polymerases from Aeropyrum pernix, an Aerobic Hyperthermophilic Crenarchaeote

    Science.gov (United States)

    Cann, Isaac K. O.; Ishino, Sonoko; Nomura, Norimichi; Sako, Yoshihiko; Ishino, Yoshizumi

    1999-01-01

    DNA polymerase activities in fractionated cell extract of Aeropyrum pernix, a hyperthermophilic crenarchaeote, were investigated. Aphidicolin-sensitive (fraction I) and aphidicolin-resistant (fraction II) activities were detected. The activity in fraction I was more heat stable than that in fraction II. Two different genes (polA and polB) encoding family B DNA polymerases were cloned from the organism by PCR using degenerated primers based on the two conserved motifs (motif A and B). The deduced amino acid sequences from their entire coding regions contained all of the motifs identified in family B DNA polymerases for 3′→5′ exonuclease and polymerase activities. The product of polA gene (Pol I) was aphidicolin resistant and heat stable up to 80°C. In contrast, the product of polB gene (Pol II) was aphidicolin sensitive and stable at 95°C. These properties of Pol I and Pol II are similar to those of fractions II and I, respectively, and moreover, those of Pol I and Pol II of Pyrodictium occultum. The deduced amino acid sequence of A. pernix Pol I exhibited the highest identities to archaeal family B DNA polymerase homologs found only in the crenarchaeotes (group I), while Pol II exhibited identities to homologs found in both euryarchaeotes and crenarchaeotes (group II). These results provide further evidence that the subdomain Crenarchaeota has two family B DNA polymerases. Furthermore, at least two DNA polymerases work in the crenarchaeal cells, as found in euryarchaeotes, which contain one family B DNA polymerase and one heterodimeric DNA polymerase of a novel family. PMID:10498710

  9. ST1710?DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators

    OpenAIRE

    Kumarevel, Thirumananseri; Tanaka, Tomoyuki; Umehara, Takashi; Yokoyama, Shigeyuki

    2009-01-01

    ST1710, a member of the multiple antibiotic resistance regulator (MarR) family of regulatory proteins in bacteria and archaea, plays important roles in development of antibiotic resistance, a global health problem. Here, we present the crystal structure of ST1710 from Sulfolobus tokodaii strain 7 complexed with salicylate, a well-known inhibitor of MarR proteins and the ST1710 complex with its promoter DNA, refined to 1.8 and 2.10 ? resolutions, respectively. The ST1710?DNA complex shares the...

  10. Novel mtDNA mutations and oxidative phosphorylation dysfunction in Russian LHON families.

    Science.gov (United States)

    Brown, M D; Zhadanov, S; Allen, J C; Hosseini, S; Newman, N J; Atamonov, V V; Mikhailovskaya, I E; Sukernik, R I; Wallace, D C

    2001-07-01

    Leber's hereditary optic neuropathy (LHON) is characterized by maternally transmitted, bilateral, central vision loss in young adults. It is caused by mutations in the mitochondrial DNA (mtDNA) encoded genes that contribute polypeptides to NADH dehydrogenase or complex I. Four mtDNA variants, the nucleotide pair (np) 3460A, 11778A, 14484C, and 14459A mutations, are known as "primary" LHON mutations and are found in most, but not all, of the LHON families reported to date. Here, we report the extensive genetic and biochemical analysis of five Russian families from the Novosibirsk region of Siberia manifesting maternally transmitted optic atrophy consistent with LHON. Three of the five families harbor known LHON primary mutations. Complete sequence analysis of proband mtDNA in the other two families has revealed novel complex I mutations at nps 3635A and 4640C, respectively. These mutations are homoplasmic and have not been reported in the literature. Biochemical analysis of complex I in patient lymphoblasts and transmitochondrial cybrids demonstrated a respiration defect with complex-I-linked substrates, although the specific activity of complex I was not reduced. Overall, our data suggests that the spectrum of mtDNA mutations associated with LHON in Russia is similar to that in Europe and North America and that the np 3635A and 4640C mutations may be additional mtDNA complex I mutations contributing to LHON expression.

  11. Structures of human exonuclease I DNA complexes suggest a unified mechanism for nuclease family

    Science.gov (United States)

    Orans, Jillian; McSweeney, Elizabeth A.; Iyer, Ravi R.; Hast, Michael A.; Hellinga, Homme W.; Modrich, Paul; Beese, Lorena S.

    2011-01-01

    Summary Human exonuclease 1 (hExo1) plays important roles in DNA repair and recombination processes that maintain genomic integrity. It is a member of the 5′ structure-specific nuclease family of exonucleases and endonucleases that includes FEN-1, XPG, and GEN1. We present structures of hExo1 in complex with a DNA substrate, followed by mutagenesis studies, and propose a common mechanism by which this nuclease family recognizes and processes diverse DNA structures. hExo1 induces a sharp bend in the DNA at nicks or gaps. Frayed 5′ ends of nicked duplexes resemble flap junctions, unifying the mechanisms of endo- and exo-nucleolytic processing. Conformational control of a mobile region in the catalytic site suggests a mechanism for allosteric regulation by binding to protein partners. The relative arrangement of substrate binding sites in these enzymes provides an elegant solution to a complex geometrical puzzle of substrate recognition and processing. PMID:21496642

  12. Genetic linkage analysis of familial amyotrophic lateral sclerosis using human chromosome 21 microsatellite DNA markers

    Energy Technology Data Exchange (ETDEWEB)

    Rosen, D.R.; Sapp, P.; O`Regan, J.; McKenna-Yasek, D.; Schlumpf, K.S.; Haines, J.L.; Gusella, J.F.; Horvitz, H.R.; Brown, R.H. Jr. [Massachusetts Institute of Technology, Cambridge, MA (United States)

    1994-05-15

    Amyotrophic lateral sclerosis (ALS; Lou Gehrig`s Disease) is a lethal neurodegenerative disease of upper and lower motorneurons in the brain and spinal cord. We previously reported linkage of a gene for familial ALS (FALS) to human chromosome 21 using 4 restriction fragment length polymorphism DNA markers and identified disease-associated mutations in the superoxide dismutase (SOD)-1 gene in some ALS families. We report here the genetic linkage data that led us to examine the SOD-1 gene for mutations. We also report a new microsatellite DNA marker for D21S63, derived from the cosmid PW517. Ten microsatellite DNA markers, including the new marker D21S63, were used to reinvestigate linkage of FALS to chromosome 21. Genetic linkage analysis performed with 13 ALS familes for these 10 DNA markers confirmed the presence of a FALS gene on chromosome 21. The highest total 2-point LOD score for all families was 4.33, obtained at a distance of 10 cM from the marker D21S223. For 5 ALS families linked to chromosome 21, a peak 2-point LOD score of 5.94 was obtained at the DNA marker D21S223. A multipoint score of 6.50 was obtained with the markers D21S213, D21S223, D21S167, and FALS for 5 chromosome 21-linked ALS families. The haplotypes of these families for the 10 DNA markers reveal recombination events that further refined the location of the FALS gene to a segment of approximately 5 megabases (Mb) between D21S213 and D21S219. The only characterized gene within this segment was SOD-1, the structural gene for Cu, Zn SOD. 30 refs., 4 figs., 4 tabs.

  13. Evidence for mobility of a new family of mouse middle repetitive DNA elements (LTR-IS).

    Science.gov (United States)

    Wirth, T; Schmidt, M; Baumruker, T; Horak, I

    1984-04-25

    Locus variation and sequence conservation of mouse LTR-IS elements, a new family of middle repetitive DNA sequences was studied. It is shown that LTR-IS sequences are present in all the inbred strains and subspecies of M. musculus tested and in M. cooki and M. caroli. Their arrangement in mouse genomes is polymorphic. Southern blot analysis and DNA sequencing revealed the existence of homologous DNA sequences with and without LTR-IS element insertion. LTR-IS sequences therefore appear to have arisen in early mouse ancestors and have, at least at some point, been mobile.

  14. Phylogenetic relationships of the family Agamidae (Reptilia : Iguania) inferred from mitochondrial DNA sequences

    OpenAIRE

    Honda, Masanao; Ota, Hidetoshi; Kobayashi, Mari; Nabhitabhata, Jarujin Mari; Yong, Hoi-Sen; Sengoku, Showichi; Hikida, Tsutomu

    2000-01-01

    Phylogenetic relationships of the family Agamidae were inferred from 860 base positions of a mitochondrial DNA sequence of 12S and 16S rRNA genes. Results confirmed the monophyly of this family including Leiolepis and Uromastyx (Leiolepidinae), and indicated the sister relationship between Agamidae and Chamaeleonidae. Our results also indicated the presence of two major clades in Agamidae. In one of these major clades, "Leiolepidinae" was first diverged, followed by the Lophognathus and Hypsi...

  15. Cloning and analysis of DnaJ family members in the silkworm, Bombyx mori.

    Science.gov (United States)

    Li, Yinü; Bu, Cuiyu; Li, Tiantian; Wang, Shibao; Jiang, Feng; Yi, Yongzhu; Yang, Huipeng; Zhang, Zhifang

    2016-01-15

    Heat shock proteins (Hsps) are involved in a variety of critical biological functions, including protein folding, degradation, and translocation and macromolecule assembly, act as molecular chaperones during periods of stress by binding to other proteins. Using expressed sequence tag (EST) and silkworm (Bombyx mori) transcriptome databases, we identified 27 cDNA sequences encoding the conserved J domain, which is found in DnaJ-type Hsps. Of the 27 J domain-containing sequences, 25 were complete cDNA sequences. We divided them into three types according to the number and presence of conserved domains. By analyzing the gene structures, intron numbers, and conserved domains and constructing a phylogenetic tree, we found that the DnaJ family had undergone convergent evolution, obtaining new domains to expand the diversity of its family members. The acquisition of the new DnaJ domains most likely occurred prior to the evolutionary divergence of prokaryotes and eukaryotes. The expression of DnaJ genes in the silkworm was generally higher in the fat body. The tissue distribution of DnaJ1 proteins was detected by western blotting, demonstrating that in the fifth-instar larvae, the DnaJ1 proteins were expressed at their highest levels in hemocytes, followed by the fat body and head. We also found that the DnaJ1 transcripts were likely differentially translated in different tissues. Using immunofluorescence cytochemistry, we revealed that in the blood cells, DnaJ1 was mainly localized in the cytoplasm. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. The Nice model can explain the dispersion of the prograde Himalia family of irregular satellites at Jupiter

    Science.gov (United States)

    Li, Daohai; Christou, Apostolos

    2017-10-01

    More than 50 irregular satellites revolve around Jupiter in which at least three distinct collisional families are identified. Among them, the Himalia family is unique in the large velocity dispersion--several hundred m/s--among its members, inconsistent with a purely collisional origin.We explore this puzzle in the context of the Nice scenario of early solar system evolution. There, the giant planets migrated significant distances due to interactions with a primordial planetesimal disk. We generate a synthetic, collisionally-produced Himalia family and follow its evolution through principal events of the Nice model. Two situations are considered: (i) The planetesimal disk is solely composed of large, moon-sized objects. In this case, the family is dramatically scattered, especially in semimajor axis and eccentricity, as the planetesimals fly by Jupiter. The velocity dispersion of $\\sim60\\%$ of family members is raised to several hundred m/s, satisfactorily explaining the observed dispersion. However, this situation is not likely as the considered planetesimals seem unphysically massive. We now consider the alternative case (ii) within the so-called ``Jumping Jupiter’’ where planetary, rather than planetesimal encounters are responsible for the observed dispersion. Here, ice giants encounter Jupiter up to a few hundred times (Nesvorn\\'{y} \\& Morbidelli 2012). We find $\\lesssim20$ such planetary encounters disperse the synthetic family to the observed degree. We also find that the family cannot survive $\\sim100$ such fly-bys as the satellites become too widely dispersed.Reference: Nesvorn\\'{y}, D., \\& Morbidelli, A. 2012, AJ, 144, 117.

  17. Determination of restriction enzyme activity when cutting DNA labeled with the TOTO dye family.

    Science.gov (United States)

    Maschmann, April; Kounovsky-Shafer, Kristy L

    2017-06-03

    Optical mapping, a single DNA molecule genome analysis platform that can determine methylation profiles, uses fluorescently labeled DNA molecules that are elongated on the surface and digested with a restriction enzyme to produce a barcode of that molecule. Understanding how the cyanine fluorochromes affect enzyme activity can lead to other fluorochromes used in the optical mapping system. The effects of restriction digestion on fluorochrome labeled DNA (Ethidium Bromide, DAPI, H33258, EthD-1, TOTO-1) have been analyzed previously. However, TOTO-1 is a part of a family of cyanine fluorochromes (YOYO-1, TOTO-1, BOBO-1, POPO-1, YOYO-3, TOTO-3, BOBO-3, and POPO-3) and the rest of the fluorochromes have not been examined in terms of their effects on restriction digestion. In order to determine if the other dyes in the TOTO-1 family inhibit restriction enzymes in the same way as TOTO-1, lambda DNA was stained with a dye from the TOTO family and digested. The restriction enzyme activity in regards to each dye, as well as each restriction enzyme, was compared to determine the extent of digestion. YOYO-1, TOTO-1, and POPO-1 fluorochromes inhibited ScaI-HF, PmlI, and EcoRI restriction enzymes. Additionally, the mobility of labeled DNA fragments in an agarose gel changed depending on which dye was intercalated.

  18. CSF studies facilitate DNA diagnosis in familial Alzheimer's disease due to a presenilin-1 mutation

    NARCIS (Netherlands)

    de Bot, Susanne T; Kremer, H P H; Dooijes, Dennis; Verbeek, Marcel M

    2009-01-01

    In sporadic Alzheimer's disease (AD), cerebrospinal fluid (CSF) analysis is becoming increasingly relevant to establish an early diagnosis. We present a case of familial AD due to a presenilin-1 mutation in which CSF studies suggested appropriate DNA diagnostics. A 38 year old Dutch man presented

  19. CSF studies facilitate DNA diagnosis in familial Alzheimer's disease due to a presenilin-1 mutation.

    NARCIS (Netherlands)

    Bot, S.T. de; Kremer, H.P.H.; Dooijes, D.; Verbeek, M.M.

    2009-01-01

    In sporadic Alzheimer's disease (AD), cerebrospinal fluid (CSF) analysis is becoming increasingly relevant to establish an early diagnosis. We present a case of familial AD due to a presenilin-1 mutation in which CSF studies suggested appropriate DNA diagnostics. A 38 year old Dutch man presented

  20. Satellite DNA methylation status and expression of selected genes in Bos indicus blastocysts produced in vivo and in vitro.

    Science.gov (United States)

    Urrego, R; Bernal-Ulloa, S M; Chavarría, N A; Herrera-Puerta, E; Lucas-Hahn, A; Herrmann, D; Winkler, S; Pache, D; Niemann, H; Rodriguez-Osorio, N

    2017-04-01

    Bovine embryos produced in vivo and in vitro differ with respect to molecular profiles, including epigenetic marks and gene expression profiles. This study investigated the CpG methylation status in bovine testis satellite I (BTS) and Bos taurus alpha satellite I (BTαS) DNA sequences, and concomitantly the relative abundance of transcripts, critically involved in DNA methylation (DNMT1 and DNMT3A), growth and development (IGF2R) and pluripotency (POU5F1) in Bos indicus embryos produced in vitro or in vivo. Results revealed that methylation of BTS were higher (P vitro compared with their in vivo produced counterparts, while the methylation status of BTαS was similar in both groups. There were no significant differences in transcript abundance for DNMT3A, IGF2R and POU5F1 between blastocysts produced in vivo and in vitro. However, a significantly lower amount of DNMT1 transcripts was found in the in vitro cultured embryos (P vitro embryo production system.

  1. Alphoid satellite DNA is tightly associated with centromere antigens in human chromosomes throughout the cell cycle

    Energy Technology Data Exchange (ETDEWEB)

    Masumoto, Hiroshi; Sugimoto, Kenji; Okazaki, Tuneko (Nagoya Univ. (Japan))

    1989-03-01

    In this study, the authors have examined a DNA element specific to the centromere domain of human chromosomes. Purified HeLa chromosomes were digested with the restriction enzyme Sau3AI and fractionated by sedimentation through a sucrose gradient. Fractions showing antigenicity to anticentromere (kinetochore) serum obtained from a scleroderma CREST patient were used to construct a DNA library. From this library they found one clone which has specifically hybridized to the centromere domain of metaphase chromosomes using a biotinylated probe DNA and FITC-conjugated avidin. The clone contained a stretch of alphoid DNA dimer. To determine precisely the relative location of the alphoid DNA stretch and the centromere antigen, a method was developed to carry out in situ hybridization of DNA and indirect immunofluorescent staining of antigen on the same cell preparation. Using this method, they have found perfect overlapping of the alphoid DNA sites with the centromere antigen in both metaphase chromosomes and nuclei at various stages in the cell cycle. They have also observed this exact correlation at the attachment sites of artificially extended sister chromatids. These results suggest the possibility that alphoid DNA repeats are a key component of kinetochore structure.

  2. Comparative analysis of DNA methyltransferase gene family in fungi: a focus on Basidiomycota

    Directory of Open Access Journals (Sweden)

    Ruirui Huang

    2016-10-01

    Full Text Available DNA methylation plays a crucial role in the regulation of gene expression in eukaryotes. Mushrooms belonging to the phylum Basidiomycota are highly valued for both nutritional and pharmaceutical uses. A growing number of studies have demonstrated the significance of DNA methylation in the development of plants and animals. However, our understanding of DNA methylation in mushrooms is limited. In this study, we identified and conducted comprehensive analyses on DNA methyltransferases (DNMtases in representative species from Basidiomycota and Ascomycota, and obtained new insights into their classification and characterization in fungi. Our results revealed that DNMtases in basidiomycetes can be divided into two classes, the Dnmt1 class and the newly defined Rad8 class. We also demonstrated that the fusion event between the characteristic domains of the DNMtases family and Snf2 family in the Rad8 class is fungi-specific, possibly indicating a functional novelty of Rad8 DNMtases in fungi. Additionally, expression profiles of DNMtases in the edible mushroom Pleurotus ostreatus revealed diverse expression patterns in various organs and developmental stages. For example, DNMtase genes displayed higher expression levels in dikaryons than in monokaryons. Consistent with the expression profiles, we found that dikaryons are more susceptible to the DNA methyltransferase inhibitor 5-azacytidine. Taken together, our findings pinpoint an important role of DNA methylation during the growth of mushrooms and provide a foundation for understanding of DNMtases in basidiomycetes.

  3. Genetic variations in the DNA replication origins of human papillomavirus family correlate with their oncogenic potential.

    Science.gov (United States)

    Yilmaz, Gulden; Biswas-Fiss, Esther E; Biswas, Subhasis B

    2017-12-27

    Human papillomaviruses (HPVs) encompasses a large family of viruses that range from benign to highly carcinogenic. The crucial differences between benign and carcinogenic types of HPV remain unknown, except that the two HPV types differ in the frequency of DNA replication. We have systematically analyzed the mechanism of HPV DNA replication initiation in low-risk and high-risk HPVs. Our results demonstrate that HPV-encoded E2 initiator protein and its four binding sites in the replication origin play pivotal roles in determining the destiny of the HPV-infected cell. We have identified strain-specific single nucleotide variations in E2 binding sites only in the high-risk HPVs. We have demonstrated that these variations result in attenuated formation of the E2-DNA complex. E2 binding to these sites is linked to the activation of the DNA replication origin as well as initiation of DNA replication. Both mobility shift assay and atomic force microscopy studies demonstrated that binding of E2 from either low- or high-risk HPVs with variant binding sequences lacked formation of multimeric E2-DNA complex formation in vitro. These results provided a molecular basis of differential DNA replication in the two types of HPVs and pointed to a correlation with the development of cancer. Copyright © 2017. Published by Elsevier B.V.

  4. Evolution of the B3 DNA binding superfamily: new insights into REM family gene diversification.

    Directory of Open Access Journals (Sweden)

    Elisson A C Romanel

    Full Text Available BACKGROUND: The B3 DNA binding domain includes five families: auxin response factor (ARF, abscisic acid-insensitive3 (ABI3, high level expression of sugar inducible (HSI, related to ABI3/VP1 (RAV and reproductive meristem (REM. The release of the complete genomes of the angiosperm eudicots Arabidopsis thaliana and Populus trichocarpa, the monocot Orysa sativa, the bryophyte Physcomitrella patens,the green algae Chlamydomonas reinhardtii and Volvox carteri and the red algae Cyanidioschyzon melorae provided an exceptional opportunity to study the evolution of this superfamily. METHODOLOGY: In order to better understand the origin and the diversification of B3 domains in plants, we combined comparative phylogenetic analysis with exon/intron structure and duplication events. In addition, we investigated the conservation and divergence of the B3 domain during the origin and evolution of each family. CONCLUSIONS: Our data indicate that showed that the B3 containing genes have undergone extensive duplication events, and that the REM family B3 domain has a highly diverged DNA binding. Our results also indicate that the founding member of the B3 gene family is likely to be similar to the ABI3/HSI genes found in C. reinhardtii and V. carteri. Among the B3 families, ABI3, HSI, RAV and ARF are most structurally conserved, whereas the REM family has experienced a rapid divergence. These results are discussed in light of their functional and evolutionary roles in plant development.

  5. The satellite DNA AflaSAT-1 in the A and B chromosomes of the grasshopper Abracris flavolineata.

    Science.gov (United States)

    Milani, Diogo; Ramos, Érica; Loreto, Vilma; Martí, Dardo Andrea; Cardoso, Adauto Lima; de Moraes, Karen Cristiane Martinez; Martins, Cesar; Cabral-de-Mello, Diogo Cavalcanti

    2017-08-29

    Satellite DNAs (satDNAs) are organized in repetitions directly contiguous to one another, forming long arrays and composing a large portion of eukaryote genomes. These sequences evolve according to the concerted evolution model, and homogenization of repeats is observed at the intragenomic level. Satellite DNAs are the primary component of heterochromatin, located primarily in centromeres and telomeres. Moreover, satDNA enrichment in specific chromosomes has been observed, such as in B chromosomes, that can provide clues about composition, origin and evolution of this chromosome. In this study, we isolated and characterized a satDNA in A and B chromosomes of Abracris flavolineata by integrating cytogenetic, molecular and genomics approaches at intra- and inter-population levels, with the aim to understand the evolution of satDNA and composition of B chromosomes. AflaSAT-1 satDNA was shared with other species and in A. flavolineata, was associated with another satDNA, AflaSAT-2. Chromosomal mapping revealed centromeric blocks variable in size in almost all chromosomes (except pair 11) of A complement for both satDNAs, whereas for B chromosome, only a small centromeric signal occurred. In distinct populations, variable number of AflaSAT-1 chromosomal sites correlated with variability in copy number. Instead of such variability, low sequence diversity was observed in A complement, but monomers from B chromosome were more variable, presenting also exclusive mutations. AflaSAT-1 was transcribed in five tissues of adults in distinct life cycle phases. The sharing of AflaSAT-1 with other species is consistent with the library hypothesis and indicates common origin in a common ancestor; however, AflaSAT-1 was highly amplified in the genome of A. flavolineata. At the population level, homogenization of repeats in distinct populations was documented, but dynamic expansion or elimination of repeats was also observed. Concerning the B chromosome, our data provided new

  6. Higher-order repeat structure in alpha satellite DNA occurs in New World monkeys and is not confined to hominoids.

    Science.gov (United States)

    Sujiwattanarat, Penporn; Thapana, Watcharaporn; Srikulnath, Kornsorn; Hirai, Yuriko; Hirai, Hirohisa; Koga, Akihiko

    2015-05-14

    Centromeres usually contain large amounts of tandem repeat DNA. Alpha satellite DNA (AS) is the most abundant tandem repeat DNA found in the centromeres of simian primates. The AS of humans contains sequences organized into higher-order repeat (HOR) structures, which are tandem arrays of larger repeat units consisting of multiple basic repeat units. HOR-carrying AS also occurs in other hominoids, but results reported to date for phylogenetically more remote taxa have been negative. Here we show direct evidence for clear HOR structures in AS of the owl monkey and common marmoset. These monkeys are New World monkey species that are located phylogenetically outside of hominoids. It is currently postulated that the presence of HOR structures in AS is unique to hominoids. Our results suggest that this view must be modified. A plausible explanation is that generation of HOR structures is a general event that occurs occasionally or frequently in primate centromeres, and that, in humans, HOR-carrying AS became predominant in the central region of the centromere. It is often difficult to assemble sequence reads of tandem repeat DNAs into accurate contig sequences; our careful sequencing strategy allowed us to overcome this problem.

  7. Family-specific vs. universal PCR primers for the study of mitochondrial DNA in plants

    Directory of Open Access Journals (Sweden)

    Aleksić Jelena M.

    2016-01-01

    Full Text Available Mitochondrial genomes (mtDNAs or mitogenomes of seed plants are characterized by a notoriously unstable organization on account of which available so-called universal or consensus primers may fail to fulfil their foreseen function - amplification of various mtDNA regions in a broad range of plant taxa. Thus, the primers developed for groups assumed to have similar organization of their mitogenomes, such as families, may facilitate a broader usage of more variable non-coding portions of these genomes in group members. Using in silico PCR method and six available complete mitogenomes of Fabaceae, it has been demonstrated that only three out of 36 published universal primer and three Medicago sativa-specific primer pairs that amplify various mtDNA regions are suitable for six representatives of the Fabaceae family upon minor modifications, and develop 21 Fabaceae-specific primer pairs for amplification of all 14 cis-splicing introns in genes of NADH subunits (nad genes which represent the most commonly used non-coding mtDNA regions in various studies in plants. Using the same method and six available complete mitogenomes of representatives of related families Cucurbitaceae, Euphorbiaceae and Rosaceae and a model plant, Arabidopsis thaliana, it has further been demonstrated that applicability of newly developed primer pairs for amplification of nad introns in more or less related taxa was dependent not only on species evolutionary distances but also on their genome sizes. A reported set of 24 primer pairs is a valuable resource which may facilitate a broader usage of mtDNA variability in future studies at both intra- and inter-specific levels in Fabaceae, which is the third largest family of flowering plants rarely studied at the mtDNA level, and in other more or less related taxa. [Projekat Ministarstva nauke Republike Srbije, br. 173005

  8. Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome.

    Science.gov (United States)

    Waye, J S; Willard, H F

    1986-09-01

    The centromeric regions of all human chromosomes are characterized by distinct subsets of a diverse tandemly repeated DNA family, alpha satellite. On human chromosome 17, the predominant form of alpha satellite is a 2.7-kilobase-pair higher-order repeat unit consisting of 16 alphoid monomers. We present the complete nucleotide sequence of the 16-monomer repeat, which is present in 500 to 1,000 copies per chromosome 17, as well as that of a less abundant 15-monomer repeat, also from chromosome 17. These repeat units were approximately 98% identical in sequence, differing by the exclusion of precisely 1 monomer from the 15-monomer repeat. Homologous unequal crossing-over is suggested as a probable mechanism by which the different repeat lengths on chromosome 17 were generated, and the putative site of such a recombination event is identified. The monomer organization of the chromosome 17 higher-order repeat unit is based, in part, on tandemly repeated pentamers. A similar pentameric suborganization has been previously demonstrated for alpha satellite of the human X chromosome. Despite the organizational similarities, substantial sequence divergence distinguishes these subsets. Hybridization experiments indicate that the chromosome 17 and X subsets are more similar to each other than to the subsets found on several other human chromosomes. We suggest that the chromosome 17 and X alpha satellite subsets may be related components of a larger alphoid subfamily which have evolved from a common ancestral repeat into the contemporary chromosome-specific subsets.

  9. Inter-familial relationships of the shorebirds (Aves: Charadriiformes based on nuclear DNA sequence data

    Directory of Open Access Journals (Sweden)

    Irestedt Martin

    2003-07-01

    Full Text Available Abstract Background Phylogenetic hypotheses of higher-level relationships in the order Charadriiformes based on morphological data, partly disagree with those based on DNA-DNA hybridisation data. So far, these relationships have not been tested by analysis of DNA sequence data. Herein we utilize 1692 bp of aligned, nuclear DNA sequences obtained from 23 charadriiform species, representing 15 families. We also test earlier suggestions that bustards and sandgrouses may be nested with the charadriiforms. The data is analysed with methods based on the parsimony and maximum-likelihood criteria. Results Several novel phylogenetic relationships were recovered and strongly supported by the data, regardless of which method of analysis was employed. These include placing the gulls and allied groups as a sistergroup to the sandpiper-like birds, and not to the plover-like birds. The auks clearly belong to the clade with the gulls and allies, and are not basal to most other charadriiform birds as suggested in analyses of morphological data. Pluvialis, which has been supposed to belong to the plover family (Charadriidae, represents a basal branch that constitutes the sister taxon to a clade with plovers, oystercatchers and avocets. The thick-knees and sheathbills unexpectedly cluster together. Conclusion The DNA sequence data contains a strong phylogenetic signal that results in a well-resolved phylogenetic tree with many strongly supported internodes. Taxonomically it is the most inclusive study of shorebird families that relies on nucleotide sequences. The presented phylogenetic hypothesis provides a solid framework for analyses of macroevolution of ecological, morphological and behavioural adaptations observed within the order Charadriiformes.

  10. Copper Inhibits the AlkB Family DNA Repair Enzymes under Wilson's Disease Condition.

    Science.gov (United States)

    Bian, Ke; Chen, Fangyi; Humulock, Zachary T; Tang, Qi; Li, Deyu

    2017-10-16

    Disturbed metabolism of copper ions can cause diseases such as Wilson's disease (WD). In this work, we investigated the inhibitory effect of Cu(II) ion in vitro on the AlkB family DNA repair enzymes, which are members of the Fe(II)/alpha-ketoglutarate-dependent dioxygenase and include human ALKBH2, ALKBH3, and E. coli AlkB proteins. None of the three proteins was significantly inhibited under normal cellular copper concentrations. However, under WD related condition, we observed that the activities of all three enzymes were strongly suppressed (from 95.2 to 100.0%). We also noted the repair efficiency under ds-DNA condition was less susceptible than ss-DNA to the inhibition.

  11. DNA analyses of the remains of the Prince Branciforte Barresi family.

    Science.gov (United States)

    Rickards, O; Martínez-Labarga, C; Favaro, M; Frezza, D; Mallegni, F

    2001-01-01

    The five skeletons found buried in the church of Militello di Catania, Sicily, were tentatively identified by morphological analysis and historical reports as the remains of Prince Branciforte Barresi, two of his children, his brother and another juvenile member of the family (sixteenth and seventeenth centuries). In order to attempt to clarify the degree of relationships of the five skeletons, sex testing and mitochondrial DNA (mtDNA) sequence analysis of the hypervariable segments I and II (HV1 and HV2) of control region were performed. Moreover, the 9 bp-deletion marker of region V (COII/tRNAlys) was examined. Molecular genetic analyses were consistent with historical expectations, although they did not directly demonstrate that these are in fact the remains of the Prince and his relatives, due to the impossibility of obtaining DNA from living maternal relatives of the Prince.

  12. Multiple DNA-binding modes for the ETS family transcription factor PU.1.

    Science.gov (United States)

    Esaki, Shingo; Evich, Marina G; Erlitzki, Noa; Germann, Markus W; Poon, Gregory M K

    2017-09-29

    The eponymous DNA-binding domain of ETS ( E 26 t ransformation- s pecific) transcription factors binds a single sequence-specific site as a monomer over a single helical turn. Following our previous observation by titration calorimetry that the ETS member PU.1 dimerizes sequentially at a single sequence-specific DNA-binding site to form a 2:1 complex, we have carried out an extensive spectroscopic and biochemical characterization of site-specific PU.1 ETS complexes. Whereas 10 bp of DNA was sufficient to support PU.1 binding as a monomer, additional flanking bases were required to invoke sequential dimerization of the bound protein. NMR spectroscopy revealed a marked loss of signal intensity in the 2:1 complex, and mutational analysis implicated the distal surface away from the bound DNA as the dimerization interface. Hydroxyl radical DNA footprinting indicated that the site-specifically bound PU.1 dimers occupied an extended DNA interface downstream from the 5'-GGAA-3' core consensus relative to its 1:1 counterpart, thus explaining the apparent site size requirement for sequential dimerization. The site-specifically bound PU.1 dimer resisted competition from nonspecific DNA and showed affinities similar to other functionally significant PU.1 interactions. As sequential dimerization did not occur with the ETS domain of Ets-1, a close structural homolog of PU.1, 2:1 complex formation may represent an alternative autoinhibitory mechanism in the ETS family at the protein-DNA level. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Uncovering the evolutionary history of neo-XY sex chromosomes in the grasshopper Ronderosia bergii (Orthoptera, Melanoplinae) through satellite DNA analysis.

    Science.gov (United States)

    Palacios-Gimenez, Octavio M; Milani, Diogo; Lemos, Bernardo; Castillo, Elio R; Martí, Dardo A; Ramos, Erica; Martins, Cesar; Cabral-de-Mello, Diogo C

    2018-01-08

    Neo-sex chromosome systems arose independently multiple times in evolution, presenting the remarkable characteristic of repetitive DNAs accumulation. Among grasshoppers, occurrence of neo-XY was repeatedly noticed in Melanoplinae. Here we analyzed the most abundant tandem repeats of R. bergii (2n = 22, neo-XY♂) using deep Illumina sequencing and graph-based clustering in order to address the neo-sex chromosomes evolution. The analyses revealed ten families of satDNAs comprising about ~1% of the male genome, which occupied mainly C-positive regions of autosomes. Regarding the sex chromosomes, satDNAs were recorded within centromeric or interstitial regions of the neo-X chromosome and four satDNAs occurred in the neo-Y, two of them being exclusive (Rber248 and Rber299). Using a combination of probes we uncovered five well-defined cytological variants for neo-Y, originated by multiple paracentric inversions and satDNA amplification, besides fragmented neo-Y. These neo-Y variants were distinct in frequency between embryos and adult males. The genomic data together with cytogenetic mapping enabled us to better understand the neo-sex chromosome dynamics in grasshoppers, reinforcing differentiation of neo-X and neo-Y and revealing the occurrence of multiple additional rearrangements involved in the neo-Y evolution of R. bergii. We discussed the possible causes that led to differences in frequency for the neo-Y variants between embryos and adults. Finally we hypothesize about the role of DNA satellites in R. bergii as well as putative historical events involved in the evolution of the R. bergii neo-XY.

  14. DNA Damage Observed in Unaffected Individuals with Family History of T2DM

    Science.gov (United States)

    Ramesh, Nikhila; Abilash, V. G.

    2017-11-01

    Diabetes has been documented to cause high levels of DNA fragmentation in some cases. As diabetes is inheritable and influenced by both genetic and environmental factors, an investigation into the genomic stability of individuals who are strongly at risk of inheriting diabetes was conducted by inducing oxidative stress, as DNA damage in unaffected individuals could be a sign of onset of the disease or the presence of genetic alterations that reduce cellular defences against reactive oxygen species. In this study, alkaline comet assay was performed on isolated human leukocytes to determine whether individuals with a family history of Type 2 Diabetes Mellitus (T2DM) are more prone to DNA damage under oxidative stress. Visual scoring of comets showed that these individuals have higher degree of DNA damage compared to a control individual with no family history of Type 2 Diabetes Mellitus. Further studies with large sample could determine the presence of disabled cellular defences against oxidative stress in unaffected individuals and intervention with antioxidants could prevent or manage Type 2 Diabetes Mellitus and its complications.

  15. Unnatural substrate repertoire of A, B, and X family DNA polymerases.

    Science.gov (United States)

    Hwang, Gil Tae; Romesberg, Floyd E

    2008-11-05

    As part of an effort to develop unnatural base pairs that are stable and replicable in DNA, we examined the ability of five different polymerases to replicate DNA containing four different unnatural nucleotides bearing predominantly hydrophobic nucleobase analogs. The unnatural pairs were developed based on intensive studies using the Klenow fragment of DNA polymerase I from E. coli (Kf) and found to be recognized to varying degrees. The five additional polymerases characterized here include family A polymerases from bacteriophage T7 and Thermus aquaticus, family B polymerases from Thermococcus litoralis and Thermococcus 9(o)N-7, and the family X polymerase, human polymerase beta. While we find that some aspects of unnatural base pair recognition are conserved among the polymerases, for example, the pair formed between two d3FB nucleotides is typically well recognized, the detailed recognition of most of the unnatural base pairs is generally polymerase dependent. In contrast, we find that the pair formed between d5SICS and dMMO2 is generally well recognized by all of the polymerases examined, suggesting that the determinants of efficient and general recognition are contained within the geometric and electronic structure of these unnatural nucleobases themselves. The data suggest that while the d3FB:d3FB pair is sufficiently well recognized by several of the polymerases for in vitro applications, the d5SICS:dMMO2 heteropair is likely uniquely promising for in vivo use. T7-mediated replication is especially noteworthy due to strong mispair discrimination.

  16. DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies.

    Science.gov (United States)

    Mahony, Shaun; Auron, Philip E; Benos, Panayiotis V

    2007-03-30

    Transcription factor (TF) proteins recognize a small number of DNA sequences with high specificity and control the expression of neighbouring genes. The evolution of TF binding preference has been the subject of a number of recent studies, in which generalized binding profiles have been introduced and used to improve the prediction of new target sites. Generalized profiles are generated by aligning and merging the individual profiles of related TFs. However, the distance metrics and alignment algorithms used to compare the binding profiles have not yet been fully explored or optimized. As a result, binding profiles depend on TF structural information and sometimes may ignore important distinctions between subfamilies. Prediction of the identity or the structural class of a protein that binds to a given DNA pattern will enhance the analysis of microarray and ChIP-chip data where frequently multiple putative targets of usually unknown TFs are predicted. Various comparison metrics and alignment algorithms are evaluated (a total of 105 combinations). We find that local alignments are generally better than global alignments at detecting eukaryotic DNA motif similarities, especially when combined with the sum of squared distances or Pearson's correlation coefficient comparison metrics. In addition, multiple-alignment strategies for binding profiles and tree-building methods are tested for their efficiency in constructing generalized binding models. A new method for automatic determination of the optimal number of clusters is developed and applied in the construction of a new set of familial binding profiles which improves upon TF classification accuracy. A software tool, STAMP, is developed to host all tested methods and make them publicly available. This work provides a high quality reference set of familial binding profiles and the first comprehensive platform for analysis of DNA profiles. Detecting similarities between DNA motifs is a key step in the comparative study

  17. DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies.

    Directory of Open Access Journals (Sweden)

    Shaun Mahony

    2007-03-01

    Full Text Available Transcription factor (TF proteins recognize a small number of DNA sequences with high specificity and control the expression of neighbouring genes. The evolution of TF binding preference has been the subject of a number of recent studies, in which generalized binding profiles have been introduced and used to improve the prediction of new target sites. Generalized profiles are generated by aligning and merging the individual profiles of related TFs. However, the distance metrics and alignment algorithms used to compare the binding profiles have not yet been fully explored or optimized. As a result, binding profiles depend on TF structural information and sometimes may ignore important distinctions between subfamilies. Prediction of the identity or the structural class of a protein that binds to a given DNA pattern will enhance the analysis of microarray and ChIP-chip data where frequently multiple putative targets of usually unknown TFs are predicted. Various comparison metrics and alignment algorithms are evaluated (a total of 105 combinations. We find that local alignments are generally better than global alignments at detecting eukaryotic DNA motif similarities, especially when combined with the sum of squared distances or Pearson's correlation coefficient comparison metrics. In addition, multiple-alignment strategies for binding profiles and tree-building methods are tested for their efficiency in constructing generalized binding models. A new method for automatic determination of the optimal number of clusters is developed and applied in the construction of a new set of familial binding profiles which improves upon TF classification accuracy. A software tool, STAMP, is developed to host all tested methods and make them publicly available. This work provides a high quality reference set of familial binding profiles and the first comprehensive platform for analysis of DNA profiles. Detecting similarities between DNA motifs is a key step in the

  18. Xanthorrhizol induced DNA fragmentation in HepG2 cells involving Bcl-2 family proteins

    Energy Technology Data Exchange (ETDEWEB)

    Tee, Thiam-Tsui, E-mail: thiamtsu@yahoo.com [School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor (Malaysia); Cheah, Yew-Hoong [School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor (Malaysia); Bioassay Unit, Herbal Medicine Research Center, Institute for Medical Research, Jalan Pahang, Kuala Lumpur (Malaysia); Meenakshii, Nallappan [Biology Department, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor (Malaysia); Mohd Sharom, Mohd Yusof; Azimahtol Hawariah, Lope Pihie [School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor (Malaysia)

    2012-04-20

    Highlights: Black-Right-Pointing-Pointer We isolated xanthorrhizol, a sesquiterpenoid compound from Curcuma xanthorrhiza. Black-Right-Pointing-Pointer Xanthorrhizol induced apoptosis in HepG2 cells as observed using SEM. Black-Right-Pointing-Pointer Apoptosis in xanthorrhizol-treated HepG2 cells involved Bcl-2 family proteins. Black-Right-Pointing-Pointer DNA fragmentation was observed in xanthorrhizol-treated HepG2 cells. Black-Right-Pointing-Pointer DNA fragmentation maybe due to cleavage of PARP and DFF45/ICAD proteins. -- Abstract: Xanthorrhizol is a plant-derived pharmacologically active sesquiterpenoid compound isolated from Curcuma xanthorrhiza. Previously, we have reported that xanthorrhizol inhibited the proliferation of HepG2 human hepatoma cells by inducing apoptotic cell death via caspase activation. Here, we attempt to further elucidate the mode of action of xanthorrhizol. Apoptosis in xanthorrhizol-treated HepG2 cells as observed by scanning electron microscopy was accompanied by truncation of BID; reduction of both anti-apoptotic Bcl-2 and Bcl-X{sub L} expression; cleavage of PARP and DFF45/ICAD proteins and DNA fragmentation. Taken together, these results suggest xanthorrhizol as a potent antiproliferative agent on HepG2 cells by inducing apoptosis via Bcl-2 family members. Hence we proposed that xanthorrhizol could be used as an anti-liver cancer drug for future studies.

  19. Dispersion of the Himalia family of jovian irregular satellites by planetesimal encounters

    Science.gov (United States)

    Li, Daohai; Christou, Apostolos

    2017-06-01

    Giant planets are believed to have migrated significant radial distances due to interaction with a primordial planetesimal disk (Tsiganis et al. 2005). This process profoundly sculpted the solar system, shaping the distribution of the different types of heliocentric objects: the giant planets, the Trojans, the Main Asteroid Belt and the KBOs. Meanwhile, the same migration may have influenced the distribution of objects in the local planetocentric system as well. Since migration is achieved mainly by planet-planetesimal encounters, we focus on irregular satellites far from the host, thus susceptible to planetesimal perturbations. Specifically, we aim to reproduce a puzzling feature of the jovian Himalia group of prograde satellites: a wide spread in $a$ and $e$, with all group members being $>200$ m/s from Himalia and apparently too high to be consistent with a purely collisional origin. Here we investigate the evolution of a pre-existing Himalia group during planetary migration.We do this in a two-step procedure. Firstly, we perform migration simulations and record the states of planetesimals approaching Jupiter. Secondly, a nascent, closely-packed Himalia group with velocity dispersion of a few 10 m/s is integrated under the gravitational disturbance of the planetesimal fly-bys. We find that these planetesimal encounters disperse the group dramatically, bumping $\\sim 60\\%$ of the members to $>200$ m/s with respect to Himalia. Particularly, $a$ and $e$ suffer the most variation while the change in $i$ is often limited, matching the actual values for the observed group fairly well.Current models posit extensive collisional processing of the irregular satellite population following the planet migration phase (Bottke et al. 2010). In evaluating the collisional probability between a group member and Himalia, we find that the closer they are, the more likely that collisions occur. This suggests that members adjacent to Himalia are more likely to be collisionally

  20. Mitochondrial DNA mutation load in a family with the m.8344A>G point mutation and lipomas

    DEFF Research Database (Denmark)

    Jeppesen, Tina Dysgaard; Al-Hashimi, Noor; Duno, Morten

    2017-01-01

    Studies have shown that difference in mtDNA mutation load among tissues is a result of postnatal modification. We present five family members with the m.8344A>G with variable phenotypes but uniform intrapersonal distribution of mutation load, indicating that there is no postnatal modification of mt......DNA mutation load in this genotype....

  1. Heritable DNA methylation in CD4+ cells among complex families displays genetic and non-genetic effects

    Science.gov (United States)

    DNA methylation at CpG sites is both heritable and influenced by environment, but the relative contributions of each to DNA methylation levels are unclear. We conducted a heritability analysis of CpG methylation in human CD4+ cells across 975 individuals from 163 families in the Genetics of Lipid-lo...

  2. Characterization of two families of tandem repeated DNA sequences in Potamogeton pectinatus L.

    Science.gov (United States)

    Ceccarelli, Marilena; Sarri, Vania; Minelli, Stefania; Gelati, Maria Teresa

    2008-11-01

    DNA sequences belonging to two families of tandem repeats, PpeRsa1 (362-364 bp in length, 62% A+T residues) and PpeRsa2 (355-359 bp in length, 59% A+T residues), have been isolated from the Potamogeton pectinatus L. genome. The two sequence families do not share significant nucleotide sequence similarity, even if an evolutionary relationship between them could be assumed. The comparison of the cleaving activity of isoschizomeres that are either sensitive or insensitive to methylation of cytosine residues in the target sequence revealed high methylation in both sequence families. The copy number per 1C DNA of PpeRsa1- and PpeRsa2-related sequences is estimated to be 4.92 x 10(4) and 7.96 x 10(4), respectively. Taken together, these sequences account for about 7.5% of the entire genome of P. pectinatus. The chromosomal organization of these sequences was investigated by fluorescent in situ hybridization. PpeRsa1 and PpeRsa2 repeats found related sequences in 52 chromosomes of the P. pectinatus complement (2n = 78). The related sequences were localized around the centromeres and at the chromosome ends in three pairs of chromosomes, while they were found only at the chromosome ends in the remaining pairs. Twenty-six chromosomes did not show any hybridization signal. The hypothesis that the species is a hybrid between a diploid parent and an allotetraploid parent is put forward.

  3. Human chromosome 1 satellite 3 DNA is decondensed, demethylated and transcribed in senescent cells and in A431 epithelial carcinoma cells.

    Science.gov (United States)

    Enukashvily, N I; Donev, R; Waisertreiger, I S-R; Podgornaya, O I

    2007-01-01

    Constitutive heterochromatin mainly consists of different classes of satellite DNAs and is defined as a transcriptionally inactive chromatin that remains compact throughout the cell cycle. The aim of this work was to investigate the level of condensation, methylation and transcriptional status of centromeric (alphoid DNA) and pericentromeric satellites (human satellite 3, HS3) in tissues (lymphocytes, placenta cells) and in cultured primary (MRC5, VH-10, AT2Sp) and malignant (A431) cells. We found that alphoid DNA remained condensed and heavily methylated in all the cell types. The HS3 of chromosome 1 (HS3-1) but not of chromosome 9 (HS3-9) was strongly decondensed and demethylated in A431 cells. The same observation was made for aged embryonic lung (MRC5) and juvenile foreskin (VH-10) fibroblasts obtained at late passages (32(nd) and 23(rd), respectively). Decondensation was also found in ataxia telangiectasia AT2Sp fibroblasts at the 16(th) passage. One of the manifestations of the disease is premature aging. The level of HS3-1 decondensation was higher in aged primary fibroblasts as compared to A431. The HS3-1 extended into the territory of neighbouring chromosomes. An RT-PCR product was detected in A431 and senescent MRC5 fibroblasts using primers specific for HS3-1. The RNA was polyadenylated and transcribed from the reverse chain. Our results demonstrate the involvement of satellite DNA in associations between human chromosomes and intermingling of chromosome territories. The invading satellite DNA can undergo decondensation to a certain level. This process is accompanied by demethylation and transcription. Copyright (c) 2007 S. Karger AG, Basel.

  4. Sea cucumber species identification of family Caudinidae from Surabaya based on morphological and mitochondrial DNA evidence

    Science.gov (United States)

    Amin, Muhammad Hilman Fu'adil; Pidada, Ida Bagus Rai; Sugiharto, Widyatmoko, Johan Nuari; Irawan, Bambang

    2016-03-01

    Species identification and taxonomy of sea cucumber remains a challenge problem in some taxa. Caudinidae family of sea cucumber was comerciallized in Surabaya, and it was used as sea cucumber chips. Members of Caudinid sea cucumber have similiar morphology, so it is hard to identify this sea cucumber only from morphological appearance. DNA barcoding is useful method to overcome this problem. The aim of this study was to determine Caudinid specimen of sea cucumber in East Java by morphological and molecular approach. Sample was collected from east coast of Surabaya, then preserved in absolute ethanol. After DNA isolation, Cytochrome Oxydase I (COI) gene amplification was performed using Echinoderm universal primer and PCR product was sequenced. Sequencing result was analyzed and identified in NCBI database using BLAST. Results showed that Caudinid specimen in have closely related to Acaudina molpadioides sequence in GenBank with 86% identity. Morphological data, especially based on ossicle, also showed that the specimen is Acaudina molpadioides.

  5. DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

    DEFF Research Database (Denmark)

    Sander, Adam F.; Lavstsen, Thomas; Rask, Thomas Salhøj

    2014-01-01

    -wide recombination hotspots in var genes, we show that during the parasite’s sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum...... falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome...... of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens....

  6. Functional studies of ssDNA binding ability of MarR family protein TcaR from Staphylococcus epidermidis.

    Science.gov (United States)

    Chang, Yu-Ming; Chen, Cammy K-M; Chang, Yuan-Chih; Jeng, Wen-Yih; Hou, Ming-Hon; Wang, Andrew H-J

    2012-01-01

    The negative transcription regulator of the ica locus, TcaR, regulates proteins involved in the biosynthesis of poly-N-acetylglucosamine (PNAG). Absence of TcaR increases PNAG production and promotes biofilm formation in Staphylococci. Previously, the 3D structure of TcaR in its apo form and its complex structure with several antibiotics have been analyzed. However, the detailed mechanism of multiple antibiotic resistance regulator (MarR) family proteins such as TcaR is unclear and only restricted on the binding ability of double-strand DNA (dsDNA). Here we show by electrophoretic mobility shift assay (EMSA), electron microscopy (EM), circular dichroism (CD), and Biacore analysis that TcaR can interact strongly with single-stranded DNA (ssDNA), thereby identifying a new role in MarR family proteins. Moreover, we show that TcaR preferentially binds 33-mer ssDNA over double-stranded DNA and inhibits viral ssDNA replication. In contrast, such ssDNA binding properties were not observed for other MarR family protein and TetR family protein, suggesting that the results from our studies are not an artifact due to simple charge interactions between TcaR and ssDNA. Overall, these results suggest a novel role for TcaR in regulation of DNA replication. We anticipate that the results of this work will extend our understanding of MarR family protein and broaden the development of new therapeutic strategies for Staphylococci.

  7. Functional studies of ssDNA binding ability of MarR family protein TcaR from Staphylococcus epidermidis.

    Directory of Open Access Journals (Sweden)

    Yu-Ming Chang

    Full Text Available The negative transcription regulator of the ica locus, TcaR, regulates proteins involved in the biosynthesis of poly-N-acetylglucosamine (PNAG. Absence of TcaR increases PNAG production and promotes biofilm formation in Staphylococci. Previously, the 3D structure of TcaR in its apo form and its complex structure with several antibiotics have been analyzed. However, the detailed mechanism of multiple antibiotic resistance regulator (MarR family proteins such as TcaR is unclear and only restricted on the binding ability of double-strand DNA (dsDNA. Here we show by electrophoretic mobility shift assay (EMSA, electron microscopy (EM, circular dichroism (CD, and Biacore analysis that TcaR can interact strongly with single-stranded DNA (ssDNA, thereby identifying a new role in MarR family proteins. Moreover, we show that TcaR preferentially binds 33-mer ssDNA over double-stranded DNA and inhibits viral ssDNA replication. In contrast, such ssDNA binding properties were not observed for other MarR family protein and TetR family protein, suggesting that the results from our studies are not an artifact due to simple charge interactions between TcaR and ssDNA. Overall, these results suggest a novel role for TcaR in regulation of DNA replication. We anticipate that the results of this work will extend our understanding of MarR family protein and broaden the development of new therapeutic strategies for Staphylococci.

  8. Impact of DNA testing for early-onset familial Alzheimer disease and frontotemporal dementia.

    Science.gov (United States)

    Steinbart, E J; Smith, C O; Poorkaj, P; Bird, T D

    2001-11-01

    DNA testing of persons at risk for hereditary, degenerative neurologic diseases is relatively new. Only anecdotal reports of such testing in familial Alzheimer disease (FAD) exist, and little is know about the personal and social impact of such testing. In a descriptive, observational study, individuals at 50% risk for autosomal dominant, early-onset FAD or frontotemporal dementia with parkinsonism linked to chromosome 17 underwent DNA testing for the genetic mutations previously identified in affected family members. Individuals were followed up for (1/2) to 3 years and were interviewed regarding attitudes toward the testing process and the impact of the results. Twenty-one (8.4%) of 251 persons at risk for FAD or frontotemporal dementia requested genetic testing. The most common reasons for requesting testing were concern about early symptoms of dementia, financial or family planning, and relief from anxiety. Twelve individuals had positive DNA test results, and 6 of these had early symptoms of dementia; 8 had negative results; and 1 has not yet received results. Of 14 asymptomatic individuals completing testing, 13 believed the testing was beneficial. Two persons reported moderate anxiety and 1 reported moderate depression. As expected, persons with negative test results had happier experiences overall, but even they had to deal with ongoing anxiety and depression. Thus far, there have been no psychiatric hospitalizations, suicide attempts, or denials of insurance. Genetic testing in early-onset FAD and frontotemporal dementia can be completed successfully. Most individuals demonstrate effective coping skills and find the testing to be beneficial, but long-term effects remain unknown.

  9. C-terminal diversity within the p53 family accounts for differences in DNA binding and transcriptional activity

    Science.gov (United States)

    Sauer, Markus; Bretz, Anne Catherine; Beinoraviciute-Kellner, Rasa; Beitzinger, Michaela; Burek, Christof; Rosenwald, Andreas; Harms, Gregory S.; Stiewe, Thorsten

    2008-01-01

    The p53 family is known as a family of transcription factors with functions in tumor suppression and development. Whereas the central DNA-binding domain is highly conserved among the three family members p53, p63 and p73, the C-terminal domains (CTDs) are diverse and subject to alternative splicing and post-translational modification. Here we demonstrate that the CTDs strongly influence DNA binding and transcriptional activity: while p53 and the p73 isoform p73γ have basic CTDs and form weak sequence-specific protein–DNA complexes, the major p73 isoforms have neutral CTDs and bind DNA strongly. A basic CTD has been previously shown to enable sliding along the DNA backbone and to facilitate the search for binding sites in the complex genome. Our experiments, however, reveal that a basic CTD also reduces protein–DNA complex stability, intranuclear mobility, promoter occupancy in vivo, target gene activation and induction of cell cycle arrest or apoptosis. A basic CTD therefore provides both positive and negative regulatory functions presumably to enable rapid switching of protein activity in response to stress. The different DNA-binding characteristics of the p53 family members could therefore reflect their predominant role in the cellular stress response (p53) or developmental processes (p73). PMID:18267967

  10. C-terminal diversity within the p53 family accounts for differences in DNA binding and transcriptional activity

    OpenAIRE

    Sauer, Markus; Bretz, Anne Catherine; Beinoraviciute-Kellner, Rasa; Beitzinger, Michaela; Burek, Christof; Rosenwald, Andreas; Harms, Gregory S.; Stiewe, Thorsten

    2008-01-01

    The p53 family is known as a family of transcription factors with functions in tumor suppression and development. Whereas the central DNA-binding domain is highly conserved among the three family members p53, p63 and p73, the C-terminal domains (CTDs) are diverse and subject to alternative splicing and post-translational modification. Here we demonstrate that the CTDs strongly influence DNA binding and transcriptional activity: while p53 and the p73 isoform p73γ have basic CTDs and form weak ...

  11. Search for unstable DNA in schizophrenia families with evidence for genetic anticipation

    Energy Technology Data Exchange (ETDEWEB)

    Petronis, A.; Vincent, J.B.; Tatuch, Y.; Sasaki, Tsukasa [Univ. of British Columbia, Vancouver (Canada)] [and others

    1996-10-01

    Evidence for genetic anticipation has recently become an important subject of research in clinical psychiatric genetics. Renewed interest in anticipation was evoked by molecular genetic findings of a novel type of mutation termed {open_quotes}unstable DNA.{close_quotes} The unstable DNA model can be construed as the {open_quotes}best fit{close_quotes} for schizophrenia twin and family epidemiological data. We have performed a large-scale Southern blot hybridization, asymmetrical PCR-based, and repeat expansion-detection screening for (CAG){sub n}/(CTG){sub n} and (CCG){sub n}/(CGG){sub n} expansions in eastern Canadian schizophrenia multiplex families demonstrating genetic anticipation. There were no differences in (CAG){sub n}/(CTG){sub n} and (CCG){sub n}/(CGG){sub n} pattern distribution either between affected and unaffected individuals or across generations. Our findings do not support the hypothesis that large (CAG){sub n}/(CTG){sub n} or (CCG){sub n}/(CGG){sub n} expansions are the major etiologic factor in schizophrenia. A separate set of experiments directed to the analysis of small (30-130 trinucleotides), Huntington disease-type expansions in individual genes is required in order to fully exclude the presence of (CAG){sub n}/(CTG){sub n}- or (CCG){sub n}/(CGG){sub n}-type unstable mutation. 38 refs., 2 figs.

  12. Familial searching: a specialist forensic DNA profiling service utilising the National DNA Database to identify unknown offenders via their relatives--the UK experience.

    Science.gov (United States)

    Maguire, C N; McCallum, L A; Storey, C; Whitaker, J P

    2014-01-01

    The National DNA Database (NDNAD) of England and Wales was established on April 10th 1995. The NDNAD is governed by a variety of legislative instruments that mean that DNA samples can be taken if an individual is arrested and detained in a police station. The biological samples and the DNA profiles derived from them can be used for purposes related to the prevention and detection of crime, the investigation of an offence and for the conduct of a prosecution. Following the South East Asian Tsunami of December 2004, the legislation was amended to allow the use of the NDNAD to assist in the identification of a deceased person or of a body part where death has occurred from natural causes or from a natural disaster. The UK NDNAD now contains the DNA profiles of approximately 6 million individuals representing 9.6% of the UK population. As the science of DNA profiling advanced, the National DNA Database provided a potential resource for increased intelligence beyond the direct matching for which it was originally created. The familial searching service offered to the police by several UK forensic science providers exploits the size and geographic coverage of the NDNAD and the fact that close relatives of an offender may share a significant proportion of that offender's DNA profile and will often reside in close geographic proximity to him or her. Between 2002 and 2011 Forensic Science Service Ltd. (FSS) provided familial search services to support 188 police investigations, 70 of which are still active cases. This technique, which may be used in serious crime cases or in 'cold case' reviews when there are few or no investigative leads, has led to the identification of 41 perpetrators or suspects. In this paper we discuss the processes, utility, and governance of the familial search service in which the NDNAD is searched for close genetic relatives of an offender who has left DNA evidence at a crime scene, but whose DNA profile is not represented within the NDNAD. We

  13. Expression of proteins involved in DNA damage response in familial and sporadic breast cancer patients.

    Science.gov (United States)

    Partipilo, Giulia; Simone, Giovanni; Scattone, Anna; Scarpi, Emanuela; Azzariti, Amalia; Mangia, Anita

    2016-01-01

    Understanding the expression of proteins involved in DNA damage response could improve knowledge of the pathways that contribute to familial and sporadic breast cancer (BC). We aimed to assess the different roles of BRCA1, poly(ADP-ribose) polymerase-1 (PARP1), BRCT-repeat inhibitor of hTERT expression (BRIT1) and novel SWItch 5 (SWI5) expression in 130 sporadic and 73 familial BC samples, by immunohistochemistry. In the sporadic group, negative nuclear BRCA1 (nBRCA1) expression was associated with positive PgR (p = 0.037). Negative association was found between nBRCA1 expression and HER2 (p = 0.001). In the familial group, nBRCA1 expression was associated with ER (p = 0.002). Reduced nBRCA1 expression was associated with higher histological grade and positive Ki67 both in sporadic (p = 0.0010, p = 0.047) and familial groups (p < 0.001, p = 0.001). Nuclear PARP1 (nPARP1) expression was associated with histological grade (p = 0.035) and positive PgR (p = 0.047) in sporadic cases. High cytoplasmic and low nuclear BRIT1 (cBRIT1 and nBRIT1) expression were associated with high histological grade in the familial group (p = 0.013, p = 0.025). Various statistical associations between the protein expressions were observed in the sporadic group, while in familial group only few associations were found. Univariate analyses showed that nPARP1 expression is able to discriminate between sporadic and familial tumors (OR 2.80, p = 0.002). Multivariate analyses proved that its overexpression is an independent factor associated with a high risk of sporadic tumor (OR 2.96, p = 0.017). Our findings indicate that nPARP1 expression is an independent factor for sporadic BCs and PARP1 inhibitors could be a promising therapy for different phenotypes. © 2015 UICC.

  14. A Viral Satellite DNA Vector (TYLCCNV) for Functional Analysis of miRNAs and siRNAs in Plants.

    Science.gov (United States)

    Ju, Zheng; Cao, Dongyan; Gao, Chao; Zuo, Jinhua; Zhai, Baiqiang; Li, Shan; Zhu, Hongliang; Fu, Daqi; Luo, Yunbo; Zhu, Benzhong

    2017-04-01

    With experimental and bioinformatical methods, numerous small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), have been found in plants, and they play vital roles in various biological regulation processes. However, most of these small RNAs remain to be functionally characterized. Until now, only several viral vectors were developed to overexpress miRNAs with limited application in plants. In this study, we report a new small RNA overexpression system via viral satellite DNA associated with Tomato yellow leaf curl China virus (TYLCCNV) vector, which could highly overexpress not only artificial and endogenous miRNAs but also endogenous siRNAs in Nicotiana benthamiana First, we constructed basic TYLCCNV-amiRPDS(319L) vector with widely used AtMIR319a backbone, but the expected photobleaching phenotype was very weak. Second, through comparing the effect of backbones (AtMIR319a, AtMIR390a, and SlMIR159) on specificity and significance of generating small RNAs, the AtMIR390a backbone was optimally selected to construct the small RNA overexpression system. Third, through sRNA-Seq and Degradome-Seq, the small RNAs from AtMIR390a backbone in TYLCCNV-amiRPDS(390) vector were confirmed to highly overexpress amiRPDS and specifically silence targeted PDS gene. Using this system, rapid functional analysis of endogenous miRNAs and siRNAs was carried out, including miR156 and athTAS3a 5'D8(+). Meanwhile, through designing corresponding artificial miRNAs, this system could also significantly silence targeted endogenous genes and show specific phenotypes, including PDS, Su, and PCNA These results demonstrated that this small RNA overexpression system could contribute to investigating not only the function of endogenous small RNAs, but also the functional genes in plants. © 2017 American Society of Plant Biologists. All Rights Reserved.

  15. A novel mtDNA ND6 gene mutation associated with LHON in a Caucasian family.

    Science.gov (United States)

    Zhadanov, Sergey I; Atamanov, Vasily V; Zhadanov, Nikolay I; Oleinikov, Oleg V; Osipova, Ludmila P; Schurr, Theodore G

    2005-07-15

    Leber's hereditary optic neuropathy (LHON) is a frequent cause of inherited blindness. A routine screening for common mtDNA mutations constitutes an important first in its diagnosis. However, a substantial number of LHON patients do not harbor known variants, both pointing to the genetic heterogeneity of LHON and bringing into question its genetic diagnosis. We report a familial case that exhibited typical features of LHON but lacked any of the common mutations. Genetic analysis revealed a novel pathogenic defect in the ND6 gene at 14279A that was not detected in any haplogroup-matched controls screened for it, nor has it been previously reported. This mutation causes a substantial conformational change in the secondary structure of the polypeptide matrix coil and may explain the LHON expression. Thus, it expands the spectrum of deleterious changes affecting ND6-encoding subunit and further highlights the functional significance of this gene, providing additional clues to the disease pathogenesis.

  16. Within-genome evolution of REPINs: a new family of miniature mobile DNA in bacteria.

    Directory of Open Access Journals (Sweden)

    Frederic Bertels

    2011-06-01

    Full Text Available Repetitive sequences are a conserved feature of many bacterial genomes. While first reported almost thirty years ago, and frequently exploited for genotyping purposes, little is known about their origin, maintenance, or processes affecting the dynamics of within-genome evolution. Here, beginning with analysis of the diversity and abundance of short oligonucleotide sequences in the genome of Pseudomonas fluorescens SBW25, we show that over-represented short sequences define three distinct groups (GI, GII, and GIII of repetitive extragenic palindromic (REP sequences. Patterns of REP distribution suggest that closely linked REP sequences form a functional replicative unit: REP doublets are over-represented, randomly distributed in extragenic space, and more highly conserved than singlets. In addition, doublets are organized as inverted repeats, which together with intervening spacer sequences are predicted to form hairpin structures in ssDNA or mRNA. We refer to these newly defined entities as REPINs (REP doublets forming hairpins and identify short reads from population sequencing that reveal putative transposition intermediates. The proximal relationship between GI, GII, and GIII REPINs and specific REP-associated tyrosine transposases (RAYTs, combined with features of the putative transposition intermediate, suggests a mechanism for within-genome dissemination. Analysis of the distribution of REPs in a range of RAYT-containing bacterial genomes, including Escherichia coli K-12 and Nostoc punctiforme, show that REPINs are a widely distributed, but hitherto unrecognized, family of miniature non-autonomous mobile DNA.

  17. Improving the specific synthetic activity of a penicillin g acylase using DNA family shuffling.

    Science.gov (United States)

    Zhou, Zheng; Zhang, Ai-Hui; Wang, Jing-Ru; Chen, Mao-Lin; Li, Ren-Bao; Yang, Sheng; Yuan, Zhong-Yi

    2003-06-01

    Penicillin G Acylas (PGA) of Providencia rettgeri (ATCC 25599) was evolved using a modified DNA family shuffling method. The identity of pga genes from Escherichia coli, Kluyvera citrophila and Providencia rettgeri ranges from 62.5% to 96.9%. The pga genes from above three species were recombined and shuffled to create interspecies pga gene fusion libraries. By substituting assembled chimaeras for corresponding region of pETPPGA, different recombinants were constructed and expressed in E. coli JM109(DE3). Mutants with obvious beta-lactam synthetic activity were selected from the plates and the ratios of synthesis to hydrolysis (S/H) were determined subsequently. It was shown that the primary structures of selected positives exhibited significant diversity among each library. The best mutant possessed 40% higher synthetic activity than the wild type enzyme of PrPGA. It was further proved in this study that the domain of alpha subunit contributed much more to improve the specific activity of synthesis. Results showed a recombinant PGA with higher synthetic activity was acquired by the method of DNA shuffling.

  18. DNA barcoding for squids of the family Gonatidae (Cephalopoda: Teuthida) from the boreal North Pacific.

    Science.gov (United States)

    Katugin, Oleg N; Chichvarkhina, Olga V; Zolotova, Anna O; Chichvarkhin, Anton Yu

    2017-01-01

    A fragment of cytochrome c oxidase I was used to assess whether species of the squid family Gonatidae from the North Pacific could be identified using DNA barcoding approach. Pairwise intra- and interspecific p-distances were assessed, and systematic relationships among species were estimated by NJ analysis. Examined species formed well-differentiated species-specific clades on the neighbor-joining and Bayesian trees. Multiple taxa formed clades supported by both tree topologies and species hypothesis-free ABGD method. Species morphologically identified as Gonatus tinro and Gonatopsis okutanii demonstrated intraspecific level of molecular genetic divergence (0.2-0.3%) indicating that they are conspecific. Genetic differences between the G. berryi clade and a squid morphologically close to that species may indicate a new cryptic species. High levels (>6.2%) of genetic differentiation within B. borealis suggested the existence of two cryptic species. This study confirms the usefulness of DNA barcoding for identifying species as well as discovering cryptic diversity in the gonatid squids, and indicates the need for further deeper insights into the phylogeny of the Gonatidae.

  19. Direct Involvement of Retinoblastoma Family Proteins in DNA Repair by Non-homologous End-Joining

    Directory of Open Access Journals (Sweden)

    Rebecca Cook

    2015-03-01

    Full Text Available Deficiencies in DNA double-strand break (DSB repair lead to genetic instability, a recognized cause of cancer initiation and evolution. We report that the retinoblastoma tumor suppressor protein (RB1 is required for DNA DSB repair by canonical non-homologous end-joining (cNHEJ. Support of cNHEJ involves a mechanism independent of RB1’s cell-cycle function and depends on its amino terminal domain with which it binds to NHEJ components XRCC5 and XRCC6. Cells with engineered loss of RB family function as well as cancer-derived cells with mutational RB1 loss show substantially reduced levels of cNHEJ. RB1 variants disabled for the interaction with XRCC5 and XRCC6, including a cancer-associated variant, are unable to support cNHEJ despite being able to confer cell-cycle control. Our data identify RB1 loss as a candidate driver of structural genomic instability and a causative factor for cancer somatic heterogeneity and evolution.

  20. Eubacterial SpoVG homologs constitute a new family of site-specific DNA-binding proteins.

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    Brandon L Jutras

    Full Text Available A site-specific DNA-binding protein was purified from Borrelia burgdorferi cytoplasmic extracts, and determined to be a member of the highly conserved SpoVG family. This is the first time a function has been attributed to any of these ubiquitous bacterial proteins. Further investigations into SpoVG orthologues indicated that the Staphylococcus aureus protein also binds DNA, but interacts preferentially with a distinct nucleic acid sequence. Site-directed mutagenesis and domain swapping between the S. aureus and B. burgdorferi proteins identified that a 6-residue stretch of the SpoVG α-helix contributes to DNA sequence specificity. Two additional, highly conserved amino acid residues on an adjacent β-sheet are essential for DNA-binding, apparently by contacts with the DNA phosphate backbone. Results of these studies thus identified a novel family of bacterial DNA-binding proteins, developed a model of SpoVG-DNA interactions, and provide direction for future functional studies on these wide-spread proteins.

  1. Imprinting mutations suggested by abnormal DNA methylation patterns in familial Angelman and Prader-Willi syndromes.

    Science.gov (United States)

    Reis, A.; Dittrich, B.; Greger, V.; Buiting, K.; Lalande, M.; Gillessen-Kaesbach, G.; Anvret, M.; Horsthemke, B.

    1994-01-01

    The D15S9 and D15S63 loci in the Prader-Willi/Angelman syndrome region on chromosome 15 are subject to parent-of-origin-specific DNA methylation. We have found two Prader-Willi syndrome families in which the patients carry a maternal methylation imprint on the paternal chromosome. In one of these families, the patients have a small deletion encompassing the gene for the small nuclear ribonucleoprotein polypeptide N, which maps 130 kb telomeric to D15S63. Furthermore, we have identified a pair of nondeletion Angelman syndrome sibs and two isolated Angelman syndrome patients who carry a paternal methylation imprint on the maternal chromosome. These Angelman and Prader-Willi syndrome patients may have a defect in the imprinting process in 15q11-13. We propose a model in which a cis-acting mutation prevents the resetting of the imprinting signal in the germ line and thus disturbs the expression of imprinted genes in this region. Images Figure 2 Figure 3 PMID:8178815

  2. Imprinting mutations suggested by abnormal DNA methylation patterns in familial angelman and Prader-Willi syndromes

    Energy Technology Data Exchange (ETDEWEB)

    Reis, A. (Freie Universitaet, Berlin (Germany)); Dittrich, B.; Buiting, K.; Gillessen-Kaesbach, G.; Horsthemke, B. (Institut fuer Humangenetik, Essen (United Kingdom)); Greger, V.; Lalande, M. (Harvard Medical School, Boston, MA (United States)); Anvret, M. (Karolinska Hospital, Stockholm (Sweden))

    1994-05-01

    The D15S9 and D15S63 loci in the Prader-Willi/Angelman syndrome region on chromosome 15 are subject to parent-of-origin-specific DNA methylation. The authors have found two Prader-Willi syndrome families in which the patients carry a maternal methylation imprint on the paternal chromosome. In one of these families, the patients have a small deletion encompassing the gene for the small nuclear ribonucleoprotein polypeptide N, which maps 130 kb telomeric to D15S63. Furthermore, they have identified a pair of nondeletion Angelman syndrome sibs and two isolated Angelman syndrome patients who carry a paternal methylation imprint on the maternal chromosome. These Angelman and Prader-Willi syndrome patients may have a defect in the imprinting process in 15q11-13. The authors propose a model in which a cis-acting mutation prevents the resetting of the imprinting signal in the germ line and thus disturbs the expression of imprinted genes in this region. 39 refs., 4 figs., 1 tab.

  3. Two X family DNA polymerases, lambda and mu, in meiotic tissues of the basidiomycete, Coprinus cinereus.

    Science.gov (United States)

    Sakamoto, Aiko; Iwabata, Kazuki; Koshiyama, Akiyo; Sugawara, Hiroko; Yanai, Takuro; Kanai, Yoshihiro; Takeuchi, Ryo; Daikuhara, Yoko; Takakusagi, Yoichi; Sakaguchi, Kengo

    2007-12-01

    The X family DNA polymerases lambda (CcPollambda) and mu (CcPolmu) were shown to be expressed during meiotic prophase in the basidiomycete, Coprinus cinereus. These two polymerases are the only members of the X family in the C. cinereus genome. The open reading frame of CcPollambda encoded a predicted product of 800 amino acid residues and that of CcPolmicro of 621 amino acid residues. Both CcPollambda and CcPolmicro required Mn(2+) ions for activity, and both were strongly inhibited by dideoxythymidine triphosphate. Unlike their mammalian counterparts, CcPollambda and CcPolmicro had no terminal deoxynucleotidyl transferase activity. Immunostaining analysis revealed that CcPollambda was present at meiotic prophase nuclei in zygotene and pachytene cells, which is the period when homologous chromosomes pair and recombine. CcPolmicro was present in a slightly wider range of cell stages, zygotene to diplotene. In analyses using D-loop recombination intermediate substrates, we found that both CcPollambda and CcPolmicro could promote primer extension of an invading strand in a D-loop structure. Moreover, both polymerases could fully extend the primer in the D-loop substrate, suggesting that D-loop extension is an activity intrinsic to CcPollambda and CcPolmicro. Based on these data, we discuss the possible roles of these polymerases in meiosis.

  4. A DNA microarray for the detection of point mutations and copy number variation causing familial hypercholesterolemia in Europe

    NARCIS (Netherlands)

    Stef, Marianne A.; Palacios, Lourdes; Olano-Martín, Estibaliz; Foe-A-Man, Carolyn; van de Kerkhof, Laura; Klaaijsen, Lisette N.; Molano, Araitz; Schuurman, Ellen J.; Tejedor, Diego; Defesche, Joep C.

    2013-01-01

    To facilitate genetic cascade screening for familial hypercholesterolemia (FH) in Europe, two versions (7 and 9) of a DNA microarray were developed to detect the most frequent point mutations in the low-density lipoprotein receptor (LDLR), apolipoprotein B (APOB), and proprotein convertase

  5. Genome-wide identification and comparative analysis of cytosine-5 DNA methyltransferases and demethylase families in wild and cultivated peanut

    Directory of Open Access Journals (Sweden)

    Pengfei eWang

    2016-02-01

    Full Text Available AbstractDNA methylation plays important roles in genome protection, regulation of gene expression and was associated with plants development. Plant DNA methylation pattern was mediated by cytosine-5 DNA methyltransferases and demethylase. Although the genomes of AA and BB wild peanuts have been fully sequence, these two gene families have not been studied. In this study we report the identification and analysis of putative cytosine-5 DNA methyltransferases (C5-MTases and demethylase in AA and BB wild peanuts. Cytosine-5 DNA methyltransferases in AA and BB wild peanuts could be classified in known MET, CMT and DRM2 groups based on their domain organization. This result was supported by the gene and protein structural characteristics and phylogenetic analysis. We found that some wild peanut DRM2 numbers didn’t contain UBA domain which was different from other plants such as Arabidopsis, maize, soybean. Five DNA demethylase were found in AA genome and five in BB genome. The selective pressure analysis showed that wild peanut C5-MTases gene mainly underwent purifying selection but many positive selection sites can be detected. Conversely, DNA demethylase genes mainly underwent positive selection during evolution. Additionally, the expression dynamic of cytosine-5 DNA methyltransferases and demethylase genes in different cultivated peanut tissues were analyzed. Expression result showed that cold, heat or drought stress could influence the expression level of C5-MTases and DNA demethylase genes in cultivated peanut. These results are useful for better understanding the complexity of these two gene families, and will facilitate epigenetic studies in peanut.

  6. Comparative molecular phylogeny and evolution of sex chromosome DNA sequences in the family Canidae (Mammalia: Carnivora).

    Science.gov (United States)

    Tsubouchi, Ayako; Fukui, Daisuke; Ueda, Miya; Tada, Kazumi; Toyoshima, Shouji; Takami, Kazutoshi; Tsujimoto, Tsunenori; Uraguchi, Kohji; Raichev, Evgeniy; Kaneko, Yayoi; Tsunoda, Hiroshi; Masuda, Ryuichi

    2012-03-01

    To investigate the molecular phylogeny and evolution of the family Canidae, nucleotide sequences of the zinc-finger-protein gene on the Y chromosome (ZFY, 924-1146 bp) and its homologous gene on the X chromosome (ZFX, 834-839 bp) for twelve canid species were determined. The phylogenetic relationships among species reconstructed by the paternal ZFY sequences closely agreed with those by mtDNA and autosomal DNA trees in previous reports, and strongly supported the phylogenetic affinity between the wolf-like canids clade and the South American canids clade. However, the branching order of some species differed between phylogenies of ZFY and ZFX genes: Cuon alpinus and Canis mesomelas were included in the wolf-like canid clades in the ZFY tree, whereas both species were clustered in a group of Chrysocyon brachyurus and Speothos venaticus in the ZFX tree. The topology difference between ZFY and ZFX trees may have resulted from the two-times higher substitution rate of the former than the latter, which was clarified in the present study. In addition, two types of transposable element sequence (SINE-I and SINE-II) were found to occur in the ZFY final intron of the twelve canid species examined. Because the SINE-I sequences were shared by all the species, they may have been inserted into the ZFY of the common ancestor before species radiation in Canidae. By contract, SINE-II found in only Canis aureus could have been inserted into ZFY independently after the speciation. The molecular diversity of SINE sequences of Canidae reflects evolutionary history of the species radiation.

  7. Characterization of family IV UDG from Aeropyrum pernix and its application in hot-start PCR by family B DNA polymerase.

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    Xi-Peng Liu

    Full Text Available Recombinant uracil-DNA glycosylase (UDG from Aeropyrum pernix (A. pernix was expressed in E. coli. The biochemical characteristics of A. pernix UDG (ApeUDG were studied using oligonucleotides carrying a deoxyuracil (dU base. The optimal temperature range and pH value for dU removal by ApeUDG were 55-65°C and pH 9.0, respectively. The removal of dU was inhibited by the divalent ions of Zn, Cu, Co, Ni, and Mn, as well as a high concentration of NaCl. The opposite base in the complementary strand affected the dU removal by ApeUDG as follows: U/C≈U/G>U/T≈U/AP≈U/->U/U≈U/I>U/A. The phosphorothioate around dU strongly inhibited dU removal by ApeUDG. Based on the above biochemical characteristics and the conservation of amino acid residues, ApeUDG was determined to belong to the IV UDG family. ApeUDG increased the yield of PCR by Pfu DNA polymerase via the removal of dU in amplified DNA. Using the dU-carrying oligonucleotide as an inhibitor and ApeUDG as an activator of Pfu DNA polymerase, the yield of undesired DNA fragments, such as primer-dimer, was significantly decreased, and the yield of the PCR target fragment was increased. This strategy, which aims to amplify the target gene with high specificity and yield, can be applied to all family B DNA polymerases.

  8. Characterization of family IV UDG from Aeropyrum pernix and its application in hot-start PCR by family B DNA polymerase.

    Science.gov (United States)

    Liu, Xi-Peng; Liu, Jian-Hua

    2011-01-01

    Recombinant uracil-DNA glycosylase (UDG) from Aeropyrum pernix (A. pernix) was expressed in E. coli. The biochemical characteristics of A. pernix UDG (ApeUDG) were studied using oligonucleotides carrying a deoxyuracil (dU) base. The optimal temperature range and pH value for dU removal by ApeUDG were 55-65°C and pH 9.0, respectively. The removal of dU was inhibited by the divalent ions of Zn, Cu, Co, Ni, and Mn, as well as a high concentration of NaCl. The opposite base in the complementary strand affected the dU removal by ApeUDG as follows: U/C≈U/G>U/T≈U/AP≈U/->U/U≈U/I>U/A. The phosphorothioate around dU strongly inhibited dU removal by ApeUDG. Based on the above biochemical characteristics and the conservation of amino acid residues, ApeUDG was determined to belong to the IV UDG family. ApeUDG increased the yield of PCR by Pfu DNA polymerase via the removal of dU in amplified DNA. Using the dU-carrying oligonucleotide as an inhibitor and ApeUDG as an activator of Pfu DNA polymerase, the yield of undesired DNA fragments, such as primer-dimer, was significantly decreased, and the yield of the PCR target fragment was increased. This strategy, which aims to amplify the target gene with high specificity and yield, can be applied to all family B DNA polymerases.

  9. The DnaJ Gene Family in Pepper (Capsicum annuum L.: Comprehensive Identification, Characterization and Expression Profiles

    Directory of Open Access Journals (Sweden)

    Yunyan Kang

    2017-05-01

    Full Text Available The DnaJ proteins which function as molecular chaperone played critical roles in plant growth and development and response to heat stress (HS and also called heat shock protein 40 based on molecular weight. However, little was reported on this gene family in pepper. Recently, the release of the whole pepper genome provided an opportunity for identifying putative DnaJ homologous. In this study, a total of 76 putative pepper DnaJ genes (CaDnaJ01 to CaDnaJ76 were identified using bioinformatics methods and classified into five groups by the presence of the complete three domains (J-domain, zinc finger domain, and C-terminal domain. Chromosome mapping suggested that segmental duplication and tandem duplication were occurred in evolution. The multiple stress-related cis-elements were found in the promoter region of these CaDnaJ genes, which indicated that the CaDnaJs might be involved in the process of responding to complex stress conditions. In addition, expression profiles based on RNA-seq showed that the 47 CaDnaJs were expressed in at least one tissue tested. The result implied that they could be involved in the process of pepper growth and development. qRT-PCR analysis found that 80.60% (54/67 CaDnaJs were induced by HS, indicated that they could participated in pepper response to high temperature treatments. In conclusion, all these results would provide a comprehensive basis for further analyzing the function of CaDnaJ members and be also significant for elucidating the evolutionary relationship in pepper.

  10. The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA.

    Science.gov (United States)

    Nakane, Shuhei; Ishikawa, Hirohito; Nakagawa, Noriko; Kuramitsu, Seiki; Masui, Ryoji

    2012-03-30

    DNA with single-nucleotide (1-nt) gaps can arise during various DNA processing events. These lesions are repaired by X-family DNA polymerases (PolXs) with high gap-filling activity. Some PolXs can bind productively to dNTPs in the absence of DNA and fill these 1-nt gaps. Although PolXs have a crucial role in efficient gap filling, currently, little is known of the kinetic and structural details of their productive dNTP binding. Here, we show that Thermus thermophilus HB8 PolX (ttPolX) had strong binding affinity for Mg(2+)-dNTPs in the absence of DNA and that it follows a Theorell-Chance (hit-and-run) mechanism with nucleotide binding first. Comparison of the intermediate crystal structures of ttPolX in a binary complex with dGTP and in a ternary complex with 1-nt gapped DNA and Mg(2+)-ddGTP revealed that the conformation of the incoming nucleotide depended on whether or not DNA was present. Furthermore, the Lys263 residue located between two guanosine conformations was essential to the strong binding affinity of the enzyme. The ability to bind to either syn-dNTP or anti-dNTP and the involvement of a Theorell-Chance mechanism are key aspects of the strong nucleotide-binding and efficient gap-filling activities of ttPolX. Copyright © 2012 Elsevier Ltd. All rights reserved.

  11. Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions

    Science.gov (United States)

    Kocman, Vojč; Plavec, Janez

    2017-05-01

    Here we describe AGCGA-quadruplexes, an unexpected addition to the well-known tetrahelical families, G-quadruplexes and i-motifs, that have been a focus of intense research due to their potential biological impact in G- and C-rich DNA regions, respectively. High-resolution structures determined by solution-state nuclear magnetic resonance (NMR) spectroscopy demonstrate that AGCGA-quadruplexes comprise four 5'-AGCGA-3' tracts and are stabilized by G-A and G-C base pairs forming GAGA- and GCGC-quartets, respectively. Residues in the core of the structure are connected with edge-type loops. Sequences of alternating 5'-AGCGA-3' and 5'-GGG-3' repeats could be expected to form G-quadruplexes, but are shown herein to form AGCGA-quadruplexes instead. Unique structural features of AGCGA-quadruplexes together with lower sensitivity to cation and pH variation imply their potential biological relevance in regulatory regions of genes responsible for basic cellular processes that are related to neurological disorders, cancer and abnormalities in bone and cartilage development.

  12. Using DNA-barcoding to make the necrobiont beetle family Cholevidae accessible for forensic entomology.

    Science.gov (United States)

    Schilthuizen, Menno; Scholte, Cindy; van Wijk, Renske E J; Dommershuijzen, Jessy; van der Horst, Devi; Zu Schlochtern, Melanie Meijer; Lievers, Rik; Groenenberg, Dick S J

    2011-07-15

    The beetle family Cholevidae (Coleoptera: Staphylinoidea), sometimes viewed as the subfamily Cholevinae of the Leiodidae, consists of some 1700 species worldwide. With the exception of specialized cave-dwelling species and species living in bird and mammal nests and burrows, the species are generalized soil-dwellers that, at least in temperate regions, are mostly found on vertebrate cadavers. Although they have been regularly reported from human corpses, and offer potential because of many species' peak activity in the cold season, they have not been a focus of forensic entomologists so far. This is probably due to their small size and the difficulty in identifying the adults and their larvae. In this paper, we show that DNA-barcoding can help make this group of necrobiont beetles available as a tool for forensic research. We collected 86 specimens of 20 species of the genera Catops, Fissocatops, Apocatops, Choleva, Nargus, Ptomaphagus, and Sciodrepoides from the Netherlands and France and show that a broad "barcoding gap" allows almost all species to be easily and unambiguously identified by the sequence of the "barcoding gene" cytochrome c oxidase I (COI). This opens up the possibility of adding Cholevidae to the set of insect taxa routinely used in forensic entomology. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  13. Mutation in cytochrome b gene of mitochondrial DNA in a family with fibromyalgia is associated with NLRP3-inflammasome activation.

    Science.gov (United States)

    Cordero, Mario D; Alcocer-Gómez, Elísabet; Marín-Aguilar, Fabiola; Rybkina, Tatyana; Cotán, David; Pérez-Pulido, Antonio; Alvarez-Suarez, José Miguel; Battino, Maurizio; Sánchez-Alcazar, José Antonio; Carrión, Angel M; Culic, Ognjen; Navarro-Pando, José M; Bullón, Pedro

    2016-02-01

    Fibromyalgia (FM) is a worldwide diffuse musculoskeletal chronic pain condition that affects up to 5% of the general population. Many symptoms associated with mitochondrial diseases are reported in patients with FM such as exercise intolerance, fatigue, myopathy and mitochondrial dysfunction. In this study, we report a mutation in cytochrome b gene of mitochondrial DNA (mtDNA) in a family with FM with inflammasome complex activation. mtDNA from blood cells of five patients with FM were sequenced. We clinically and genetically characterised a patient with FM and family with a new mutation in mtCYB. Mitochondrial mutation phenotypes were determined in skin fibroblasts and transmitochondrial cybrids. After mtDNA sequence in patients with FM, we found a mitochondrial homoplasmic mutation m.15804T>C in the mtCYB gene in a patient and family, which was maternally transmitted. Mutation was observed in several tissues and skin fibroblasts showed a very significant mitochondrial dysfunction and oxidative stress. Increased NLRP3-inflammasome complex activation was observed in blood cells from patient and family. We propose further studies on mtDNA sequence analysis in patients with FM with evidences for maternal inheritance. The presence of similar symptoms in mitochondrial myopathies could unmask mitochondrial diseases among patients with FM. On the other hand, the inflammasome complex activation by mitochondrial dysfunction could be implicated in the pathophysiology of mitochondrial diseases. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  14. Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation.

    Science.gov (United States)

    Velazquez Camacho, Oscar; Galan, Carmen; Swist-Rosowska, Kalina; Ching, Reagan; Gamalinda, Michael; Karabiber, Fethullah; De La Rosa-Velazquez, Inti; Engist, Bettina; Koschorz, Birgit; Shukeir, Nicholas; Onishi-Seebacher, Megumi; van de Nobelen, Suzanne; Jenuwein, Thomas

    2017-08-01

    The Suv39h1 and Suv39h2 histone lysine methyltransferases are hallmark enzymes at mammalian heterochromatin. We show here that the mouse Suv39h2 enzyme differs from Suv39h1 by containing an N-terminal basic domain that facilitates retention at mitotic chromatin and provides an additional affinity for major satellite repeat RNA. To analyze an RNA-dependent interaction with chromatin, we purified native nucleosomes from mouse ES cells and detect that Suv39h1 and Suv39h2 exclusively associate with poly-nucleosomes. This association was attenuated upon RNaseH incubation and entirely lost upon RNaseA digestion of native chromatin. Major satellite repeat transcripts remain chromatin-associated and have a secondary structure that favors RNA:DNA hybrid formation. Together, these data reveal an RNA-mediated mechanism for the stable chromatin interaction of the Suv39h KMT and suggest a function for major satellite non-coding RNA in the organization of an RNA-nucleosome scaffold as the underlying structure of mouse heterochromatin.

  15. A C-terminal Myb extension domain defines a novel family of double-strand telomeric DNA-binding proteins in Arabidopsis.

    Science.gov (United States)

    Karamysheva, Zemfira N; Surovtseva, Yulia V; Vespa, Laurent; Shakirov, Eugene V; Shippen, Dorothy E

    2004-11-12

    Little is known about the protein composition of plant telomeres. We queried the Arabidopsis thaliana genome data base in search of genes with similarity to the human telomere proteins hTRF1 and hTRF2. hTRF1/hTRF2 are distinguished by the presence of a single Myb-like domain in their C terminus that is required for telomeric DNA binding in vitro. Twelve Arabidopsis genes fitting this criterion, dubbed TRF-like (TRFL), fell into two distinct gene families. Notably, TRFL family 1 possessed a highly conserved region C-terminal to the Myb domain called Myb-extension (Myb-ext) that is absent in TRFL family 2 and hTRF1/hTRF2. Immunoprecipitation experiments revealed that recombinant proteins from TRFL family 1, but not those from family 2, formed homodimers and heterodimers in vitro. DNA binding studies with isolated C-terminal fragments from TRFL family 1 proteins, but not family 2, showed specific binding to double-stranded plant telomeric DNA in vitro. Removal of the Myb-ext domain from TRFL1, a family 1 member, abolished DNA binding. However, when the Myb-ext domain was introduced into the corresponding region in TRFL3, a family 2 member, telomeric DNA binding was observed. Thus, Myb-ext is required for binding plant telomeric DNA and defines a novel class of proteins in Arabidopsis.

  16. Distribution of cytotoxic and DNA ADP-ribosylating activity in crude extracts from butterflies among the family Pieridae

    Science.gov (United States)

    Matsumoto, Yasuko; Nakano, Tsuyoshi; Yamamoto, Masafumi; Matsushima-Hibiya, Yuko; Odagiri, Ken-Ichi; Yata, Osamu; Koyama, Kotaro; Sugimura, Takashi; Wakabayashi, Keiji

    2008-01-01

    Cabbage butterflies, Pieris rapae and Pieris brassicae, contain strong cytotoxic proteins, designated as pierisin-1 and -2, against cancer cell lines. These proteins exhibit DNA ADP-ribosylating activity. To determine the distribution of substances with cytotoxicity and DNA ADP-ribosylating activity among other species, crude extracts from 20 species of the family Pieridae were examined for cytotoxicity in HeLa cells and DNA ADP-ribosylating activity. Both activities were detected in extracts from 13 species: subtribes Pierina (Pieris rapae, Pieris canidia, Pieris napi, Pieris melete, Pieris brassicae, Pontia daplidice, and Talbotia naganum), Aporiina (Aporia gigantea, Aporia crataegi, Aporia hippia, and Delias pasithoe), and Appiadina (Appias nero and Appias paulina). All of these extracts contained substances recognized by anti-pierisin-1 antibodies, with a molecular mass of ≈100 kDa established earlier for pierisin-1. Moreover, sequences containing NAD-binding sites, conserved in ADP-ribosyltransferases, were amplified from genomic DNA from 13 species of butterflies with cytotoxicity and DNA ADP-ribosylating activity by PCR. Extracts from seven species, Appias lyncida, Leptosia nina, Anthocharis scolymus, Eurema hecabe, Catopsilia pomona, Catopsilia scylla, and Colias erate, showed neither cytotoxicity nor DNA ADP-ribosylating activity, and did not contain substances recognized by anti-pierisin-1 antibodies. Sequences containing NAD-binding sites were not amplified from genomic DNA from these seven species. Thus, pierisin-like proteins, showing cytotoxicity and DNA ADP-ribosylating activity, are suggested to be present in the extracts from butterflies not only among the subtribe Pierina, but also among the subtribes Aporiina and Appiadina. These findings offer insight to understanding the nature of DNA ADP-ribosylating activity in the butterfly. PMID:18256183

  17. Use of DNA profiles for investigation using a simulated national DNA database: Part II. Statistical and ethical considerations on familial searching.

    Science.gov (United States)

    Hicks, T; Taroni, F; Curran, J; Buckleton, J; Castella, V; Ribaux, O

    2010-10-01

    Familial searching consists of searching for a full profile left at a crime scene in a National DNA Database (NDNAD). In this paper we are interested in the circumstance where no full match is returned, but a partial match is found between a database member's profile and the crime stain. Because close relatives share more of their DNA than unrelated persons, this partial match may indicate that the crime stain was left by a close relative of the person with whom the partial match was found. This approach has successfully solved important crimes in the UK and the USA. In a previous paper, a model, which takes into account substructure and siblings, was used to simulate a NDNAD. In this paper, we have used this model to test the usefulness of familial searching and offer guidelines for pre-assessment of the cases based on the likelihood ratio. Siblings of "persons" present in the simulated Swiss NDNAD were created. These profiles (N=10,000) were used as traces and were then compared to the whole database (N=100,000). The statistical results obtained show that the technique has great potential confirming the findings of previous studies. However, effectiveness of the technique is only one part of the story. Familial searching has juridical and ethical aspects that should not be ignored. In Switzerland for example, there are no specific guidelines to the legality or otherwise of familial searching. This article both presents statistical results, and addresses criminological and civil liberties aspects to take into account risks and benefits of familial searching. Copyright © 2009 Elsevier Ireland Ltd. All rights reserved.

  18. Genome wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/EXK nuclease family protein HVO_A0006

    Directory of Open Access Journals (Sweden)

    Matthew eOuellette

    2015-04-01

    Full Text Available Restriction-modification (RM systems have evolved to protect the cell from invading DNAs and are composed of two enzymes: a DNA methyltransferase and a restriction endonuclease. Although RM systems are present in both archaeal and bacterial genomes, DNA methylation in archaea has not been well defined. In order to characterize the function of RM systems in archaeal species, we have made use of the model haloarchaeon Haloferax volcanii. A genomic DNA methylation analysis of H. volcanii strain H26 was performed using PacBio single molecule real-time (SMRT sequencing. This analysis was also performed on a strain of H. volcanii in which an annotated DNA methyltransferase gene HVO_A0006 was deleted from the genome. Sequence analysis of H26 revealed two motifs which are modified in the genome: Cm4TAG and GCAm6BN6VTGC. Analysis of the ∆HVO_A0006 strain indicated that it exhibited reduced adenine methylation compared to the parental strain and altered the detected adenine motif. However, protein domain architecture analysis and amino acid alignments revealed that HVO_A0006 is homologous only to the N-terminal endonuclease region of Type IIG RM proteins and contains a PD-(D/EXK nuclease motif, suggesting that HVO_A0006 is a PD-(D/EXK nuclease family protein. Further bioinformatic analysis of the HVO_A0006 gene demonstrating that the gene is rare among the Halobacteria. It is surrounded by two transposition genes suggesting that HVO_A0006 is a fragment of a Type IIG RM gene, which has likely been acquired through gene transfer, and affects restriction-modification activity by interacting with another RM system component(s. Here, we present the first genome-wide characterization of DNA methylation in an archaeal species and examine the function of a DNA methyltransferase related gene HVO_A0006.

  19. Segregation pattern and biochemical effect of the G3460A mtDNA mutation in 27 members of LHON family.

    Science.gov (United States)

    Kaplanová, Vilma; Zeman, Jirí; Hansíková, Hana; Cerná, Leona; Houst'ková, Hana; Misovicová, Nadezda; Houstek, Josef

    2004-08-30

    Inheritance and expression of mitochondrial DNA (mtDNA) mutations are crucial for the pathogenesis of Leber hereditary optic neuropathy (LHON). We have investigated the segregation and functional consequences of G3460A mtDNA mutation in 27 members of a three-generation family with LHON syndrome. Specific activity of respiratory chain complex I in platelets was reduced in average to 56%, but no direct correlation between the mutation load and its biochemical expression was found. Heteroplasmy in blood, platelets and hair follicles varied from 7% to 100%. Segregation pattern exhibited tissue specificity and influence of different nuclear backgrounds in four branches of the pedigree. Longitudinal analysis revealed a significant (p=0.02) decrease in blood mutation load. Although enzyme assay showed reduction of complex I activity, our results give additional support to the hypothesis that expression of LHON mutation depends on complex nuclear-mitochondrial interaction.

  20. Detection of common sequence variations of familial hypercholesterolemia in Taiwan using DNA mass spectrometry.

    Science.gov (United States)

    Chiou, Kuan-Rau; Charng, Min-Ji

    Familial hypercholesterolemia (FH) is a heterogeneous autosomal dominant disease. The genetic heterogeneity of FH requires low-cost, high-throughput, and rapid mutation detection technology to efficiently integrate genetic screening into clinical practice. The aims of the study were to customize the MassARRAY assay to (1) establish an FH mutation assay panel, comprising known point mutations located on FH-causing genes and (2) test the feasibility of the assay for screening FH patients residing in Taiwan who fit the clinical criteria of FH diagnosis. We designed a custom Agena iPLEX assay to detect 68 point mutations on FH-causing genes. First, the assay performance was verified by analyzing 180 previously sequenced subjects (120 with point mutations and 60 healthy controls), with the results being compared with those of Sanger DNA sequencing. Second, a blind study was carried out on 185 FH probands (44 definite FH and 141 probable/possible FH). In the first part of this study, only 1 discrepancy was found between the Agena iPLEX and Sanger sequencing genotyping results. In the blind study, a total of 62 probands with mutations were identified by both techniques. Five mutations were detected by Sanger sequencing assay only. The detection sensitivity and specificity rates of Agena iPLEX were 92.5% and 100%, respectively, in the blind study. The hands-on time for the Agena iPLEX assay was around 1 day. The custom-designed Agena iPLEX assay has high specificity and sensitivity for FH genetic screening. Considering its low cost, rapidity, and flexibility, the assay has great potential to be incorporated into FH screening in Taiwan. Copyright © 2017 National Lipid Association. Published by Elsevier Inc. All rights reserved.

  1. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.

    Directory of Open Access Journals (Sweden)

    Jason Gertz

    2011-08-01

    Full Text Available The methylation of cytosines in CpG dinucleotides is essential for cellular differentiation and the progression of many cancers, and it plays an important role in gametic imprinting. To assess variation and inheritance of genome-wide patterns of DNA methylation simultaneously in humans, we applied reduced representation bisulfite sequencing (RRBS to somatic DNA from six members of a three-generation family. We observed that 8.1% of heterozygous SNPs are associated with differential methylation in cis, which provides a robust signature for Mendelian transmission and relatedness. The vast majority of differential methylation between homologous chromosomes (>92% occurs on a particular haplotype as opposed to being associated with the gender of the parent of origin, indicating that genotype affects DNA methylation of far more loci than does gametic imprinting. We found that 75% of genotype-dependent differential methylation events in the family are also seen in unrelated individuals and that overall genotype can explain 80% of the variation in DNA methylation. These events are under-represented in CpG islands, enriched in intergenic regions, and located in regions of low evolutionary conservation. Even though they are generally not in functionally constrained regions, 22% (twice as many as expected by chance of genes harboring genotype-dependent DNA methylation exhibited allele-specific gene expression as measured by RNA-seq of a lymphoblastoid cell line, indicating that some of these events are associated with gene expression differences. Overall, our results demonstrate that the influence of genotype on patterns of DNA methylation is widespread in the genome and greatly exceeds the influence of imprinting on genome-wide methylation patterns.

  2. Variants of sequence family B Thermococcus kodakaraensis DNA polymerase with increased mismatch extension selectivity.

    Directory of Open Access Journals (Sweden)

    Claudia Huber

    Full Text Available Fidelity and selectivity of DNA polymerases are critical determinants for the biology of life, as well as important tools for biotechnological applications. DNA polymerases catalyze the formation of DNA strands by adding deoxynucleotides to a primer, which is complementarily bound to a template. To ensure the integrity of the genome, DNA polymerases select the correct nucleotide and further extend the nascent DNA strand. Thus, DNA polymerase fidelity is pivotal for ensuring that cells can replicate their genome with minimal error. DNA polymerases are, however, further optimized for more specific biotechnological or diagnostic applications. Here we report on the semi-rational design of mutant libraries derived by saturation mutagenesis at single sites of a 3'-5'-exonuclease deficient variant of Thermococcus kodakaraensis DNA polymerase (KOD pol and the discovery for variants with enhanced mismatch extension selectivity by screening. Sites of potential interest for saturation mutagenesis were selected by their proximity to primer or template strands. The resulting libraries were screened via quantitative real-time PCR. We identified three variants with single amino acid exchanges-R501C, R606Q, and R606W-which exhibited increased mismatch extension selectivity. These variants were further characterized towards their potential in mismatch discrimination. Additionally, the identified enzymes were also able to differentiate between cytosine and 5-methylcytosine. Our results demonstrate the potential in characterizing and developing DNA polymerases for specific PCR based applications in DNA biotechnology and diagnostics.

  3. A Naturally Occurring Defective DNA Satellite Associated with a Monopartite Begomovirus: Evidence for Recombination between Alphasatellite and Betasatellite

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    Zhenghe Li

    2013-09-01

    Full Text Available Monopartite begomoviruses and their associated satellites form unique disease complexes that have emerged as a serious threat to agriculture worldwide. It is well known that frequent recombination contributes to the diversification and evolution of geminiviruses. In this study, we identified a novel defective satellite molecule (RecSat in association with Tobacco leaf curl Yunnan virus (TbLCYNV in a naturally infected tobacco plant. Sequence analysis showed that Recsat comprises 754 nucleotides in size and is a chimera involving alphasatellite and betasatellite sequences, containing both betasatellite-conserved region and alphasatellite stem-loop structure. Recombination analysis revealed that RecSat has arisen from three independent recombination events likely involving Tomato yellow leaf curl China betasatellite, Ageratum yellow vein China betasatellite and Tobacco curly shoot alphasatellite. Co-inoculation of RecSat with TbLCYNV induced symptoms indistinguishable from those induced by TbLCYNV alone in Nicotiana benthamiana. Southern blot hybridization showed that RecSat could be trans-replicated stably in N. benthamiana plants by TbLCYNV, and impaired the accumulation of helper virus and co-inoculated alphasatellite. Our results provide the first evidence for recombination between two distinct types of satellites among geminivirus complex and highlight recombination as a driving force for geminivirus evolution.

  4. Regulation of the DNA Methylation Landscape in Human Somatic Cell Reprogramming by the miR-29 Family

    Directory of Open Access Journals (Sweden)

    Eriona Hysolli

    2016-07-01

    Full Text Available Reprogramming to pluripotency after overexpression of OCT4, SOX2, KLF4, and MYC is accompanied by global genomic and epigenomic changes. Histone modification and DNA methylation states in induced pluripotent stem cells (iPSCs have been shown to be highly similar to embryonic stem cells (ESCs. However, epigenetic differences still exist between iPSCs and ESCs. In particular, aberrant DNA methylation states found in iPSCs are a major concern when using iPSCs in a clinical setting. Thus, it is critical to find factors that regulate DNA methylation states in reprogramming. Here, we found that the miR-29 family is an important epigenetic regulator during human somatic cell reprogramming. Our global DNA methylation and hydroxymethylation analysis shows that DNA demethylation is a major event mediated by miR-29a depletion during early reprogramming, and that iPSCs derived from miR-29a depletion are epigenetically closer to ESCs. Our findings uncover an important miRNA-based approach to generate clinically robust iPSCs.

  5. Domain Structures and Inter-Domain Interactions Defining the Holoenzyme Architecture of Archaeal D-Family DNA Polymerase

    Directory of Open Access Journals (Sweden)

    Hideshi Yokoyama

    2013-07-01

    Full Text Available Archaea-specific D-family DNA polymerase (PolD forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain topology of the PolD holoenzyme is proposed. The experimental evidence supports various aspects of the model. The conserved amphipathic nature of the N-terminal putative α-helix of the large subunit plays a key role in the homodimeric assembly and the self-cyclization of the large subunit and is deeply involved in the archaeal PolD stability and activity. We also discuss the evolutional transformation from archaeal D-family to eukaryotic B-family polymerase on the basis of the structural information.

  6. Domain structures and inter-domain interactions defining the holoenzyme architecture of archaeal d-family DNA polymerase.

    Science.gov (United States)

    Matsui, Ikuo; Matsui, Eriko; Yamasaki, Kazuhiko; Yokoyama, Hideshi

    2013-07-05

    Archaea-specific D-family DNA polymerase (PolD) forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain topology of the PolD holoenzyme is proposed. The experimental evidence supports various aspects of the model. The conserved amphipathic nature of the N-terminal putative α-helix of the large subunit plays a key role in the homodimeric assembly and the self-cyclization of the large subunit and is deeply involved in the archaeal PolD stability and activity. We also discuss the evolutional transformation from archaeal D-family to eukaryotic B-family polymerase on the basis of the structural information.

  7. Mitochondrial DNA mutations distinguish bilateral multifocal renal oncocytomas from familial Birt-Hogg-Dubé tumors

    Science.gov (United States)

    Lang, Martin; Vocke, Cathy D.; Merino, Maria J.; Schmidt, Laura S.; Linehan, W. Marston

    2015-01-01

    Oncocytomas are mostly benign tumors characterized by accumulation of defective mitochondria, and in sporadic cases, are associated with disruptive mitochondrial DNA (mtDNA) mutations. However, the role mtDNA mutations play in renal tumors of Birt-Hogg-Dubé (BHD) patients and other renal oncocytomas with an apparent genetic component has not been investigated to date. Here we characterize the mitochondrial genome in different renal tumors and investigate the possibility of employing mtDNA sequencing analyses of biopsy specimens to aid in the differential diagnosis of oncocytomas. The entire mitochondrial genome was sequenced in 25 samples of bilateral and multifocal (BMF) renal oncocytomas, 30 renal tumors from BHD patients and 36 non-oncocytic renal tumors of different histologies as well as in biopsy samples of kidney tumors. mtDNA sequencing in BMF oncocytomas revealed that all tumors carry disruptive mutations, which impair the assembly of the NADH-ubiquinone oxidoreductase. Multiple tumors from a given BMF oncocytoma patient mainly harbor the same somatic mutation and the kidneys of these patients display diffuse oncocytosis. In contrast, renal oncocytomas of patients with BHD syndrome and renal tumors with different histologies do not show disruptive mtDNA mutations. Moreover, we demonstrate that it is feasible to amplify and sequence the entire mtDNA in biopsy specimens, and that these sequences are representative of the tumor DNA. These results show that pathogenic mtDNA mutations affecting complex I of the respiratory chain are strongly correlated with the oncocytoma phenotype in non-BHD-related renal tumors and that mtDNA sequences from biopsies are predictive of the tumor genotype. This work supports a role for mtDNA mutations in respiratory chain complexes as diagnostic markers for renal oncocytomas. PMID:26428318

  8. Human circulating ribosomal DNA content significantly increases while circulating satellite III (1q12) content decreases under chronic occupational exposure to low-dose gamma- neutron and tritium beta-radiation.

    Science.gov (United States)

    Korzeneva, Inna B; Kostuyk, Svetlana V; Ershova, Elizaveta S; Skorodumova, Elena N; Zhuravleva, Veronika F; Pankratova, Galina V; Volkova, Irina V; Stepanova, Elena V; Porokhovnik, Lev N; Veiko, Natalia N

    A single exposure to ionizing radiation (IR) results in an elevated cell-free DNA (cfDNA) content in the blood plasma. In this case, the cfDNA concentration can be a marker of the cell death in the organism. However, a chronic exposure to a low-dose IR enhances both the endonuclease activity and titer of antibodies to DNA in blood plasma, resulting in a decrease of the total concentration of circulating cfDNA in exposed people. In this case, the total cfDNA concentration should not be considered as a marker of the cell death in an exposed body. We assumed that a pool of the cfDNA circulating in the exposed people contains DNA fragments, which are resistant to a double-strand break formation in the environment of the elevated plasma endonuclease activity, and can be accumulated in the blood plasma. In order to test this hypothesis, we studied the content of GC-rich sequences (69%GC) of the transcribed region of human ribosomal repeat (rDNA), as well as the content of AT-rich repeat (63%AT) of satellite III (1q12) in the cfDNA samples obtained from 285 individuals. We have found that a chronic exposure to gamma-neutron radiation (N=88) and tritium β-radiation (N=88) evokes an increase of the rDNA content (RrDNA index) and a decrease of the satellite III content (RsatIII index) in the circulating cfDNA as compared with the cfDNA of non-exposed people (N=109). Such index that simultaneously displays both the increase of rDNA content and decrease of satellite III content in the cfDNA (RrDNA/RsatIII) can be recommended as a marker of chronic processes in the body that involve the elevated cell death rate and/or increased blood plasma endonuclease activity. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. When molecules support morphology: Phylogenetic reconstruction of the family Onuphidae (Eunicida, Annelida) based on 16S rDNA and 18S rDNA.

    Science.gov (United States)

    Budaeva, Nataliya; Schepetov, Dmitry; Zanol, Joana; Neretina, Tatiana; Willassen, Endre

    2016-01-01

    Onuphid polychaetes are tubicolous marine worms commonly reported worldwide from intertidal areas to hadal depths. They often dominate in benthic communities and have economic importance in aquaculture and recreational fishing. Here we report the phylogeny of the family Onuphidae based on the combined analyses of nuclear (18S rDNA) and mitochondrial (16S rDNA) genes. Results of Bayesian and Maximum Likelihood analyses supported the monophyly of Onuphidae and its traditional subdivision into two monophyletic subfamilies: Onuphinae and Hyalinoeciinae. Ten of 22 recognized genera were monophyletic with strong node support; four more genera included in this study were either monotypic or represented by a single species. None of the genera appeared para- or polyphyletic and this indicates a strong congruence between the traditional morphology-based systematics of the family and the newly obtained molecular-based phylogenetic reconstructions. Intergeneric relationships within Hyalinoeciinae were not resolved. Two strongly supported monophyletic groups of genera were recovered within Onuphinae: ((Onuphis, Aponuphis), Diopatra, Paradiopatra) and (Hirsutonuphis, (Paxtonia, (Kinbergonuphis, Mooreonuphis))). A previously accepted hypothesis on the subdivision of Onuphinae into the Onuphis group of genera and the Diopatra group of genera was largely rejected. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  10. The Toll-like receptor gene family is integrated into human DNA damage and p53 networks.

    Directory of Open Access Journals (Sweden)

    Daniel Menendez

    2011-03-01

    Full Text Available In recent years the functions that the p53 tumor suppressor plays in human biology have been greatly extended beyond "guardian of the genome." Our studies of promoter response element sequences targeted by the p53 master regulatory transcription factor suggest a general role for this DNA damage and stress-responsive regulator in the control of human Toll-like receptor (TLR gene expression. The TLR gene family mediates innate immunity to a wide variety of pathogenic threats through recognition of conserved pathogen-associated molecular motifs. Using primary human immune cells, we have examined expression of the entire TLR gene family following exposure to anti-cancer agents that induce the p53 network. Expression of all TLR genes, TLR1 to TLR10, in blood lymphocytes and alveolar macrophages from healthy volunteers can be induced by DNA metabolic stressors. However, there is considerable inter-individual variability. Most of the TLR genes respond to p53 via canonical as well as noncanonical promoter binding sites. Importantly, the integration of the TLR gene family into the p53 network is unique to primates, a recurrent theme raised for other gene families in our previous studies. Furthermore, a polymorphism in a TLR8 response element provides the first human example of a p53 target sequence specifically responsible for endogenous gene induction. These findings-demonstrating that the human innate immune system, including downstream induction of cytokines, can be modulated by DNA metabolic stress-have many implications for health and disease, as well as for understanding the evolution of damage and p53 responsive networks.

  11. Leber's hereditary optic neuroretinopathy (LHON) associated with mitochondrial DNA point mutation G11778A in two Croatian families.

    Science.gov (United States)

    Martin-Kleiner, Irena; Gabrilovac, Jelka; Bradvica, Mario; Vidović, Tomislav; Cerovski, Branimir; Fumić, Ksenija; Boranić, Milivoj

    2006-03-01

    Leber's hereditary optic neuroretinopathy (LHON) is manifested as a bilateral acute or subacute loss of central vision due to optic atrophy. It is linked to point mutations of mitochondrial DNA, which is inherited maternally. The most common mitochondrial DNA point mutations associated with LHON are G3460A, G11778A and T14484C. These mutations are linked with the defects of subunits of the complex I (NADH-dehydrogenase-ubiquinone reductase) in mitochondria. The G11778A mitochondrial DNA point mutation is manifested by a severe visual impairment. In this paper two Croatian families with the LHON G11778A mutation are presented. Three LHON patients from two families were younger males which had the visual acuity of 0.1 or below, the ophthalmoscopy revealed telangiectatic microangiopathy and papilloedema, while Goldmann kinetic perimetry showed a central scotoma. The mothers and female relatives were LHON mutants without symptoms, whereas their sons suffered from a severe visual impairment. Molecular diagnosis helps to explain the cause of LHON disease.

  12. Homoplasmy of the G7444A mtDNA and heterozygosity of the GJB2 c.35delG mutations in a family with hearing loss

    DEFF Research Database (Denmark)

    Kokotas, Haris; Grigoriadou, Maria; Li, Yang

    2011-01-01

    Mitochondrial mutations have been shown to be responsible for syndromic as well as non-syndromic hearing loss. The G7444A mitochondrial DNA mutation affects COI/the precursor of tRNA(Ser(UCN)), encoding the first subunit of cytochrome oxidase. Here we report on the first Greek family with the G7444......A mitochondrial DNA mutation....

  13. Detection of a mariner-like element and a miniature inverted-repeat transposable element (MITE) associated with the heterochromatin from ants of the genus Messor and their possible involvement for satellite DNA evolution.

    Science.gov (United States)

    Palomeque, Teresa; Antonio Carrillo, José; Muñoz-López, Martín; Lorite, Pedro

    2006-04-26

    The satellite DNA of ants Messor bouvieri, M. barbarus and M. structor, studied in a previous paper, is organized as tandemly repeated 79-bp monomers in the three species showing high sequence similarity. In the present paper, a mariner-like element (Mboumar) and a new MITE (miniature inverted-repeat transposable element) called IRE-130, inserted into satellite DNA from M. bouvieri, are analyzed. The study of Mboumar element, of its transcription and the putative transposase that it would encode, suggests that it could be an active element. Mboumar elements inserted into IRE-130 elements have also been detected. It is the first time, to our knowledge, that a MITE has been described in Hymenoptera and it is also the first time that a mariner-like element inserted into a MITE has been detected. A mariner-like element, inserted into satellite DNA from M. structor and in M. barbarus, also has been found. The results seem to indicate that transposition events have participated in the satellite DNA mobilization and evolution.

  14. DNA hairpins promote temperature controlled cargo encapsulation in a truncated octahedral nanocage structure family

    DEFF Research Database (Denmark)

    Franch, Oskar; Iacovelli, Federico; Falconi, Mattia

    2016-01-01

    In the present study we investigate the mechanism behind temperature controlled cargo uptake using a truncated octahedral DNA cage scaffold functionalized with one, two, three or four hairpin forming DNA strands inserted in one corner of the structure. This investigation was inspired by our...... previous demonstration of temperature controlled reversible encapsulation of the cargo enzyme, horseradish peroxidase, in the cage with four hairpin forming strands. However, in this previous study the mechanism of cargo uptake was not directly addressed (Juul, et al., Temperature-Controlled Encapsulation...... and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage, ACS Nano, 2013, 7, 9724–9734). In the present study we use a combination of molecular dynamics simulations and in vitro analyses to unravel the mechanism of cargo uptake in hairpin containing DNA cages. We find that two hairpin...

  15. Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae

    Directory of Open Access Journals (Sweden)

    Catherine Jan

    2016-09-01

    Full Text Available The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni. From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.

  16. Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes

    Czech Academy of Sciences Publication Activity Database

    Puterová, J.; Razumova, O.; Martínek, T.; Alexandrov, O.; Divashuk, M.; Kubát, Z.; Hobza, Roman; Karlov, G.; Kejnovský, E.

    2017-01-01

    Roč. 9, č. 1 (2017), s. 197-212 ISSN 1759-6653 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:61389030 Keywords : sex-chromosomes * repetitive sequences * silene-latifolia * molecular cytogenetics * arabidopsis-thaliana * genome size * evolution * organization * alignment * database * sex chromosomes * genome composition * chromosomal localization * repetitive DNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.979, year: 2016

  17. First freshwater member ever reported for the family Bathycoccaceae (Chlorophyta; Archaeplastida) from Argentinean Patagonia revealed by environmental DNA survey.

    Science.gov (United States)

    Lara, Enrique; Fernández, Leonardo D; Schiaffino, M Romina; Izaguirre, Irina

    2017-08-01

    We characterized molecularly the first freshwater member ever reported for the family Bathycoccaceae in Lake Musters (Argentinean Patagonia). Members of this family are extremely numerous and play a key ecological role in marine systems as primary producers. We cloned a fragment comprising the SSU rRNA gene+ITS region from environmental DNA using specific mamiellophyte primers. The unique SSU rRNA gene sequence obtained clustered robustly with Bathycoccus prasinos. Analysis of the two-dimensional structure of the ITS region showed the presence of a typical supplementary helix in the ITS-2 region, a synapomorphy of Bathycoccaceae, which confirmed further its phylogenetic placement. We finally discuss the possible causes for the presence of this organism in Lake Musters. Copyright © 2017 Elsevier GmbH. All rights reserved.

  18. Molecular mechanisms of ligand-mediated attenuation of DNA binding by MarR family transcriptional regulators.

    Science.gov (United States)

    Perera, Inoka C; Grove, Anne

    2010-10-01

    Bacteria and archaea encode members of the large multiple antibiotic resistance regulator (MarR) family of transcriptional regulators. Generally, MarR homologs regulate activity of genes involved in antibiotic resistance, stress responses, virulence or catabolism of aromatic compounds. They constitute a diverse group of transcriptional regulators that includes both repressors and activators, and the conventional mode of regulation entails a genetic locus in which the MarR homolog and a gene under its regulation are encoded divergently; binding of the MarR homolog to the intergenic region typically represses transcription of both genes, while binding of a specific ligand to the transcription factor results in attenuated DNA binding and hence activated gene expression. For many homologs, the natural ligand is unknown. Crystal structures reveal a common architecture with a characteristic winged helix domain for DNA binding, and recent structural information of homologs solved both in the absence and presence of their respective ligands, as well as biochemical data, is finally converging to illuminate the mechanisms by which ligand-binding causes attenuated DNA binding. As MarR homologs regulate pathways that are critical to bacterial physiology, including virulence, a molecular understanding of mechanisms by which ligands affect a regulation of gene activity is essential. Specifying the position of ligand-binding pockets further has the potential to aid in identifying the ligands for MarR homologs for which the ligand remains unknown.

  19. Disposable magnetic DNA sensors for the determination at the attomolar level of a specific enterobacteriaceae family gene.

    Science.gov (United States)

    Loaiza, Oscar A; Campuzano, Susana; Pedrero, María; Pividori, M Isabel; García, Pedro; Pingarrón, José M

    2008-11-01

    Disposable magnetic DNA sensors using an enzyme-amplified strategy for the specific detection of a gene related to the Enterobacteriaceae bacterial family, based on the coupling of streptavidin-peroxidase to biotinylated lacZ gene target sequences, has been developed. A biotinylated 25-mer capture probe was attached to streptavidin-modified magnetic beads and hybridization with the biotinylated target was allowed to proceed. Then, a streptavidin-peroxidase polymer was attached to the biotinylated target, and the resulting modified magnetic beads were captured by a magnetic field on the surface of tetrathiafulvalene (TTF) modified gold screen-printed electrodes (Au/SPEs). The amperometric response obtained at -0.15 V after the addition of hydrogen peroxide was used to detect the hybridization process. In order to improve the sensitivity of the determination and reduce the assay time, different variables of the assay protocol were optimized. A low detection limit (5.7 fmol) with good stability (RSD = 7.1%, n = 10) was obtained. The DNA nonspecific adsorption at the magnetic beads was negligible, the obtained results thus demonstrating the possibility to detect the hybridization event with great specificity and sensitivity. The developed method was used for the analysis of Escherichia coli DNA fragments (326 bases) in polymerase chain reaction (PCR) amplicons extracted from a cell culture. As low as 2.5 aM asymmetric PCR product could be detected with the developed methodology.

  20. Nek11, a new member of the NIMA family of kinases, involved in DNA replication and genotoxic stress responses.

    Science.gov (United States)

    Noguchi, Kohji; Fukazawa, Hidesuke; Murakami, Yuko; Uehara, Yoshimasa

    2002-10-18

    DNA replication and genotoxic stresses activate various checkpoint-associated protein kinases, and checkpoint dysfunction often leads to cell lethality. Here, we have identified new members of the mammalian NIMA family of kinases, termed Nek11L and Nek11S (NIMA-related kinase 11 Long and Short isoform) as novel DNA replication/damage stresses-responsive kinases. Molecular cloning and biochemical studies showed that the catalytic domain of Nek11 is most similar to Nek4 and Nek3, and substrate specificity of Nek11L is distinguishable from those of NIMA and Nek2. The expression of nek11L mRNA increased through S to G(2)/M phase, and subcellular localization of Nek11 protein altered between interphase and prometaphase, suggesting multiple roles of Nek11. We found an activation of Nek11 kinase activity when cells were treated with various DNA-damaging agents and replication inhibitors, and this activation of Nek11 was suppressed by caffeine in HeLaS3 cells. The transient expression of wild-type Nek11L enhanced the aphidicolin-induced S-phase arrest, whereas the aphidicolin-induced S-phase arrest was reduced in the U2OS cell lines expressing kinase-negative Nek11L (K61R), and these cells were more sensitive to aphidicolin-induced cell lethality. Collectively, these results suggest that Nek11 has a role in the S-phase checkpoint downstream of the caffeine-sensitive pathway.

  1. Identification of BC005512 as a DNA damage responsive murine endogenous retrovirus of GLN family involved in cell growth regulation.

    Directory of Open Access Journals (Sweden)

    Yuanfeng Wu

    Full Text Available Genotoxicity assessment is of great significance in drug safety evaluation, and microarray is a useful tool widely used to identify genotoxic stress responsive genes. In the present work, by using oligonucleotide microarray in an in vivo model, we identified an unknown gene BC005512 (abbreviated as BC, official full name: cDNA sequence BC005512, whose expression in mouse liver was specifically induced by seven well-known genotoxins (GTXs, but not by non-genotoxins (NGTXs. Bioinformatics revealed that BC was a member of the GLN family of murine endogenous retrovirus (ERV. However, the relationship to genotoxicity and the cellular function of GLN are largely unknown. Using NIH/3T3 cells as an in vitro model system and quantitative real-time PCR, BC expression was specifically induced by another seven GTXs, covering diverse genotoxicity mechanisms. Additionally, dose-response and linear regression analysis showed that expression level of BC in NIH/3T3 cells strongly correlated with DNA damage, measured using the alkaline comet assay,. While in p53 deficient L5178Y cells, GTXs could not induce BC expression. Further functional studies using RNA interference revealed that down-regulation of BC expression induced G1/S phase arrest, inhibited cell proliferation and thus suppressed cell growth in NIH/3T3 cells. Together, our results provide the first evidence that BC005512, a member from GLN family of murine ERV, was responsive to DNA damage and involved in cell growth regulation. These findings could be of great value in genotoxicity predictions and contribute to a deeper understanding of GLN biological functions.

  2. Analytical Performance of a Multiplex Real-Time PCR Assay Using TaqMan Probes for Quantification of Trypanosoma cruzi Satellite DNA in Blood Samples

    Science.gov (United States)

    Abate, Teresa; Cayo, Nelly M.; Parrado, Rudy; Bello, Zoraida Diaz; Velazquez, Elsa; Muñoz-Calderon, Arturo; Juiz, Natalia A.; Basile, Joaquín; Garcia, Lineth; Riarte, Adelina; Nasser, Julio R.; Ocampo, Susana B.; Yadon, Zaida E.; Torrico, Faustino; de Noya, Belkisyole Alarcón; Ribeiro, Isabela; Schijman, Alejandro G.

    2013-01-01

    Background The analytical validation of sensitive, accurate and standardized Real-Time PCR methods for Trypanosoma cruzi quantification is crucial to provide a reliable laboratory tool for diagnosis of recent infections as well as for monitoring treatment efficacy. Methods/Principal Findings We have standardized and validated a multiplex Real-Time quantitative PCR assay (qPCR) based on TaqMan technology, aiming to quantify T. cruzi satellite DNA as well as an internal amplification control (IAC) in a single-tube reaction. IAC amplification allows rule out false negative PCR results due to inhibitory substances or loss of DNA during sample processing. The assay has a limit of detection (LOD) of 0.70 parasite equivalents/mL and a limit of quantification (LOQ) of 1.53 parasite equivalents/mL starting from non-boiled Guanidine EDTA blood spiked with T. cruzi CL-Brener stock. The method was evaluated with blood samples collected from Chagas disease patients experiencing different clinical stages and epidemiological scenarios: 1- Sixteen Venezuelan patients from an outbreak of oral transmission, 2- Sixty three Bolivian patients suffering chronic Chagas disease, 3- Thirty four Argentinean cases with chronic Chagas disease, 4- Twenty seven newborns to seropositive mothers, 5- A seronegative receptor who got infected after transplantation with a cadaveric kidney explanted from an infected subject. Conclusions/Significance The performing parameters of this assay encourage its application to early assessment of T. cruzi infection in cases in which serological methods are not informative, such as recent infections by oral contamination or congenital transmission or after transplantation with organs from seropositive donors, as well as for monitoring Chagas disease patients under etiological treatment. PMID:23350002

  3. The use of DNA markers in the pre-clinical diagnosis of familial ...

    African Journals Online (AJOL)

    D5S6), but not probes Pi227 (D5S37) and C11 p11 (D5S71). Haplotype analysis allowed the pre- clinical diagnosis of FAP in 5 subjects. S Atr Med J 1995; 85: 269-271. Familial adenomatous polyposis (FAP) is an autosomal dominant genetic ...

  4. Phylogenetic relationships among the family Ommastrephidae (Mollusca: Cephalopoda) inferred from two mitochondrial DNA gene sequences.

    Science.gov (United States)

    Wakabayashi, T; Suzuki, N; Sakai, M; Ichii, T; Chow, S

    2012-09-01

    Squids of the family Ommastrephidae are distributed worldwide, and the family includes many species of commercial importance. To investigate phylogenetic relationships among squid species of the family Ommastrephidae, partial nucleotide sequences of two mitochondrial gene loci (cytochrome c oxidase subunit I [1277bp] and 16S rRNA [443bp]) of 15 ommastrephid species and two outgroup species from the families Loliginidae and Enoploteuthidae were determined and used to construct parsimony and distance based phylogenetic trees. The molecular data provided several new phylogenetic inferences. The monophyletic status of three subfamilies (Illicinae, Todarodinae and Ommastrephinae) was well supported, although phylogenetic relationships between the subfamilies were not resolved. Inclusion of a problematic species, Ornithoteuthis volatilis, to Todarodinae was indicated. Within Todarodinae, the Japanese common squid Todarodes pacificus was observed to have much closer relationship to the species of the genus Nototodarus than to its congener (Todarodes filippovae). These results indicate that re-evaluation of several morphological key characters for ommastrephid taxonomy may be necessary. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Genomic DNA copy-number alterations of the let-7 family in human cancers.

    Directory of Open Access Journals (Sweden)

    Yanling Wang

    Full Text Available In human cancer, expression of the let-7 family is significantly reduced, and this is associated with shorter survival times in patients. However, the mechanisms leading to let-7 downregulation in cancer are still largely unclear. Since an alteration in copy-number is one of the causes of gene deregulation in cancer, we examined copy number alterations of the let-7 family in 2,969 cancer specimens from a high-resolution SNP array dataset. We found that there was a reduction in the copy number of let-7 genes in a cancer-type specific manner. Importantly, focal deletion of four let-7 family members was found in three cancer types: medulloblastoma (let-7a-2 and let-7e, breast cancer (let-7a-2, and ovarian cancer (let-7a-3/let-7b. For example, the genomic locus harboring let-7a-3/let-7b was deleted in 44% of the specimens from ovarian cancer patients. We also found a positive correlation between the copy number of let-7b and mature let-7b expression in ovarian cancer. Finally, we showed that restoration of let-7b expression dramatically reduced ovarian tumor growth in vitro and in vivo. Our results indicate that copy number deletion is an important mechanism leading to the downregulation of expression of specific let-7 family members in medulloblastoma, breast, and ovarian cancers. Restoration of let-7 expression in tumor cells could provide a novel therapeutic strategy for the treatment of cancer.

  6. Sequence conservation in avian CR1: an interspersed repetitive DNA family evolving under functional constraints.

    Science.gov (United States)

    Chen, Z Q; Ritzel, R G; Lin, C C; Hodgetts, R B

    1991-07-01

    CR1 is a short interspersed repetitive DNA element originally identified in the domestic chicken (Gallus gallus). However, unlike virtually all other such sequences described to date, CR1 is not confined to one or a few closely related species. It is probably a ubiquitous component of the avian genome, having been detected in representatives of nine orders encompassing a wide spectrum of the class Aves. This identification was made possible by using the polymerase chain reaction (PCR), which revealed interspecific similarities not detected by conventional Southern analysis. DNA sequence comparisons between a CR1 element isolated from a sarus crane (Grus antigone) and those isolated from an emu (Dromaius novaehollandiae) showed that two short highly conserved regions are present. These are included within two regions previously characterized in the CR1 units of domestic fowl. One of these behaves as a transcriptional silencer and the other is a binding site for a nuclear protein. Our observations suggest that CR1 has evolved under functional constraints and that interspersed repetitive sequences as a class may constitute a more significant component of the eukaryotic genome than is generally acknowledged.

  7. Cloning of a Syrian hamster cDNA related to sexual dimorphism: establishment of a new family of proteins.

    Science.gov (United States)

    Domínguez, P

    1995-12-04

    The clone FHG22, isolated from a female minus male subtracted cDNA library obtained from the sexually dimorphic Syrian hamster Harderian glands (HG) is 440 bp long with a 95 amino acids ORF, and hybridizes to a female HG-specific 0.6 kb mRNA. The FHG22 nucleotide and amino acid sequences are similar to the subunits from prostatein, uteroglobin, major cat allergen Fel dI (chain 1) and mouse salivary androgen binding proteins (subunit alpha). Therefore I propose that all those polypeptides belong to a common new family. The hamster genome has a single copy of the FHG22 gene, without homologous genes. FHG22 mRNA is also found in male and female parotid (higher levels in females) and submandibular glands, indicating a tissue and sex-dependent control of expression.

  8. DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family

    Directory of Open Access Journals (Sweden)

    Miller M Clarke

    2009-07-01

    Full Text Available Abstract Background Genes orthologous to the ybaB loci of Escherichia coli and Haemophilus influenzae are widely distributed among eubacteria. Several years ago, the three-dimensional structures of the YbaB orthologs of both E. coli and H. influenzae were determined, revealing a novel "tweezer"-like structure. However, a function for YbaB had remained elusive, with an early study of the H. influenzae ortholog failing to detect DNA-binding activity. Our group recently determined that the Borrelia burgdorferi YbaB ortholog, EbfC, is a DNA-binding protein. To reconcile those results, we assessed the abilities of both the H. influenzae and E. coli YbaB proteins to bind DNA to which B. burgdorferi EbfC can bind. Results Both the H. influenzae and the E. coli YbaB proteins bound to tested DNAs. DNA-binding was not well competed with poly-dI-dC, indicating some sequence preferences for those two proteins. Analyses of binding characteristics determined that both YbaB orthologs bind as homodimers. Different DNA sequence preferences were observed between H. influenzae YbaB, E. coli YbaB and B. burgdorferi EbfC, consistent with amino acid differences in the putative DNA-binding domains of these proteins. Conclusion Three distinct members of the YbaB/EbfC bacterial protein family have now been demonstrated to bind DNA. Members of this protein family are encoded by a broad range of bacteria, including many pathogenic species, and results of our studies suggest that all such proteins have DNA-binding activities. The functions of YbaB/EbfC family members in each bacterial species are as-yet unknown, but given the ubiquity of these DNA-binding proteins among Eubacteria, further investigations are warranted.

  9. Heritable DNA Methylation in CD4+ Cells among Complex Families Displays Genetic and Non-Genetic Effects.

    Directory of Open Access Journals (Sweden)

    Kenneth Day

    Full Text Available DNA methylation at CpG sites is both heritable and influenced by environment, but the relative contributions of each to DNA methylation levels are unclear. We conducted a heritability analysis of CpG methylation in human CD4+ cells across 975 individuals from 163 families in the Genetics of Lipid-lowering Drugs and Diet Network (GOLDN. Based on a broad-sense heritability (H2 value threshold of 0.4, we identified 20,575 highly heritable CpGs among the 174,445 most variable autosomal CpGs (SD > 0.02. Tests for associations of heritable CpGs with genotype at 2,145,360 SNPs using 717 of 975 individuals showed that ~74% were cis-meQTLs (1 Mb away from the CpG or located on a different chromosome, and 20% of CpGs showed no strong significant associations with genotype (based on a p-value threshold of 1e-7. Genes proximal to the genotype independent heritable CpGs were enriched for functional terms related to regulation of T cell activation. These CpGs were also among those that distinguished T cells from other blood cell lineages. Compared to genes proximal to meQTL-associated heritable CpGs, genotype independent heritable CpGs were moderately enriched in the same genomic regions that escape erasure during primordial germ cell development and could carry potential for generational transmission.

  10. A family of DNA repeats in Aspergillus nidulans has assimilated degenerated retrotransposons

    DEFF Research Database (Denmark)

    Nielsen, M.L.; Hermansen, T.D.; Aleksenko, Alexei Y.

    2001-01-01

    In the course of a chromosomal walk towards the centromere of chromosome IV of Aspergillus nidulans, several cross- hybridizing genomic cosmid clones were isolated. Restriction mapping of two such clones revealed that their restriction patterns were similar in a region of at least 15 kb, indicati......) phenomenon, first described in Neurospora crassa, may have operated in A. nidulans. The data indicate that this family of repeats has assimilated mobile elements that subsequently degenerated but then underwent further duplications as a part of the host repeats....

  11. Illegitimacy and sibship assignments in oil palm (Elaeis guineensis Jacq.) half-sib families using single locus DNA microsatellite markers.

    Science.gov (United States)

    Hama-Ali, Emad Omer; Alwee, Sharifah Shahrul Rabiah Syed; Tan, Soon Guan; Panandam, Jothi Malar; Ling, Ho Chai; Namasivayam, Parameswari; Peng, Hoh Boon

    2015-05-01

    Oil palm breeding has been progressing very well in Southeast Asia, especially in Malaysia and Indonesia. Despite this progress, there are still problems due to the difficulty of controlled crossing in oil palm. Contaminated/illegitimate progeny has appeared in some breeding programs; late and failure of detection by the traditional method causes a waste of time and labor. The use of molecular markers improves the integrity of breeding programs in perennial crops such as oil palm. Four half-sib families with a total of 200 progeny were used in this study. Thirty polymorphic single locus DNA microsatellites markers were typed to identify the illegitimate individuals and to obtain the correct parental and progeny assignments by using the CERVUS and COLONY programs. Three illegitimate palms (1.5%) were found, and 16 loci proved to be sufficient for sibship assignments without parental genotypes by using the COLONY program. The pairwise-likelihood score (PLS) method was better for half-sib family assignments than the full likelihood (FL) method.

  12. A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and dideoxyribonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Tabor, S.; Richardson, C.C. [Harvard Medical School, Boston, MA (United States)

    1995-07-03

    Bacteriophage T7 DNA polymerase efficiently incorporates a chain-terminating dideoxynucleotide into DNA, in contrast to the DNA polymerases from Escherichia coli and Thermus aquaticus. The molecular basis for this difference has been determined by constructing active site hybrids of these polymerases. A single hydroxyl group on the polypeptide chain is critical for selectivity. Replacing tyrosine-526 of T7 DNA polymerase with phenylalanine increases discrimination against the four dideoxynucleotides by >2000-fold, while replacing the phenylalanine at the homologous position in E. coli DNA polymerase I (position 762) or T. aquaticus DNA polymerase (position 667) with tyrosine decreases discrimination against the four dideoxynucleotides 250- to 8000-fold. These mutations allow the engineering of new DNA polymerases with enhanced properties for use in DNA sequence analysis. 29 refs., 4 figs., 2 tabs.

  13. DNA methylation at a bovine alpha satellite I repeat CpG site during development following fertilization and somatic cell nuclear transfer.

    Directory of Open Access Journals (Sweden)

    Christine Couldrey

    Full Text Available Incomplete epigenetic reprogramming is postulated to contribute to the low developmental success following somatic cell nuclear transfer (SCNT. Here, we describe the epigenetic reprogramming of DNA methylation at an alpha satellite I CpG site (αsatI-5 during development of cattle generated either by artificial insemination (AI or in vitro fertilization (IVF and SCNT. Quantitative methylation analysis identified that SCNT donor cells were highly methylated at αsatI-5 and resulting SCNT blastocysts showed significantly more methylation than IVF blastocysts. At implantation, no difference in methylation was observed between SCNT and AI in trophoblast tissue at αsatI-5, however, SCNT embryos were significantly hyper-methylated compared to AI controls at this time point. Following implantation, DNA methylation at αsatI-5 decreased in AI but not SCNT placental tissues. In contrast to placenta, the proportion of methylation at αsatI-5 remained high in adrenal, kidney and muscle tissues during development. Differences in the average proportion of methylation were smaller in somatic tissues than placental tissues but, on average, SCNT somatic tissues were hyper-methylated at αsatI-5. Although sperm from all bulls was less methylated than somatic tissues at αsatI-5, on average this site remained hyper-methylated in sperm from cloned bulls compared with control bulls. This developmental time course confirms that epigenetic reprogramming does occur, at least to some extent, following SCNT. However, the elevated methylation levels observed in SCNT blastocysts and cellular derivatives implies that there is either insufficient time or abundance of appropriate reprogramming factors in oocytes to ensure complete reprogramming. Incomplete reprogramming at this CpG site may be a contributing factor to low SCNT success rates, but more likely represents the tip of the iceberg in terms of incompletely reprogramming. Until protocols ensure the epigenetic

  14. Molecular Identification and Phylogenetic Relationships of Threadfin Breams (Family: Nemipteridae Using mtDNA Marker

    Directory of Open Access Journals (Sweden)

    Vaithilingam RAVITCHANDIRANE

    2012-05-01

    Full Text Available Cytochrome c oxidase-1 gene sequences of mitochondrial genome were analyzed for species identification and phylogenetic relationship among the commercially important Nemipterus species. Sequence analysis of COI gene clearly indicated that all the nine fish species fell into distinct clads, which are genetically distant from each other and exhibited identical phylogenetic reservation. All the COI gene sequences provide sufficient phylogenetic information and evolutionary relationship to distinguish the nine Nemipterus species unambiguously. As per the neighbour-joining (NJ and maximum likelihood (ML trees, all the nine species are genetically distant from each other and exhibited identical phylogenetic reservation. Based on the NJ and ML phylogenetic trees N. mesoprion, N. zysron, N. hexodon, N. nematophorus, N. virgatus and N. bipunctatus were closely related with high bootstrap value (97. The overall mean Kimura two parameter (K2P distances between the nine species was 0.109. The intra species K2P distance was high in N. japonicus (0.069 followed by N. peronii (0.050 and N. mesoprion (0.002. This study proves the use of mtDNA COI gene sequence based approach is an alternative tool for identifying fish species at a faster pace.

  15. Impact of a novel homozygous mutation in nicotinamide nucleotide transhydrogenase on mitochondrial DNA integrity in a case of familial glucocorticoid deficiency

    Directory of Open Access Journals (Sweden)

    Yasuko Fujisawa

    2015-06-01

    General significance: By studying a family affected with a novel point mutation in the NNT gene, a gene–dose response was found for various mitochondrial outcomes providing for novel insights into the role of NNT in the maintenance of mtDNA integrity beyond that described for preventing oxidative stress.

  16. Domain organization within repeated DNA sequences: application to the study of a family of transposable elements.

    Science.gov (United States)

    Tempel, Sébastien; Giraud, Mathieu; Lavenier, Dominique; Lerman, Israël-César; Valin, Anne-Sophie; Couée, Ivan; Amrani, Abdelhak El; Nicolas, Jacques

    2006-08-15

    The analysis of repeated elements in genomes is a fascinating domain of research that is lacking relevant tools for transposable elements (TEs), the most complex ones. The dynamics of TEs, which provides the main mechanism of mutation in some genomes, is an essential component of genome evolution. In this study we introduce a new concept of domain, a segmentation unit useful for describing the architecture of different copies of TEs. Our method extracts occurrences of a terminus-defined family of TEs, aligns the sequences, finds the domains in the alignment and searches the distribution of each domain in sequences. After a classification step relative to the presence or the absence of domains, the method results in a graphical view of sequences segmented into domains. Analysis of the new non-autonomous TE AtREP21 in the model plant Arabidopsis thaliana reveals copies of very different sizes and various combinations of domains which show the potential of our method. DomainOrganizer web page is available at www.irisa.fr/symbiose/DomainOrganizer/.

  17. Conserved amino acid motifs from the novel Piv/MooV family of transposases and site-specific recombinases are required for catalysis of DNA inversion by Piv.

    Science.gov (United States)

    Tobiason, D M; Buchner, J M; Thiel, W H; Gernert, K M; Karls, A C

    2001-02-01

    Piv, a site-specific invertase from Moraxella lacunata, exhibits amino acid homology with the transposases of the IS110/IS492 family of insertion elements. The functions of conserved amino acid motifs that define this novel family of both transposases and site-specific recombinases (Piv/MooV family) were examined by mutagenesis of fully conserved amino acids within each motif in Piv. All Piv mutants altered in conserved residues were defective for in vivo inversion of the M. lacunata invertible DNA segment, but competent for in vivo binding to Piv DNA recognition sequences. Although the primary amino acid sequences of the Piv/MooV recombinases do not contain a conserved DDE motif, which defines the retroviral integrase/transposase (IN/Tnps) family, the predicted secondary structural elements of Piv align well with those of the IN/Tnps for which crystal structures have been determined. Molecular modelling of Piv based on these alignments predicts that E59, conserved as either E or D in the Piv/MooV family, forms a catalytic pocket with the conserved D9 and D101 residues. Analysis of Piv E59G confirms a role for E59 in catalysis of inversion. These results suggest that Piv and the related IS110/IS492 transposases mediate DNA recombination by a common mechanism involving a catalytic DED or DDD motif.

  18. Successful DNA Profiling for Identification of burnt Families from their bones using AmpFℓSTR Identifiler® Plus Kit

    Directory of Open Access Journals (Sweden)

    Muhamamd Shahzad

    2016-02-01

    Full Text Available Background: DNA profiling plays a vital role in the identification of dead bodies during mass disasters. Severe fragmentation, decomposition, burning and intermixing of the remains can occur in the mass disasters. DNA analysis faces many challenges especially when the dead bodies are completely decomposed or burnt. This report presents the identification of 32 completely burnt individuals including three families from their remains in a bus using AmpFlSTR Identifiler Plus® Kit and AmpFlSTR Y-filer® Kit. Methods: DNA was extracted from provided remains of burnt bodies and reference samples by organic extraction procedure. The extracted quantity of DNA was calculated on ABI SDS7500 real time PCR with Quantifiler® Human DNA Quantification Kit (Applied Biosystems. DNA samples of 32 completely burnt individuals including three families were amplified using AmpFlSTR Identifiler Plus® Kit and AmpFlSTR Y-filer® Kit. The genotyping of these amplified samples was performed on ABI 3130xl Genetic Analyzer. Results: The resulting data obtained from Genetic Analyzer was analyzed using GeneMapper ID software version 3.2 (Applied Biosystems. Seventeen burnt individuals including 3 burnt families were identified with the help of 16 autosomal STRs and 6 were identified through Y-STR analysis by allele sharing of their provided reference samples of parents and brothers respectively. Conclusion: For the identification of unknown individuals particularly burnt deceased victims, STR analysis has become the gold standard in forensic science. Successful DNA profiling through the amplification of STR markers of AmpFlSTR Identifiler Plus® Kit proved to be very helpful in identifying the remains of burnt individuals even in the presence of inhibition observed in the Real Time PCR.

  19. An unusual DNA sequence observed in the. gamma. globin gene loci of two members of a Chinese family

    Energy Technology Data Exchange (ETDEWEB)

    Ryan, Q.C.

    1989-01-01

    There are two nonallelic human {gamma} globin genes located on the short arm of chromosome No. 11 in the order 5{prime}-{sup G}{sub {gamma}}-{sup A}{sub {gamma}}-3{prime}. Various modifications of the two {gamma} genes have been reported and include: deletions, triplications, quadruplications and recently a quintuplication. These are generally created by one or more unequal crossovers in the {gamma} globin gene regions on adjacent chromosomes. During the course of looking for a {gamma}{sup {degree}} thalassemia, which might be due to a crossover of looking for a {gamma} genes, two cases were found in the family W. Bgl II mapping studies showed a 5 kb deletion at the {gamma} gene loci in these individuals. The Bgl II fragment from the {gamma} gene loci of R.W. was cloned into the phage vector QR1. Phage mapping showed that two out of the three Pst I sites within the Bgl II fragment were missing which suggested that the crossover might have occurred within the {gamma} gene, possibly within the {gamma}IVS II region. Sequence analysis of the cloned fragment revealed an unusual sequence which had no sequence homology with the {gamma} gene region except for a small 264 bp region near the 3{prime} end. The orientation of the 264 bp fragment is inverted relative to homologous sequences in the {sup G}{sub {gamma}} and {sup A}{sub {gamma}} IVS II. The unusual sequence was computer analyzed for homology with every DNA sequence file in the EMBL database and GenBank and did not show any significant homologies to all the available DNA sequences except for the 264 bp {gamma}IVS II homology.

  20. Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus tokodaii and a function of tyrosine 170 in DNA binding.

    Science.gov (United States)

    Kawai, Akito; Higuchi, Shigesada; Tsunoda, Masaru; Nakamura, Kazuo T; Yamagata, Yuriko; Miyamoto, Shuichi

    2015-09-14

    Uracil-DNA glycosylases (UDGs) excise uracil from DNA by catalyzing the N-glycosidic bond hydrolysis. Here we report the first crystal structures of an archaeal UDG (stoUDG). Compared with other UDGs, stoUDG has a different structure of the leucine-intercalation loop, which is important for DNA binding. The stoUDG-DNA complex model indicated that Leu169, Tyr170, and Asn171 in the loop are involved in DNA intercalation. Mutational analysis showed that Tyr170 is critical for substrate DNA recognition. These results indicate that Tyr170 occupies the intercalation site formed after the structural change of the leucine-intercalation loop required for the catalysis. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  1. Satellite reconnaissance

    Science.gov (United States)

    Deloor, G. P.

    1984-06-01

    The potential of the observation equipment in remote sensing satellites is described. United States meteorology, land use and oceanography satellites and the major US Earth observation programs are listed. Imaging satellite systems are described such as: visible light and near infrared, thermal IR window, and microwave window. It is concluded that a geometrical resolution between 10 and 40 m can be expected. In order to reduce the data flow from the satellite system the input side of the system (the object-sensor interaction) has to be known. Satellites with synthetic aperture radar are increasingly important, but satellites can never fully replace observations with aircraft and drones.

  2. A dispersed family of repetitive DNA sequences exhibits characteristics of a transposable element in the genus Lycopersicon.

    Science.gov (United States)

    Young, R J; Francis, D M; St Clair, D A; Taylor, B H

    1994-06-01

    A segment of DNA 5' to the transcribed region of an auxin-regulated gene, ARPI, from Lycopersicon esculentum Mill. cv. VFN8 contains a sequence with the structural characteristics of a transposable element. The putative element (Lyt1) is 1340 bp long, has terminal inverted repeats of approximately 235 bp and is flanked by 9-bp direct repeats. Lyt1 has a structure similar to the Robertson's Mutator (Mu) family from maize. The terminal inverted repeats are 80% AT-rich, are 96.6% identical, and define a larger family of repetitive elements. Southern analysis and genomic dot-blot reconstructions detected at least 41 copies of Lyt1-hybridizing sequences in red-fruited Lycopersicon spp. (L. esculentum, L. pimpinellifolium and L. cheesmanii), and 2-8 copies in the green-fruited species (L. hirsutum, L. pennellii, L. peruvianum, L. chilense and L. chmielewskii). There were two to four copies in the Solanum spp. closely allied with the genus Lycopersicon (S. lycopersicoides, S. ochranthum and S. juglandifolium), while the more distantly related Solanum spp. showed little (one to two copies in S. tuberosum) to no (S. quitoense) detectable hybridization under stringent conditions. Linkage analysis in the F2 progeny of a cross between L. esculentum and L. cheesmanii indicated that at least six loci that hybridize to the Lyt1 sequence are dispersed in the genome. Polymerase chain reaction and Southern analyses revealed that some red-fruited accessions and L. chmielewskii lacked Lyt1 5' to the transcribed region of ARPI. Subsequent sequence analysis indicated that only one copy of the 9-bp direct repeat (target site) was present, suggesting that transposition of the element into the ARPI gene occurred after the divergence of the red-fruited and green-fruited Lycopersicon species.

  3. RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family.

    Science.gov (United States)

    Bies-Etheve, Natacha; Pontier, Dominique; Lahmy, Sylvie; Picart, Claire; Vega, Danielle; Cooke, Richard; Lagrange, Thierry

    2009-06-01

    Recent studies have identified a conserved WG/GW-containing motif, known as the Argonaute (AGO) hook, which is involved in the recruitment of AGOs to distinct components of the eukaryotic RNA silencing pathways. By using this motif as a model to detect new components in plant RNA silencing pathways, we identified SPT5-like, a plant-specific AGO4-interacting member of the nuclear SPT5 (Suppressor of Ty insertion 5) RNA polymerase (RNAP) elongation factor family that is characterized by the presence of a carboxy-terminal extension with more than 40 WG/GW motifs. Knockout SPT5-like mutants show a decrease in the accumulation of several 24-nt RNAs and hypomethylation at different loci revealing an implication in RNA-directed DNA methylation (RdDM). Here, we propose that SPT5-like emerged in plants as a facultative RNAP elongation factor. Its plant-specific origin and role in RdDM might reflect functional interactions with plant-specific RNA Pols required for RdDM.

  4. Suppression of RNA silencing by a plant DNA virus satellite requires a host calmodulin-like protein to repress RDR6 expression.

    Directory of Open Access Journals (Sweden)

    Fangfang Li

    2014-02-01

    Full Text Available In plants, RNA silencing plays a key role in antiviral defense. To counteract host defense, plant viruses encode viral suppressors of RNA silencing (VSRs that target different effector molecules in the RNA silencing pathway. Evidence has shown that plants also encode endogenous suppressors of RNA silencing (ESRs that function in proper regulation of RNA silencing. The possibility that these cellular proteins can be subverted by viruses to thwart host defense is intriguing but has not been fully explored. Here we report that the Nicotiana benthamiana calmodulin-like protein Nbrgs-CaM is required for the functions of the VSR βC1, the sole protein encoded by the DNA satellite associated with the geminivirus Tomato yellow leaf curl China virus (TYLCCNV. Nbrgs-CaM expression is up-regulated by the βC1. Transgenic plants over-expressing Nbrgs-CaM displayed developmental abnormities reminiscent of βC1-associated morphological alterations. Nbrgs-CaM suppressed RNA silencing in an Agrobacterium infiltration assay and, when over-expressed, blocked TYLCCNV-induced gene silencing. Genetic evidence showed that Nbrgs-CaM mediated the βC1 functions in silencing suppression and symptom modulation, and was required for efficient virus infection. Moreover, the tobacco and tomato orthologs of Nbrgs-CaM also possessed ESR activity, and were induced by betasatellite to promote virus infection in these Solanaceae hosts. We further demonstrated that βC1-induced Nbrgs-CaM suppressed the production of secondary siRNAs, likely through repressing RNA-DEPENDENT RNA POLYMERASE 6 (RDR6 expression. RDR6-deficient N. benthamiana plants were defective in antiviral response and were hypersensitive to TYLCCNV infection. More significantly, TYLCCNV could overcome host range restrictions to infect Arabidopsis thaliana when the plants carried a RDR6 mutation. These findings demonstrate a distinct mechanism of VSR for suppressing PTGS through usurpation of a host ESR, and

  5. Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses

    Science.gov (United States)

    Krupovic, Mart; Koonin, Eugene V.

    2014-06-01

    Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. However, viruses of the family Bidnaviridae, instead of the endonuclease, encode a protein-primed type B DNA polymerase (PolB) and hence break this pattern. We investigated the provenance of all bidnavirus genes and uncover an unexpected turbulent evolutionary history of these unique viruses. Our analysis strongly suggests that bidnaviruses evolved from a parvovirus ancestor from which they inherit a jelly-roll capsid protein and a superfamily 3 helicase. The radiation of bidnaviruses from parvoviruses was probably triggered by integration of the ancestral parvovirus genome into a large virus-derived DNA transposon of the Polinton (polintovirus) family resulting in the acquisition of the polintovirus PolB gene along with terminal inverted repeats. Bidnavirus genes for a receptor-binding protein and a potential novel antiviral defense modulator are derived from dsRNA viruses (Reoviridae) and dsDNA viruses (Baculoviridae), respectively. The unusual evolutionary history of bidnaviruses emphasizes the key role of horizontal gene transfer, sometimes between viruses with completely different genomes but occupying the same niche, in the emergence of new viral types.

  6. Evidence for 5S rDNA horizontal transfer in the toadfish Halobatrachus didactylus (Schneider, 1801) based on the analysis of three multigene families.

    Science.gov (United States)

    Merlo, Manuel A; Cross, Ismael; Palazón, José L; Ubeda-Manzanaro, María; Sarasquete, Carmen; Rebordinos, Laureana

    2012-10-07

    The Batrachoididae family is a group of marine teleosts that includes several species with more complicated physiological characteristics, such as their excretory, reproductive, cardiovascular and respiratory systems. Previous studies of the 5S rDNA gene family carried out in four species from the Western Atlantic showed two types of this gene in two species but only one in the other two, under processes of concerted evolution and birth-and-death evolution with purifying selection. Here we present results of the 5S rDNA and another two gene families in Halobatrachus didactylus, an Eastern Atlantic species, and draw evolutionary inferences regarding the gene families. In addition we have also mapped the genes on the chromosomes by two-colour fluorescence in situ hybridization (FISH). Two types of 5S rDNA were observed, named type α and type β. Molecular analysis of the 5S rDNA indicates that H. didactylus does not share the non-transcribed spacer (NTS) sequences with four other species of the family; therefore, it must have evolved in isolation. Amplification with the type β specific primers amplified a specific band in 9 specimens of H. didactylus and two of Sparus aurata. Both types showed regulatory regions and a secondary structure which mark them as functional genes. However, the U2 snRNA gene and the ITS-1 sequence showed one electrophoretic band and with one type of sequence. The U2 snRNA sequence was the most variable of the three multigene families studied. Results from two-colour FISH showed no co-localization of the gene coding from three multigene families and provided the first map of the chromosomes of the species. A highly significant finding was observed in the analysis of the 5S rDNA, since two such distant species as H. didactylus and Sparus aurata share a 5S rDNA type. This 5S rDNA type has been detected in other species belonging to the Batrachoidiformes and Perciformes orders, but not in the Pleuronectiformes and Clupeiformes orders. Two

  7. Evidence for 5S rDNA Horizontal Transfer in the toadfish Halobatrachus didactylus (Schneider, 1801) based on the analysis of three multigene families

    Science.gov (United States)

    2012-01-01

    Background The Batrachoididae family is a group of marine teleosts that includes several species with more complicated physiological characteristics, such as their excretory, reproductive, cardiovascular and respiratory systems. Previous studies of the 5S rDNA gene family carried out in four species from the Western Atlantic showed two types of this gene in two species but only one in the other two, under processes of concerted evolution and birth-and-death evolution with purifying selection. Here we present results of the 5S rDNA and another two gene families in Halobatrachus didactylus, an Eastern Atlantic species, and draw evolutionary inferences regarding the gene families. In addition we have also mapped the genes on the chromosomes by two-colour fluorescence in situ hybridization (FISH). Results Two types of 5S rDNA were observed, named type α and type β. Molecular analysis of the 5S rDNA indicates that H. didactylus does not share the non-transcribed spacer (NTS) sequences with four other species of the family; therefore, it must have evolved in isolation. Amplification with the type β specific primers amplified a specific band in 9 specimens of H. didactylus and two of Sparus aurata. Both types showed regulatory regions and a secondary structure which mark them as functional genes. However, the U2 snRNA gene and the ITS-1 sequence showed one electrophoretic band and with one type of sequence. The U2 snRNA sequence was the most variable of the three multigene families studied. Results from two-colour FISH showed no co-localization of the gene coding from three multigene families and provided the first map of the chromosomes of the species. Conclusions A highly significant finding was observed in the analysis of the 5S rDNA, since two such distant species as H. didactylus and Sparus aurata share a 5S rDNA type. This 5S rDNA type has been detected in other species belonging to the Batrachoidiformes and Perciformes orders, but not in the Pleuronectiformes

  8. Exome sequencing of germline DNA from non-BRCA1/2 familial breast cancer cases selected on the basis of aCGH tumor profiling.

    Directory of Open Access Journals (Sweden)

    Florentine S Hilbers

    Full Text Available The bulk of familial breast cancer risk (∼70% cannot be explained by mutations in the known predisposition genes, primarily BRCA1 and BRCA2. Underlying genetic heterogeneity in these cases is the probable explanation for the failure of all attempts to identify further high-risk alleles. While exome sequencing of non-BRCA1/2 breast cancer cases is a promising strategy to detect new high-risk genes, rational approaches to the rigorous pre-selection of cases are needed to reduce heterogeneity. We selected six families in which the tumours of multiple cases showed a specific genomic profile on array comparative genomic hybridization (aCGH. Linkage analysis in these families revealed a region on chromosome 4 with a LOD score of 2.49 under homogeneity. We then analysed the germline DNA of two patients from each family using exome sequencing. Initially focusing on the linkage region, no potentially pathogenic variants could be identified in more than one family. Variants outside the linkage region were then analysed, and we detected multiple possibly pathogenic variants in genes that encode DNA integrity maintenance proteins. However, further analysis led to the rejection of all variants due to poor co-segregation or a relatively high allele frequency in a control population. We concluded that using CGH results to focus on a sub-set of families for sequencing analysis did not enable us to identify a common genetic change responsible for the aggregation of breast cancer in these families. Our data also support the emerging view that non-BRCA1/2 hereditary breast cancer families have a very heterogeneous genetic basis.

  9. 3-O-Methylfunicone, a Selective Inhibitor of Mammalian Y-Family DNA Polymerases from an Australian Sea Salt Fungal Strain

    Directory of Open Access Journals (Sweden)

    Fumio Sugawara

    2009-11-01

    Full Text Available We isolated a pol inhibitor from the cultured mycelia extract of a fungal strain isolated from natural salt from a sea salt pan in Australia, which was identified as 3-O-methylfunicone by spectroscopic analyses. This compound selectively inhibited the activities of mammalian Y-family DNA polymerases (pols (i.e., pols η, ι and κ. Among these pols, human pol κ activity was most strongly inhibited, with an IC50 value of 12.5 μM. On the other hand, the compound barely influenced the activities of the other families of mammalian pols, such as A-family (i.e., pol γ, B-family (i.e., pols α, δ and ε or X-family (i.e., pols β, λ and terminal deoxynucleotidyl transferase, and showed no effect on the activities of fish pol δ, plant pols, prokaryotic pols and other DNA metabolic enzymes, such as calf primase of pol α, human immunodeficiency virus type-1 (HIV-1 reverse transcriptase, human telomerase, T7 RNA polymerase, mouse IMP dehydrogenase (type II, human topoisomerases I and II, T4 polynucleotide kinase or bovine deoxyribonuclease I. This compound also suppressed the growth of two cultured human cancer cell lines, HCT116 (colon carcinoma cells and HeLa (cervix carcinoma cells, and UV-treated HeLa cells exhibited lower clonogenic survival in the presence of inhibitor.

  10. Diagnostic validation of a familial hypercholesterolaemia cohort provides a model for using targeted next generation DNA sequencing in the clinical setting.

    Science.gov (United States)

    Hinchcliffe, Marcus; Le, Huong; Fimmel, Anthony; Molloy, Laura; Freeman, Lucinda; Sullivan, David; Trent, Ronald J

    2014-01-01

    Our aim was to assess the sensitivity and specificity of a next generation DNA sequencing (NGS) platform using a capture based DNA library preparation method. Data and experience gained from this diagnostic validation can be used to progress the applications of NGS in the wider molecular diagnostic setting. A technical cross-validation comparing the current molecular diagnostic gold standard methods of Sanger DNA sequencing and multiplex ligation-dependant probe amplification (MLPA) versus a customised capture based targeted re-sequencing method on a SOLiD 5500 sequencing platform was carried out using a cohort of 96 familial hypercholesterolaemia (FH) samples. We compared a total of 595 DNA variations (488 common single nucleotide polymorphisms, 73 missense mutations, 9 nonsense mutations, 3 splice site point mutations, 13 small indels, 2 multi-exonic duplications and 7 multi-exonic deletions) found previously in the 96 FH samples. DNA variation detection sensitivity and specificity were both 100% for the SOLiD 5500 NGS platform compared with Sanger sequencing and MLPA only when both LifeScope and Integrative Genomics Viewer softwares were utilised. The methods described here offer a high-quality strategy for the detection of a wide range of DNA mutations in diseases with a moderate number of well described causative genes. However, there are important issues related to the bioinformatic algorithms employed to detect small indels.

  11. Evolutionary Dynamics of 5S rDNA and Recurrent Association of Transposable Elements in Electric Fish of the Family Gymnotidae (Gymnotiformes): The Case of Gymnotus mamiraua.

    Science.gov (United States)

    da Silva, Maelin; Barbosa, Patricia; Artoni, Roberto F; Feldberg, Eliana

    2016-01-01

    Gymnotidae is a family of electric fish endemic to the Neotropics consisting of 2 genera: Electrophorus and Gymnotus. The genus Gymnotus is widely distributed and is found in all of the major Brazilian river systems. Physical and molecular mapping data for the ribosomal DNA (rDNA) in this genus are still scarce, with its chromosomal location known in only 11 species. As other species of Gymnotus with 2n = 54 chromosomes from the Paraná-Paraguay basin, G. mamiraua was found to have a large number of 5S rDNA sites. Isolation and cloning of the 5S rDNA sequences from G. mamiraua identified a fragment of a transposable element similar to the Tc1/mariner transposon associated with a non-transcribed spacer. Double fluorescence in situ hybridization analysis of this element and the 5S rDNA showed that they were colocalized on several chromosomes, in addition to acting as nonsyntenic markers on others. Our data show the association between these sequences and suggest that the Tc1 retrotransposon may be the agent that drives the spread of these 5S rDNA-like sequences in the G. mamiraua genome. © 2016 S. Karger AG, Basel.

  12. Identification and characterization of C106R, a novel mutation in the DNA-binding domain of GCMB, in a family with autosomal-dominant hypoparathyroidism.

    Science.gov (United States)

    Yi, Hyon-Seung; Eom, Young Sil; Park, Ie Byung; Lee, Sangho; Hong, Suntaek; Jüppner, Harald; Mannstadt, Michael; Lee, Sihoon

    2012-05-01

    Glial cells missing B (GCMB) is a transcription factor that is expressed in the parathyroid hormone (PTH)-secreting cells of the parathyroid glands. Several mutations in GCMB have been reported to cause hypoparathyroidism (HP). We identified a family with two individuals in two generations (mother and son), who are affected by autosomal-dominant hypoparathyroidism (AD-HP). A novel heterozygous mutation in exon 2 of GCMB was identified in both affected individuals that changes cysteine at position 106 of the putative DNA-binding domain of GCMB to arginine (C106R). We performed mutational analysis of the genes encoding GCMB, pre-pro PTH, GATA3 and CaSR using polymerase chain reaction (PCR)-amplified genomic DNA. The identified GCMB mutant was characterized by functional studies including nuclear localization, electrophoretic mobility shift assays (EMSA) and luciferase reporter assays, and homology modelling was performed to generate a three-dimensional structural model for the DNA-binding domain of GCMB to predict the structural consequences of the identified mutation. The C106R mutant of GCMB failed to interact with the DNA consensus recognition motif, as determined by EMSA. Furthermore, in comparison with wild-type GCMB, the C106R mutant demonstrated reduced transactivation in luciferase reporter assays; however, the mutant GCMB failed to reduce the activity of the wild-type protein. Consistent with the EMSA findings, homology modelling analysis suggested that replacement of cysteine 106 with arginine would interfere with DNA binding. We have identified a novel GCMB mutation that may explain AD-HP in our family. However, the exact mechanism by which this heterozygous mutation leads to the disease in the described family remains to be elucidated. © 2012 Blackwell Publishing Ltd.

  13. Androgen Insensitivity Syndrome in a Family of Warmblood Horses Caused by a 25-bp Deletion of the DNA-Binding Domain of the Androgen Receptor Gene

    DEFF Research Database (Denmark)

    Eastman Welsford, G.; Munk, Rikke; Villagómez, Daniel A.F.

    2017-01-01

    Testicular feminization, an earlier term coined for describing a syndrome resulting from failure of masculinization of target organs by androgen secretions during embryo development, has been well documented not only in humans but also in the domestic horse. The pathology, actually referred to as...... pedigree segregating AIS, where the molecular analyses of the androgen receptor gene in the family provided evidences that a 25-bp deletion of the DNA-binding domain is causative of this equine syndrome....

  14. Characterization of a DNA sequence family in the Prader-Willi/Angelman syndrome chromosome region in 15q11-q13

    Energy Technology Data Exchange (ETDEWEB)

    Dittrich, B.; Knoblauch, H.; Buiting, K.; Horsthemke, B. (Universitaetsklinikum Essen (Germany))

    1993-04-01

    IR4-3R (D15S11) is an anonymous DNA sequence from human chromosome 15. Using YAC cloning and restriction enzyme analysis, the authors have found that IR4-3R detects five related DNA sequences, which are spread over 700 kb within the Prader-Willi/Angelman syndrome chromosome region in 15q11-q 13. The RsaI and StyI polymorphisms, which were described previously, are associated with the most proximal copy of IR4-3R and are in strong linkage disequilibrium. IR4-3R represents the third DNA sequence family that has been identified in 15q11-q13. 14 refs., 2 figs., 1 tab.

  15. Satellite RNAs and Satellite Viruses.

    Science.gov (United States)

    Palukaitis, Peter

    2016-03-01

    Satellite RNAs and satellite viruses are extraviral components that can affect either the pathogenicity, the accumulation, or both of their associated viruses while themselves being dependent on the associated viruses as helper viruses for their infection. Most of these satellite RNAs are noncoding RNAs, and in many cases, have been shown to alter the interaction of their helper viruses with their hosts. In only a few cases have the functions of these satellite RNAs in such interactions been studied in detail. In particular, work on the satellite RNAs of Cucumber mosaic virus and Turnip crinkle virus have provided novel insights into RNAs functioning as noncoding RNAs. These effects are described and potential roles for satellite RNAs in the processes involved in symptom intensification or attenuation are discussed. In most cases, models describing these roles involve some aspect of RNA silencing or its suppression, either directly or indirectly involving the particular satellite RNA.

  16. DNA barcoding in native plants of the Labiatae (Lamiaceae) family from Chios Island (Greece) and the adjacent Çeşme-Karaburun Peninsula (Turkey).

    Science.gov (United States)

    Theodoridis, Spyros; Stefanaki, Anastasia; Tezcan, Meltem; Aki, Cuneyt; Kokkini, Stella; Vlachonasios, Konstantinos E

    2012-07-01

    The plant family Labiatae (Lamiaceae) is known for its fine medicinal and aromatic herbs like lavender, mint, oregano, sage and thyme and is a rich source of essential oils for the food, pharmaceutical and cosmetic industry. Besides its great economic importance, the Labiatae family contributes significantly to the endemic flora of Greece and Turkey. Owing to its economic and biological significance and to the difficult identification based on morphological characters of several of its taxa, the Labiatae family is an ideal case for developing DNA barcodes. The purpose of this study is to evaluate the utility of DNA barcoding on a local scale in discriminating Labiatae species in Chios Island (Greece) and the adjacent Çeşme-Karaburun Peninsula (Turkey). We chose three cpDNA regions (matK, rbcL, trnH-psbA) that were proposed by previous studies and tested them either as single region or as multiregion barcodes based on the criteria determined by Consortium for the Barcode of Life (CBOL). Our results show that matK and trnH-psbA taken as useful in discriminating species of the Labiatae, for the species we examined, as any multiregion combination. matK and trnH-psbA could serve as single-region barcodes for Labiatae species contributing to the conservation and the trade control of valuable plant resources. © 2012 Blackwell Publishing Ltd.

  17. Centriolar satellites

    DEFF Research Database (Denmark)

    Tollenaere, Maxim A X; Mailand, Niels; Bekker-Jensen, Simon

    2015-01-01

    , emerging evidence points to these structures as important hubs for dynamic, multi-faceted regulation in response to a variety of cues. In this review, we summarize the current knowledge of the roles of centriolar satellites in regulating centrosome functions, ciliogenesis, and neurogenesis. We also...... highlight newly discovered regulatory mechanisms targeting centriolar satellites and their functional status, and we discuss how defects in centriolar satellite components are intimately linked to a wide spectrum of human diseases....

  18. Lack of involvement of known DNA methyltransferases in familial hydatidiform mole implies the involvement of other factors in establishment of imprinting in the human female germline

    Directory of Open Access Journals (Sweden)

    Picton H M

    2003-01-01

    Full Text Available Abstract Background Differential methylation of the two alleles is a hallmark of imprinted genes. Correspondingly, loss of DNA methyltransferase function results in aberrant imprinting and abnormal post-fertilization development. In the mouse, mutations of the oocyte-specific isoform of the DNA methyltransferase Dnmt1 (Dnmt1o and of the methyltransferase-like Dnmt3L gene result in specific failures of imprint establishment or maintenance, at multiple loci. We have previously shown in humans that an analogous inherited failure to establish imprinting at multiple loci in the female germline underlies a rare phenotype of recurrent hydatidiform mole. Results We have identified a human homologue of the murine Dnmt1o and assessed its pattern of expression. Human DNMT1o mRNA is detectable in mature oocytes and early fertilized embryos but not in any somatic tissues analysed. The somatic isoform of DNMT1 mRNA, in contrast, is not detectable in human oocytes. In the previously-described family with multi-locus imprinting failure, mutation of DNMT1o and of the other known members of this gene family has been excluded. Conclusions Mutation of the known DNMT genes does not underlie familial hydatidiform mole, at least in the family under study. This suggests that trans-acting factors other than the known methyltransferases are required for imprint establishment in humans, a concept that has indirect support from recent biochemical studies of DNMT3L.

  19. Primary structure of rat cardiac beta-adrenergic and muscarinic cholinergic receptors obtained by automated DNA sequence analysis: further evidence for a multigene family.

    Science.gov (United States)

    Gocayne, J; Robinson, D A; FitzGerald, M G; Chung, F Z; Kerlavage, A R; Lentes, K U; Lai, J; Wang, C D; Fraser, C M; Venter, J C

    1987-12-01

    Two cDNA clones, lambda RHM-MF and lambda RHB-DAR, encoding the muscarinic cholinergic receptor and the beta-adrenergic receptor, respectively, have been isolated from a rat heart cDNA library. The cDNA clones were characterized by restriction mapping and automated DNA sequence analysis utilizing fluorescent dye primers. The rat heart muscarinic receptor consists of 466 amino acids and has a calculated molecular weight of 51,543. The rat heart beta-adrenergic receptor consists of 418 amino acids and has a calculated molecular weight of 46,890. The two cardiac receptors have substantial amino acid homology (27.2% identity, 50.6% with favored substitutions). The rat cardiac beta receptor has 88.0% homology (92.5% with favored substitutions) with the human brain beta receptor and the rat cardiac muscarinic receptor has 94.6% homology (97.6% with favored substitutions) with the porcine cardiac muscarinic receptor. The muscarinic cholinergic and beta-adrenergic receptors appear to be as conserved as hemoglobin and cytochrome c but less conserved than histones and are clearly members of a multigene family. These data support our hypothesis, based upon biochemical and immunological evidence, that suggests considerable structural homology and evolutionary conservation between adrenergic and muscarinic cholinergic receptors. To our knowledge, this is the first report utilizing automated DNA sequence analysis to determine the structure of a gene.

  20. Expression of an X-family DNA polymerase, pol lambda, in the respiratory epithelium of non-small cell lung cancer patients with habitual smoking.

    Science.gov (United States)

    Ohba, Taro; Kometani, Takurou; Shoji, Fumihiro; Yano, Tokujiro; Yoshino, Ichiro; Ichiro, Yoshino; Taguchi, Kenichi; Kuraoka, Isao; Oda, Shinya; Maehara, Yoshihiko

    2009-01-01

    DNA polymerase lambda, pol lambda, is a eukaryotic member of the X-family DNA polymerases that is involved in two modes of DNA repair, i.e. base excision repair (BER) or non-homologous end joining (NHEJ). Using immunohistochemical approaches, we have observed pol lambda expression in human tissues, particularly in the respiratory system of lung cancer patients. pol lambda proteins were distributed in the nuclei of the epithelial cells in the bronchi, bronchioles and alveoli. Intriguingly, the level of pol lambda expression in the bronchiolar epithelia significantly correlated with the amount of habitual smoking in the individuals. Conversely, pol lambda expression in cancer tissues did not correlate with the smoking status of the patients. Pol lambda expression was sometimes discrepant between the tumor tissues and adjacent bronchioles. More importantly, tumors without pol lambda expression that occurred in heavy smokers significantly tended to be at an advanced clinical stage. Pol lambda may thus be involved in the DNA repair processes counteracting DNA damage caused by tobacco smoke in the respiratory system.

  1. Association studies using family pools of outcrossing crops based on allele-frequency estimates from DNA sequencing

    DEFF Research Database (Denmark)

    Ashraf, Bilal; Jensen, Just; Asp, Torben

    2014-01-01

    F2 families are frequently used in breeding of outcrossing species, for instance to obtain trait measurements on plots. We propose to perform association studies by obtaining a matching “family genotype” from sequencing a pooled sample of the family, and to directly use allele frequencies compute...

  2. Analysis of the DNA-Binding Activities of the Arabidopsis R2R3-MYB Transcription Factor Family by One-Hybrid Experiments in Yeast.

    Directory of Open Access Journals (Sweden)

    Zsolt Kelemen

    Full Text Available The control of growth and development of all living organisms is a complex and dynamic process that requires the harmonious expression of numerous genes. Gene expression is mainly controlled by the activity of sequence-specific DNA binding proteins called transcription factors (TFs. Amongst the various classes of eukaryotic TFs, the MYB superfamily is one of the largest and most diverse, and it has considerably expanded in the plant kingdom. R2R3-MYBs have been extensively studied over the last 15 years. However, DNA-binding specificity has been characterized for only a small subset of these proteins. Therefore, one of the remaining challenges is the exhaustive characterization of the DNA-binding specificity of all R2R3-MYB proteins. In this study, we have developed a library of Arabidopsis thaliana R2R3-MYB open reading frames, whose DNA-binding activities were assayed in vivo (yeast one-hybrid experiments with a pool of selected cis-regulatory elements. Altogether 1904 interactions were assayed leading to the discovery of specific patterns of interactions between the various R2R3-MYB subgroups and their DNA target sequences and to the identification of key features that govern these interactions. The present work provides a comprehensive in vivo analysis of R2R3-MYB binding activities that should help in predicting new DNA motifs and identifying new putative target genes for each member of this very large family of TFs. In a broader perspective, the generated data will help to better understand how TF interact with their target DNA sequences.

  3. Identification of fungal DNA barcode targets and PCR primers based on Pfam protein families and taxonomic hierarchy

    NARCIS (Netherlands)

    Lewis, C.T.; Bilkhu, S.; Robert, V.; Eberhardt, U.; Szoke, S.; Seifert, K.A.; Lévesque, C.A.

    2011-01-01

    Abstract: DNA barcoding is the application of DNA sequences of standardized genetic markers for the identification of eukaryotic organisms. We attempted to identify alternative candidate barcode gene targets for the fungal biota from available fungal genomes using a taxonomy-aware processing

  4. Satellite Communications

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Satellite Communications. Arthur C Clarke wrote a seminal paper in 1945 in wireless world. Use three satellites in geo-synchronous orbit to enable intercontinental communications. System could be realised in '50 to 100 years'

  5. Contrasting patterns of evolution of 45S and 5S rDNA families uncover new aspects in the genome constitution of the agronomically important grass Thinopyrum intermedium (Triticeae).

    Science.gov (United States)

    Mahelka, Václav; Kopecky, David; Baum, Bernard R

    2013-09-01

    We employed sequencing of clones and in situ hybridization (genomic and fluorescent in situ hybridization [GISH and rDNA-FISH]) to characterize both the sequence variation and genomic organization of 45S (herein ITS1-5.8S-ITS2 region) and 5S (5S gene + nontranscribed spacer) ribosomal DNA (rDNA) families in the allohexaploid grass Thinopyrum intermedium. Both rDNA families are organized within several rDNA loci within all three subgenomes of the allohexaploid species. Both families have undergone different patterns of evolution. The 45S rDNA family has evolved in a concerted manner: internal transcribed spacer (ITS) sequences residing within the arrays of two subgenomes out of three got homogenized toward one major ribotype, whereas the third subgenome contained a minor proportion of distinct unhomogenized copies. Homogenization mechanisms such as unequal crossover and/or gene conversion were coupled with the loss of certain 45S rDNA loci. Unlike in the 45S family, the data suggest that neither interlocus homogenization among homeologous chromosomes nor locus loss occurred in 5S rDNA. Consistently with other Triticeae, the 5S rDNA family in intermediate wheatgrass comprised two distinct array types-the long- and short-spacer unit classes. Within the long and short units, we distinguished five and three different types, respectively, likely representing homeologous unit classes donated by putative parental species. Although the major ITS ribotype corresponds in our phylogenetic analysis to the E-genome species, the minor ribotype corresponds to Dasypyrum. 5S sequences suggested the contributions from Pseudoroegneria, Dasypyrum, and Aegilops. The contribution from Aegilops to the intermediate wheatgrass' genome is a new finding with implications in wheat improvement. We discuss rDNA evolution and potential origin of intermediate wheatgrass.

  6. Molecular phylogeny and systematics of the banana family (Musaceae) inferred from multiple nuclear and chloroplast DNA fragments, with a special reference to the genus Musa.

    Science.gov (United States)

    Li, Lin-Feng; Häkkinen, Markku; Yuan, Yong-Ming; Hao, Gang; Ge, Xue-Jun

    2010-10-01

    Musaceae is a small paleotropical family. Three genera have been recognised within this family although the generic delimitations remain controversial. Most species of the family (around 65 species) have been placed under the genus Musa and its infrageneric classification has long been disputed. In this study, we obtained nuclear ribosomal ITS and chloroplast (atpB-rbcL, rps16, and trnL-F) DNA sequences of 36 species (42 accessions of ingroups representing three genera) together with 10 accessions of ingroups retrieved from GenBank database and 4 accessions of outgroups, to construct the phylogeny of the family, with a special reference to the infrageneric classification of the genus Musa. Our phylogenetic analyses elaborated previous results in supporting the monophyly of the family and suggested that Musella and Ensete may be congeneric or at least closely related, but refuted the previous infrageneric classification of Musa. None of the five sections of Musa previously defined based on morphology was recovered as monophyletic group in the molecular phylogeny. Two infrageneric clades were identified, which corresponded well to the basic chromosome numbers of x=11 and 10/9/7, respectively: the former clade comprises species from the sections Musa and Rhodochlamys while the latter contains sections of Callimusa, Australimusa, and Ingentimusa. Copyright 2010 Elsevier Inc. All rights reserved.

  7. The miR-200 family and miR-205 are repressed by Twist1 and concurrently silenced and DNA hypermethylated in invasive bladder cancer

    DEFF Research Database (Denmark)

    Wiklund, Erik Digman

    MicroRNAs (miRNA) are small non-coding RNAs commonly deregulated in cancer. The miR-200 family (miR-200a, -200b, -200c, -141 and -429) and miR-205 are encoded in three separate genomic loci and are frequently silenced in advanced cancer. The miR-200 family and miR-205 have been implicated in tumo...... demonstrating concerted transcriptional regulation of the three miR-200 loci. Our data also indicate that DNA hypermethylation of the miR-200 family and miR-205 are possible prognostic markers in bladder cancer.  ......MicroRNAs (miRNA) are small non-coding RNAs commonly deregulated in cancer. The miR-200 family (miR-200a, -200b, -200c, -141 and -429) and miR-205 are encoded in three separate genomic loci and are frequently silenced in advanced cancer. The miR-200 family and miR-205 have been implicated in tumour...... invasion and metastasis by negatively regulating the transcriptional repressors of E-cadherin, ZEB1 and ZEB2. Loss of miR-200 expression leads to silencing of E-cadherin, thereby promoting epithelial to mesenchymal transition (EMT) and loss of cell adhesion. However, little is known about...

  8. Comparative Genomics of Chrysochromulina Ericina Virus and Other Microalga-Infecting Large DNA Viruses Highlights Their Intricate Evolutionary Relationship with the Established Mimiviridae Family.

    Science.gov (United States)

    Gallot-Lavallée, Lucie; Blanc, Guillaume; Claverie, Jean-Michel

    2017-07-15

    Chrysochromulina ericina virus CeV-01B (CeV) was isolated from Norwegian coastal waters in 1998. Its icosahedral particle is 160 nm in diameter and encloses a 474-kb double-stranded DNA (dsDNA) genome. This virus, although infecting a microalga (the haptophyceae Haptolina ericina, formerly Chrysochromulina ericina), is phylogenetically related to members of the Mimiviridae family, initially established with the acanthamoeba-infecting mimivirus and megavirus as prototypes. This family was later split into two genera (Mimivirus and Cafeteriavirus) following the characterization of a virus infecting the heterotrophic stramenopile Cafeteria roenbergensis (CroV). CeV, as well as two of its close relatives, which infect the unicellular photosynthetic eukaryotes Phaeocystis globosa (Phaeocystis globosa virus [PgV]) and Aureococcus anophagefferens (Aureococcus anophagefferens virus [AaV]), are currently unclassified by the International Committee on Viral Taxonomy (ICTV). The detailed comparative analysis of the CeV genome presented here confirms the phylogenetic affinity of this emerging group of microalga-infecting viruses with the Mimiviridae but argues in favor of their classification inside a distinct clade within the family. Although CeV, PgV, and AaV share more common features among them than with the larger Mimiviridae, they also exhibit a large complement of unique genes, attesting to their complex evolutionary history. We identified several gene fusion events and cases of convergent evolution involving independent lateral gene acquisitions. Finally, CeV possesses an unusual number of inteins, some of which are closely related despite being inserted in nonhomologous genes. This appears to contradict the paradigm of allele-specific inteins and suggests that the Mimiviridae are especially efficient in spreading inteins while enlarging their repertoire of homing genes.IMPORTANCE Although it infects the microalga Chrysochromulina ericina, CeV is more closely related

  9. Editing of misaligned 3'-termini by an intrinsic 3'-5' exonuclease activity residing in the PHP domain of a family X DNA polymerase.

    Science.gov (United States)

    Baños, Benito; Lázaro, José M; Villar, Laurentino; Salas, Margarita; de Vega, Miguel

    2008-10-01

    Bacillus subtilis gene yshC encodes a family X DNA polymerase (PolX(Bs)), whose biochemical features suggest that it plays a role during DNA repair processes. Here, we show that, in addition to the polymerization activity, PolX(Bs) possesses an intrinsic 3'-5' exonuclease activity specialized in resecting unannealed 3'-termini in a gapped DNA substrate. Biochemical analysis of a PolX(Bs) deletion mutant lacking the C-terminal polymerase histidinol phosphatase (PHP) domain, present in most of the bacterial/archaeal PolXs, as well as of this separately expressed protein region, allow us to state that the 3'-5' exonuclease activity of PolX(Bs) resides in its PHP domain. Furthermore, site-directed mutagenesis of PolX(Bs) His339 and His341 residues, evolutionary conserved in the PHP superfamily members, demonstrated that the predicted metal binding site is directly involved in catalysis of the exonucleolytic reaction. The implications of the unannealed 3'-termini resection by the 3'-5' exonuclease activity of PolX(Bs) in the DNA repair context are discussed.

  10. Satellite Communications

    CERN Document Server

    Pelton, Joseph N

    2012-01-01

    The field of satellite communications represents the world's largest space industry. Those who are interested in space need to understand the fundamentals of satellite communications, its technology, operation, business, economic, and regulatory aspects. This book explains all this along with key insights into the field's future growth trends and current strategic challenges. Fundamentals of Satellite Communications is a concise book that gives all of the key facts and figures as well as a strategic view of where this dynamic industry is going. Author Joseph N. Pelton, PhD, former Dean of the International Space University and former Director of Strategic Policy at Intelstat, presents a r

  11. Satellite myths

    Science.gov (United States)

    Easton, Roger L.; Hall, David

    2008-01-01

    Richard Corfield's article “Sputnik's legacy” (October 2007 pp23-27) states that the satellite on board the US Vanguard rocket, which exploded during launch on 6 December 1957 two months after Sputnik's successful take-off, was “a hastily put together contraption of wires and circuitry designed only to send a radio signal back to Earth”. In fact, the Vanguard satellite was developed over a period of several years and put together carefully using the best techniques and equipment available at the time - such as transistors from Bell Laboratories/Western Electric. The satellite contained not one but two transmitters, in which the crystal-controlled oscillators had been designed to measure both the temperature of the satellite shell and of the internal package.

  12. Satellite Geomagnetism

    DEFF Research Database (Denmark)

    Olsen, Nils; Stolle, Claudia

    2012-01-01

    Observations of Earth’s magnetic field from space began more than 50 years ago. A continuous monitoring of the field using low Earth orbit (LEO) satellites, however, started only in 1999, and three satellites have taken highprecision measurements of the geomagnetic field during the past decade....... The unprecedented time-space coverage of their data opened revolutionary new possibilities for monitoring, understanding, and exploring Earth’s magnetic field. In the near future, the three-satellite constellation Swarm will ensure continuity of such measurement and provide enhanced possibilities to improve our...... ability to characterize and understand the many sources that contribute to Earth’s magnetic field. In this review, we summarize investigations of Earth’s interior and environment that have been possible through the analysis of high-precision magnetic field observations taken by LEO satellites....

  13. Legendrian satellites

    OpenAIRE

    Etnyre, John; Vértesi, Vera

    2016-01-01

    In this paper we study Legendrian knots in the knot types of satellite knots. In particular, we classify Legendrian Whitehead patterns and learn a great deal about Legendrian braided patterns. We also show how the classification of Legendrian patterns can lead to a classification of the associated satellite knots if the companion knot is Legendrian simple and uniformly thick. This leads to new Legendrian and transverse classification results for knots in the 3-sphere with its standard contact...

  14. Scientific Satellites

    Science.gov (United States)

    1967-01-01

    igniters, and restrictors, can provide dozens of precision bursts of thrust upon command. Solid-rocket throttling ( vernier -thrusting) is more difficult...Here is a very straightforward micromete - oroid detector. A particle penetrates a pressurized vessel, usually a cylinder; the gas inside escapes; and a...The first Explorer satellites carried wire grids. The Micromete - oroid Satellite series used 46 cards, like those sketched in figure 11-85. Explorer

  15. Boomerang Satellites

    Science.gov (United States)

    Hesselbrock, Andrew; Minton, David A.

    2017-10-01

    We recently reported that the orbital architecture of the Martian environment allows for material in orbit around the planet to ``cycle'' between orbiting the planet as a ring, or as coherent satellites. Here we generalize our previous analysis to examine several factors that determine whether satellites accreting at the edge of planetary rings will cycle. In order for the orbiting material to cycle, tidal evolution must decrease the semi-major axis of any accreting satellites. In some systems, the density of the ring/satellite material, the surface mass density of the ring, the tidal parameters of the system, and the rotation rate of the primary body contribute to a competition between resonant ring torques and tidal dissipation that prevent this from occurring, either permanently or temporarily. Analyzing these criteria, we examine various bodies in our solar system (such as Saturn, Uranus, and Eris) to identify systems where cycling may occur. We find that a ring-satellite cycle may give rise to the current Uranian ring-satellite system, and suggest that Miranda may have formed from an early, more massive Uranian ring.

  16. The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays.

    Science.gov (United States)

    Pinhal, Danillo; Yoshimura, Tatiana S; Araki, Carlos S; Martins, Cesar

    2011-05-31

    Ribosomal 5S genes are well known for the critical role they play in ribosome folding and functionality. These genes are thought to evolve in a concerted fashion, with high rates of homogenization of gene copies. However, the majority of previous analyses regarding the evolutionary process of rDNA repeats were conducted in invertebrates and plants. Studies have also been conducted on vertebrates, but these analyses were usually restricted to the 18S, 5.8S and 28S rRNA genes. The recent identification of divergent 5S rRNA gene paralogs in the genomes of elasmobranches and teleost fishes indicate that the eukaryotic 5S rRNA gene family has a more complex genomic organization than previously thought. The availability of new sequence data from lower vertebrates such as teleosts and elasmobranches enables an enhanced evolutionary characterization of 5S rDNA among vertebrates. We identified two variant classes of 5S rDNA sequences in the genomes of Potamotrygonidae stingrays, similar to the genomes of other vertebrates. One class of 5S rRNA genes was shared only by elasmobranches. A broad comparative survey among 100 vertebrate species suggests that the 5S rRNA gene variants in fishes originated from rounds of genome duplication. These variants were then maintained or eliminated by birth-and-death mechanisms, under intense purifying selection. Clustered multiple copies of 5S rDNA variants could have arisen due to unequal crossing over mechanisms. Simultaneously, the distinct genome clusters were independently homogenized, resulting in the maintenance of clusters of highly similar repeats through concerted evolution. We believe that 5S rDNA molecular evolution in fish genomes is driven by a mixed mechanism that integrates birth-and-death and concerted evolution.

  17. Does risk of endometrial cancer for women without a germline mutation in a DNA mismatch repair gene depend on family history of endometrial cancer or colorectal cancer?

    Science.gov (United States)

    Bharati, Rajani; Jenkins, Mark A; Lindor, Noralane M; Le Marchand, Loïc; Gallinger, Steven; Haile, Robert W; Newcomb, Polly A; Hopper, John L; Win, Aung Ko

    2014-05-01

    To determine whether risk of endometrial cancer for women without a germline mutation in a DNA mismatch repair (MMR) gene depends on family history of endometrial or colorectal cancer. We retrospectively followed a cohort of 79,166 women who were recruited to the Colon Cancer Family Registry, after exclusion of women who were relatives of a carrier of a MMR gene mutation. The Kaplan-Meier failure method was used to estimate the cumulative risk of endometrial cancer. Cox regression was used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for association between family history of endometrial or colorectal cancer and risk of endometrial cancer. A total of 628 endometrial cancer cases were observed, with mean age at diagnosis of 54.4 (standard deviation: 15.7) years. The cumulative risk of endometrial cancer to age 70 years was estimated to be 0.94% (95% CI 0.83-1.05) for women with no family history of endometrial cancer, and 3.80% (95% CI 2.75-4.98) for women with at least one first- or second-degree relative with endometrial cancer. Compared with women without family history, we found an increased risk of endometrial cancer for women with at least one first- or second-degree relative with endometrial cancer (HR 3.66, 95% CI 2.63-5.08), and for women with one first-degree relative with colorectal cancer diagnosed at age cancer is associated with a family history of endometrial cancer or early-onset colorectal cancer for women without a MMR gene mutation, indicating for potential underlying genetic and environmental factors shared by colorectal and endometrial cancers other than caused by MMR gene mutations. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. cDNA cloning and characterization of mouse DTEF-1 and ETF, members of the TEA/ATTS family of transcription factors.

    Science.gov (United States)

    Yockey, C E; Shimizu, N

    1998-02-01

    Members of the TEA/ATTS family of transcription factors have been found in most representative eukaryotic organisms. In vertebrates, the TEA family contains at least four members, which share overlapping DNA-binding specificity and have similar transcriptional activation properties. In this article, we describe the cDNA cloning and characterization of the murine TEA proteins DTEF-1 (mDTEF-1) and ETF. Using in situ hybridization analysis of mouse embryos, we found that mDTEF-1 and ETF transcript distributions substantially overlap. ETF is expressed throughout the embryo except in the myocardium early in development, whereas late in development, it is enriched in lung and neuroectoderm. Mouse DTEF-1 is expressed at a much lower level throughout development and is substantially enriched in ectoderm and skin, as well as in the developing pituitary at midgestation. Northern blot analysis of adult mouse tissue total RNA showed that both ETF and mDTEF-1 are abundant in uterus and lung relative to other tissues. Using gel mobility shift assays and GAL4-fusion protein analysis, we demonstrated that the full coding sequences of ETF and mDTEF-1 encode M-CAT/GT-IIC-binding proteins containing activation domains.

  19. Crystal structures of the DNA-binding domain tetramer of the p53 tumor suppressor family member p73 bound to different full-site response elements.

    Science.gov (United States)

    Ethayathulla, Abdul S; Nguyen, H Thien; Viadiu, Hector

    2013-02-15

    How cells choose between developmental pathways remains a fundamental biological question. In the case of the p53 protein family, its three transcription factors (p73, p63, and p53) each trigger a gene expression pattern that leads to specific cellular pathways. At the same time, these transcription factors recognize the same response element (RE) consensus sequences, and their transactivation of target genes overlaps. We aimed to understand target gene selectivity at the molecular level by determining the crystal structures of the p73 DNA-binding domain (DBD) in complex with full-site REs that vary in sequence. We report two structures of the p73 DBD bound as a tetramer to 20-bp full-site REs based on two distinct quarter-sites: GAACA and GAACC. Our study confirms that the DNA-binding residues are conserved within the p53 family, whereas the dimerization and tetramerization interfaces diverge. Moreover, a conserved lysine residue in loop L1 of the DBD senses the presence of guanines in positions 2 and 3 of the quarter-site RE, whereas a conserved arginine in loop 3 adapts to changes in position 5. Sequence variations in the RE elicit a p73 conformational response that might explain target gene specificity.

  20. Is There any Alternative to Canonical DNA Barcoding of Multicellular Eukaryotic Species? A Case for the Tubulin Gene Family.

    Science.gov (United States)

    Breviario, Diego

    2017-04-13

    Modern taxonomy is largely relying on DNA barcoding, a nucleotide sequence-based approach that provides automated species identification using short orthologous DNA regions, mainly of organellar origin when applied to multicellular Eukaryotic species. Target DNA loci have been selected that contain a minimal amount of nucleotide sequence variation within species while diverging among species. This strategy is quite effective for the identification of vertebrates and other animal lineages but poses a problem in plants where different combinations of two or three loci are constantly used. Even so, species discrimination in such plant categories as ornamentals and herbals remain problematic as well as the confident identification of subspecies, ecotypes, and closely related or recently evolved species. All these limitations may be successfully solved by the application of a different strategy, based on the use of a multi-locus, ubiquitous, nuclear marker, that is tubulin. In fact, the tubulin-based polymorphism method can release specific genomic profiles to any plant species independently from its taxonomic group. This offers the rare possibility of an effective yet generic genomic fingerprint. In a more general context, the issue is raised about the possibility that approaches alternative to systematic DNA sequencing may still provide useful and simple solutions.

  1. Mutation-Induced Population Shift in the MexR Conformational Ensemble Disengages DNA Binding: A Novel Mechanism for MarR Family Derepression.

    Science.gov (United States)

    Anandapadamanaban, Madhanagopal; Pilstål, Robert; Andresen, Cecilia; Trewhella, Jill; Moche, Martin; Wallner, Björn; Sunnerhagen, Maria

    2016-08-02

    MexR is a repressor of the MexAB-OprM multidrug efflux pump operon of Pseudomonas aeruginosa, where DNA-binding impairing mutations lead to multidrug resistance (MDR). Surprisingly, the crystal structure of an MDR-conferring MexR mutant R21W (2.19 Å) presented here is closely similar to wild-type MexR. However, our extended analysis, by molecular dynamics and small-angle X-ray scattering, reveals that the mutation stabilizes a ground state that is deficient of DNA binding and is shared by both mutant and wild-type MexR, whereas the DNA-binding state is only transiently reached by the more flexible wild-type MexR. This population shift in the conformational ensemble is effected by mutation-induced allosteric coupling of contact networks that are independent in the wild-type protein. We propose that the MexR-R21W mutant mimics derepression by small-molecule binding to MarR proteins, and that the described allosteric model based on population shifts may also apply to other MarR family members. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. The Roles of P53 and its Family Proteins, P63 and P73, in the DNA Damage Stress Response in Organogenesis Stage Mouse Embryos.

    Science.gov (United States)

    El Husseini, Nazem; Hales, Barbara F

    2017-12-07

    Members of the P53 transcription factor family, P53, P63 and P73, play important roles in normal development and in regulating the expression of genes that control apoptosis and cell cycle progression in response to genotoxic stress. P53 is involved in the DNA damage response pathway that is activated by hydroxyurea in organogenesis-stage murine embryos. The extent to which P63 and P73 contribute to this stress response is not known. To address this question, we examined the roles of P53, P63 and P73 in mediating the response of Trp53-positive and Trp53-deficient murine embryos to a single dose of hydroxyurea (400 mg/kg) on gestational day 9. Hydroxyurea treatment downregulated the expression of Trp63 and upregulated Trp73 in the absence of effects on the levels of Trp53 transcripts; Trp73 upregulation was P53-dependent. At the protein level, hydroxyurea treatment increased the levels and phosphorylation of P53 in the absence of effects on P63 and P73. Upregulation of the expression of genes that regulate cell cycle arrest and apoptosis, Cdkn1a, Rb1, Fas, Trp53inp1 and Pmaip1, was P53-dependent in hydroxyurea-treated embryos. The increase in cleaved caspase-3 and cleaved mammalian sterile-20 like-1 (MST-1) kinase levels induced by hydroxyurea was also P53-dependent; in contrast, the increase in phosphorylated H2AX, a marker of DNA double strand breaks, in response to hydroxyurea treatment was only partially P53 dependent. Together, our data show that P53 is the principal P53 family member that is activated in the embryonic DNA damage response. © The Author 2017. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  3. Sequence Discrimination by DNA-binding Domain of ETS Family Transcription Factor PU.1 Is Linked to Specific Hydration of Protein-DNA Interface*

    Science.gov (United States)

    Poon, Gregory M. K.

    2012-01-01

    PU.1 is an essential transcription factor in normal hematopoietic lineage development. It recognizes a large number of promoter sites differing only in bases flanking a core consensus of 5′-GGAA-3′. DNA binding is mediated by its ETS domain, whose sequence selectivity directly corresponds to the transactivational activity and frequency of binding sites for full-length PU.1 in vivo. To better understand the basis of sequence discrimination, we characterized its binding properties to a high affinity and low affinity site. Despite sharing a homologous structural framework as confirmed by DNase I and hydroxyl radical footprinting, the two complexes exhibit striking heterogeneity in terms of hydration properties. High affinity binding is destabilized by osmotic stress, whereas low affinity binding is insensitive. Dimethyl sulfate footprinting showed that the major groove at the core consensus is protected in the high affinity complex but accessible in the low affinity one. Finally, destabilization of low affinity binding by salt is in quantitative agreement with the number of phosphate contacts but is substantially attenuated in high affinity binding. These observations support a mechanism of sequence discrimination wherein specifically bound water molecules couple flanking backbone contacts with base-specific interactions in a sequestered cavity at the core consensus. The implications of this model with respect to other ETS paralogs are discussed. PMID:22474303

  4. Satellite broadcasting

    Science.gov (United States)

    Gregory, D.; Rainger, P.; Harvey, R. V.; Jennings, A.

    Questions related to direct broadcasting satellites are addressed with attention given to celestial mechanics, synchronous orbits, propagation, international plans, domestic installation, related laws and system costs. The role of the World Administrative Planning Conference (WARC) organization is discussed and contrasted with that of the regional administrative radio conference. Topics related to the field of law include coverage and overspill, regulation and control, copyrights and international organizations. Alternative ways of estimating direct broadcasting system costs are presented with consideration given to satellite costs as a function of mass, launch costs and system costs as a function of power.

  5. Hyperresistance to 4-nitroquinoline 1-oxide cytotoxicity and reduced DNA damage formation in dermal fibroblast strains derived from five members of a cancer-prone family.

    Science.gov (United States)

    Mirzayans, R; Sabour, M; Rauth, A M; Paterson, M C

    1993-11-01

    Dermal fibroblasts cultured from members of a family presenting multiple polyps and sarcomas were compared with fibroblast strains from unrelated healthy donors for sensitivity to killing by four genotoxic agents. Cells from the sister of the male proband (strain 3437T), mother (strain 3703T), two of his paternal aunts (3701T and 3704T) and one paternal uncle (3702T) displayed marked resistance (1.8 to 4.3 times greater than the normal mean) to 4-nitroquinoline 1-oxide (4NQO), a procarcinogen whose DNA-damaging properties encompass those of both far (254 nm) ultraviolet (UV) light and ionising radiation. These same 4NQO-resistant cells, however, responded normally to reproductive inactivation by UV light, 60Co gamma radiation or the alkylating agent methylnitrosourea, signifying that the abnormal resistance of these cells to 4NQO is not associated with aberrant DNA metabolism. In keeping with this conclusion, exposure to a given dose of 4NQO produced decreased amounts of DNA damage and stimulated lower levels of repair DNA synthesis in all five 4NQO-resistant strains than in normal controls. Moreover, exogenous radiolabelled 4NQO accumulated to a lesser extent in the 4NQO-resistant than in the normal fibroblasts. Cell sonicates of strains 3437T, 3701T and 3702T exhibited reduced capacities (40-60% of normal) to catalise the conversion of 4NQO to the proximate carcinogen 4-hydroxyaminoquinoline 1-oxide. However, the 4NQO-resistant strains 3703T and 3704T carried out 4NQO bioreduction at normal rates. Our data therefore indicate that enhanced resistance to 4NQO cytotoxicity in 3437T, 3701T and 3702T is a consequence of anomalies in both intracellular accumulation and enzymatic reduction of 4NQO, whereas 4NQO resistance in 3703T and 3704T appears to result solely from reduced intracellular drug accumulation.

  6. Karakteristik genetik pada famili cervidae (Cervus unicolor, Cervus timorensis, dan Axis kuhlii) berdasarkan 12SrRNA mtDNA

    OpenAIRE

    Wirdateti; Gono Semiadi; Toshinao Okayama

    2004-01-01

    Genetic analysis from three species of Indonesia Cervidae (sambar deer, Cervus unicolor; rusa deer, Cervus timorensis; andBawean deer, Axis kuhlii) was conducted to analyze their relationship. Tissues and blood from twelve sambar deer, one rusa deer andthree Bawean deer were collected and analyzed for 12SrRNA using Primer forward (L1091) and reverse (H1478). The results indicatedthe amplication of mtDNA were 389 base nucleotide. There were 22 polimorphic sites, which were dominated by transit...

  7. Differential promoter methylation of kinesin family member 1a in plasma is associated with breast cancer and DNA repair capacity

    Science.gov (United States)

    GUERRERO-PRESTON, RAFAEL; HADAR, TAL; OSTROW, KIMBERLY LASKIE; SOUDRY, ETHAN; ECHENIQUE, MIGUEL; ILI-GANGAS, CARMEN; PÉREZ, GABRIELA; PEREZ, JIMENA; BREBI-MIEVILLE, PRISCILLA; DESCHAMPS, JOSÉ; MORALES, LUISA; BAYONA, MANUEL; SIDRANSKY, DAVID; MATTA, JAIME

    2014-01-01

    Methylation alterations of CpG islands, CpG island shores and first exons are key events in the formation and progression of human cancer, and an increasing number of differentially methylated regions and genes have been identified in breast cancer. Recent studies of the breast cancer methylome using deep sequencing and microarray platforms are providing a novel insight on the different roles aberrant methylation plays in molecular subtypes of breast cancer. Accumulating evidence from a subset of studies suggests that promoter methylation of tumor-suppressor genes associated with breast cancer can be quantified in circulating DNA. However, there is a paucity of studies that examine the combined presence of genetic and epigenetic alterations associated with breast cancer using blood-based assays. Dysregulation of DNA repair capacity (DRC) is a genetic risk factor for breast cancer that has been measured in lymphocytes. We isolated plasma DNA from 340 participants in a breast cancer case control project to study promoter methylation levels of five genes previously shown to be associated with breast cancer in frozen tissue and in cell line DNA: MAL, KIF1A, FKBP4, VGF and OGDHL. Methylation of at least one gene was found in 49% of the cases compared to 20% of the controls. Three of the four genes had receiver characteristic operator curve values of ≥0.50: MAL (0.64), KIF1A (0.51) and OGDHL (0.53). KIF1A promoter methylation was associated with breast cancer and inversely associated with DRC. This is the first evidence of a significant association between genetic and epigenetic alterations in breast cancer using blood-based tests. The potential diagnostic utility of these biomarkers and their relevance for breast cancer risk prediction should be examined in larger cohorts. PMID:24927296

  8. Incomplete sequence homogenization in 45S rDNA multigene families: intermixed IGS heterogeneity within the single NOR locus of the polyploid species Medicago arborea (Fabaceae).

    Science.gov (United States)

    Galián, José A; Rosato, Marcela; Rosselló, Josep A

    2014-08-01

    Ribosomal sequences have become the classical example of the genomic homogenization of nuclear multigene families. Despite theoretical advantages and modelling predictions that support concerted evolution of the 45S rDNA, several reports have found intragenomic polymorphisms. However, the origins and causes of these rDNA polymorphisms are difficult to assess because seed plants show a wide range of 45S rDNA loci number variation, especially in polyploids. Medicago arborea is a tetraploid species that has a single 45S rDNA locus. This feature makes this species a suitable case study to assess the fate of ribosomal IGS homogenization in polyploid species showing nucleolus organizer region (NOR) reduction. The intergenic spacer (IGS) region was amplified by long PCR and the fragments were cloned and sequenced by a primer-walking strategy. The physical mapping of the whole and partial IGS variants was assessed by fluorescent in situ hybridization (FISH) and fibre-FISH methods on mitotic chromosomes and extended DNA fibres, respectively. Two IGS fragments of 4·8 and 3·5 kb were obtained showing structural features of functional sequences. The shorter variant appears to be a truncated copy of the 4·8 kb fragment that lacks the duplication of the transcription initiation site region and the entire D region. The physical localization of the two IGS variants on metaphase chromosomes and extended DNA fibres using FISH corroborated their joint presence within the same locus. In addition, no spatial structure of the two variants was detected within the NOR. The results suggest that full sequence homogenization is not operating within the NOR locus of M. arborea. The structure of the NOR locus reported here departs from the models of IGS heterogeneity present in plants and caution against assuming the widespread belief that intragenomic ribosomal heterogeneity is mainly due to sequence variation between paralogous loci. © The Author 2014. Published by Oxford University

  9. Organization and evolution of Gorilla centromeric DNA from old strategies to new approaches.

    Science.gov (United States)

    Catacchio, C R; Ragone, R; Chiatante, G; Ventura, M

    2015-09-21

    The centromere/kinetochore interaction is responsible for the pairing and segregation of replicated chromosomes in eukaryotes. Centromere DNA is portrayed as scarcely conserved, repetitive in nature, quickly evolving and protein-binding competent. Among primates, the major class of centromeric DNA is the pancentromeric α-satellite, made of arrays of 171 bp monomers, repeated in a head-to-tail pattern. α-satellite sequences can either form tandem heterogeneous monomeric arrays or assemble in higher-order repeats (HORs). Gorilla centromere DNA has barely been characterized, and data are mainly based on hybridizations of human alphoid sequences. We isolated and finely characterized gorilla α-satellite sequences and revealed relevant structure and chromosomal distribution similarities with other great apes as well as gorilla-specific features, such as the uniquely octameric structure of the suprachromosomal family-2 (SF2). We demonstrated for the first time the orthologous localization of alphoid suprachromosomal families-1 and -2 (SF1 and SF2) between human and gorilla in contrast to chimpanzee centromeres. Finally, the discovery of a new 189 bp monomer type in gorilla centromeres unravels clues to the role of the centromere protein B, paving the way to solve the significance of the centromere DNA's essential repetitive nature in association with its function and the peculiar evolution of the α-satellite sequence.

  10. The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive.

    Science.gov (United States)

    Larracuente, Amanda M

    2014-11-25

    Satellite DNA can make up a substantial fraction of eukaryotic genomes and has roles in genome structure and chromosome segregation. The rapid evolution of satellite DNA can contribute to genomic instability and genetic incompatibilities between species. Despite its ubiquity and its contribution to genome evolution, we currently know little about the dynamics of satellite DNA evolution. The Responder (Rsp) satellite DNA family is found in the pericentric heterochromatin of chromosome 2 of Drosophila melanogaster. Rsp is well-known for being the target of Segregation Distorter (SD)- an autosomal meiotic drive system in D. melanogaster. I present an evolutionary genetic analysis of the Rsp family of repeats in D. melanogaster and its closely-related species in the melanogaster group (D. simulans, D. sechellia, D. mauritiana, D. erecta, and D. yakuba) using a combination of available BAC sequences, whole genome shotgun Sanger reads, Illumina short read deep sequencing, and fluorescence in situ hybridization. I show that Rsp repeats have euchromatic locations throughout the D. melanogaster genome, that Rsp arrays show evidence for concerted evolution, and that Rsp repeats exist outside of D. melanogaster, in the melanogaster group. The repeats in these species are considerably diverged at the sequence level compared to D. melanogaster, and have a strikingly different genomic distribution, even between closely-related sister taxa. The genomic organization of the Rsp repeat in the D. melanogaster genome is complex-it exists of large blocks of tandem repeats in the heterochromatin and small blocks of tandem repeats in the euchromatin. My discovery of heterochromatic Rsp-like sequences outside of D. melanogaster suggests that SD evolved after its target satellite and that the evolution of the Rsp satellite family is highly dynamic over a short evolutionary time scale (<240,000 years).

  11. Functional Annotation, Genome Organization and Phylogeny of the Grapevine (Vitis vinifera Terpene Synthase Gene Family Based on Genome Assembly, FLcDNA Cloning, and Enzyme Assays

    Directory of Open Access Journals (Sweden)

    Toub Omid

    2010-10-01

    Full Text Available Abstract Background Terpenoids are among the most important constituents of grape flavour and wine bouquet, and serve as useful metabolite markers in viticulture and enology. Based on the initial 8-fold sequencing of a nearly homozygous Pinot noir inbred line, 89 putative terpenoid synthase genes (VvTPS were predicted by in silico analysis of the grapevine (Vitis vinifera genome assembly 1. The finding of this very large VvTPS family, combined with the importance of terpenoid metabolism for the organoleptic properties of grapevine berries and finished wines, prompted a detailed examination of this gene family at the genomic level as well as an investigation into VvTPS biochemical functions. Results We present findings from the analysis of the up-dated 12-fold sequencing and assembly of the grapevine genome that place the number of predicted VvTPS genes at 69 putatively functional VvTPS, 20 partial VvTPS, and 63 VvTPS probable pseudogenes. Gene discovery and annotation included information about gene architecture and chromosomal location. A dense cluster of 45 VvTPS is localized on chromosome 18. Extensive FLcDNA cloning, gene synthesis, and protein expression enabled functional characterization of 39 VvTPS; this is the largest number of functionally characterized TPS for any species reported to date. Of these enzymes, 23 have unique functions and/or phylogenetic locations within the plant TPS gene family. Phylogenetic analyses of the TPS gene family showed that while most VvTPS form species-specific gene clusters, there are several examples of gene orthology with TPS of other plant species, representing perhaps more ancient VvTPS, which have maintained functions independent of speciation. Conclusions The highly expanded VvTPS gene family underpins the prominence of terpenoid metabolism in grapevine. We provide a detailed experimental functional annotation of 39 members of this important gene family in grapevine and comprehensive information

  12. Functional Annotation, Genome Organization and Phylogeny of the Grapevine (Vitis vinifera) Terpene Synthase Gene Family Based on Genome Assembly, FLcDNA Cloning, and Enzyme Assays

    Science.gov (United States)

    2010-01-01

    Background Terpenoids are among the most important constituents of grape flavour and wine bouquet, and serve as useful metabolite markers in viticulture and enology. Based on the initial 8-fold sequencing of a nearly homozygous Pinot noir inbred line, 89 putative terpenoid synthase genes (VvTPS) were predicted by in silico analysis of the grapevine (Vitis vinifera) genome assembly [1]. The finding of this very large VvTPS family, combined with the importance of terpenoid metabolism for the organoleptic properties of grapevine berries and finished wines, prompted a detailed examination of this gene family at the genomic level as well as an investigation into VvTPS biochemical functions. Results We present findings from the analysis of the up-dated 12-fold sequencing and assembly of the grapevine genome that place the number of predicted VvTPS genes at 69 putatively functional VvTPS, 20 partial VvTPS, and 63 VvTPS probable pseudogenes. Gene discovery and annotation included information about gene architecture and chromosomal location. A dense cluster of 45 VvTPS is localized on chromosome 18. Extensive FLcDNA cloning, gene synthesis, and protein expression enabled functional characterization of 39 VvTPS; this is the largest number of functionally characterized TPS for any species reported to date. Of these enzymes, 23 have unique functions and/or phylogenetic locations within the plant TPS gene family. Phylogenetic analyses of the TPS gene family showed that while most VvTPS form species-specific gene clusters, there are several examples of gene orthology with TPS of other plant species, representing perhaps more ancient VvTPS, which have maintained functions independent of speciation. Conclusions The highly expanded VvTPS gene family underpins the prominence of terpenoid metabolism in grapevine. We provide a detailed experimental functional annotation of 39 members of this important gene family in grapevine and comprehensive information about gene structure and

  13. SmTRC1, a novel Schistosoma mansoni DNA transposon, discloses new families of animal and fungi transposons belonging to the CACTA superfamily

    Directory of Open Access Journals (Sweden)

    Verjovski-Almeida Sergio

    2006-11-01

    Full Text Available Abstract Background The CACTA (also called En/Spm superfamily of DNA-only transposons contain the core sequence CACTA in their Terminal Inverted Repeats (TIRs and so far have only been described in plants. Large transcriptome and genome sequence data have recently become publicly available for Schistosoma mansoni, a digenetic blood fluke that is a major causative agent of schistosomiasis in humans, and have provided a comprehensive repository for the discovery of novel genes and repetitive elements. Despite the extensive description of retroelements in S. mansoni, just a single DNA-only transposon belonging to the Merlin family has so far been reported in this organism. Results We describe a novel S. mansoni transposon named SmTRC1, for S. mansoni Transposon Related to CACTA 1, an element that shares several characteristics with plant CACTA transposons. Southern blotting indicates approximately 30–300 copies of SmTRC1 in the S. mansoni genome. Using genomic PCR followed by cloning and sequencing, we amplified and characterized a full-length and a truncated copy of this element. RT-PCR using S. mansoni mRNA followed by cloning and sequencing revealed several alternatively spliced transcripts of this transposon, resulting in distinct ORFs coding for different proteins. Interestingly, a survey of complete genomes from animals and fungi revealed several other novel TRC elements, indicating new families of DNA transposons belonging to the CACTA superfamily that have not previously been reported in these kingdoms. The first three bases in the S. mansoni TIR are CCC and they are identical to those in the TIRs of the insects Aedes aegypti and Tribolium castaneum, suggesting that animal TRCs may display a CCC core sequence. Conclusion The DNA-only transposable element SmTRC1 from S. mansoni exhibits various characteristics, such as generation of multiple alternatively-spliced transcripts, the presence of terminal inverted repeats at the extremities of

  14. Strikingly different penetrance of LHON in two Chinese families with primary mutation G11778A is independent of mtDNA haplogroup background and secondary mutation G13708A.

    Science.gov (United States)

    Wang, Hua-Wei; Jia, Xiaoyun; Ji, Yanli; Kong, Qing-Peng; Zhang, Qingjiong; Yao, Yong-Gang; Zhang, Ya-Ping

    2008-08-25

    The penetrance of Leber's hereditary optic neuropathy (LHON) in families with primary mitochondrial DNA (mtDNA) mutations is very complex. Matrilineal and nuclear genetic background, as well as environmental factors, have been reported to be involved in different affected pedigrees. Here we describe two large Chinese families that show a striking difference in the penetrance of LHON, in which 53.3% and 15.0% of members were affected (PLHON in the two Chinese families is independent of both their mtDNA haplotype background and a secondary mutation G13708A. As a result, it is likely that unknown nuclear gene involvement and/or other factors contribute to the strikingly different penetrance of LHON.

  15. Karakteristik genetik pada famili cervidae (Cervus unicolor, Cervus timorensis, dan Axis kuhlii berdasarkan 12SrRNA mtDNA

    Directory of Open Access Journals (Sweden)

    Wirdateti

    2004-12-01

    Full Text Available Genetic analysis from three species of Indonesia Cervidae (sambar deer, Cervus unicolor; rusa deer, Cervus timorensis; andBawean deer, Axis kuhlii was conducted to analyze their relationship. Tissues and blood from twelve sambar deer, one rusa deer andthree Bawean deer were collected and analyzed for 12SrRNA using Primer forward (L1091 and reverse (H1478. The results indicatedthe amplication of mtDNA were 389 base nucleotide. There were 22 polimorphic sites, which were dominated by transition and gave9 haplotypes that were 5 in sambar deer, 1 in rusa deer and 3 in Bawean deer.

  16. Cloning of a cDNA encoding a novel human nuclear phosphoprotein belonging to the WD-40 family

    DEFF Research Database (Denmark)

    Honoré, B; Leffers, H; Madsen, Peder

    1994-01-01

    We have cloned and expressed in vaccinia virus a cDNA encoding an ubiquitous 501-amino-acid (aa) phosphoprotein that corresponds to protein IEF SSP 9502 (79,400 Da, pI 4.5) in the master 2-D-gel keratinocyte protein database [Celis et al., Electrophoresis 14 (1993) 1091-1198]. The deduced aa......-134]. The protein contains a nuclear targeting signal (KKKGK), and fractionation of transformed human amnion cells (AMA) in karyoplasts and cytoplasts confirmed that it is predominantly localized in the nucleus. Database searching indicated that IEF SSP 9502 is a putative human homologue of the Saccharomyces...

  17. Archaeal DNA polymerases in biotechnology.

    Science.gov (United States)

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Huang, Yanchao

    2015-08-01

    DNA polymerase (pol) is a ubiquitous enzyme that synthesizes DNA strands in all living cells. In vitro, DNA pol is used for DNA manipulation, including cloning, PCR, site-directed mutagenesis, sequencing, and several other applications. Family B archaeal DNA pols have been widely used for molecular biological methods. Biochemical and structural studies reveal that each archaeal DNA pol has different characteristics with respect to fidelity, processivity and thermostability. Due to their high fidelity and strong thermostability, family B archaeal DNA pols have the extensive application on high-fidelity PCR, DNA sequencing, and site-directed mutagenesis while family Y archaeal DNA pols have the potential for error-prone PCR and random mutagenesis because of their low fidelity and strong thermostability. This information combined with mutational analysis has been used to construct novel DNA pols with altered properties that enhance their use as biotechnological reagents. In this review, we focus on the development and use of family B archaeal DNA pols.

  18. Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family

    Science.gov (United States)

    2010-01-01

    Background In flowering plants and animals the most common ribosomal RNA genes (rDNA) organisation is that in which 35S (encoding 18S-5.8S-26S rRNA) and 5S genes are physically separated occupying different chromosomal loci. However, recent observations established that both genes have been unified to a single 35S-5S unit in the genus Artemisia (Asteraceae), a genomic arrangement typical of primitive eukaryotes such as yeast, among others. Here we aim to reveal the origin, distribution and mechanisms leading to the linked organisation of rDNA in the Asteraceae by analysing unit structure (PCR, Southern blot, sequencing), gene copy number (quantitative PCR) and chromosomal position (FISH) of 5S and 35S rRNA genes in ~200 species representing the family diversity and other closely related groups. Results Dominant linked rDNA genotype was found within three large groups in subfamily Asteroideae: tribe Anthemideae (93% of the studied cases), tribe Gnaphalieae (100%) and in the "Heliantheae alliance" (23%). The remaining five tribes of the Asteroideae displayed canonical non linked arrangement of rDNA, as did the other groups in the Asteraceae. Nevertheless, low copy linked genes were identified among several species that amplified unlinked units. The conserved position of functional 5S insertions downstream from the 26S gene suggests a unique, perhaps retrotransposon-mediated integration event at the base of subfamily Asteroideae. Further evolution likely involved divergence of 26S-5S intergenic spacers, amplification and homogenisation of units across the chromosomes and concomitant elimination of unlinked arrays. However, the opposite trend, from linked towards unlinked arrangement was also surmised in few species indicating possible reversibility of these processes. Conclusions Our results indicate that nearly 25% of Asteraceae species may have evolved unusual linked arrangement of rRNA genes. Thus, in plants, fundamental changes in intrinsic structure of rDNA units

  19. Distinct evolutionary histories of the DNA-A and DNA-B components of bipartite begomoviruses

    Directory of Open Access Journals (Sweden)

    Nawaz-ul-Rehman Muhammad

    2010-04-01

    Full Text Available Abstract Background Viruses of the genus Begomovirus (family Geminiviridae have genomes consisting of either one or two genomic components. The component of bipartite begomoviruses known as DNA-A is homologous to the genomes of all geminiviruses and encodes proteins required for replication, control of gene expression, overcoming host defenses, encapsidation and insect transmission. The second component, referred to as DNA-B, encodes two proteins with functions in intra- and intercellular movement in host plants. The origin of the DNA-B component remains unclear. The study described here was initiated to investigate the relationship between the DNA-A and DNA-B components of bipartite begomoviruses with a view to unraveling their evolutionary histories and providing information on the possible origin of the DNA-B component. Results Comparative phylogenetic and exhaustive pairwise sequence comparison of all DNA-A and DNA-B components of begomoviruses demonstrates that the two molecules have very distinct molecular evolutionary histories and likely are under very different evolutionary pressures. The analysis highlights that component exchange has played a far greater role in diversification of begomoviruses than previously suspected, although there are distinct differences in the apparent ability of different groups of viruses to utilize this "sexual" mechanism of genetic exchange. Additionally we explore the hypothesis that DNA-B originated as a satellite that was captured by the monopartite progenitor of all extant bipartite begomoviruses and subsequently evolved to become the integral (essential genome component that we recognize today. The situation with present-day satellites associated with begomoviruses provides some clues to the processes and selection pressures that may have led to the "domestication" of a wild progenitor of the DNA-B component. Conclusions The analysis has highlighted the greater genetic variation of DNA-B components, in

  20. Strikingly different penetrance of LHON in two Chinese families with primary mutation G11778A is independent of mtDNA haplogroup background and secondary mutation G13708A

    Energy Technology Data Exchange (ETDEWEB)

    Wang Huawei [Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223 (China)]|[Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091 (China); Jia Xiaoyun; Ji Yanli [State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060 (China); Kong Qingpeng [State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 (China); Zhang Qingjiong [State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060 (China)], E-mail: qingjiongzhang@yahoo.com; Yao Yonggang [Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223 (China)]|[State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 (China)], E-mail: ygyaozh@yahoo.com; Zhang Yaping [Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091 (China)]|[State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 (China)

    2008-08-25

    The penetrance of Leber's hereditary optic neuropathy (LHON) in families with primary mitochondrial DNA (mtDNA) mutations is very complex. Matrilineal and nuclear genetic background, as well as environmental factors, have been reported to be involved in different affected pedigrees. Here we describe two large Chinese families that show a striking difference in the penetrance of LHON, in which 53.3% and 15.0% of members were affected (P < 0.02), respectively. Analysis of the complete mtDNA genome of the two families revealed the presence of the primary mutation G11778A and several other variants suggesting the same haplogroup status G2a. The family with higher penetrance contained a previously described secondary mutation G13708A, which presents a polymorphism in normal Chinese samples and does not affect in vivo mitochondrial oxidative metabolism as described in a previous study. Evolutionary analysis failed to indicate any putatively pathogenic mutation that cosegregated with G11778A in these two pedigrees. Our results suggest that the variable penetrance of LHON in the two Chinese families is independent of both their mtDNA haplotype background and a secondary mutation G13708A. As a result, it is likely that unknown nuclear gene involvement and/or other factors contribute to the strikingly different penetrance of LHON.

  1. Intravascular persistence of Anaplasma platys, Ehrlichia chaffeensis, and Ehrlichia ewingii DNA in the blood of a dog and two family members.

    Science.gov (United States)

    Breitschwerdt, Edward B; Hegarty, Barbara C; Qurollo, Barbara A; Saito, Tais B; Maggi, Ricardo G; Blanton, Lucas S; Bouyer, Donald H

    2014-07-01

    Anaplasmosis, caused by Anaplasma phagocytophilum and Anaplasma platys, and ehrlichiosis, caused by Ehrlichia chaffeensis, Ehrlichia ewingii, the "Panola Mountain Ehrlichia" and Ehrlichia muris-like pathogens have been identified as emerging tick borne infectious diseases in dogs and human patients. Persistent intravascular infection with these bacteria is well documented in dogs, but is less well documented in human beings. Serology and PCR targeting multiple microbial genes, followed by DNA sequencing, was used to test sequential blood samples. Tissue culture isolation was attempted in two laboratories. A. platys, E. chaffeensis, and E. ewingii DNA was amplified from two Anaplasma and Ehrlichia seronegative family members and their dog, all lacking typical symptoms of anaplasmosis or ehrlichiosis. Following treatment with doxycycline, the dog and mother were Anaplasma and Ehrlichia spp. PCR negative. Sequential PCR testing provided molecular evidence supporting intravascular persistence of A. platys and Ehrlichia spp. in two humans and their dog. Diagnosticians and clinicians should consider the potential for co-infections due to these tick borne organisms.

  2. Deficiency of CCAAT/enhancer binding protein family DNA binding prevents malignant conversion of adenoma to carcinoma in NNK-induced lung carcinogenesis in the mouse

    Directory of Open Access Journals (Sweden)

    Kimura Shioko

    2012-12-01

    Full Text Available Abstract Background The CCAAT/enhancer binding proteins (C/EBPs play important roles in carcinogenesis of many tumors including the lung. Since multiple C/EBPs are expressed in lung, the combinatorial expression of these C/EBPs on lung carcinogenesis is not known. Methods A transgenic mouse line expressing a dominant negative A-C/EBP under the promoter of lung epithelial Clara cell secretory protein (CCSP gene in doxycycline dependent fashion was subjected to 4-(methylnitrosamino-1-(3-pyridyl-1-butanone (NNK-induced lung carcinogenesis bioassay in the presence and absence of doxycycline, and the effect of abolition of DNA binding activities of C/EBPs on lung carcinogenesis was examined. Results A-C/EBP expression was found not to interfere with tumor development; however, it suppressed the malignant conversion of adenoma to carcinoma during NNK-induced lung carcinogenesis. The results suggested that Ki67 may be used as a marker for lung carcinomas in mouse. Conclusions The DNA binding of C/EBP family members can be used as a potential molecular target for lung cancer therapy.

  3. A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family geminiviridae implicated in grapevine redleaf disease by next-generation sequencing.

    Directory of Open Access Journals (Sweden)

    Sudarsana Poojari

    Full Text Available A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L. cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s associated with this emerging disease, designated as grapevine redleaf disease (GRD. High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleaf-associated virus (GRLaV, and Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac Walsh from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Franc-associated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family Geminiviridae with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms.

  4. A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family geminiviridae implicated in grapevine redleaf disease by next-generation sequencing.

    Science.gov (United States)

    Poojari, Sudarsana; Alabi, Olufemi J; Fofanov, Viacheslav Y; Naidu, Rayapati A

    2013-01-01

    A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L.) cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s) associated with this emerging disease, designated as grapevine redleaf disease (GRD). High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleaf-associated virus (GRLaV), and Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac Walsh) from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Franc-associated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family Geminiviridae with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms.

  5. Solar satellites

    Energy Technology Data Exchange (ETDEWEB)

    Poher, C.

    1982-01-01

    A reference system design, projected costs, and the functional concepts of a satellite solar power system (SSPS) for converting sunlight falling on solar panels of a satellite in GEO to a multi-GW beam which could be received by a rectenna on earth are outlined. Electricity transmission by microwaves has been demonstrated, and a reference design system for supplying 5 GW dc to earth was devised. The system will use either monocrystalline Si or concentrator GaAs solar cells for energy collection in GEO. Development is still needed to improve the lifespan of the cells. Currently, the cell performance degrades 50 percent in efficiency after 7-8 yr in space. Each SSPS satellite would weigh either 34,000 tons (Si) or 51,000 tons (GaAs), thereby requiring the fabrication of a heavy lift launch vehicle or a single-stage-to-orbit transport in order to minimize launch costs. Costs for the solar panels have been estimated at $500/kW using the GaAs technology, with transport costs for materials to GEO being $40/kg.

  6. Functional Studies of ssDNA Binding Ability of MarR Family Protein TcaR from Staphylococcus epidermidis

    OpenAIRE

    Yu-Ming Chang; Cammy K-M Chen; Yuan-Chih Chang; Wen-Yih Jeng; Ming-Hon Hou; Andrew H-J Wang

    2012-01-01

    The negative transcription regulator of the ica locus, TcaR, regulates proteins involved in the biosynthesis of poly-N-acetylglucosamine (PNAG). Absence of TcaR increases PNAG production and promotes biofilm formation in Staphylococci. Previously, the 3D structure of TcaR in its apo form and its complex structure with several antibiotics have been analyzed. However, the detailed mechanism of multiple antibiotic resistance regulator (MarR) family proteins such as TcaR is unclear and only restr...

  7. FANCM c.5791C>T nonsense mutation (rs144567652) induces exon skipping, affects DNA repair activity and is a familial breast cancer risk factor

    Science.gov (United States)

    Peterlongo, Paolo; Catucci, Irene; Colombo, Mara; Caleca, Laura; Mucaki, Eliseos; Bogliolo, Massimo; Marin, Maria; Damiola, Francesca; Bernard, Loris; Pensotti, Valeria; Volorio, Sara; Dall'Olio, Valentina; Meindl, Alfons; Bartram, Claus; Sutter, Christian; Surowy, Harald; Sornin, Valérie; Dondon, Marie-Gabrielle; Eon-Marchais, Séverine; Stoppa-Lyonnet, Dominique; Andrieu, Nadine; Sinilnikova, Olga M.; Mitchell, Gillian; James, Paul A.; Thompson, Ella; Marchetti, Marina; Verzeroli, Cristina; Tartari, Carmen; Capone, Gabriele Lorenzo; Putignano, Anna Laura; Genuardi, Maurizio; Medici, Veronica; Marchi, Isabella; Federico, Massimo; Tognazzo, Silvia; Matricardi, Laura; Agata, Simona; Dolcetti, Riccardo; Puppa, Lara Della; Cini, Giulia; Gismondi, Viviana; Viassolo, Valeria; Perfumo, Chiara; Mencarelli, Maria Antonietta; Baldassarri, Margherita; Peissel, Bernard; Roversi, Gaia; Silvestri, Valentina; Rizzolo, Piera; Spina, Francesca; Vivanet, Caterina; Tibiletti, Maria Grazia; Caligo, Maria Adelaide; Gambino, Gaetana; Tommasi, Stefania; Pilato, Brunella; Tondini, Carlo; Corna, Chiara; Bonanni, Bernardo; Barile, Monica; Osorio, Ana; Benitez, Javier; Balestrino, Luisa; Ottini, Laura; Manoukian, Siranoush; Pierotti, Marco A.; Renieri, Alessandra; Varesco, Liliana; Couch, Fergus J.; Wang, Xianshu; Devilee, Peter; Hilbers, Florentine S.; van Asperen, Christi J.; Viel, Alessandra; Montagna, Marco; Cortesi, Laura; Diez, Orland; Balmaña, Judith; Hauke, Jan; Schmutzler, Rita K.; Papi, Laura; Pujana, Miguel Angel; Lázaro, Conxi; Falanga, Anna; Offit, Kenneth; Vijai, Joseph; Campbell, Ian; Burwinkel, Barbara; Kvist, Anders; Ehrencrona, Hans; Mazoyer, Sylvie; Pizzamiglio, Sara; Verderio, Paolo; Surralles, Jordi; Rogan, Peter K.; Radice, Paolo

    2015-01-01

    Numerous genetic factors that influence breast cancer risk are known. However, approximately two-thirds of the overall familial risk remain unexplained. To determine whether some of the missing heritability is due to rare variants conferring high to moderate risk, we tested for an association between the c.5791C>T nonsense mutation (p.Arg1931*; rs144567652) in exon 22 of FANCM gene and breast cancer. An analysis of genotyping data from 8635 familial breast cancer cases and 6625 controls from different countries yielded an association between the c.5791C>T mutation and breast cancer risk [odds ratio (OR) = 3.93 (95% confidence interval (CI) = 1.28–12.11; P = 0.017)]. Moreover, we performed two meta-analyses of studies from countries with carriers in both cases and controls and of all available data. These analyses showed breast cancer associations with OR = 3.67 (95% CI = 1.04–12.87; P = 0.043) and OR = 3.33 (95% CI = 1.09–13.62; P = 0.032), respectively. Based on information theory-based prediction, we established that the mutation caused an out-of-frame deletion of exon 22, due to the creation of a binding site for the pre-mRNA processing protein hnRNP A1. Furthermore, genetic complementation analyses showed that the mutation influenced the DNA repair activity of the FANCM protein. In summary, we provide evidence for the first time showing that the common p.Arg1931* loss-of-function variant in FANCM is a risk factor for familial breast cancer. PMID:26130695

  8. A whisper-game perspective on the family communication of DNA-test results: A retrospective study on the communication process of BRCA1/2-test results between proband and relatives

    NARCIS (Netherlands)

    J. Vos (Jeroen); F. Menko (Fred); A.M. Jansen (Anna); C.J. van Asperen (Christi); A.M. Stiggelbout (Anne); A. Tibben (Arend)

    2011-01-01

    textabstractObjective of this paper is to study how DNA-test result information was communicated and perceived within families. A retrospective descriptive study in 13 probands with a BRCA1/2 unclassified variant, 7 with a pathogenic mutation, 5 with an uninformative result, and in 44, 14, and 12 of

  9. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  10. The discovery of Iberobaeniidae (Coleoptera: Elateroidea): a new family of beetles from Spain, with immatures detected by environmental DNA sequencing.

    Science.gov (United States)

    Bocak, L; Kundrata, R; Fernández, C Andújar; Vogler, A P

    2016-05-11

    The ongoing exploration of biodiversity and the implementation of new molecular tools continue to unveil hitherto unknown lineages. Here, we report the discovery of three species of neotenic beetles for which we propose the new family Iberobaeniidae. Complete mitochondrial genomes and rRNA genes recovered Iberobaeniidae as a deep branch in Elateroidea, as sister to Lycidae (net-winged beetles). Two species of the new genus Iberobaenia, Iberobaenia minuta sp. nov. and Iberobaenia lencinai sp. nov. were found in the adult stage. In a separate incidence, a related sequence was identified in bulk samples of soil invertebrates subjected to shotgun sequencing and mitogenome assembly, which was traced to a larval voucher specimen of a third species of Iberobaenia Iberobaenia shows characters shared with other elateroid neotenic lineages, including soft-bodiedness, the hypognathous head, reduced mouthparts with reduced labial palpomeres, and extremely small-bodied males without strengthening structures due to miniaturization. Molecular dating shows that Iberobaeniidae represents an ancient relict lineage originating in the Lower Jurassic, which possibly indicates a long history of neoteny, usually considered to be evolutionarily short-lived. The apparent endemism of Iberobaeniidae in the Mediterranean region highlights the importance of this biodiversity hotspot and the need for further species exploration even in the well-studied European continent. © 2016 The Author(s).

  11. New insight into multifunctional role of peroxiredoxin family protein: Determination of DNA protection properties of bacterioferritin comigratory protein under hyperthermal and oxidative stresses

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sangmin, E-mail: taeinlee2011@kangwon.ac.kr [Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, South Korea (Korea, Republic of); Chung, Jeong Min [Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, South Korea (Korea, Republic of); Yun, Hyung Joong; Won, Jonghan [Advanced Nano Surface Research Group, Korea Basic Science Institute, 169-148 Gwahak-ro, Daejeon, 305-333 (Korea, Republic of); Jung, Hyun Suk, E-mail: hsjung@kangwon.ac.kr [Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, South Korea (Korea, Republic of)

    2016-01-22

    Bacterioferritin comigratory protein (BCP) is a monomeric conformer acting as a putative thiol-dependent bacterial peroxidase, however molecular basis of DNA-protection via DNA-binding has not been clearly understood. In this study, we characterized the DNA binding properties of BCP using various lengths and differently shaped architectures of DNA. An electrophoretic mobility shift assay and electron microscopy analysis showed that recombinant TkBCP bound to DNA of a circular shape (double-stranded DNA and single-stranded DNA) and a linear shape (16–1000 bp) as well as various architectures of DNA. In addition, DNA protection experiments indicated that TkBCP can protect DNA against hyperthermal and oxidative stress by removing highly reactive oxygen species (ROS) or by protecting DNA from thermal degradation. Based on these results, we suggest that TkBCP is a multi-functional DNA-binding protein which has DNA chaperon and antioxidant functions. - Highlights: • Bacterioferritin comigratory protein (BCP) protects DNA from oxidative stress by reducing ROS. • TkBCP does not only scavenge ROS, but also protect DNA from hyperthermal stress. • BCP potentially adopts the multi-functional role in DNA binding activities and anti-oxidant functions.

  12. Lesion-Induced Mutation in the Hyperthermophilic Archaeon Sulfolobus acidocaldarius and Its Avoidance by the Y-Family DNA Polymerase Dbh.

    Science.gov (United States)

    Sakofsky, Cynthia J; Grogan, Dennis W

    2015-10-01

    Hyperthermophilic archaea offer certain advantages as models of genome replication, and Sulfolobus Y-family polymerases Dpo4 (S. solfataricus) and Dbh (S. acidocaldarius) have been studied intensively in vitro as biochemical and structural models of trans-lesion DNA synthesis (TLS). However, the genetic functions of these enzymes have not been determined in the native context of living cells. We developed the first quantitative genetic assays of replication past defined DNA lesions and error-prone motifs in Sulfolobus chromosomes and used them to measure the efficiency and accuracy of bypass in normal and dbh(-) strains of Sulfolobus acidocaldarius. Oligonucleotide-mediated transformation allowed low levels of abasic-site bypass to be observed in S. acidocaldarius and demonstrated that the local sequence context affected bypass specificity; in addition, most erroneous TLS did not require Dbh function. Applying the technique to another common lesion, 7,8-dihydro-8-oxo-deoxyguanosine (8-oxo-dG), revealed an antimutagenic role of Dbh. The efficiency and accuracy of replication past 8-oxo-dG was higher in the presence of Dbh, and up to 90% of the Dbh-dependent events inserted dC. A third set of assays, based on phenotypic reversion, showed no effect of Dbh function on spontaneous -1 frameshifts in mononucleotide tracts in vivo, despite the extremely frequent slippage at these motifs documented in vitro. Taken together, the results indicate that a primary genetic role of Dbh is to avoid mutations at 8-oxo-dG that occur when other Sulfolobus enzymes replicate past this lesion. The genetic evidence that Dbh is recruited to 8-oxo-dG raises questions regarding the mechanism of recruitment, since Sulfolobus spp. have eukaryotic-like replisomes but no ubiquitin. Copyright © 2015 by the Genetics Society of America.

  13. White Matter Hyperintensities on T2-Weighted MRI Images among DNA-Verified Older Familial Hypercholesterolemia Patients

    Energy Technology Data Exchange (ETDEWEB)

    Hyttinen, L. (Dept. of Internal Medicine, North Karelia Central Hospital, Joensuu (Finland)); Autti, T.; Soljanlahti, S. (Medical Imaging Center, Helsinki Univ. Central Hospital, Helsinki (Finland)); Rauma, S. (Dept. of Radiology, North Karelia Central Hospital, Joensuu (Finland)); Vuorio, A.F. (Dept. of Medicine, Univ. of Helsinki, Helsinki (Finland)); Strandberg, T.E. (Dept. of Health Sciences/Geriatrics, Univ. of Oulu, Oulu (Finland))

    2009-04-15

    Background: Familial hypercholesterolemia (FH) is a genetic disorder, causing an increased risk of coronary heart disease (CHD) if untreated. Silent brain infarctions and white matter hyperintensities (WMHIs) observed on T2-weighted magnetic resonance images (MRI) are associated with increased risk for stroke and myocardial infarction. Age is a strong predictor of WMHIs. Purpose: To use MRI to assess the presence of clinically silent brain lesions in older FH patients, and to compare the occurrence and size of these lesions in older FH patients with middle-aged FH patients and healthy controls. Material and Methods: A total of 43 older (age = 65 years) FH patients with the same FH North Karelia mutation, living in Finland, were identified. In this comprehensive cohort, 1.5T brain MRI was available for 33 individuals (age 65-84 years, M/F 9/24, mean duration of statin treatment 15.3 years). This group was divided into two age categories: 65-74 years (FHe1 group, n=23) and 75-84 years (FHe2 group, n=10). Infarcts, including lacunas, and WMHIs on T2-weighted images were recorded. Data from brain MRI were compared to those of a group of middle-aged FH patients with CHD (n=19, age 48-64 years) and with middle-aged healthy controls (n=29, age 49-63 years). Results: Only two (6%) of the older FH patients had clinically silent brain infarcts detected by MRI. The amount of large WMHIs (>5 mm in diameter) was similar in the FHe1 group compared with the groups of middle-aged FH patients and healthy controls, even though the FHe1 group was 13 years older. The total amount of WMHIs and the amount of large WMHIs were greatest in the FHe2 group. Conclusion: FH patients aged 65 to 74 years receiving long-term statin treatment (15 years) did not have more WMHIs on brain MRI compared to middle-aged FH patients and healthy controls.

  14. Use of DNA-damaging agents and RNA pooling to assess expression profiles associated with BRCA1 and BRCA2 mutation status in familial breast cancer patients.

    Directory of Open Access Journals (Sweden)

    Logan C Walker

    2010-02-01

    Full Text Available A large number of rare sequence variants of unknown clinical significance have been identified in the breast cancer susceptibility genes, BRCA1 and BRCA2. Laboratory-based methods that can distinguish between carriers of pathogenic mutations and non-carriers are likely to have utility for the classification of these sequence variants. To identify predictors of pathogenic mutation status in familial breast cancer patients, we explored the use of gene expression arrays to assess the effect of two DNA-damaging agents (irradiation and mitomycin C on cellular response in relation to BRCA1 and BRCA2 mutation status. A range of regimes was used to treat 27 lymphoblastoid cell-lines (LCLs derived from affected women in high-risk breast cancer families (nine BRCA1, nine BRCA2, and nine non-BRCA1/2 or BRCAX individuals and nine LCLs from healthy individuals. Using an RNA-pooling strategy, we found that treating LCLs with 1.2 microM mitomycin C and measuring the gene expression profiles 1 hour post-treatment had the greatest potential to discriminate BRCA1, BRCA2, and BRCAX mutation status. A classifier was built using the expression profile of nine QRT-PCR validated genes that were associated with BRCA1, BRCA2, and BRCAX status in RNA pools. These nine genes could distinguish BRCA1 from BRCA2 carriers with 83% accuracy in individual samples, but three-way analysis for BRCA1, BRCA2, and BRCAX had a maximum of 59% prediction accuracy. Our results suggest that, compared to BRCA1 and BRCA2 mutation carriers, non-BRCA1/2 (BRCAX individuals are genetically heterogeneous. This study also demonstrates the effectiveness of RNA pools to compare the expression profiles of cell-lines from BRCA1, BRCA2, and BRCAX cases after treatment with irradiation and mitomycin C as a method to prioritize treatment regimes for detailed downstream expression analysis.

  15. Geostationary Satellite (GOES) Images

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Visible and Infrared satellite imagery taken from radiometer instruments on SMS (ATS) and GOES satellites in geostationary orbit. These satellites produced...

  16. Conectando famílias de construções genéticas: testes de DNA na reunificação da família somali na Finlândia Connecting genes-building families: DNA testing in somali family reunification in Finland

    Directory of Open Access Journals (Sweden)

    Petri Hautaniemi

    2007-12-01

    Full Text Available Os temas centrais desse artigo, reunificação familiar em geral e teste de DNA em particular, surgiram a partir de uma pesquisa em andamento acerca de jovens da Somália na Finlândia. Desde 1996, realizo uma pesquisa etnográfica - em escolas, clubes de jovens, ruas e cafés - com jovens da Somália que chegaram à Finlândia por volta de 1994 e que freqüentam escolas finlandesas nos subúrbios de Helsinki. Meu interesse geral nesta pesquisa longitudinal era conhecer as experiências de passagem para a vida adulta em contextos altamente diferenciados, não apenas do ponto de vista do país anfitrião, mas também cultural e transnacionalmente. O tema, testes de DNA, toca na questão central desta pesquisa de modo profundo. Aqui, crescer não é visto como uma simples questão biológica. É um processo social no qual as relações, como laços de parentesco, são constituídas, vivenciadas e contestadas. Essas relações são poderosas para a identificação individual e social. A testagem-DNA pode violar simbólica e fisicamente o processo social de identificações íntimas e de integridade pessoal.The central themes of this article, family reunification in general, and DNA testing in particular, came to the fore during a research project about young Somalians in Finland. Since 1996, I have been conducting ethnographic research - in schools, youth clubs, streets and cafés - with youngsters from Somalia who arrived in Finland around 1994, and who attend Finnish schools in the suburbs of Helsinki. My general interest in this longitudinal study was to learn about the experiences of coming of age in highly dispersed settings, not only in the vein of a local host country, but also culturally and transnationally. Here, growing up is seen not as a simple biological question. It is a social process in which relationships such as kinship ties are constituted, experienced, and contested. These are powerful relations for individual and social

  17. Iodine Satellite

    Science.gov (United States)

    Dankanich, John; Kamhawi, Hani; Szabo, James

    2015-01-01

    This project is a collaborative effort to mature an iodine propulsion system while reducing risk and increasing fidelity of a technology demonstration mission concept. 1 The FY 2014 tasks include investments leveraged throughout NASA, from multiple mission directorates, as a partnership with NASA Glenn Research Center (GRC), a NASA Marshall Space Flight Center (MSFC) Technology Investment Project, and an Air Force partnership. Propulsion technology is often a critical enabling technology for space missions. NASA is investing in technologies to enable high value missions with very small and low-cost spacecraft, even CubeSats. However, these small spacecraft currently lack any appreciable propulsion capability. CubeSats are typically deployed and drift without any ability to transfer to higher value orbits, perform orbit maintenance, or deorbit. However, the iodine Hall system can allow the spacecraft to transfer into a higher value science orbit. The iodine satellite (iSAT) will be able to achieve a (Delta)V of >500 m/s with 1,300 s. The iSAT spacecraft, illustrated in figure 1, is currently a 12U CubeSat. The spacecraft chassis will be constructed from aluminum with a finish to prevent iodine-driven corrosion. The iSAT spacecraft includes full three-axis control using wheels, magnetic torque rods, inertial management unit, and a suite of sensors and optics. The spacecraft will leverage heat generated by spacecraft components and radiators for a passive thermal control system.

  18. The 5S rDNA gene family in mollusks: characterization of transcriptional regulatory regions, prediction of secondary structures, and long-term evolution, with special attention to Mytilidae mussels.

    Science.gov (United States)

    Vizoso, Miguel; Vierna, Joaquín; González-Tizón, Ana M; Martínez-Lage, Andrés

    2011-01-01

    Several reports on the characterization of 5S ribosomal DNA (5S rDNA) in various animal groups have been published to date, but there is a lack of studies analyzing this gene family in a much broader context. Here, we have studied 5S rDNA variation in several molluskan species, including bivalves, gastropods, and cephalopods. The degree of conservation of transcriptional regulatory regions was analyzed in these lineages, revealing a conserved TATA-like box in the upstream region. The evolution of the 120 bp coding region (5S) was also studied, suggesting the occurrence of paralogue groups in razor clams, clams, and cockles. In addition, 5S rDNA sequences from 11 species and 7 genus of Mytilidae Rafinesque, 1815 mussels were sampled and studied in detail. Four different 5S rDNA types, based on the nontranscribed spacer region were identified. The phylogenetic analyses performed within each type showed a between-species gene clustering pattern, suggesting ancestral polymorphism. Moreover, some putative pseudogenized 5S copies were also identified. Our report, together with previous studies that found high degree of intragenomic divergence in bivalve species, suggests that birth-and-death evolution may be the main force driving the evolution of 5S rDNA in these animals, even at the genus level.

  19. Iodine Satellite

    Science.gov (United States)

    Kamhawi, Hani; Dankanich, John; Martinez, Andres; Petro, Andrew

    2015-01-01

    The Iodine Satellite (iSat) spacecraft will be the first CubeSat to demonstrate high change in velocity from a primary propulsion system by using Hall thruster technology and iodine as a propellant. The mission will demonstrate CubeSat maneuverability, including plane change, altitude change and change in its closest approach to Earth to ensure atmospheric reentry in less than 90 days. The mission is planned for launch in fall 2017. Hall thruster technology is a type of electric propulsion. Electric propulsion uses electricity, typically from solar panels, to accelerate the propellant. Electric propulsion can accelerate propellant to 10 times higher velocities than traditional chemical propulsion systems, which significantly increases fuel efficiency. To enable the success of the propulsion subsystem, iSat will also demonstrate power management and thermal control capabilities well beyond the current state-of-the-art for spacecraft of its size. This technology is a viable primary propulsion system that can be used on small satellites ranging from about 22 pounds (10 kilograms) to more than 1,000 pounds (450 kilograms). iSat's fuel efficiency is ten times greater and its propulsion per volume is 100 times greater than current cold-gas systems and three times better than the same system operating on xenon. iSat's iodine propulsion system consists of a 200 watt (W) Hall thruster, a cathode, a tank to store solid iodine, a power processing unit (PPU) and the feed system to supply the iodine. This propulsion system is based on a 200 W Hall thruster developed by Busek Co. Inc., which was previously flown using xenon as the propellant. Several improvements have been made to the original system to include a compact PPU, targeting greater than 80 percent reduction in mass and volume of conventional PPU designs. The cathode technology is planned to enable heaterless cathode conditioning, significantly increasing total system efficiency. The feed system has been designed to

  20. Satellited 4q identified in amniotic fluid cells

    Energy Technology Data Exchange (ETDEWEB)

    Miller, I.; Hsieh, C.L.; Songster, G. [Stanford Univ. Medical Center, Stanford, CA (United States)] [and others

    1995-01-16

    Extra material was identified on the distal long arm of a chromosome 4 in an amniotic fluid specimen sampled at 16.6 weeks of gestational age. There was no visible loss of material from chromosome 4, and no evidence for a balanced rearrangement. The primary counseling issue in this case was advanced maternal age. Ultrasound findings were normal, and family history was unremarkable. The identical 4qs chromosome was observed in cells from a paternal peripheral blood specimen and appeared to be an unbalanced rearrangement. This extra material was NOR positive in lymphocytes from the father, but was negative in the fetal amniocytes. Father`s relatives were studied to verify the familial origin of this anomaly. In situ hybridization with both exon and intron sequences of ribosomal DNA demonstrated that ribosomal DNA is present at the terminus of the 4qs chromosome in the fetus, father, and paternal grandmother. This satellited 4q might have been derived from a translocation event that resulted in very little or no loss from the 4q and no specific phenotype. This derivative chromosome 4 has been inherited through at least 3 generations of phenotypically normal individuals. 8 refs., 3 figs.

  1. The Two Cryptochrome/Photolyase Family Proteins Fulfill Distinct Roles in DNA Photorepair and Regulation of Conidiation in the Gray Mold Fungus Botrytis cinerea.

    Science.gov (United States)

    Cohrs, Kim C; Schumacher, Julia

    2017-09-01

    The plant-pathogenic leotiomycete Botrytis cinerea is known for the strict regulation of its asexual differentiation programs by environmental light conditions. Sclerotia are formed in constant darkness; black/near-UV (NUV) light induces conidiation; and blue light represses both differentiation programs. Sensing of black/NUV light is attributed to proteins of the cryptochrome/photolyase family (CPF). To elucidate the molecular basis of the photoinduction of conidiation, we functionally characterized the two CPF proteins encoded in the genome of B. cinerea as putative positive-acting components. B. cinerea CRY1 (BcCRY1), a cyclobutane pyrimidine dimer (CPD) photolyase, acts as the major enzyme of light-driven DNA repair (photoreactivation) and has no obvious role in signaling. In contrast, BcCRY2, belonging to the cry-DASH proteins, is dispensable for photorepair but performs regulatory functions by repressing conidiation in white and especially black/NUV light. The transcription of bccry1 and bccry2 is induced by light in a White Collar complex (WCC)-dependent manner, but neither light nor the WCC is essential for the repression of conidiation through BcCRY2 when bccry2 is constitutively expressed. Further, BcCRY2 affects the transcript levels of both WCC-induced and WCC-repressed genes, suggesting a signaling function downstream of the WCC. Since both CPF proteins are dispensable for photoinduction by black/NUV light, the origin of this effect remains elusive and may be connected to a yet unknown UV-light-responsive system.IMPORTANCEBotrytis cinerea is an economically important plant pathogen that causes gray mold diseases in a wide variety of plant species, including high-value crops and ornamental flowers. The spread of disease in the field relies on the formation of conidia, a process that is regulated by different light qualities. While this feature has been known for a long time, we are just starting to understand the underlying molecular mechanisms

  2. The phylogeny of the family Lacertidae (Reptilia) based on nuclear DNA sequences: convergent adaptations to arid habitats within the subfamily Eremiainae.

    Science.gov (United States)

    Mayer, Werner; Pavlicev, Mihaela

    2007-09-01

    The family Lacertidae encompasses more than 250 species distributed in the Palearctis, Ethiopis and Orientalis. Lacertids have been subjected in the past to several morphological and molecular studies to establish their phylogeny. However, the problems of convergent adaptation in morphology and of excessively variable molecular markers have hampered the establishment of well supported deeper phylogenetic relationships. Particularly the adaptations to xeric environments have often been used to establish a scenario for the origin and radiation of major lineages within lacertids. Here we present a molecular phylogenetic study based on two nuclear marker genes and representatives of 37 lacertid genera and distinct species groups (as in the case of the collective genus Lacerta). Roughly 1600 bp of the nuclear rag1 and c-mos genes were sequenced and analyzed. While the results provide good support to the hitherto suggested main subfamilies of Gallotiinae (Gallotia and Psammodromus), Eremiainae and Lacertinae [Harris, D.J., Arnold, E.N., Thomas, R.H., 1998. Relationships of lacertid lizards (Reptilia: Lacertidae) estimated from mitochondrial DNA sequences and morphology. Proc. R. Soc. Lond. B 265, 1939-1948], they also suggest unexpected relationships. In particular, the oriental genus Takydromus, previously considered the sister-group to the three subfamilies, is nested within Lacertinae. Moreover, the genera within the Eremiainae are further divided into two groups, roughly corresponding to their respective geographical distributions in the Ethiopian and the Saharo-Eurasian ranges. The results support an independent origin of adaptations to xeric conditions in different subfamilies. The relationships within the subfamily Lacertinae could not be resolved with the markers used. The species groups of the collective genus Lacerta show a bush-like topology in the inferred Bayesian tree, suggesting rapid radiation. The composition of the subfamilies Eremiainae and Lacertinae

  3. Feasibility of microminiature satellites

    Science.gov (United States)

    Imai, Ryouichi

    1991-07-01

    A conceptual study is conducted on technical problems and system design techniques to accomplish higher performance microminiature satellites by smaller systems. Applications of microminiature satellite technology to practical satellite mission are mentioned. Concepts of microminiature satellites, measures to miniaturize satellites, and micro-miniaturization technologies for communication and data processing, electric solar power paddle, attitude and orbit control, structure, thermal control, propulsion, and instrumentation systems are outlined. Examples of miniaturizing satellite missions such as planet exploration, low-altitude communication networks, space positioning system, low-altitude earth observation mission, clustered satellites, tethered satellites, and timely observation are described. Satellite miniaturizing technology can also be used to launch systems by lasers, and superconductive linear catapults (space escalator). It is pointed out that keys to promote satellite miniaturization are electronics, precision machining, raw material, electric power source technologies, and system design technology to integrate those technologies.

  4. Infectivity, effects on helper viruses and whitefly transmission of the deltasatellites associated with sweepoviruses (genus Begomovirus, family Geminiviridae).

    Science.gov (United States)

    Hassan, Ishtiaq; Orílio, Anelise F; Fiallo-Olivé, Elvira; Briddon, Rob W; Navas-Castillo, Jesús

    2016-07-25

    Begomoviruses (family Geminiviridae) are whitefly-transmitted viruses with single-stranded DNA genomes that are frequently associated with DNA satellites. These satellites include non-coding satellites, for which the name deltasatellites has been proposed. Although the first deltasatellite was identified in the late 1990s, little is known about the effects they have on infections of their helper begomoviruses. Recently a group of deltasatellites were identified associated with sweepoviruses, a group of phylogenetically distinct begomoviruses that infect plants of the family Convolvulaceae including sweet potato. In this work, the deltasatellites associated with sweepoviruses are shown to be transreplicated and maintained in plants by the virus with which they were identified, sweet potato leaf curl virus (SPLCV). These deltasatellites were shown generally to reduce symptom severity of the virus infection by reducing virus DNA levels. Additionally they were shown to be maintained in plants, and reduce the symptoms induced by two Old World monopartite begomoviruses, tomato yellow leaf curl virus and tomato yellow leaf curl Sardinia virus. Finally one of the satellites was shown to be transmitted plant-to-plant in the presence of SPLCV by the whitefly vector of the virus, Bemisia tabaci, being the first time a deltasatellite has been shown to be insect transmitted.

  5. Trends in communications satellites

    CERN Document Server

    Curtin, Denis J

    1979-01-01

    Trends in Communications Satellites offers a comprehensive look at trends and advances in satellite communications, including experimental ones such as NASA satellites and those jointly developed by France and Germany. The economic aspects of communications satellites are also examined. This book consists of 16 chapters and begins with a discussion on the fundamentals of electrical communications and their application to space communications, including spacecraft, earth stations, and orbit and wavelength utilization. The next section demonstrates how successful commercial satellite communicati

  6. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  7. Molecular biology of fuselloviruses and their satellites

    DEFF Research Database (Denmark)

    Contursi, Patrizia; Fusco, Salvatore; Cannio, Raffaele

    2014-01-01

    Fuselloviruses, also known as Sulfolobus Spindle-shaped viruses (SSVs), are "lemon"- or "spindle"-shaped double-stranded DNA viruses. Among them, SSV1, SSV2 and the satellite viruses pSSVx and pSSVi have been investigated at the structural, genetic, transcriptomic, proteomic and biochemical level...

  8. De novo DNMTs and DNA methylation: novel insights into disease pathogenesis and therapy from epigenomics.

    Science.gov (United States)

    Leppert, Sylwia; Matarazzo, Maria R

    2014-01-01

    DNA methylation plays an important role in epigenetics signaling, having an impact on gene regulation, chromatin structure and development. Within the family of de novo DNA methyltransferases two active enzymes, DNMT3A and DNMT3B, are responsible for the establishment of the proper cytosine methylation profile during development. Defects in DNMT3s function correlate with pathogenesis and progression of monogenic diseases and cancers. Among monogenic diseases, Immunodeficiency, Centromeric instability and Facial anomalies (ICF) syndrome is the only Mendelian disorder associated with DNMT3B mutations and DNA methylation defects of satellite and non-satellite regions. Similar CpG hypomethylation of the repetitive elements and gene-specific hypermethylation are observed in many types of cancer. DNA hyper-methylation sites provide targets for the epigenetic therapy. Generally, we can distinguish two groups of epi-drugs affecting DNMTs activity, i) nucleoside inhibitors, covalently trapping the enzymes, and bringing higher cytotoxic effect and (ii) nonnucleoside inhibitors, which block their active sites, showing less side-effects. Moreover, combining drugs targeting chromatin and those targeting DNA methylation enhances the efficacy of the therapy and gives more chances of patient recovery. However, development of more specific and effective epigenetic therapies requires more complete understanding of epigenomic landscapes. Here, we give an overview of the recent findings in the epigenomics field, focusing on those related to DNA methylation defects in disease pathogenesis and therapy.

  9. Handbook of satellite applications

    CERN Document Server

    Madry, Scott; Camacho-Lara, Sergio

    2017-01-01

    The first edition of this ground breaking reference work was the most comprehensive reference source available about the key aspects of the satellite applications field. This updated second edition covers the technology, the markets, applications and regulations related to satellite telecommunications, broadcasting and networking—including civilian and military systems; precise satellite navigation and timing networks (i.e. GPS and others); remote sensing and meteorological satellite systems. Created under the auspices of the International Space University based in France, this brand new edition is now expanded to cover new innovative small satellite constellations, new commercial launching systems, innovation in military application satellites and their acquisition, updated appendices, a useful glossary and more.

  10. Satellite orbit predictor

    Science.gov (United States)

    Friedman, Morton l.; Garrett, James, Major

    An analog aid to determine satellite coverage of Emergency Locator Transmitters Emergency Position Indicating Radio Beacon (ELT/EPIRB) distress incidence is discussed. The satellite orbit predictor is a graphical aid for determining the relationship between the satellite orbit, antenna coverage of the spacecraft and coverage of the Local User Terminal. The predictor allows the user to quickly visualize if a selected position will probably be detected and is composed of a base map and a satellite track overlay for each satellite.A table of equator crossings for each satellite is included.

  11. Galileo satellite antenna modeling

    Science.gov (United States)

    Steigenberger, Peter; Dach, Rolf; Prange, Lars; Montenbruck, Oliver

    2015-04-01

    The space segment of the European satellite navigation system Galileo currently consists of six satellites. Four of them belong to the first generation of In-Orbit Validation (IOV) satellites whereas the other two are Full Operational Capability (FOC) satellites. High-precision geodetic applications require detailed knowledge about the actual phase center of the satellite and receiver antenna. The deviation of this actual phase center from a well-defined reference point is described by phase center offsets (PCOs) and phase center variations (PCVs). Unfortunately, no public information is available about the Galileo satellite antenna PCOs and PCVs, neither for the IOV, nor the FOC satellites. Therefore, conventional values for the IOV satellite antenna PCOs have been adopted for the Multi-GNSS experiment (MGEX) of the International GNSS Service (IGS). The effect of the PCVs is currently neglected and no PCOs for the FOC satellites are available yet. To overcome this deficiency in GNSS observation modeling, satellite antenna PCOs and PCVs are estimated for the Galileo IOV satellites based on global GNSS tracking data of the MGEX network and additional stations of the legacy IGS network. Two completely independent solutions are computed with the Bernese and Napeos software packages. The PCO and PCV values of the individual satellites are analyzed and the availability of two different solutions allows for an accuracy assessment. The FOC satellites are built by a different manufacturer and are also equipped with another type of antenna panel compared to the IOV satellites. Signal transmission of the first FOC satellite has started in December 2014 and activation of the second satellite is expected for early 2015. Based on the available observations PCO estimates and, optionally PCVs of the FOC satellites will be presented as well. Finally, the impact of the new antenna model on the precision and accuracy of the Galileo orbit determination is analyzed.

  12. GPS Satellite Simulation Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The GPS satellite simulation facility consists of a GPS satellite simulator controlled by either a Silicon Graphics Origin 2000 or PC depending upon unit under test...

  13. Satellite Tags- Hawaii EEZ

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Satellite tagging was implemented in 2013. Satellite tagging is conducted using a Dan Inject air rifle and deployment arrows designed by Wildlife Computers. Two...

  14. Characterization of a Leber's hereditary optic neuropathy (LHON) family harboring two primary LHON mutations m.11778G>A and m.14484T>C of the mitochondrial DNA.

    Science.gov (United States)

    Catarino, Claudia B; Ahting, Uwe; Gusic, Mirjana; Iuso, Arcangela; Repp, Birgit; Peters, Katrin; Biskup, Saskia; von Livonius, Bettina; Prokisch, Holger; Klopstock, Thomas

    2017-09-01

    Leber's hereditary optic neuropathy (LHON) is an inherited mitochondrial disease that usually leads to acute or subacute bilateral central vision loss. In 95% of cases, LHON is caused by one of three primary mutations of the mitochondrial DNA (mtDNA), m.11778G>A in the MT-ND4 gene, m.14484T>C in the MT-ND6 gene, or m.3460G>A in the MT-ND1 gene. Here we characterize clinically, genetically, and biochemically a LHON family with multiple patients harboring two of these primary LHON mutations, m.11778G>A homoplasmic and m.14484T>C heteroplasmic. The unusually low male-to-female ratio of affected family members is also seen among the other patients previously reported with two primary LHON mutations m.11778G>A and m.14484T>C. While the index patient had very late onset of symptoms at 75years and severe visual loss, her two daughters had both onset in childhood (6 and 9years), with moderate to mild visual loss. A higher degree of heteroplasmy of the m.14484T>C mutation was found to correlate with an earlier age at onset in this family. Ours is the first LHON family harboring two primary LHON mutations where functional studies were performed in several affected family members. A more pronounced bioenergetic defect was found to correlate with an earlier age at onset. The patient with the earliest age at onset had a more significant complex I dysfunction than all controls, including the LHON patient with only the m.11778G>A mutation, suggesting a synergistic effect of the two primary LHON mutations in this patient. Copyright © 2017 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

  15. Editing of misaligned 3′-termini by an intrinsic 3′–5′ exonuclease activity residing in the PHP domain of a family X DNA polymerase

    Science.gov (United States)

    Baños, Benito; Lázaro, José M.; Villar, Laurentino; de Vega, Miguel

    2008-01-01

    Bacillus subtilis gene yshC encodes a family X DNA polymerase (PolXBs), whose biochemical features suggest that it plays a role during DNA repair processes. Here, we show that, in addition to the polymerization activity, PolXBs possesses an intrinsic 3′–5′ exonuclease activity specialized in resecting unannealed 3′-termini in a gapped DNA substrate. Biochemical analysis of a PolXBs deletion mutant lacking the C-terminal polymerase histidinol phosphatase (PHP) domain, present in most of the bacterial/archaeal PolXs, as well as of this separately expressed protein region, allow us to state that the 3′–5′ exonuclease activity of PolXBs resides in its PHP domain. Furthermore, site-directed mutagenesis of PolXBs His339 and His341 residues, evolutionary conserved in the PHP superfamily members, demonstrated that the predicted metal binding site is directly involved in catalysis of the exonucleolytic reaction. The implications of the unannealed 3′-termini resection by the 3′–5′ exonuclease activity of PolXBs in the DNA repair context are discussed. PMID:18776221

  16. Lack of involvement of known DNA methyltransferases in familial hydatidiform mole implies the involvement of other factors in establishment of imprinting in the human female germline

    OpenAIRE

    Picton H M; Huntriss J; Hodge D; Judson H; de Vos M; Hayward B E; Sheridan E; Bonthron DT

    2003-01-01

    Abstract Background Differential methylation of the two alleles is a hallmark of imprinted genes. Correspondingly, loss of DNA methyltransferase function results in aberrant imprinting and abnormal post-fertilization development. In the mouse, mutations of the oocyte-specific isoform of the DNA methyltransferase Dnmt1 (Dnmt1o) and of the methyltransferase-like Dnmt3L gene result in specific failures of imprint establishment or maintenance, at multiple loci. We have previously shown in humans ...

  17. Werner Helicase Wings DNA Binding

    OpenAIRE

    Hoadley, Kelly A.; Keck, James L.

    2010-01-01

    In this issue of Structure, Kitano et al. describe the structure of the DNA-bound winged-helix domain from the Werner helicase. This structure of a RecQ/DNA complex offers insights into the DNA unwinding mechanisms of RecQ family helicases.

  18. Werner helicase wings DNA binding.

    Science.gov (United States)

    Hoadley, Kelly A; Keck, James L

    2010-02-10

    In this issue of Structure, Kitano et al. describe the structure of the DNA-bound winged-helix domain from the Werner helicase. This structure of a RecQ/DNA complex offers insights into the DNA-unwinding mechanisms of RecQ family helicases. Copyright 2010 Elsevier Inc. All rights reserved.

  19. Theory of geostationary satellites

    CERN Document Server

    Zee, Chong-Hung

    1989-01-01

    Geostationary or equatorial synchronous satellites are a daily reminder of our space efforts during the past two decades. The nightly television satellite weather picture, the intercontinental telecommunications of television transmissions and telephone conversations, and the establishrnent of educational programs in remote regions on Earth are constant reminders of the presence of these satellites. As used here, the term 'geo­ stationary' must be taken loosely because, in the long run, the satellites will not remain 'stationary' with respect to an Earth-fixed reference frame. This results from the fact that these satellites, as is true for all satellites, are incessantly subject to perturbations other than the central-body attraction of the Earth. Among the more predominant pertur­ bations are: the ellipticity of the Earth's equator, the Sun and Moon, and solar radiation pressure. Higher harmonics of the Earth's potential and tidal effects also influence satellite motion, but they are of second­ order whe...

  20. Meteorological satellite systems

    CERN Document Server

    Tan, Su-Yin

    2014-01-01

    “Meteorological Satellite Systems” is a primer on weather satellites and their Earth applications. This book reviews historic developments and recent technological advancements in GEO and polar orbiting meteorological satellites. It explores the evolution of these remote sensing technologies and their capabilities to monitor short- and long-term changes in weather patterns in response to climate change. Satellites developed by various countries, such as U.S. meteorological satellites, EUMETSAT, and Russian, Chinese, Japanese and Indian satellite platforms are reviewed. This book also discusses international efforts to coordinate meteorological remote sensing data collection and sharing. This title provides a ready and quick reference for information about meteorological satellites. It serves as a useful tool for a broad audience that includes students, academics, private consultants, engineers, scientists, and teachers.

  1. Cryptic satellites rich in inverted repeats comprise 30% of the genome of a hermit crab

    Energy Technology Data Exchange (ETDEWEB)

    Fowler, R.F.; Skinner, D.M.

    1985-01-25

    One major very highly repeated (VHR) DNA (approx. 7 x 10W copies/genome; repeat unit = 156 base pairs (bp)), a family of three minor VHR DNAs (approx. 2.8 x 10W copies/genome; repeat units = 71-74 bp), and a number of trace components account for almost 30% of the genome of a hermit crab. The repeat units of the three minor variants are defined by identical 14-bp G + C-rich inverted repeats that might form cruciforms. Two copies of the repeat unit (CCTA) of one of two patent satellites of this crab occur at the center of one in seven of the G + C-rich inverted repeats; copies of the other patent satellite are found in main component DNA. The sequences of both the major and minor VHR DNAs are characterized by short tracts of A/sub n/ and/or T/sub n/ (n = 4-7) residues whose presence would permit the formation of perfectly matched stems separated by loops of 8-16 bp. The A/sub n/ and/or T/sub n/ tracts are interspersed with segments of G + C-rich DNA and are arranged differently in the major and minor VHR DNAs. Although the repeat units of the major and the three minor VHR DNAs are arranged in tandem, the composition and sequence of their bases are such that they do not form distinct bands in CsCl gradients; they are cryptic satellites. 42 references, 7 figures, 1 table.

  2. Familial paragangliomas

    Directory of Open Access Journals (Sweden)

    Lips CJM

    2006-10-01

    Full Text Available Abstract Paragangliomas are rare tumours of the autonomic nervous system and occur in sporadic and hereditary forms. They are usually benign and have a low mortality. However, they cause significant morbidity related to their mass effect. Genetic predisposition can occur within the familial tumour syndromes multiple endocrine neoplasia type 2 (MEN 2, von Hippel-Lindau (VHL and neurofibromatosis type 1 (NF-1, or be due to mutations in genes specific to the development of paraganglioma only. Compared to sporadic forms, familial paragangliomas tend to present at a younger age and at multiple sites. Tumours should be diagnosed and resected as early as possible, as it has been shown that morbidity is related to tumour size. This article gives an overview of the current literature on the origin of the different forms of paragangliomas, DNA diagnosis, as well as biochemical and radiological screening guidelines.

  3. High-resolution melting of 12S rRNA and cytochrome b DNA sequences for discrimination of species within distinct European animal families.

    Directory of Open Access Journals (Sweden)

    Jana Naue

    Full Text Available The cheap and easy identification of species is necessary within multiple fields of molecular biology. The use of high-resolution melting (HRM of DNA provides a fast closed-tube method for analysis of the sequence composition of the mitochondrial genes 12S rRNA and cytochrome b. We investigated the potential use of HRM for species identification within eleven different animal groups commonly found in Europe by animal-group-specific DNA amplification followed by DNA melting. Influence factors as DNA amount, additional single base alterations, and the existence of mixed samples were taken into consideration. Visual inspection combined with mathematical evaluation of the curve shapes did resolve nearly all species within an animal group. The assay can therefore not only be used for identification of animal groups and mixture analysis but also for species identification within the respective groups. The use of a universal 12S rRNA system additionally revealed a possible approach for species discrimination, mostly by exclusion. The use of the HRM assay showed to be a reliable, fast, and cheap method for species discrimination within a broad range of different animal species and can be used in a flexible "modular" manner depending on the question to be solved.

  4. Methods of satellite oceanography

    Science.gov (United States)

    Stewart, R. H.

    1985-01-01

    The theoretical basis for remote sensing measurements of climate and ocean dynamics is examined. Consideration is given to: the absorption of electromagnetic radiation in the atmosphere; scattering in the atmosphere; and satellite observations using visible light. Consideration is also given to: the theory of radio scatter from the sea; scatter of centimeter waves from the sea; and the theory of operation of synthetic aperture radars. Additional topics include: the coordinate systems of satellite orbits for oceanographic remote sensing applications; the operating features of the major U.S. satellite systems for viewing the ocean; and satellite altimetry.

  5. Epigenetic regulation by Z-DNA silencer function controls cancer-associated ADAM-12 expression in breast cancer: cross-talk between MeCP2 and NF1 transcription factor family.

    Science.gov (United States)

    Ray, Bimal K; Dhar, Srijita; Henry, Carolyn; Rich, Alexander; Ray, Alpana

    2013-01-15

    A disintegrin and metalloprotease domain-containing protein 12 (ADAM-12) is upregulated in many human cancers and promotes cancer metastasis. Increased urinary level of ADAM-12 in breast and bladder cancers correlates with disease progression. However, the mechanism of its induction in cancer remains less understood. Previously, we reported a Z-DNA-forming negative regulatory element (NRE) in ADAM-12 that functions as a transcriptional suppressor to maintain a low-level expression of ADAM-12 in most normal cells. We now report here that overexpression of ADAM-12 in triple-negative MDA-MB-231 breast cancer cells and breast cancer tumors is likely due to a marked loss of this Z-DNA-mediated transcriptional suppression function. We show that Z-DNA suppressor operates by interaction with methyl-CpG-binding protein, MeCP2, a prominent epigenetic regulator, and two members of the nuclear factor 1 family of transcription factors, NF1C and NF1X. While this tripartite interaction is highly prevalent in normal breast epithelial cells, both in vitro and in vivo, it is significantly lower in breast cancer cells. Western blot analysis has revealed significant differences in the levels of these 3 proteins between normal mammary epithelial and breast cancer cells. Furthermore, we show, by NRE mutation analysis, that interaction of these proteins with the NRE is necessary for effective suppressor function. Our findings unveil a new epigenetic regulatory process in which Z-DNA/MeCP2/NF1 interaction leads to transcriptional suppression, loss of which results in ADAM-12 overexpression in breast cancer cells.

  6. De novo COX2 mutation in a LHON family of Caucasian origin: implication for the role of mtDNA polymorphism in human pathology.

    Science.gov (United States)

    Zhadanov, Sergey I; Atamanov, Vasiliy V; Zhadanov, Nikolay I; Schurr, Theodore G

    2006-01-01

    Recent studies suggest that certain mutations with phylogeographic importance as haplogroup markers may also influence the phenotypic expression of particular mitochondrial disorders. One such disorder, Leber's hereditary optic neuropathy (LHON), demonstrates a clear expression bias in mtDNAs belonging to haplogroup J, a West Eurasian maternal lineage defined by polymorphic markers that have been called 'secondary' disease mutations. In this report, we present evidence for a de novo heteroplasmic COX2 mutation associated with a LHON clinical phenotype. This particular mutation-at nucleotide position 7,598-occurs in West Eurasian haplogroup H, the most common maternal lineage among individuals of European descent, whereas previous studies have detected this mutation only in East Eurasian haplogroup E. A review of the available mtDNA sequence data indicates that the COX2 7598 mutation occurs as a homoplasic event at the tips of these phylogenetic branches, suggesting that it could be a variant that is rapidly eliminated by selection. This finding points to the potential background influence of polymorphisms on the expression of mild deleterious mutations such as LHON mtDNA defects and further highlights the difficulties in distinguishing deleterious mtDNA changes from neutral polymorphisms and their significance in the development of mitochondriopathies.

  7. Planets and satellites galore

    Science.gov (United States)

    Marsden, B. G.

    1980-10-01

    The facts and controversies surrounding the discoveries of Uranus, Neptune, Pluto and their satellites are reviewed. Earth-approaching and earth-crossing minor planets are discussed with attention to the work of Helin and Giclas. The problems attending satellite discoveries are examined, and the criteria for 1978 P 1 is evaluated.

  8. Satellite Communications Industry

    Science.gov (United States)

    1993-04-01

    Ariane $loom SAJAC 1 Hughes Satellite Japan 06/94 $150m SAJAC 2 Hughes Satellite Japan -- (spare) $150m SatcomHl GE GE Americom /95 $50m SOLIDARIDAD ...1 Hughes SCT (Mexico) 11/93 Ariane $loom SOLIDARIDAD 2 Hughes SCT (Mexico) /94 $loom Superbird Al Loral Space Com Gp (Jap) 11/92 Ariane $175m

  9. Progress in satellite quantum key distribution

    Science.gov (United States)

    Bedington, Robert; Arrazola, Juan Miguel; Ling, Alexander

    2017-08-01

    Quantum key distribution (QKD) is a family of protocols for growing a private encryption key between two parties. Despite much progress, all ground-based QKD approaches have a distance limit due to atmospheric losses or in-fibre attenuation. These limitations make purely ground-based systems impractical for a global distribution network. However, the range of communication may be extended by employing satellites equipped with high-quality optical links. This manuscript summarizes research and development which is beginning to enable QKD with satellites. It includes a discussion of protocols, infrastructure, and the technical challenges involved with implementing such systems, as well as a top level summary of on-going satellite QKD initiatives around the world.

  10. A Tandemly Arranged Pattern of Two 5S rDNA Arrays in Amolops mantzorum (Anura, Ranidae).

    Science.gov (United States)

    Liu, Ting; Song, Menghuan; Xia, Yun; Zeng, Xiaomao

    2017-01-01

    In an attempt to extend the knowledge of the 5S rDNA organization in anurans, the 5S rDNA sequences of Amolops mantzorum were isolated, characterized, and mapped by FISH. Two forms of 5S rDNA, type I (209 bp) and type II (about 870 bp), were found in specimens investigated from various populations. Both of them contained a 118-bp coding sequence, readily differentiated by their non-transcribed spacer (NTS) sizes and compositions. Four probes (the 5S rDNA coding sequences, the type I NTS, the type II NTS, and the entire type II 5S rDNA sequences) were respectively labeled with TAMRA or digoxigenin to hybridize with mitotic chromosomes for samples of all localities. It turned out that all probes showed the same signals that appeared in every centromeric region and in the telomeric regions of chromosome 5, without differences within or between populations. Obviously, both type I and type II of the 5S rDNA arrays arranged in tandem, which was contrasting with other frogs or fishes recorded to date. More interestingly, all the probes detected centromeric regions in all karyotypes, suggesting the presence of a satellite DNA family derived from 5S rDNA. © 2017 S. Karger AG, Basel.

  11. [The analysis of mitochondrial DNA haplogroups and variants for Leber's hereditary optic neuropathy in Chinese families carrying the m.14484T >C mutation].

    Science.gov (United States)

    Meng, Xiangjuan; Zhu, Jinping; Gao, Min; Zhang, Sai; Zhao, Fuxin; Zhang, Juanjuan; Liu, Xiaoling; Wei, Qiping; Tong, Yi; Zhang, Minglian; Qu, Jia; Guan, Minxin

    2014-04-01

    The m.14484T>C mutation in mitochondrial ND6 gene (MT-ND6) is a primary mutation underlying the development of Leber's hereditary optic neuropathy (LHON) , but by itself not enough to cause visual loss. To explore the role of mitochondrial haplogroups on the expression of LHON for the people carrying the m.14484T>C mutation, we performed systematic and extended mutational screening of MT-ND6 gene in a cohort of 1177 Han Chinese patients with LHON. A total of 67 affected subjects carried the homoplasmic m.14484T>C mutation, accounting for 5.7% of this LHON population. The penetrances of optic neuropathy among 51 pedigrees carrying the m.14484T>C mutation ranged from 5.6% to 100.0%, with the average of 21.5%. The sequence analysis of entire mitochondrial genomes of 51 probands exhibited distinct sets of polymorphisms belonging to 18 Eastern Asian haplogroups. The frequencies of haplogroup A and haplogroup F were sig-nificantly less in the LHON mtDNA samples than those in 106 Chinese controls. On the other hand, the haplogroup M10a accounted for 9.8% of the patient's mtDNA samples but was absent in 106 Chinese controls. Strikingly, the average pene-trance (46.13%) of optic neuropathy for the pedigrees carrying mitochondrial haplogroup M10a was higher than those car-rying other mtDNA haplogroups. These observations indicated that mitochondrial haplogroup M10a may increase the risk of visual loss.

  12. Cellular responses to a prolonged delay in mitosis are determined by a DNA damage response controlled by Bcl-2 family proteins.

    Science.gov (United States)

    Colin, Didier J; Hain, Karolina O; Allan, Lindsey A; Clarke, Paul R

    2015-03-01

    Anti-cancer drugs that disrupt mitosis inhibit cell proliferation and induce apoptosis, although the mechanisms of these responses are poorly understood. Here, we characterize a mitotic stress response that determines cell fate in response to microtubule poisons. We show that mitotic arrest induced by these drugs produces a temporally controlled DNA damage response (DDR) characterized by the caspase-dependent formation of γH2AX foci in non-apoptotic cells. Following exit from a delayed mitosis, this initial response results in activation of DDR protein kinases, phosphorylation of the tumour suppressor p53 and a delay in subsequent cell cycle progression. We show that this response is controlled by Mcl-1, a regulator of caspase activation that becomes degraded during mitotic arrest. Chemical inhibition of Mcl-1 and the related proteins Bcl-2 and Bcl-xL by a BH3 mimetic enhances the mitotic DDR, promotes p53 activation and inhibits subsequent cell cycle progression. We also show that inhibitors of DDR protein kinases as well as BH3 mimetics promote apoptosis synergistically with taxol (paclitaxel) in a variety of cancer cell lines. Our work demonstrates the role of mitotic DNA damage responses in determining cell fate in response to microtubule poisons and BH3 mimetics, providing a rationale for anti-cancer combination chemotherapies.

  13. Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response

    Directory of Open Access Journals (Sweden)

    Sakaki Yoshiyuki

    2007-12-01

    Full Text Available Abstract Background Cassava, an allotetraploid known for its remarkable tolerance to abiotic stresses is an important source of energy for humans and animals and a raw material for many industrial processes. A full-length cDNA library of cassava plants under normal, heat, drought, aluminum and post harvest physiological deterioration conditions was built; 19968 clones were sequence-characterized using expressed sequence tags (ESTs. Results The ESTs were assembled into 6355 contigs and 9026 singletons that were further grouped into 10577 scaffolds; we found 4621 new cassava sequences and 1521 sequences with no significant similarity to plant protein databases. Transcripts of 7796 distinct genes were captured and we were able to assign a functional classification to 78% of them while finding more than half of the enzymes annotated in metabolic pathways in Arabidopsis. The annotation of sequences that were not paired to transcripts of other species included many stress-related functional categories showing that our library is enriched with stress-induced genes. Finally, we detected 230 putative gene duplications that include key enzymes in reactive oxygen species signaling pathways and could play a role in cassava stress response features. Conclusion The cassava full-length cDNA library here presented contains transcripts of genes involved in stress response as well as genes important for different areas of cassava research. This library will be an important resource for gene discovery, characterization and cloning; in the near future it will aid the annotation of the cassava genome.

  14. DNA methylation in plants.

    Science.gov (United States)

    Vanyushin, B F

    2006-01-01

    DNA in plants is highly methylated, containing 5-methylcytosine (m5C) and N6-methyladenine (m6A); m5C is located mainly in symmetrical CG and CNG sequences but it may occur also in other non-symmetrical contexts. m6A but not m5C was found in plant mitochondrial DNA. DNA methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by phytohormones and changes on seed germination, flowering and under the influence of various pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development, with particular involvement in regulation of gene expression and DNA replication. DNA replication is accompanied by the appearance of under-methylated, newly formed DNA strands including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of the cell cycle. A model for regulation of DNA replication by methylation is suggested. Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is carried out by the families of specific enzymes that belong to at least three classes of DNA methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria replication. Like in animals, DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is methylated both at cytosine and adenine residues; thus, at least two different, and probably interdependent, systems of DNA modification are present in plants. Plants seem to have a restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in plants; it involves de novo methylation of almost all cytosine residues in a region of siRNA-DNA

  15. Satellite Operations in Alaska

    Science.gov (United States)

    Kreller, M. A.

    2016-12-01

    Numerous observational challenges exist across Alaska impacting National Weather Service (NWS) forecast operations and providing decision support services (DSS) to critical core partners and customers. These observational challenges range from limited utility of GOES imagery at higher latitudes, scarcity of observing platforms, to limited radar coverage. Although we are fortunate to receive these valuable and limited data sets, there still remain extensive spatial and temporal data gaps across Alaska. Many forecast challenges in Alaska are similar to those in the CONUS with the detection and monitoring of wildfire conditions, severe thunderstorms, river flooding, and coastal flooding, etc. There are additional unique DSS provided in Alaska including sea ice forecasting, ivu (ice shoves onshore), coastal erosion due to permafrost melt, and extreme hazardous winter conditions (temperatures as low as -80F). In addition to the observational and forecast challenges, the sheer size of the area of responsibility in Alaska is a challenge. NWS operations have always heavily relied on satellite imagery to quickly assess the current weather situation and provide forecast guidance. NWS operations have established several partnerships with the satellite community to help with these challenges. In particular the GOES-R and Joint Polar Satellite System (JPSS) OCONUS Satellite Proving Ground (PG) Programs have not only improved Alaska's observational challenges, but continue to identify new capabilities with the next generation geostationary and polar-orbiting satellite products.. For example, River ice and flood detection products derived from the Suomi-NPP VIIRS satellite imagery with the support of the JPSS Proving Ground and Risk Reduction Program. This presentation will provide examples of how new satellite capabilities are being used in NWS Alaska forecast operations to support DSS, with emphasis on JPSS satellite products. Future satellite utilization or operational needs

  16. Skeletal muscle satellite cells

    Science.gov (United States)

    Schultz, E.; McCormick, K. M.

    1994-01-01

    Evidence now suggests that satellite cells constitute a class of myogenic cells that differ distinctly from other embryonic myoblasts. Satellite cells arise from somites and first appear as a distinct myoblast type well before birth. Satellite cells from different muscles cannot be functionally distinguished from one another and are able to provide nuclei to all fibers without regard to phenotype. Thus, it is difficult to ascribe any significant function to establishing or stabilizing fiber type, even during regeneration. Within a muscle, satellite cells exhibit marked heterogeneity with respect to their proliferative behavior. The satellite cell population on a fiber can be partitioned into those that function as stem cells and those which are readily available for fusion. Recent studies have shown that the cells are not simply spindle shaped, but are very diverse in their morphology and have multiple branches emanating from the poles of the cells. This finding is consistent with other studies indicating that the cells have the capacity for extensive migration within, and perhaps between, muscles. Complexity of cell shape usually reflects increased cytoplasmic volume and organelles including a well developed Golgi, and is usually associated with growing postnatal muscle or muscles undergoing some form of induced adaptive change or repair. The appearance of activated satellite cells suggests some function of the cells in the adaptive process through elaboration and secretion of a product. Significant advances have been made in determining the potential secretion products that satellite cells make. The manner in which satellite cell proliferative and fusion behavior is controlled has also been studied. There seems to be little doubt that cellcell coupling is not how satellite cells and myofibers communicate. Rather satellite cell regulation is through a number of potential growth factors that arise from a number of sources. Critical to the understanding of this form

  17. Molecular and cytogenetic characterization of repetitive DNA in the Antarctic polyplacophoran Nuttallochiton mirandus.

    Science.gov (United States)

    Biscotti, Maria Assunta; Barucca, Marco; Capriglione, Teresa; Odierna, Gaetano; Olmo, Ettore; Canapa, Adriana

    2008-01-01

    Two highly repeated DNAs, designated NmE1/NmE2 and NmE5, were identified by EcoRV digestion in the chiton Nuttallochiton mirandus (Mollusca: Polyplacophora). The comparison of the sequences obtained showed high similarity in 5' and 3' regions and the NmE5 sequence displayed an inserted sequence that might arise from a transposable element. Southern blotting analyses suggested a tandem organization of both satellite DNA families identified. Moreover, dot blot analyses, performed on several molluscan species, revealed a different degree of conservation of the repeated DNAs. Fluorescence in-situ hybridizations (FISH) on metaphase chromosomes showed that both satellite DNAs are located at centromeric regions.

  18. DNA Methyltransferase Activity Assays: Advances and Challenges

    OpenAIRE

    Poh, Wan Jun; Wee, Cayden Pang Pee; Gao,Zhiqiang

    2016-01-01

    DNA methyltransferases (MTases), a family of enzymes that catalyse the methylation of DNA, have a profound effect on gene regulation. A large body of evidence has indicated that DNA MTase is potentially a predictive biomarker closely associated with genetic disorders and genetic diseases like cancer. Given the attention bestowed onto DNA MTases in molecular biology and medicine, highly sensitive detection of DNA MTase activity is essential in determining gene regulation, epigenetic modificati...

  19. DNA-Encoded Flagellin Activates Toll-Like Receptor 5 (TLR5), Nod-like Receptor Family CARD Domain-Containing Protein 4 (NRLC4), and Acts as an Epidermal, Systemic, and Mucosal-Adjuvant

    Science.gov (United States)

    Nyström, Sanna; Bråve, Andreas; Falkeborn, Tina; Devito, Claudia; Rissiek, Björn; Johansson, Daniel X.; Schröder, Ulf; Uematsu, Satoshi; Akira, Shizuo; Hinkula, Jorma; Applequist, Steven E.

    2013-01-01

    Eliciting effective immune responses using non-living/replicating DNA vaccines is a significant challenge. We have previously shown that ballistic dermal plasmid DNA-encoded flagellin (FliC) promotes humoral as well as cellular immunity to co-delivered antigens. Here, we observe that a plasmid encoding secreted FliC (pFliC(-gly)) produces flagellin capable of activating two innate immune receptors known to detect flagellin; Toll-like Receptor 5 (TLR5) and Nod-like Receptor family CARD domain-containing protein 4 (NRLC4). To test the ability of pFliC(-gly) to act as an adjuvant we immunized mice with plasmid encoding secreted FliC (pFliC(-gly)) and plasmid encoding a model antigen (ovalbumin) by three different immunization routes representative of dermal, systemic, and mucosal tissues. By all three routes we observed increases in antigen-specific antibodies in serum as well as MHC Class I-dependent cellular immune responses when pFliC(-gly) adjuvant was added. Additionally, we were able to induce mucosal antibody responses and Class II-dependent cellular immune responses after mucosal vaccination with pFliC(-gly). Humoral immune responses elicited by heterologus prime-boost immunization with a plasmid encoding HIV-1 from gp160 followed by protein boosting could be enhanced by use of pFliC(-gly). We also observed enhancement of cross-clade reactive IgA as well as a broadening of B cell epitope reactivity. These observations indicate that plasmid-encoded secreted flagellin can activate multiple innate immune responses and function as an adjuvant to non-living/replicating DNA immunizations. Moreover, the capacity to elicit mucosal immune responses, in addition to dermal and systemic properties, demonstrates the potential of flagellin to be used with vaccines designed to be delivered by various routes. PMID:26344341

  20. Construction of an Infectious cDNA Clone of Aichi Virus (a New Member of the Family Picornaviridae) and Mutational Analysis of a Stem-Loop Structure at the 5′ End of the Genome

    Science.gov (United States)

    Sasaki, Jun; Kusuhara, Yasuhiro; Maeno, Yoshimasa; Kobayashi, Nobumichi; Yamashita, Teruo; Sakae, Kenji; Takeda, Naokazu; Taniguchi, Koki

    2001-01-01

    Aichi virus is the type species of a new genus, Kobuvirus, of the family Picornaviridae. In this study, we constructed a full-length cDNA clone of Aichi virus whose in vitro transcripts were infectious to Vero cells. During construction of the infectious cDNA clone, a novel sequence of 32 nucleotides was identified at the 5′ end of the genome. Computer-assisted prediction of the secondary structure of the 5′ end of the genome, including the novel sequence, suggested the formation of a stable stem-loop structure consisting of 42 nucleotides. The function of this stem-loop in virus replication was investigated using various site-directed mutants derived from the infectious cDNA clone. Our data indicated that correct folding of the stem-loop at the 5′ end of the positive strand, but not at the 3′ end of the negative strand, is critical for viral RNA replication. The primary sequence in the lower part of the stem was also suggested to be crucial for RNA replication. In contrast, nucleotide changes in the loop segment did not so severely reduce the efficiency of virus replication. A double mutant, in which both nucleotide stretches of the middle part of the stem were replaced by their complementary nucleotides, had efficient RNA replication and translation abilities but was unable to produce viruses. These results indicate that the stem-loop at the 5′ end of the Aichi virus genome is an element involved in both viral RNA replication and production of infectious virus particles. PMID:11483747

  1. [The first experience in Russia of using DNA diagnosis in Alport's syndrome in a family with a unique morphological picture of the kidney lesion].

    Science.gov (United States)

    Tsalikova, F D; Ignatova, M S; Krasnopol'skaia, K D; Tverskaia, S M; Brydun, A V

    1995-01-01

    Clinicomorphological findings are reported for two children from families with hereditary predisposition to hematuria characterized by early occurrence of chronic renal insufficiency, neurosensory hypoacusis, congenital ocular abnormalities inherited by sex-linked dominant type. Light microscopy of nephrobiopsies revealed diffuse mesangial proliferation in both children. Final diagnosis of Alport's syndrome was feasible only on molecular-genetic level after polymerase chain reactions had identified mutation in collagen type 4 alpha-5-chain gene on a long arm of X-chromosome in genotypes of both patients and their mothers. Genetical, clinical, morphological, evolutional and diagnostic aspects of Alport's syndrome are reviewed.

  2. First record and five new species of Xylographellini (Coleoptera: Ciidae) from China, with online DNA barcode library of the family.

    Science.gov (United States)

    Lopes-Andrade, Cristiano; Grebennikov, Vasily V

    2015-08-25

    We report the first record of the beetle tribe Xylographellini (Ciidae) from the continental Palaearctic Region, represented by five new species discovered in Yunnan and Sichuan provinces, China: Scolytocis danae sp. nov., Syncosmetus euryale sp. nov., Sync. medusa sp. nov., Sync. perseus sp. nov. and Sync. stheno sp. nov. Illustrations and identification keys are provided for these new species, and in order to facilitate further research of Ciidae we present an open-access DNA barcode library (dx.doi.org/10.5883/DS-SYNCOSM) containing 114 records (of 44 species in 14 genera), 15 of which belong to the newly described species. A phylogenetic analysis based on the barcode fragment of the cytochrome oxidase I gene did not recover much tree structure within Ciidae, however both Xylographus Mellié and Syncosmetus Sharp were recovered as clades, with a single Scolytocis Blair being the sister to the latter.

  3. Small Satellite Transporter Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The primary objective is to determine whether this small satellite transporter is capable of transporting at least four 6U CubeSats is possible for a given set of...

  4. Handbook of satellite applications

    CERN Document Server

    Madry, Scott; Camacho-Lara, Sergio

    2013-01-01

    Top space experts from around the world have collaborated to produce this comprehensive, authoritative, and clearly illustrated reference guide to the fast growing, multi-billion dollar field of satellite applications and space communications. This handbook, done under the auspices of the International Space University based in France, addresses not only system technologies but also examines market dynamics, technical standards and regulatory constraints. The handbook is a completely multi-disciplinary reference book that covers, in an in-depth fashion, the fields of satellite telecommunications, Earth observation, remote sensing, satellite navigation, geographical information systems, and geosynchronous meteorological systems. It covers current practices and designs as well as advanced concepts and future systems. It provides a comparative analysis of the common technologies and design elements for satellite application bus structures, thermal controls, power systems, stabilization techniques, telemetry, com...

  5. Multiple Satellite Trajectory Optimization

    National Research Council Canada - National Science Library

    Mendy Jr, Paul B

    2004-01-01

    This thesis develops and validates a satellite trajectory optimization model. A summary is given of the general mathematical principles of dynamic optimal control to minimize fuel consumed or transfer time...

  6. DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA

    DEFF Research Database (Denmark)

    Christensen, H.; Angen, Øystein; Mutters, R.

    2000-01-01

    The present study was aimed at reducing the time and labour used to perform DNA-DNA hybridizations for classification of bacteria at the species level. A micro-well-format DNA hybridization method was developed and validated. DNA extractions were performed by a small-scale method and DNA...... was sheared mechanically into fragments of between 400 and 700 bases. The hybridization conditions were calibrated according to DNA similarities obtained by the spectrophotometric method using strains within the family Pasteurellaceae, Optimal conditions were obtained with 300 ng DNA added per well and bound...... by covalent attachment to NucleoLink. Hybridization was performed with 500 ng DNA, 5% (w/w) of which was labelled with photo-activatable biotin (competitive hybridization) for 2.5 h at 65 degrees C in 2 x SSC followed by stringent washing with 2 x SSC at the same temperature. The criteria for acceptance...

  7. Saturn's outer satellite, Phoebe

    Science.gov (United States)

    1981-01-01

    Voyager 2 took this photo of Saturn's outer satellite, Phoebe, on Sept. 4, 1981, from 2.2 million kilometers (1.36 million miles) away. The photo shows that Phoebe is about 200 kilometers (120 miles) in diameter, about twice the size of Earth-based measurements; and dark, with five percent reflectivity -- much darker than any other Saturnian satellite. That, and information from Earth-based observations, indicates Phoebe is almost certainly a captured asteroid, and did not form in the original Saturn nebula as Saturn's other satellites did. Phoebe is the only Saturnian satellite that does not always show the same face to Saturn: Its orbital period is 550 days. Its rotation period (length of day), determined from Voyager 2 observations, is nine to ten hours. Other ground-based observations that indicate that Phoebe is a captured asteroid: It orbits Saturn in the ecliptic plane (the plane in which Earth and most other planets orbit the Sun), rather than in Saturn's equatorial plane as the other Saturn satellites do. And Phoebe's orbit is retrograde -- in the direction opposite to that of the other satellites. Voyager is managed for NASA's Office of Space Science by the Jet Propulsion Laboratory.

  8. Induction studies with satellite data

    DEFF Research Database (Denmark)

    Olsen, Nils

    1999-01-01

    satellites. The results of several induction studies with scalar satellite data (from the POGO satellites) and with vector data (from the Magsat mission) demonstrate the ability to probe the Earth's conductivity from space. However, compared to the results obtained with ground data the satellite results...

  9. Chilean Pitavia more closely related to Oceania and Old World Rutaceae than to Neotropical groups: evidence from two cpDNA non-coding regions, with a new subfamilial classification of the family.

    Science.gov (United States)

    Groppo, Milton; Kallunki, Jacquelyn A; Pirani, José Rubens; Antonelli, Alexandre

    2012-01-01

    The position of the plant genus Pitavia within an infrafamilial phylogeny of Rutaceae (rue, or orange family) was investigated with the use of two non-coding regions from cpDNA, the trnL-trnF region and the rps16 intron. The only species of the genus, Pitavia punctata Molina, is restricted to the temperate forests of the Coastal Cordillera of Central-Southern Chile and threatened by loss of habitat. The genus traditionally has been treated as part of tribe Zanthoxyleae (subfamily Rutoideae) where it constitutes the monogeneric tribe Pitaviinae. This tribe and genus are characterized by fruits of 1 to 4 fleshy drupelets, unlike the dehiscent fruits typical of the subfamily. Fifty-five taxa of Rutaceae, representing 53 genera (nearly one-third of those in the family) and all subfamilies, tribes, and almost all subtribes of the family were included. Parsimony and Bayesian inference were used to infer the phylogeny; six taxa of Meliaceae, Sapindaceae, and Simaroubaceae, all members of Sapindales, were also used as out-groups. Results from both analyses were congruent and showed Pitavia as sister to Flindersia and Lunasia, both genera with species scattered through Australia, Philippines, Moluccas, New Guinea and the Malayan region, and phylogenetically far from other Neotropical Rutaceae, such as the Galipeinae (Galipeeae, Rutoideae) and Pteleinae (Toddalieae, former Toddalioideae). Additionally, a new circumscription of the subfamilies of Rutaceae is presented and discussed. Only two subfamilies (both monophyletic) are recognized: Cneoroideae (including Dictyolomatoideae, Spathelioideae, Cneoraceae, and Ptaeroxylaceae) and Rutoideae (including not only traditional Rutoideae but also Aurantioideae, Flindersioideae, and Toddalioideae). As a consequence, Aurantioideae (Citrus and allies) is reduced to tribal rank as Aurantieae.

  10. ISDN - The case for satellites

    Science.gov (United States)

    Pelton, J. N.; McDougal, P. J.

    1987-05-01

    The role of satellites in the proposed Integrated Services Digital Network (ISDN) is examined. ISDN is to be a unified global network providing international telecommunication services. The delay time connected with satellite communications is considered. The advantages of using satellites in ISDN are: (1) the digital services available with satellites (time-division multiple access, intermediate data rate, and Intelsat business services); (2) satellite networking features; (3) flexibility; and (4) global interconnectivity. It is noted that with the use of powerful transmitters on satellites, the growth of small earth stations, and developments in band switching and intersatellite links that satellites are applicable to ISDN.

  11. Families of Keplerian orbits

    Energy Technology Data Exchange (ETDEWEB)

    Butikov, Eugene I [St Petersburg State University, St Petersburg (Russian Federation)

    2003-03-01

    Various properties of Keplerian orbits traced by satellites that are launched from one and the same spatial point with different initial velocities are discussed. Two families of elliptical orbits are investigated, namely the sets of orbits produced by a common direction but different magnitudes of the initial velocities, and by a common magnitude but various directions of the initial velocities. For the latter family, the envelope of all the orbits is found, which is the boundary of the spatial region occupied by the orbits.

  12. Families of Keplerian orbits

    CERN Document Server

    Butikov, E I

    2003-01-01

    Various properties of Keplerian orbits traced by satellites that are launched from one and the same spatial point with different initial velocities are discussed. Two families of elliptical orbits are investigated, namely the sets of orbits produced by a common direction but different magnitudes of the initial velocities, and by a common magnitude but various directions of the initial velocities. For the latter family, the envelope of all the orbits is found, which is the boundary of the spatial region occupied by the orbits.

  13. Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family.

    Science.gov (United States)

    Das, Ushati; Smith, Paul; Shuman, Stewart

    2012-01-01

    LigD 3'-phosphoesterase (PE) enzymes perform end-healing reactions at DNA breaks. Here we characterize the 3'-ribonucleoside-resecting activity of Candidatus Korarchaeum PE. CkoPE prefers a single-stranded substrate versus a primer-template. Activity is abolished by vanadate (10 mM), but is less sensitive to phosphate (IC(50) 50 mM) or chloride (IC(50) 150 mM). The metal requirement is satisfied by manganese, cobalt, copper or cadmium, but not magnesium, calcium, nickel or zinc. Insights to CkoPE metal specificity were gained by solving new 1.5 Å crystal structures of CkoPE in complexes with Co(2+) and Zn(2+). His9, His15 and Asp17 coordinate cobalt in an octahedral complex that includes a phosphate anion, which is in turn coordinated by Arg19 and His51. The cobalt and phosphate positions and the atomic contacts in the active site are virtually identical to those in the CkoPE·Mn(2+) structure. By contrast, Zn(2+) binds in the active site in a tetrahedral complex, wherein the position, orientation and atomic contacts of the phosphate are shifted and its interaction with His51 is lost. We conclude that: (i) PE selectively binds to 'soft' metals in either productive or non-productive modes and (ii) PE catalysis depends acutely on proper metal and scissile phosphate geometry.

  14. Familial hypercholesterolemia and atherosclerosis in cloned minipigs created by DNA transposition of a human PCSK9 gain-of-function mutant.

    Science.gov (United States)

    Al-Mashhadi, Rozh H; Sørensen, Charlotte B; Kragh, Peter M; Christoffersen, Christina; Mortensen, Martin B; Tolbod, Lars P; Thim, Troels; Du, Yutao; Li, Juan; Liu, Ying; Moldt, Brian; Schmidt, Mette; Vajta, Gabor; Larsen, Torben; Purup, Stig; Bolund, Lars; Nielsen, Lars B; Callesen, Henrik; Falk, Erling; Mikkelsen, Jacob Giehm; Bentzon, Jacob F

    2013-01-02

    Lack of animal models with human-like size and pathology hampers translational research in atherosclerosis. Mouse models are missing central features of human atherosclerosis and are too small for intravascular procedures and imaging. Modeling the disease in minipigs may overcome these limitations, but it has proven difficult to induce rapid atherosclerosis in normal pigs by high-fat feeding alone, and genetically modified models similar to those created in mice are not available. D374Y gain-of-function mutations in the proprotein convertase subtilisin/kexin type 9 (PCSK9) gene cause severe autosomal dominant hypercholesterolemia and accelerates atherosclerosis in humans. Using Sleeping Beauty DNA transposition and cloning by somatic cell nuclear transfer, we created Yucatan minipigs with liver-specific expression of human D374Y-PCSK9. D374Y-PCSK9 transgenic pigs displayed reduced hepatic low-density lipoprotein (LDL) receptor levels, impaired LDL clearance, severe hypercholesterolemia, and spontaneous development of progressive atherosclerotic lesions that could be visualized by noninvasive imaging. This model should prove useful for several types of translational research in atherosclerosis.

  15. Phylogeographic distribution of mitochondrial DNA ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 88; Issue 1 ... mtDNA; macrohaplogroup M; haplogroups; castes and tribes; linguistic families. ... belonging to the same linguistic family but inhabiting different geographical regions (Dravidian and Austro–Asiatic speakers) exhibited differences in their haplogroup diversity.

  16. Geostationary satellites collocation

    CERN Document Server

    Li, Hengnian

    2014-01-01

    Geostationary Satellites Collocation aims to find solutions for deploying a safe and reliable collocation control. Focusing on the orbital perturbation analysis, the mathematical foundations for orbit and control of the geostationary satellite are summarized. The mathematical and physical principle of orbital maneuver and collocation strategies for multi geostationary satellites sharing with the same dead band is also stressed. Moreover, the book presents some applications using the above algorithms and mathematical models to help readers master the corrective method for planning station keeping maneuvers. Engineers and scientists in the fields of aerospace technology and space science can benefit from this book. Hengnian Li is the Deputy Director of State Key Laboratory of Astronautic Dynamics, China.

  17. Solar Power Satellites

    CERN Document Server

    Flournoy, Don M

    2012-01-01

    Communication satellites are a $144 billion industry. Is there any space-based industry that could possibly beat that market? 'Solar Power Satellites' shows why and how the space satellite industry will soon begin expanding its market from relaying signals to Earth to generating energy in space and delivering it to the ground as electricity. In all industrialized nations, energy demand is growing exponentially. In the developing world, the need for energy is as basic as food and water. The Sun's energy is available everywhere, and it is non-polluting. As business plans demonstrate its technical feasibility, commercial potential, and environmental acceptability, every country on Earth will look to space for the power it needs.

  18. Family Therapy

    Science.gov (United States)

    Family therapy Overview By Mayo Clinic Staff Family therapy is a type of psychological counseling (psychotherapy) that can help family members improve communication and resolve conflicts. Family therapy is usually provided ...

  19. Dissolved families

    DEFF Research Database (Denmark)

    Christoffersen, Mogens

    The situation in the family preceding a family separation is studied here, to identify risk factors for family dissolution. Information registers covering prospective statistics about health aspects, demographic variables, family violence, self-destructive behaviour, unemployment, and the spousal...

  20. Functional Overload Enhances Satellite Cell Properties in Skeletal Muscle

    Directory of Open Access Journals (Sweden)

    Shin Fujimaki

    2016-01-01

    Full Text Available Skeletal muscle represents a plentiful and accessible source of adult stem cells. Skeletal-muscle-derived stem cells, termed satellite cells, play essential roles in postnatal growth, maintenance, repair, and regeneration of skeletal muscle. Although it is well known that the number of satellite cells increases following physical exercise, functional alterations in satellite cells such as proliferative capacity and differentiation efficiency following exercise and their molecular mechanisms remain unclear. Here, we found that functional overload, which is widely used to model resistance exercise, causes skeletal muscle hypertrophy and converts satellite cells from quiescent state to activated state. Our analysis showed that functional overload induces the expression of MyoD in satellite cells and enhances the proliferative capacity and differentiation potential of these cells. The changes in satellite cell properties coincided with the inactivation of Notch signaling and the activation of Wnt signaling and likely involve modulation by transcription factors of the Sox family. These results indicate the effects of resistance exercise on the regulation of satellite cells and provide insight into the molecular mechanism of satellite cell activation following physical exercise.

  1. GPS satellite surveying

    CERN Document Server

    Leick, Alfred; Tatarnikov, Dmitry

    2015-01-01

    THE MOST COMPREHENSIVE, UP-TO-DATE GUIDE ON GPS TECHNOLOGY FOR SURVEYING Three previous editions have established GPS Satellite Surveying as the definitive industry reference. Now fully updated and expanded to reflect the newest developments in the field, this Fourth Edition features cutting-edge information on GNSS antennas, precise point positioning, real-time relative positioning, lattice reduction, and much more. Expert authors examine additional tools and applications, offering complete coverage of geodetic surveying using satellite technologies. The past decade has seen a major evolut

  2. First evidence of DNA methylation in insect Tribolium castaneum: environmental regulation of DNA methylation within heterochromatin.

    Science.gov (United States)

    Feliciello, Isidoro; Parazajder, Josip; Akrap, Ivana; Ugarković, Durđica

    2013-05-01

    DNA methylation has been studied in many eukaryotic organisms, in particular vertebrates, and was implicated in developmental and phenotypic variations. Little is known about the role of DNA methylation in invertebrates, although insects are considered as excellent models for studying the evolution of DNA methylation. In the red flour beetle, Tribolium castaneum (Tenebrionidae, Coleoptera), no evidence of DNA methylation has been found till now. In this paper, a cytosine methylation in Tribolium castaneum embryos was detected by methylation sensitive restriction endonucleases and immuno-dot blot assay. DNA methylation in embryos is followed by a global demethylation in larvae, pupae and adults. DNA demethylation seems to proceed actively through 5-hydroxymethylcytosine, most probably by the action of TET enzyme. Bisulfite sequencing of a highly abundant satellite DNA located in pericentromeric heterochromatin revealed similar profile of cytosine methylation in adults and embryos. Cytosine methylation was not only restricted to CpG sites but was found at CpA, CpT and CpC sites. In addition, complete cytosine demethylation of heterochromatic satellite DNA was induced by heat stress. The results reveal existence of DNA methylation cycling in T. castaneum ranging from strong overall cytosine methylation in embryos to a weak DNA methylation in other developmental stages. Nevertheless, DNA methylation is preserved within heterochromatin during development, indicating its role in heterochromatin formation and maintenance. It is, however, strongly affected by heat stress, suggesting a role for DNA methylation in heterochromatin structure modulation during heat stress response.

  3. Diversity of Dicotyledenous-Infecting Geminiviruses and Their Associated DNA Molecules in Southern Africa, Including the South-West Indian Ocean Islands

    Directory of Open Access Journals (Sweden)

    Lindy L. Esterhuizen

    2012-09-01

    Full Text Available The family Geminiviridae comprises a group of plant-infecting circular ssDNA viruses that severely constrain agricultural production throughout the temperate regions of the world, and are a particularly serious threat to food security in sub-Saharan Africa. While geminiviruses exhibit considerable diversity in terms of their nucleotide sequences, genome structures, host ranges and insect vectors, the best characterised and economically most important of these viruses are those in the genus Begomovirus. Whereas begomoviruses are generally considered to be either monopartite (one ssDNA component or bipartite (two circular ssDNA components called DNA-A and DNA-B, many apparently monopartite begomoviruses are associated with additional subviral ssDNA satellite components, called alpha- (DNA-as or betasatellites (DNA-βs. Additionally, subgenomic molecules, also known as defective interfering (DIs DNAs that are usually derived from the parent helper virus through deletions of parts of its genome, are also associated with bipartite and monopartite begomoviruses. The past three decades have witnessed the emergence and diversification of various new begomoviral species and associated DI DNAs, in southern Africa, East Africa, and proximal Indian Ocean islands, which today threaten important vegetable and commercial crops such as, tobacco, cassava, tomato, sweet potato, and beans. This review aims to describe what is known about these viruses and their impacts on sustainable production in this sensitive region of the world.

  4. Satellite orbit determination and gravity field recovery from satellite-to-satellite tracking

    Science.gov (United States)

    Wakker, K. F.; Ambrosius, B. A. C.; Leenman, H.

    1989-07-01

    Studies on satellite-to-satellite tracking (SST) with POPSAT (a geodetic satellite concept) and a ERS-class (Earth observation) satellite, a Satellite-to-Satellite Tracking (SST) gravity mission, and precise gravity field determination methods and mission requirements are reported. The first two studies primarily address the application of SST between the high altitude POPSAT and an ERS-class or GRM (Geopotential Research Mission) satellite to the orbit determination of the latter two satellites. Activities focussed on the determination of the tracking coverage of the lower altitude satellite by ground based tracking systems and by POPSAT, orbit determination error analysis and the determination of the surface forces acting on GRM. The third study surveys principles of SST, uncertainties of existing drag models, effects of direct luni-solar attraction and tides on orbit and the gravity gradient observable. Detailed ARISTOTELES (which replaced POPSAT) orbit determination error analyses were performed for various ground based tracking networks.

  5. Mitochondrial DNA.

    Science.gov (United States)

    Wright, Russell G.; Bottino, Paul J.

    1986-01-01

    Provides background information for teachers on mitochondrial DNA, pointing out that it may have once been a free-living organism. Includes a ready-to-duplicate exercise titled "Using Microchondrial DNA to Measure Evolutionary Distance." (JN)

  6. Rotation of Synchronous Satellites: Application to the Galilean Satellites

    Science.gov (United States)

    Henrard, Jacques; Schwanen, Gabriel

    2004-03-01

    An analytical theory of the rotation of a synchronous satellite is developed for the application to the rotation of the Galilean satellites. The theory is developed in the framework of Hamiltonian mechanics, using Andoyer variables. Special attention is given to the frequencies of libration as functions of the moments of inertia of the satellite.

  7. Cibola flight experiment satellite

    Science.gov (United States)

    Davies, P.; Liddle, Doug; Paffett, John; Sweeting, Martin; Curiel, A.; Sun, Wei; Eves, Stuart

    2004-11-01

    In order to achieve an "economy of scale" with respect to payload capacity the major trend in telecommunications satellites is for larger and larger platforms. With these large platforms the level of integration between platform and payload is increasing leading to longer delivery schedules. The typical lifecycle for procurement of these large telecommunications satellites is now 3-6 years depending on the level of non-recurring engineering needed. Surrey Satellite Technology Ltd (SSTL) has designed a low-cost platform aimed at telecommunications and navigation applications. SSTL's Geostationary Minisatellite Platform (GMP) is a new entrant addressing the lower end of the market with payloads up to 250kg requiring less than 1.5 kW power. The British National Space Centre through the MOSAIC Small Satellite Initiative supported the development of GMP. The main design goals for GMP are low-cost for the complete mission including launch and operations and a platform allowing flexible payload accommodation. GMP is specifically designed to allow rapid development and deployment with schedules typically between 1 and 2 years from contract signature to flight readiness. GMP achieves these aims by a modular design where the level of integration between the platform and payload is low. The modular design decomposes the satellite into three major components - the propulsion bay, the avionics bay and the payload module. Both the propulsion and avionics bays are reusable, largely unchanged, and independent of the payload configuration. Such a design means that SSTL or a 3rd party manufacturer can manufacture the payload in parallel to the platform with integration taking place quite late in the schedule. In July 2003 SSTL signed a contract for ESA's first Galileo navigation satellite known as GSTBV2/A. The satellite is based on GMP and ESA plan to launch it into a MEO orbit late in 2005. The second flight of GMP is likely to be in 2006 carrying a geostationary payload

  8. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  9. Defense Meteorological Satellite Program (DMSP)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Defense Meteorological Satellite Program (DMSP) satellites collect visible and infrared cloud imagery as well as monitoring the atmospheric, oceanographic,...

  10. Satellite Ocean Heat Content Suite

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This collection contains an operational Satellite Ocean Heat Content Suite (SOHCS) product generated by NOAA National Environmental Satellite, Data, and Information...

  11. CDDIS_GNSS_satellite_data

    Data.gov (United States)

    National Aeronautics and Space Administration — Global Navigation Satellite System (GNSS) data consists of the U.S. Global Positioning System (GPS) and the Russian GLObal NAvigation Satellite System (GLONASS)...

  12. Satellite transmission of oceanographic data

    Digital Repository Service at National Institute of Oceanography (India)

    Desa, E.S.; Desai, R.G.P.; DeSa, E.J.

    Oceanographic data collected on a research vessel has been transmitted to a shore laboratory using the INMARSAT maritime satellite The system configuration used, consisted of Satellite Communication Terminals interfaced to desk top computers...

  13. Students Partner with Laboratory Staff to Modernize LES-9 Satellite Communications

    Science.gov (United States)

    2016-04-29

    orbiting counterpart, a satellite model built by Minuteman Technical High School students and Laboratory staff hangs reminiscent of one of the...communications satellite was developed for the U.S. Air Force and designed to operate in coplanar, circular, inclined, and geosynchronous orbits . Royster...Laboratory’s first pioneering inventions, the Lincoln Experimental Satellite (LES) family. Launched on 14 March 1976, LES-9 is the last in a series of

  14. Family functioning in neglectful families.

    Science.gov (United States)

    Gaudin, J M; Polansky, N A; Kilpatrick, A C; Shilton, P

    1996-04-01

    Family functioning in 103 neglectful and 102 non-neglectful low-income families is examined using self-report and observational measures. Neglectful mothers reported their families as having more family conflict and less expression of feelings, but not less cohesive. Ratings of observed and videotaped family interactions indicated neglect families were less organized, more chaotic, less verbally expressive, showed less positive and more negative affect than comparison families. However, there were wide differences on measures of functioning among neglect families. Three distinct types of neglectful family functioning are identified and interventions for each type are suggested to improve parental-family functioning.

  15. Variations in brain DNA

    Directory of Open Access Journals (Sweden)

    Jesus eAvila

    2014-11-01

    Full Text Available It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain.

  16. Random DNA libraries from three species of the stick insect genus Bacillus (Insecta: Phasmida): repetitive DNA characterization and first observation of polyneopteran MITEs.

    Science.gov (United States)

    Ricci, Marco; Luchetti, Andrea; Bonandin, Livia; Mantovani, Barbara

    2013-12-01

    The repetitive DNA content of the stick insect species Bacillus rossius (facultative parthenogenetic), Bacillus grandii (gonochoric), and Bacillus atticus (obligate parthenogenetic) was analyzed through the survey of random genomic libraries roughly corresponding to 0.006% of the genome. By repeat masking, 19 families of transposable elements were identified (two LTR and six non-LTR retrotransposons; 11 DNA transposons). Moreover, a de novo analysis revealed, among the three libraries, the first MITE family observed in polyneopteran genomes. On the whole, transposable element abundance represented 23.3% of the genome in B. rossius, 22.9% in B. atticus, and 18% in B. grandii. Tandem repeat content in the three libraries is much lower: 1.32%, 0.64%, and 1.86% in B. rossius, B. grandii, and B. atticus, respectively. Microsatellites are the most abundant in all species. Minisatellites were only found in B. rossius and B. atticus, and five monomers belonging to the Bag320 satellite family were detected in B. atticus. Assuming the survey provides adequate representation of the relative genome, the obligate parthenogenetic species (B. atticus), compared with the other two species analyzed, does not show a lower transposable element content, as expected from some theoretical and empirical studies.

  17. miR-29 Represses the Activities of DNA Methyltransferases and DNA Demethylases

    Directory of Open Access Journals (Sweden)

    Izuho Hatada

    2013-07-01

    Full Text Available Members of the microRNA-29 (miR-29 family directly target the DNA methyltransferases, DNMT3A and DNMT3B. Disturbances in the expression levels of miR-29 have been linked to tumorigenesis and tumor aggressiveness. Members of the miR-29 family are currently thought to repress DNA methylation and suppress tumorigenesis by protecting against de novo methylation. Here, we report that members of the miR-29 family repress the activities of DNA methyltransferases and DNA demethylases, which have opposing roles in control of DNA methylation status. Members of the miR-29 family directly inhibited DNA methyltransferases and two major factors involved in DNA demethylation, namely tet methylcytosine dioxygenase 1 (TET1 and thymine DNA glycosylase (TDG. Overexpression of miR-29 upregulated the global DNA methylation level in some cancer cells and downregulated DNA methylation in other cancer cells, suggesting that miR-29 suppresses tumorigenesis by protecting against changes in the existing DNA methylation status rather than by preventing de novo methylation of DNA.

  18. Saturn's outer satellite - Phoebe

    Science.gov (United States)

    1999-01-01

    Voyager 2 took these images of Saturn's outer satellite Phoebe, on Sept. 4, 1981, from 2.2 million kilometers (1.36 million miles)away. This pair shows two different hemispheres of the satellite. The left image shows a bright mountain on the upper right edge reflecting the light of the setting sun. This mountain is possibly the central peak of a large impact crater taking up most of the upper right quadrant of Phoebe in this view. The right images shows a hemisphere with an intrinsically bright spot in the top portion of the image as well as the ridges appearing bright in the sunset light of the lower right. These images were processed by the Multimission Image Processing Laboratory of the Jet Propulsion Laboratory. The Jet Propulsion Laboratory manages the Voyager Project for NASA's Office of Space Science and Applications.

  19. Expert systems for satellite stationkeeping

    Science.gov (United States)

    Mekaru, M. M.; Wright, M. A.

    The feasibility of implementing artificial intelligence on satellites is evaluated, with the aim of using an onboard expert system to perform effective stationkeeping functions without assistance from the ground. The Defense Satellite Communication System (DSCS III) is used as an example. The cost for implementing a satellite stationkeeping expert system is analyzed. A ground-based expert system could reduce the current number of support personnel for the stationkeeping task. Results of analyzing a possible flight system are quite promising. An expert system for satellite stationkeeping seems feasible, appears cost-effective, and offers increased satellite endurance through autonomous operations.

  20. Thematic mapping from satellite imagery

    CERN Document Server

    Denègre, J

    2013-01-01

    Thematic Mapping from Satellite Imagery: A Guidebook discusses methods in producing maps using satellite images. The book is comprised of five chapters; each chapter covers one stage of the process. Chapter 1 tackles the satellite remote sensing imaging and its cartographic significance. Chapter 2 discusses the production processes for extracting information from satellite data. The next chapter covers the methods for combining satellite-derived information with that obtained from conventional sources. Chapter 4 deals with design and semiology for cartographic representation, and Chapter 5 pre

  1. Cooperative and cognitive satellite systems

    CERN Document Server

    Chatzinotas, Symeon; De Gaudenzi, Riccardo

    2015-01-01

    Cooperative and Cognitive Satellite Systems provides a solid overview of the current research in the field of cooperative and cognitive satellite systems, helping users understand how to incorporate state-of-the-art communication techniques in innovative satellite network architectures to enable the next generation of satellite systems. The book is edited and written by top researchers and practitioners in the field, providing a comprehensive explanation of current research that allows users to discover future technologies and their applications, integrate satellite and terrestrial systems

  2. ASPEC: Solar power satellite

    Science.gov (United States)

    1991-01-01

    The solar power satellite (SPS) will provide a clean, reliable source of energy for large-scale consumption. The system will use satellites in geostationary orbits around the Earth to capture the Sun's energy. The intercepted sunlight will be converted to laser beam energy that can be transmitted to the Earth's surface. Ground systems on the Earth will convert the transmissions from space into electric power. The preliminary design for the SPS consists of one satellite in orbit around the Earth transmitting energy to a single ground station. The SPS design uses multilayer solar cell technology arranged on a 20 km squared planar array to intercept sunlight and convert it to an electric voltage. Power conditioning devices then send the electricity to a laser, which transmits the power to the surface of the Earth. A ground station will convert the beam into electricity. Typically, a single SPS will supply 5 GW of power to the ground station. Due to the large mass of the SPS, about 41 million kg, construction in space is needed in order to keep the structural mass low. The orbit configuration for this design is to operate a single satellite in geosynchronous orbit (GEO). The GEO allows the system to be positioned above a single receiving station and remain in sunlight 99 percent of the time. Construction will take place in low Earth orbit (LEO); array sections, 20 in total, will be sailed on solar wind out to the GEO location in 150 days. These individual transportation sections are referred to as solar sailing array panels (SSAP's). The primary truss elements used to support the array are composed of composite tubular members in a pentahedral arrangement. Smart segments consisting of passive and active damping devices will increase the control of dynamic SPS modes.

  3. Family Meals

    Science.gov (United States)

    ... Late for the Flu Vaccine? Eating Disorders Arrhythmias Family Meals KidsHealth > For Parents > Family Meals Print A ... even more important as kids get older. Making Family Meals Happen It can be a big challenge ...

  4. Family Issues

    Science.gov (United States)

    ... and grandparents raise grandchildren. Some children live in foster families, adoptive families, or in stepfamilies. Families are much more than groups of people who share the same genes or the ...

  5. Family Life

    Science.gov (United States)

    ... Family and Friends > Family Life Request Permissions Family Life Approved by the Cancer.Net Editorial Board , 11/ ... treatment become as overwhelming for others in your life as they are for you. Understanding the potential ...

  6. Familial hypertriglyceridemia

    Science.gov (United States)

    Familial hypertriglyceridemia is a common disorder passed down through families. It causes a higher-than-normal level of ... Familial hypertriglyceridemia is caused by a genetic defect, which is passed on in an autosomal dominant fashion. This ...

  7. Satellite-Friendly Protocols and Standards

    Science.gov (United States)

    Koudelka, O.; Schmidt, M.; Ebert, J.; Schlemmer, H.; Kastner, S.; Riedler, W.

    2002-01-01

    We are currently observing a development unprecedented with other services, the enormous growth of the Internet. Video, voice and data applications can be supported via this network in high quality. Multi-media applications require high bandwidth which may not be available in many areas. When making proper use of the broadcast feature of a communications satellite, the performance of the satellite-based system can compare favourably to terrestrial solutions. Internet applications are in many cases highly asymmetric, making them very well suited to applications using small and inexpensive terminals. Data from one source may be used simultaneously by a large number of users. The Internet protocol suite has become the de-facto standard. But this protocol family in its original form has not been designed to support guaranteed quality of service, a prerequisite for real-time, high quality traffic. The Internet Protocol has to be adapted for the satellite environment, because long roundtrip delays and the error behaviour of the channel could make it inefficient over a GEO satellite. Another requirement is to utilise the satellite bandwidth as efficiently as possible. This can be achieved by adapting the access system to the nature of IP frames, which are variable in length. In the framework of ESA's ARTES project a novel satellite multimedia system was developed which utilises Multi-Frequency TDMA in a meshed network topology. The system supports Quality of Service (QoS) by reserving capacity with different QoS requirements. The system is centrally controlled by a master station with the implementation of a demand assignment (DAMA) system. A lean internal signalling system has been adopted. Network management is based on the SNMP protocol and industry-standard network management platforms, making interfaces to standard accounting and billing systems easy. Modern communication systems will have to be compliant to different standards in a very flexible manner. The

  8. Laser satellite power systems

    Energy Technology Data Exchange (ETDEWEB)

    Walbridge, E.W.

    1980-01-01

    A laser satellite power system (SPS) converts solar power captured by earth-orbiting satellites into electrical power on the earth's surface, the satellite-to-ground transmission of power being effected by laser beam. The laser SPS may be an alternative to the microwave SPS. Microwaves easily penetrate clouds while laser radiation does not. Although there is this major disadvantage to a laser SPS, that system has four important advantages over the microwave alternative: (1) land requirements are much less, (2) radiation levels are low outside the laser ground stations, (3) laser beam sidelobes are not expected to interfere with electromagnetic systems, and (4) the laser system lends itself to small-scale demonstration. After describing lasers and how they work, the report discusses the five lasers that are candidates for application in a laser SPS: electric discharge lasers, direct and indirect solar pumped lasers, free electron lasers, and closed-cycle chemical lasers. The Lockheed laser SPS is examined in some detail. To determine whether a laser SPS will be worthy of future deployment, its capabilities need to be better understood and its attractiveness relative to other electric power options better assessed. First priority should be given to potential program stoppers, e.g., beam attenuation by clouds. If investigation shows these potential program stoppers to be resolvable, further research should investigate lasers that are particularly promising for SPS application.

  9. Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model.

    Science.gov (United States)

    Oliver, Patricia; Peralta-Gil, Martín; Tabche, María-Luisa; Merino, Enrique

    2016-08-27

    The goal of most programs developed to find transcription factor binding sites (TFBSs) is the identification of discrete sequence motifs that are significantly over-represented in a given set of sequences where a transcription factor (TF) is expected to bind. These programs assume that the nucleotide conservation of a specific motif is indicative of a selective pressure required for the recognition of a TF for its corresponding TFBS. Despite their extensive use, the accuracies reached with these programs remain low. In many cases, true TFBSs are excluded from the identification process, especially when they correspond to low-affinity but important binding sites of regulatory systems. We developed a computational protocol based on molecular and structural criteria to perform biologically meaningful and accurate phylogenetic footprinting analyses. Our protocol considers fundamental aspects of the TF-DNA binding process, such as: i) the active homodimeric conformations of TFs that impose symmetric structures on the TFBSs, ii) the cooperative binding of TFs, iii) the effects of the presence or absence of co-inducers, iv) the proximity between two TFBSs or one TFBS and a promoter that leads to very long spurious motifs, v) the presence of AT-rich sequences not recognized by the TF but that are required for DNA flexibility, and vi) the dynamic order in which the different binding events take place to determine a regulatory response (i.e., activation or repression). In our protocol, the abovementioned criteria were used to analyze a profile of consensus motifs generated from canonical Phylogenetic Footprinting Analyses using a set of analysis windows of incremental sizes. To evaluate the performance of our protocol, we analyzed six members of the LysR-type TF family in Gammaproteobacteria. The identification of TFBSs based exclusively on the significance of the over-representation of motifs in a set of sequences might lead to inaccurate results. The consideration of

  10. Eukaryotic DNA Replicases

    KAUST Repository

    Zaher, Manal S.

    2014-11-21

    The current model of the eukaryotic DNA replication fork includes three replicative DNA polymerases, polymerase α/primase complex (Pol α), polymerase δ (Pol δ), and polymerase ε (Pol ε). The primase synthesizes 8–12 nucleotide RNA primers that are extended by the DNA polymerization activity of Pol α into 30–35 nucleotide RNA-DNA primers. Replication factor C (RFC) opens the polymerase clamp-like processivity factor, proliferating cell nuclear antigen (PCNA), and loads it onto the primer-template. Pol δ utilizes PCNA to mediate highly processive DNA synthesis, while Pol ε has intrinsic high processivity that is modestly stimulated by PCNA. Pol ε replicates the leading strand and Pol δ replicates the lagging strand in a division of labor that is not strict. The three polymerases are comprised of multiple subunits and share unifying features in their large catalytic and B subunits. The remaining subunits are evolutionarily not related and perform diverse functions. The catalytic subunits are members of family B, which are distinguished by their larger sizes due to inserts in their N- and C-terminal regions. The sizes of these inserts vary among the three polymerases, and their functions remain largely unknown. Strikingly, the quaternary structures of Pol α, Pol δ, and Pol ε are arranged similarly. The catalytic subunits adopt a globular structure that is linked via its conserved C-terminal region to the B subunit. The remaining subunits are linked to the catalytic and B subunits in a highly flexible manner.

  11. Family Privilege

    Science.gov (United States)

    Seita, John R.

    2014-01-01

    Family privilege is defined as "strengths and supports gained through primary caring relationships." A generation ago, the typical family included two parents and a bevy of kids living under one roof. Now, every variation of blended caregiving qualifies as family. But over the long arc of human history, a real family was a…

  12. Satellite Laser Ranging Satellite Orbit Product from NASA CDDIS

    Data.gov (United States)

    National Aeronautics and Space Administration — SLR Satellite Orbit solutions available from the Crustal Dynamics Data Information System (CDDIS). Precise Orbit Determination (POD) solutions in Standard Product 3...

  13. Radio broadcasting via satellite

    Science.gov (United States)

    Helm, Neil R.; Pritchard, Wilbur L.

    1990-10-01

    Market areas offering potential for future narrowband broadcast satellites are examined, including international public diplomacy, government- and advertising-supported, and business-application usages. Technical issues such as frequency allocation, spacecraft types, transmission parameters, and radio receiver characteristics are outlined. Service and system requirements, advertising revenue, and business communications services are among the economic issues discussed. The institutional framework required to provide an operational radio broadcast service is studied, and new initiatives in direct broadcast audio radio systems, encompassing studies, tests, in-orbit demonstrations of, and proposals for national and international commercial broadcast services are considered.

  14. The Galilean Satellites

    Science.gov (United States)

    1998-01-01

    This composite includes the four largest moons of Jupiter which are known as the Galilean satellites. The Galilean satellites were first seen by the Italian astronomer Galileo Galilei in 1610. Shown from left to right in order of increasing distance from Jupiter, Io is closest, followed by Europa, Ganymede, and Callisto.The order of these satellites from the planet Jupiter helps to explain some of the visible differences among the moons. Io is subject to the strongest tidal stresses from the massive planet. These stresses generate internal heating which is released at the surface and makes Io the most volcanically active body in our solar system. Europa appears to be strongly differentiated with a rock/iron core, an ice layer at its surface, and the potential for local or global zones of water between these layers. Tectonic resurfacing brightens terrain on the less active and partially differentiated moon Ganymede. Callisto, furthest from Jupiter, appears heavily cratered at low resolutions and shows no evidence of internal activity.North is to the top of this composite picture in which these satellites have all been scaled to a common factor of 10 kilometers (6 miles) per picture element.The Solid State Imaging (CCD) system aboard NASA's Galileo spacecraft acquired the Io and Ganymede images in June 1996, the Europa images in September 1996, and the Callisto images in November 1997.Launched in October 1989, the spacecraft's mission is to conduct detailed studies of the giant planet, its largest moons and the Jovian magnetic environment. The Jet Propulsion Laboratory, Pasadena, CA, manages the mission for NASA's Office of Space Science, Washington, DC.The Jet Propulsion Laboratory, Pasadena, CA manages the Galileo mission for NASA's Office of Space Science, Washington, DC. JPL is an operating division of California Institute of Technology (Caltech).This image and other images and data received from Galileo are posted on the World Wide Web, on the Galileo mission

  15. China Satellite Navigation Conference

    CERN Document Server

    Liu, Jingnan; Yang, Yuanxi; Fan, Shiwei; Yu, Wenxian

    2017-01-01

    These proceedings present selected research papers from CSNC2017, held during 23th-25th May in Shanghai, China. The theme of CSNC2017 is Positioning, Connecting All. These papers discuss the technologies and applications of the Global Navigation Satellite System (GNSS), and the latest progress made in the China BeiDou System (BDS) especially. They are divided into 12 topics to match the corresponding sessions in CSNC2017, which broadly covered key topics in GNSS. Readers can learn about the BDS and keep abreast of the latest advances in GNSS techniques and applications.

  16. Understanding satellite navigation

    CERN Document Server

    Acharya, Rajat

    2014-01-01

    This book explains the basic principles of satellite navigation technology with the bare minimum of mathematics and without complex equations. It helps you to conceptualize the underlying theory from first principles, building up your knowledge gradually using practical demonstrations and worked examples. A full range of MATLAB simulations is used to visualize concepts and solve problems, allowing you to see what happens to signals and systems with different configurations. Implementation and applications are discussed, along with some special topics such as Kalman Filter and Ionosphere. W

  17. China Satellite Navigation Conference

    CERN Document Server

    Liu, Jingnan; Fan, Shiwei; Wang, Feixue

    2016-01-01

    These Proceedings present selected research papers from CSNC2016, held during 18th-20th May in Changsha, China. The theme of CSNC2016 is Smart Sensing, Smart Perception. These papers discuss the technologies and applications of the Global Navigation Satellite System (GNSS), and the latest progress made in the China BeiDou System (BDS) especially. They are divided into 12 topics to match the corresponding sessions in CSNC2016, which broadly covered key topics in GNSS. Readers can learn about the BDS and keep abreast of the latest advances in GNSS techniques and applications.

  18. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  19. DNA Vaccines

    Indian Academy of Sciences (India)

    research interests include: eukaryotic gene expres- sion and infectious diseases. Keywords. DNA vaccine, immune response, antibodies, infectious diseases. GENERAL I ... T -cells: Lymphocytes that differentiate primarily in the thymus and are central to the control and ... enhance DNA delivery into skeletal muscle.

  20. Collision matrix for Leo satellites

    Science.gov (United States)

    McKnight, Darren; Lorenzen, Gary

    The Low Earth Orbit (LEO) is becoming cluttered with thousands of satellites, rocket bodies, and a variety of space garbage. This collection of objects crossing paths at speeds on the order of 10 km/s is creating an increasing collision hazard to many operational systems. The effect that the destruction of LEO satellites will have on other users of the near-Earth environment is of great concern. A model is examined which quantifies the effect of one satellite fragmentation on neighboring satellites. This model is used to evaluate the interdependent hazard to a series of satellite systems. A number of space system fragmentation events are numerically simulated and the collision hazard to each is tabulated. Once all satellites in the matrix have been fragmented separately, a complete collision hazard representation can be depicted. This model has potential for developing an enhanced understanding of a number of aspects of the growing debris hazard in LEO.

  1. Public Service Communication Satellite Program

    Science.gov (United States)

    Brown, J. P.

    1977-01-01

    The proposed NASA Public Service Communication Satellite Program consists of four different activities designed to fulfill the needs of public service sector. These are: interaction with the users, experimentation with existing satellites, development of a limited capability satellite for the earliest possible launch, and initiation of an R&D program to develop the greatly increased capability that future systems will require. This paper will discuss NASA efforts in each of these areas.

  2. Living antennas on communication satellites

    DEFF Research Database (Denmark)

    Lumholt, Michael

    2003-01-01

    Crises change the global pattern of communication. The communications problems occur because the satellites are optimized to cover specific geographic areas, and these areas cannot be altered once the satellites are in Earth orbit. An effective solution to the problem is to equip communication...... satellites with "living" antennas that can adjust their radiation coverage areas according to the new demands. The development of living antennas is, therefore, among the focus areas identified and supported by the European Space Agency, ESA....

  3. Asteroid 243 IDA and its satellite. [Abstract only

    Science.gov (United States)

    Chapman, C. R.; Klaasen, K.; Belton, M. J. S.; Veverka, J.

    1994-01-01

    A high-resolution mosaic of Ida shows a highly irregular body (roughly 56 km long), heavily covered with craters, with many interesting geological features, including grooves, blocks, chutes, dark-floored craters, and crater chains. A satellite of Ida, with a preliminary designation of 1993 (243) 1, was discovered in orbit around Ida. It is approximately 1.5 km in diameter, has an albedo and spectral reflectance not grossly different from Ida, and orbits Ida in a prograde direction with a period of roughly 20 hr. No other comparable-sized satellites have been found near Ida. New pictures of the opposite side of Ida reveal an irregular, dog-bone shape, with a prominent gouge that seems to separate Ida into two chief components. A V-shaped valley, well shown in the highest-resolution view of Ida returned in April, may mark a modest expression on the September face of the more dramatic feature on the back side. Ida's dense population of craters shows a wide diversity of morphologies, consistent with the surface having been subjected to saturated bombardment by smaller projectiles. Assuming the same projectile flux applies to Ida was used in deriving Gaspra's cratering age of about 200 m.y., and assuming that Gaspra and Ida both have the same impact strength, then the age of Ida's surface is calculated to be 1-2 b.y. This is considerably older than expected from other evidence concerning the Koronis family. Our favored explanation of Ida's satellite is that it (or a precursor satellite from which the present satellite was derived) formed during the catastrophic disruption event that formed Ida itself and formed the Koronis family of asteroids. Perhaps, instead, the satellite is a block ejected from a cratering impact. In any case, smaller blocks visible on some parts of Ida are more certain to be crater ejecta, whether or not they were ever temporary satellites.

  4. Jupiter's Galilean Satellites

    Science.gov (United States)

    McGrath, Melissa A.

    2005-01-01

    Jupiter's Galilean satellites Io, Europa, Ganymede and Callisto encompass some of the most bizarre environments known in the solar system, spanning that of Io, the most volcanically active and perhaps the most inhospitable body known, to Europa, currently the focus of a search for life in the solar system because of its subsurface ocean. One of the premier areas of scientific return in solar system research in the past 10 years, due in large part to the Galileo mission and observations by the Hubble Space Telescope, has been a remarkable increase in our knowledge about these satellites. Discoveries have been made of tenuous molecular oxygen atmospheres on Europa and Ganymede, a magnetic field and accompanying auroral emissions at the poles of Ganymede, and of ozone and sulfur dioxide embedded in the surfaces of Europa, Ganymede and Callisto. Io's unusual sulfur dioxide atmosphere, including its volcanic plumes and strong electrodynamic interaction with magnetospheric plasma, has finally been quantitatively characterized. This talk will present highlights from the recent discoveries and advances in our understanding of these fascinating objects.

  5. Magnetic Satellite Missions and Data

    DEFF Research Database (Denmark)

    Olsen, Nils; Kotsiaros, Stavros

    2011-01-01

    Although the first satellite observations of the Earth’s magnetic field were already taken more than 50 years ago, continuous geomagnetic measurements from space are only available since 1999. The unprecedented time-space coverage of this recent data set opened revolutionary new possibilities...... for exploring the Earth’s magnetic field from space. In this chapter we discuss characteristics of satellites measuring the geomagnetic field and report on past, present and upcoming magnetic satellite missions. We conclude with some basics about space magnetic gradiometry as a possible path for future...... exploration of Earth’s magnetic field with satellites....

  6. Expression of cassini, a murine gamma-satellite sequence conserved in evolution, is regulated in normal and malignant hematopoietic cells.

    Science.gov (United States)

    Arutyunyan, Anna; Stoddart, Sonia; Yi, Sun-ju; Fei, Fei; Lim, Min; Groffen, Paula; Feldhahn, Niklas; Groffen, John; Heisterkamp, Nora

    2012-08-23

    Acute lymphoblastic leukemia (ALL) cells treated with drugs can become drug-tolerant if co-cultured with protective stromal mouse embryonic fibroblasts (MEFs). We performed transcriptional profiling on these stromal fibroblasts to investigate if they were affected by the presence of drug-treated ALL cells. These mitotically inactivated MEFs showed few changes in gene expression, but a family of sequences of which transcription is significantly increased was identified. A sequence related to this family, which we named cassini, was selected for further characterization. We found that cassini was highly upregulated in drug-treated ALL cells. Analysis of RNAs from different normal mouse tissues showed that cassini expression is highest in spleen and thymus, and can be further enhanced in these organs by exposure of mice to bacterial endotoxin. Heat shock, but not other types of stress, significantly induced the transcription of this locus in ALL cells. Transient overexpression of cassini in human 293 embryonic kidney cells did not increase the cytotoxic or cytostatic effects of chemotherapeutic drugs but provided some protection. Database searches revealed that sequences highly homologous to cassini are present in rodents, apicomplexans, flatworms and primates, indicating that they are conserved in evolution. Moreover, CASSINI RNA was induced in human ALL cells treated with vincristine. Surprisingly, cassini belongs to the previously reported murine family of γ-satellite/major satellite DNA sequences, which were not known to be present in other species. Our results show that the transcription of at least one member of these sequences is regulated, suggesting that this has a function in normal and transformed immune cells. Expression of these sequences may protect cells when they are exposed to specific stress stimuli.

  7. Expression of cassini, a murine gamma-satellite sequence conserved in evolution, is regulated in normal and malignant hematopoietic cells

    Directory of Open Access Journals (Sweden)

    Arutyunyan Anna

    2012-08-01

    Full Text Available Abstract Background Acute lymphoblastic leukemia (ALL cells treated with drugs can become drug-tolerant if co-cultured with protective stromal mouse embryonic fibroblasts (MEFs. Results We performed transcriptional profiling on these stromal fibroblasts to investigate if they were affected by the presence of drug-treated ALL cells. These mitotically inactivated MEFs showed few changes in gene expression, but a family of sequences of which transcription is significantly increased was identified. A sequence related to this family, which we named cassini, was selected for further characterization. We found that cassini was highly upregulated in drug-treated ALL cells. Analysis of RNAs from different normal mouse tissues showed that cassini expression is highest in spleen and thymus, and can be further enhanced in these organs by exposure of mice to bacterial endotoxin. Heat shock, but not other types of stress, significantly induced the transcription of this locus in ALL cells. Transient overexpression of cassini in human 293 embryonic kidney cells did not increase the cytotoxic or cytostatic effects of chemotherapeutic drugs but provided some protection. Database searches revealed that sequences highly homologous to cassini are present in rodents, apicomplexans, flatworms and primates, indicating that they are conserved in evolution. Moreover, CASSINI RNA was induced in human ALL cells treated with vincristine. Surprisingly, cassini belongs to the previously reported murine family of γ-satellite/major satellite DNA sequences, which were not known to be present in other species. Conclusions Our results show that the transcription of at least one member of these sequences is regulated, suggesting that this has a function in normal and transformed immune cells. Expression of these sequences may protect cells when they are exposed to specific stress stimuli.

  8. Tracking the evolution of sex chromosome systems in Melanoplinae grasshoppers through chromosomal mapping of repetitive DNA sequences.

    Science.gov (United States)

    Palacios-Gimenez, Octavio M; Castillo, Elio R; Martí, Dardo A; Cabral-de-Mello, Diogo C

    2013-08-09

    The accumulation of repetitive DNA during sex chromosome differentiation is a common feature of many eukaryotes and becomes more evident after recombination has been restricted or abolished. The accumulated repetitive sequences include multigene families, microsatellites, satellite DNAs and mobile elements, all of which are important for the structural remodeling of heterochromatin. In grasshoppers, derived sex chromosome systems, such as neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀, are frequently observed in the Melanoplinae subfamily. However, no studies concerning the evolution of sex chromosomes in Melanoplinae have addressed the role of the repetitive DNA sequences. To further investigate the evolution of sex chromosomes in grasshoppers, we used classical cytogenetic and FISH analyses to examine the repetitive DNA sequences in six phylogenetically related Melanoplinae species with X0♂/XX♀, neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀ sex chromosome systems. Our data indicate a non-spreading of heterochromatic blocks and pool of repetitive DNAs (C0t-1 DNA) in the sex chromosomes; however, the spreading of multigene families among the neo-sex chromosomes of Eurotettix and Dichromatos was remarkable, particularly for 5S rDNA. In autosomes, FISH mapping of multigene families revealed distinct patterns of chromosomal organization at the intra- and intergenomic levels. These results suggest a common origin and subsequent differential accumulation of repetitive DNAs in the sex chromosomes of Dichromatos and an independent origin of the sex chromosomes of the neo-XY and neo-X1X2Y systems. Our data indicate a possible role for repetitive DNAs in the diversification of sex chromosome systems in grasshoppers.

  9. Gigabit Satellite Network for NASA's Advanced Communication Technology Satellite (ACTS)

    Science.gov (United States)

    Hoder, Douglas; Bergamo, Marcos

    1996-01-01

    The advanced communication technology satellite (ACTS) gigabit satellite network provides long-haul point-to-point and point-to-multipoint full-duplex SONET services over NASA's ACTS. at rates up to 622 Mbit/s (SONET OC-12), with signal quality comparable to that obtained with terrestrial fiber networks. Data multiplexing over the satellite is accomplished using time-division multiple access (TDMA) techniques coordinated with the switching and beam hopping facilities provided by ACTS. Transmissions through the satellite are protected with Reed-Solomon encoding. providing virtually error-free transmission under most weather conditions. Unique to the system are a TDMA frame structure and satellite synchronization mechanism that allow: (a) very efficient utilization of the satellite capacity: (b) over-the-satellite dosed-loop synchronization of the network in configurations with up to 64 ground stations: and (c) ground station initial acquisition without collisions with existing signalling or data traffic. The user interfaces are compatible with SONET standards, performing the function of conventional SONET multiplexers and. as such. can be: readily integrated with standard SONET fiber-based terrestrial networks. Management of the network is based upon the simple network management protocol (SNMP). and includes an over-the-satellite signalling network and backup terrestrial internet (IP-based) connectivity. A description of the ground stations is also included.

  10. [Phylogenetic analysis of DNA demethylase genes in angiosperm].

    Science.gov (United States)

    Liu, Qiuxiang; Xue, Qingzhong; Xu, Jianhong

    2014-03-01

    The DNA methylation patterns and levels are depended on the function of DNA methyltransferase and DNA demethylase, and DNA demethylase plays a critical role in active DNA demethylation. In this paper, all homologous DNA demethylase gene copies were identified in monocots (O. sativa and S. bicolor) and dicotyledon (A.thaliana and P. trichocarpa) based on ten known DNA demethylase genes from rice and Arabidopsis. Two types of new DNA demethy-lase-like genes (DML4 and DML5) were identified. Tandem duplication, segmental duplication and whole genome duplica-tion exist in DNA demethylase gene family in plants, which result in neofunctionalization and subfunctionalization upon the phylogeny of conserved glycosylase domains and chromosomal locations of genes. Furthermore, the expression of DNA demethylase genes was investigated in different tissues. This study will facilitate our understanding of the relationship be-tween function and evolution of DNA demethylase, and utilizing the DNA demethylase genes in plants.

  11. Molecular organization and chromosomal localization of 5S rDNA in Amazonian Engystomops (Anura, Leiuperidae).

    Science.gov (United States)

    Rodrigues, Débora Silva; Rivera, Miryan; Lourenço, Luciana Bolsoni

    2012-03-20

    For anurans, knowledge of 5S rDNA is scarce. For Engystomops species, chromosomal homeologies are difficult to recognize due to the high level of inter- and intraspecific cytogenetic variation. In an attempt to better compare the karyotypes of the Amazonian species Engystomops freibergi and Engystomops petersi, and to extend the knowledge of 5S rDNA organization in anurans, the 5S rDNA sequences of Amazonian Engystomops species were isolated, characterized, and mapped. Two types of 5S rDNA, which were readily differentiated by their NTS (non-transcribed spacer) sizes and compositions, were isolated from specimens of E. freibergi from Brazil and E. petersi from two Ecuadorian localities (Puyo and Yasuní). In the E. freibergi karyotypes, the entire type I 5S rDNA repeating unit hybridized to the pericentromeric region of 3p, whereas the entire type II 5S rDNA repeating unit mapped to the distal region of 6q, suggesting a differential localization of these sequences. The type I NTS probe clearly detected the 3p pericentromeric region in the karyotypes of E. freibergi and E. petersi from Puyo and the 5p pericentromeric region in the karyotype of E. petersi from Yasuní, but no distal or interstitial signals were observed. Interestingly, this probe also detected many centromeric regions in the three karyotypes, suggesting the presence of a satellite DNA family derived from 5S rDNA. The type II NTS probe detected only distal 6q regions in the three karyotypes, corroborating the differential distribution of the two types of 5S rDNA. Because the 5S rDNA types found in Engystomops are related to those of Physalaemus with respect to their nucleotide sequences and chromosomal locations, their origin likely preceded the evolutionary divergence of these genera. In addition, our data indicated homeology between Chromosome 5 in E. petersi from Yasuní and Chromosomes 3 in E. freibergi and E. petersi from Puyo. In addition, the chromosomal location of the type II 5S rDNA

  12. Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression.

    Science.gov (United States)

    Aze, Antoine; Sannino, Vincenzo; Soffientini, Paolo; Bachi, Angela; Costanzo, Vincenzo

    2016-06-01

    Half of the human genome is made up of repetitive DNA. However, mechanisms underlying replication of chromosome regions containing repetitive DNA are poorly understood. We reconstituted replication of defined human chromosome segments using bacterial artificial chromosomes in Xenopus laevis egg extract. Using this approach we characterized the chromatin assembly and replication dynamics of centromeric alpha-satellite DNA. Proteomic analysis of centromeric chromatin revealed replication-dependent enrichment of a network of DNA repair factors including the MSH2-6 complex, which was required for efficient centromeric DNA replication. However, contrary to expectations, the ATR-dependent checkpoint monitoring DNA replication fork arrest could not be activated on highly repetitive DNA due to the inability of the single-stranded DNA binding protein RPA to accumulate on chromatin. Electron microscopy of centromeric DNA and supercoil mapping revealed the presence of topoisomerase I-dependent DNA loops embedded in a protein matrix enriched for SMC2-4 proteins. This arrangement suppressed ATR signalling by preventing RPA hyper-loading, facilitating replication of centromeric DNA. These findings have important implications for our understanding of repetitive DNA metabolism and centromere organization under normal and stressful conditions.

  13. Satellite Control Laboratory

    DEFF Research Database (Denmark)

    Wisniewski, Rafal; Bak, Thomas

    2001-01-01

    The Satellite Laboratory at the Department of Control Engineering of Aalborg University (SatLab) is a dynamic motion facility designed for analysis and test of micro spacecraft. A unique feature of the laboratory is that it provides a completely gravity-free environment. A test spacecraft...... of the laboratory is to conduct dynamic tests of the control and attitude determination algorithms during nominal operation and in abnormal conditions. Further it is intended to use SatLab for validation of various algorithms for fault detection, accommodation and supervisory control. Different mission objectives...... can be implemented in the laboratory, e.g. three-axis attitude control, slew manoeuvres, spins stabilization using magnetic actuation and/or reaction wheels. The spacecraft attitude can be determined applying magnetometer measurements...

  14. The solar power satellite

    Energy Technology Data Exchange (ETDEWEB)

    Combes, P.F.

    1982-01-01

    The construction, launch, components, and operations of satellite solar power systems (SSPS) for direct beaming of solar energy converted to electricity to earth stations are outlined. The reference designs of either Si or concentrator GaAs solar cell assemblies large enough to project 5 GW of power are described. The beam will be furnished by klystrons or amplitrons for reception by rectennas on earth. Conforming to the law of amplitude and the equiphase law will permit high efficiencies, pointing accuracy, and low power deposition/sq cm, thus avoiding environmental problems, although some telecommunications systems may suffer interference. The construction of the dipole rectenna grid is sketched, noting that one receiver would be an ellipse sized at 10 x 13 km. Various forms of pollution which could result from the construction of an SSPS are examined.

  15. Satellite Rings Movie

    Science.gov (United States)

    2000-01-01

    This brief movie clip (of which the release image is a still frame), taken by NASA's Cassini spacecraft as it approached Jupiter, shows the motions, over a 16 hour-period, of two satellites embedded in Jupiter's ring. The moon Adrastea is the fainter of the two, and Metis the brighter. Images such as these will be used to refine the orbits of the two bodies.The movie was made from images taken during a 40-hour sequence of the Jovian ring on December 11, 2000.Cassini is a cooperative mission of NASA, the European Space Agency and the Italian Space Agency. JPL, a division of the California Institute of Technology in Pasadena, manages Cassini for NASA's Office of Space Science, Washington, D.C.

  16. Satellite Control Laboratory

    DEFF Research Database (Denmark)

    Wisniewski, Rafal; Bak, Thomas

    2001-01-01

    The Satellite Laboratory at the Department of Control Engineering of Aalborg University (SatLab) is a dynamic motion facility designed for analysis and test of micro spacecraft. A unique feature of the laboratory is that it provides a completely gravity-free environment. A test spacecraft...... of the laboratory is to conduct dynamic tests of the control and attitude determination algorithms during nominal operation and in abnormal conditions. Further it is intended to use SatLab for validation of various algorithms for fault detection, accommodation and supervisory control. Different mission objectives...... can be implemented in the laboratory, e.g. three-axis attitude control, slew manoeuvres, spins stabilization using magnetic actuation and/or reaction wheels. The spacecraft attitude can be determined applying magnetometer measurements....

  17. Study of satellite microminiaturization technology

    Science.gov (United States)

    Obara, Hiroaki; Oomura, Katsutoshi

    1992-07-01

    The characteristics, objectives, and missions, such as those for message relaying, low orbit broadcasting, monitoring and warning, scientific observation and space environment monitoring, planet exploration, and technology development of microminiature satellites are outlined. An overview of the study of satellite microminiaturization technologies for communication, information processing, sensing for navigation and observation missions, power supply, actuators, structure and thermal control, and overall system is presented.

  18. Integrated Satellite-HAP Systems

    DEFF Research Database (Denmark)

    Cianca, Ernestina; De Sanctis, Mauro; De Luise, Aldo

    2005-01-01

    Thus far, high-altitude platform (HAP)-based systems have been mainly conceived as an alternative to satellites for complementing the terrestrial network. This article aims to show that HAP should no longer be seen as a competitor technology by investors of satellites, but as a key element for an...

  19. The Skeletal Muscle Satellite Cell

    Science.gov (United States)

    2011-01-01

    The skeletal muscle satellite cell was first described and named based on its anatomic location between the myofiber plasma and basement membranes. In 1961, two independent studies by Alexander Mauro and Bernard Katz provided the first electron microscopic descriptions of satellite cells in frog and rat muscles. These cells were soon detected in other vertebrates and acquired candidacy as the source of myogenic cells needed for myofiber growth and repair throughout life. Cultures of isolated myofibers and, subsequently, transplantation of single myofibers demonstrated that satellite cells were myogenic progenitors. More recently, satellite cells were redefined as myogenic stem cells given their ability to self-renew in addition to producing differentiated progeny. Identification of distinctively expressed molecular markers, in particular Pax7, has facilitated detection of satellite cells using light microscopy. Notwithstanding the remarkable progress made since the discovery of satellite cells, researchers have looked for alternative cells with myogenic capacity that can potentially be used for whole body cell-based therapy of skeletal muscle. Yet, new studies show that inducible ablation of satellite cells in adult muscle impairs myofiber regeneration. Thus, on the 50th anniversary since its discovery, the satellite cell’s indispensable role in muscle repair has been reaffirmed. PMID:22147605

  20. Mobility management in satellite networks

    Science.gov (United States)

    Johanson, Gary A.

    1995-01-01

    This paper addresses the methods used or proposed for use in multi-beam and/or multi-satellite networks designed to provide Mobile Satellite Services (MSS). Specific topics include beam crossover in the North American Mobile Satellite (MSAT) system as well as registration and live call hand-off for a multi-regional geosynchronous (GEO) satellite based system and a global coverage Low Earth Orbiting (LEO) system. In the MSAT system, the individual satellite beams cover very large geographic areas so the need for live call hand-off was not anticipated. This paper discusses the methods used to keep track of the beam location of the users so that incoming call announcements or other messages may be directed to them. Proposed new GEO systems with large numbers of beams will provide much smaller geographic coverage in individual beams and thus the need arises to keep track of the user's location as well as to provide live call hand-off as the user traverses from beam to beam. This situation also occurs in proposed LEO systems where the problems are worsened by the need for satellite to satellite hand-off as well as beam to beam hand-off within a single satellite. The paper discusses methods to accomplish these handoffs and proposes system architectures to address the various hand-off scenarios.

  1. Interference in Cellular Satellite Systems

    OpenAIRE

    Kilic, Ozlem; Zaghloul, Amir I.

    2010-01-01

    Co-channel beam interference in multi-beam satellite communications systems was investigated particularly for the downlink. Concept of frequency reuse was explained and the role of satellite antenna size and pattern was examined. Conventional spot beam coverage and its impact on determining the antenna size on board was discussed.

  2. Epigenetics, epidemiology and mitochondrial DNA diseases

    OpenAIRE

    Chinnery, Patrick F; Elliott, Hannah R; Hudson, Gavin; Samuels, David C; Relton, Caroline L

    2012-01-01

    Over the last two decades, the mutation of mitochondrial DNA (mtDNA) has emerged as a major cause of inherited human disease. The disorders present clinically in at least 1 in 10 000 adults, but pathogenic mutations are found in approximately 1 in 200 of the background population. Mitochondrial DNA is maternally inherited and there can be marked phenotypic variability within the same family. Heteroplasmy is a significant factor and environmental toxins also appear to modulate the phenotype. A...

  3. Familial gigantism

    NARCIS (Netherlands)

    W.W. de Herder (Wouter)

    2012-01-01

    textabstractFamilial GH-secreting tumors are seen in association with three separate hereditary clinical syndromes: multiple endocrine neoplasia type 1, Carney complex, and familial isolated pituitary adenomas.

  4. Familial gigantism

    Directory of Open Access Journals (Sweden)

    Wouter W. de Herder

    2012-01-01

    Full Text Available Familial GH-secreting tumors are seen in association with three separate hereditary clinical syndromes: multiple endocrine neoplasia type 1, Carney complex, and familial isolated pituitary adenomas.

  5. Advanced satellite communication system

    Science.gov (United States)

    Staples, Edward J.; Lie, Sen

    1992-05-01

    The objective of this research program was to develop an innovative advanced satellite receiver/demodulator utilizing surface acoustic wave (SAW) chirp transform processor and coherent BPSK demodulation. The algorithm of this SAW chirp Fourier transformer is of the Convolve - Multiply - Convolve (CMC) type, utilizing off-the-shelf reflective array compressor (RAC) chirp filters. This satellite receiver, if fully developed, was intended to be used as an on-board multichannel communications repeater. The Advanced Communications Receiver consists of four units: (1) CMC processor, (2) single sideband modulator, (3) demodulator, and (4) chirp waveform generator and individual channel processors. The input signal is composed of multiple user transmission frequencies operating independently from remotely located ground terminals. This signal is Fourier transformed by the CMC Processor into a unique time slot for each user frequency. The CMC processor is driven by a waveform generator through a single sideband (SSB) modulator. The output of the coherent demodulator is composed of positive and negative pulses, which are the envelopes of the chirp transform processor output. These pulses correspond to the data symbols. Following the demodulator, a logic circuit reconstructs the pulses into data, which are subsequently differentially decoded to form the transmitted data. The coherent demodulation and detection of BPSK signals derived from a CMC chirp transform processor were experimentally demonstrated and bit error rate (BER) testing was performed. To assess the feasibility of such advanced receiver, the results were compared with the theoretical analysis and plotted for an average BER as a function of signal-to-noise ratio. Another goal of this SBIR program was the development of a commercial product. The commercial product developed was an arbitrary waveform generator. The successful sales have begun with the delivery of the first arbitrary waveform generator.

  6. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  7. DNA nanotechnology

    Science.gov (United States)

    Seeman, Nadrian C.; Sleiman, Hanadi F.

    2018-01-01

    DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

  8. In vitro assays for DNA pairing and recombination-associated DNA synthesis.

    Science.gov (United States)

    Liu, Jie; Sneeden, Jessica; Heyer, Wolf-Dietrich

    2011-01-01

    Homologous recombination (HR) is a high-fidelity DNA repair pathway that maintains genome integrity, by repairing double strand breaks (DSBs) and single-stranded DNA (ssDNA) gaps and by supporting stalled/collapsed replication forks. The RecA/Rad51 family of proteins are the key enzymes in this homology-directed repair pathway, as they perform DNA strand invasion and exchange, in concert with a host of ancillary factors. In vitro, the RecA/Rad51 family of proteins share similar enzymatic activities including catalyzing ssDNA-stimulated ATP hydrolysis, formation of displacement loops (D-loops), and DNA strand exchange. After successful DNA strand invasion, DNA synthesis restores the lost genetic information using an undamaged DNA template. In this chapter, we describe two well-established biochemical assays to investigate the signature DNA strand transfer activity of RecA/Rad51 family of proteins: the D-loop assay and the DNA strand exchange reaction. Moreover, we describe a D-loop extension assay coupling D-loop formation with DNA synthesis, which can be used to define the roles of DNA polymerases in HR. Additionally, we present a protocol to investigate protein-mediated DNA annealing, a critical step in the synthesis-dependent strand annealing (SDSA) and double-Holliday junction (dHJ) pathways as well as the single-strand annealing (SSA) pathway. The quality of supercoiled plasmid DNA is critical in reconstituted HR reactions, and a protocol describing the preparation of this DNA substrate is included.

  9. Family Ties

    OpenAIRE

    Alesina, Alberto; Giuliano, Paola

    2009-01-01

    We study the role of the most primitive institution in society: the family. Its organization and relationship between generations shape values formation, economic outcomes and influences national institutions. We use a measure of family ties, constructed from the World Values Survey, to review and extend the literature on the effect of family ties on economic behavior and economic attitudes. We show that strong family ties are negatively correlated with generalized trust; they imply more hous...

  10. DNA Chip

    Indian Academy of Sciences (India)

    involved in the pathology of schizophrenia. In the human ge- nome, the ratio between coding and non-coding DNA is very low (less than 3% of the human .... construction of a Tm-specific chip, i.e. all the oligos/cDNA on the chip will hybridize at the same temperature. The techniques available are still not able to create a chip ...

  11. Sky alert! when satellites fail

    CERN Document Server

    Johnson, Les

    2013-01-01

    How much do we depend on space satellites? Defense, travel, agriculture, weather forecasting, mobile phones and broadband, commerce...the list seems endless. But what would our live be like if the unimaginable happened and, by accident or design, those space assets disappeared? Sky Alert! explores what our world would be like, looking in turn at areas where the loss could have catastrophic effects. The book - demonstrates our dependence on space technology and satellites; - outlines the effect on our economy, defense, and daily lives if satellites and orbiting spacecraft were destroyed; - illustrates the danger of dead satellites, spent rocket stages, and space debris colliding with a functioning satellites; - demonstrates the threat of dramatically increased radiation levels associated with geomagnetic storms; - introduces space as a potential area of conflict between nations.

  12. Direct Broadcast Satellite: Radio Program

    Science.gov (United States)

    Hollansworth, James E.

    1992-01-01

    NASA is committed to providing technology development that leads to the introduction of new commercial applications for communications satellites. The Direct Broadcast Satellite-Radio (DBS-R) Program is a joint effort between The National Aeronautics and Space Administration (NASA) and The United States Information Agency/Voice of America (USIA/VOA) directed at this objective. The purpose of this program is to define the service and develop the technology for a direct-to-listener satellite sound broadcasting system. The DBS-R Program, as structured by NASA and VOA, is now a three-phase program designed to help the U.S. commercial communications satellite and receiver industry bring about this new communications service. Major efforts are being directed towards frequency planning hardware and service development, service demonstration, and experimentation with new satellite and receiver technology.

  13. IS4 family goes genomic

    OpenAIRE

    Mahillon Jacques; Siguier Patricia; De Palmenaer Daniel

    2008-01-01

    Abstract Background Insertion sequences (ISs) are small, mobile DNA entities able to expand in prokaryotic genomes and trigger important rearrangements. To understand their role in evolution, accurate IS taxonomy is essential. The IS4 family is composed of ~70 elements and, like some other families, displays extremely elevated levels of internal divergence impeding its classification. The increasing availability of complete genome sequences provides a valuable source for the discovery of addi...

  14. Exponential families

    NARCIS (Netherlands)

    Hallin, M.; Piegorsch, W.; El Shaarawi, A.

    2012-01-01

    Exponential families of distributions are parametric dominated families in which the logarithm of probability densities take a simple bilinear form (bilinear in the parameter and a statistic). As a consequence of that special form, sampling models in those families admit a finite-dimensional

  15. Family Matters.

    Science.gov (United States)

    Featherstone, Joseph

    1979-01-01

    Emphasizing the family as the center of political/policy debates is the result of the tradition of romanticizing family virtues and a set of events ("the sixities"). Author sees the family emerging as a symbol in communal social policy development. Warns of dangers inherent in seeking private solutions to collective problems. (Author/CSS)

  16. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  17. IP voice over ATM satellite: experimental results over satellite channels

    Science.gov (United States)

    Saraf, Koroush A.; Butts, Norman P.

    1999-01-01

    IP telephony, a new technology to provide voice communication over traditional data networks, has the potential to revolutionize telephone communication within the modern enterprise. This innovation uses packetization techniques to carry voice conversations over IP networks. This packet switched technology promises new integrated services, and lower cost long-distance communication compared to traditional circuit switched telephone networks. Future satellites will need to carry IP traffic efficiently in order to stay competitive in servicing the global data- networking and global telephony infrastructure. However, the effects of Voice over IP over switched satellite channels have not been investigated in detail. To fully understand the effects of satellite channels on Voice over IP quality; several experiments were conducted at Lockheed Martin Telecommunications' Satellite Integration Lab. The result of those experiments along with suggested improvements for voice communication over satellite are presented in this document. First, a detailed introduction of IP telephony as a suitable technology for voice communication over future satellites is presented. This is followed by procedures for the experiments, along with results and strategies. In conclusion we hope that these capability demonstrations will alleviate any uncertainty regarding the applicability of this technology to satellite networks.

  18. Polar-Orbiting Satellite (POES) Images

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Visible and Infrared satellite imagery taken from camera systems or radiometer instruments on satellites in orbit around the poles. Satellite campaigns include...

  19. A ranking index for quality assessment of forensic DNA profiles forensic DNA profiles.

    Science.gov (United States)

    Hedman, Johannes; Ansell, Ricky; Nordgaard, Anders

    2010-11-09

    Assessment of DNA profile quality is vital in forensic DNA analysis, both in order to determine the evidentiary value of DNA results and to compare the performance of different DNA analysis protocols. Generally the quality assessment is performed through manual examination of the DNA profiles based on empirical knowledge, or by comparing the intensities (allelic peak heights) of the capillary electrophoresis electropherograms. We recently developed a ranking index for unbiased and quantitative quality assessment of forensic DNA profiles, the forensic DNA profile index (FI) (Hedman et al. Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles, Biotechniques 47 (2009) 951-958). FI uses electropherogram data to combine the intensities of the allelic peaks with the balances within and between loci, using Principal Components Analysis. Here we present the construction of FI. We explain the mathematical and statistical methodologies used and present details about the applied data reduction method. Thereby we show how to adapt the ranking index for any Short Tandem Repeat-based forensic DNA typing system through validation against a manual grading scale and calibration against a specific set of DNA profiles. The developed tool provides unbiased quality assessment of forensic DNA profiles. It can be applied for any DNA profiling system based on Short Tandem Repeat markers. Apart from crime related DNA analysis, FI can therefore be used as a quality tool in paternal or familial testing as well as in disaster victim identification.

  20. A ranking index for quality assessment of forensic DNA profiles forensic DNA profiles

    Directory of Open Access Journals (Sweden)

    Ansell Ricky

    2010-11-01

    Full Text Available Abstract Background Assessment of DNA profile quality is vital in forensic DNA analysis, both in order to determine the evidentiary value of DNA results and to compare the performance of different DNA analysis protocols. Generally the quality assessment is performed through manual examination of the DNA profiles based on empirical knowledge, or by comparing the intensities (allelic peak heights of the capillary electrophoresis electropherograms. Results We recently developed a ranking index for unbiased and quantitative quality assessment of forensic DNA profiles, the forensic DNA profile index (FI (Hedman et al. Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles, Biotechniques 47 (2009 951-958. FI uses electropherogram data to combine the intensities of the allelic peaks with the balances within and between loci, using Principal Components Analysis. Here we present the construction of FI. We explain the mathematical and statistical methodologies used and present details about the applied data reduction method. Thereby we show how to adapt the ranking index for any Short Tandem Repeat-based forensic DNA typing system through validation against a manual grading scale and calibration against a specific set of DNA profiles. Conclusions The developed tool provides unbiased quality assessment of forensic DNA profiles. It can be applied for any DNA profiling system based on Short Tandem Repeat markers. Apart from crime related DNA analysis, FI can therefore be used as a quality tool in paternal or familial testing as well as in disaster victim identification.

  1. A ranking index for quality assessment of forensic DNA profiles forensic DNA profiles

    Science.gov (United States)

    2010-01-01

    Background Assessment of DNA profile quality is vital in forensic DNA analysis, both in order to determine the evidentiary value of DNA results and to compare the performance of different DNA analysis protocols. Generally the quality assessment is performed through manual examination of the DNA profiles based on empirical knowledge, or by comparing the intensities (allelic peak heights) of the capillary electrophoresis electropherograms. Results We recently developed a ranking index for unbiased and quantitative quality assessment of forensic DNA profiles, the forensic DNA profile index (FI) (Hedman et al. Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles, Biotechniques 47 (2009) 951-958). FI uses electropherogram data to combine the intensities of the allelic peaks with the balances within and between loci, using Principal Components Analysis. Here we present the construction of FI. We explain the mathematical and statistical methodologies used and present details about the applied data reduction method. Thereby we show how to adapt the ranking index for any Short Tandem Repeat-based forensic DNA typing system through validation against a manual grading scale and calibration against a specific set of DNA profiles. Conclusions The developed tool provides unbiased quality assessment of forensic DNA profiles. It can be applied for any DNA profiling system based on Short Tandem Repeat markers. Apart from crime related DNA analysis, FI can therefore be used as a quality tool in paternal or familial testing as well as in disaster victim identification. PMID:21062433

  2. The exterior tidal potential acting on a satellite. [satellite orbits/satellite perturbation - gravitation effects

    Science.gov (United States)

    Musen, P.

    1975-01-01

    A theory is presented that points out the existence of several long period and 'cross effects' in the coefficients in the expansion of the geopotential and in the motion of satellites. The tidal potential, defined as small periodic variations in the geopotential, was calculated. The influence of these geopotential variations on satellite perturbation is examined. Spherical harmonics were employed.

  3. Targeted DNA methylation in pericentromeres with genome editing-based artificial DNA methyltransferase.

    Science.gov (United States)

    Yamazaki, Taiga; Hatano, Yu; Handa, Tetsuya; Kato, Sakiko; Hoida, Kensuke; Yamamura, Rui; Fukuyama, Takashi; Uematsu, Takayuki; Kobayashi, Noritada; Kimura, Hiroshi; Yamagata, Kazuo

    2017-01-01

    To study the impact of epigenetic changes on biological functions, the ability to manipulate the epigenetic status of certain genomic regions artificially could be an indispensable technology. "Epigenome editing" techniques have gradually emerged that apply TALE or CRISPR/Cas9 technologies with various effector domains isolated from epigenetic code writers or erasers such as DNA methyltransferase, 5-methylcytosine oxidase, and histone modification enzymes. Here we demonstrate that a TALE recognizing a major satellite, consisting of a repeated sequence in pericentromeres, could be fused with the bacterial CpG methyltransferase, SssI. ChIP-qPCR assays demonstrated that the fusion protein TALMaj-SssI preferentially bound to major chromosomal satellites in cultured cell lines. Then, TALMaj-SssI was expressed in fertilized mouse oocytes with hypomethylated major satellites (10-20% CpG islands). Bisulfite sequencing revealed that the DNA methylation status was increased specifically in major satellites (50-60%), but not in minor satellites or other repeat elements, such as Intracisternal A-particle (IAP) or long interspersed nuclear elements-1 (Line1) when the expression level of TALMaj-SssI is optimized in the cell. At a microscopic level, distal ends of chromosomes at the first mitotic stage were dramatically highlighted by the mCherry-tagged methyl CpG binding domain of human MBD1 (mCherry-MBD-NLS). Moreover, targeted DNA methylation to major satellites did not interfere with kinetochore function during early embryonic cleavages. Co-injection of dCas9 fused with SssI and guide RNA (gRNA) recognizing major satellite sequences enabled increment of the DNA methylation in the satellites, but a few off-target effects were also observed in minor satellites and retrotransposons. Although CRISPR can be applied instead of the TALE system, technical improvements to reduce off-target effects are required. We have demonstrated a new method of introducing DNA methylation without

  4. Targeted DNA methylation in pericentromeres with genome editing-based artificial DNA methyltransferase.

    Directory of Open Access Journals (Sweden)

    Taiga Yamazaki

    Full Text Available To study the impact of epigenetic changes on biological functions, the ability to manipulate the epigenetic status of certain genomic regions artificially could be an indispensable technology. "Epigenome editing" techniques have gradually emerged that apply TALE or CRISPR/Cas9 technologies with various effector domains isolated from epigenetic code writers or erasers such as DNA methyltransferase, 5-methylcytosine oxidase, and histone modification enzymes. Here we demonstrate that a TALE recognizing a major satellite, consisting of a repeated sequence in pericentromeres, could be fused with the bacterial CpG methyltransferase, SssI. ChIP-qPCR assays demonstrated that the fusion protein TALMaj-SssI preferentially bound to major chromosomal satellites in cultured cell lines. Then, TALMaj-SssI was expressed in fertilized mouse oocytes with hypomethylated major satellites (10-20% CpG islands. Bisulfite sequencing revealed that the DNA methylation status was increased specifically in major satellites (50-60%, but not in minor satellites or other repeat elements, such as Intracisternal A-particle (IAP or long interspersed nuclear elements-1 (Line1 when the expression level of TALMaj-SssI is optimized in the cell. At a microscopic level, distal ends of chromosomes at the first mitotic stage were dramatically highlighted by the mCherry-tagged methyl CpG binding domain of human MBD1 (mCherry-MBD-NLS. Moreover, targeted DNA methylation to major satellites did not interfere with kinetochore function during early embryonic cleavages. Co-injection of dCas9 fused with SssI and guide RNA (gRNA recognizing major satellite sequences enabled increment of the DNA methylation in the satellites, but a few off-target effects were also observed in minor satellites and retrotransposons. Although CRISPR can be applied instead of the TALE system, technical improvements to reduce off-target effects are required. We have demonstrated a new method of introducing DNA

  5. Community families

    DEFF Research Database (Denmark)

    Jensen, Lotte Groth; Lou, Stina; Aagaard, Jørgen

    2017-01-01

    Background: Social interventions targeted at people with severe mental illness (SMI) often include volunteers. Volunteers' perspectives are important for these interventions to work. The present paper investigates the experiences of volunteer families who befriend a person with SMI. Material......: Qualitative interviews with members of volunteer families. Discussion: The families were motivated by helping a vulnerable person and to engaging in a rewarding relationship. However, the families often doubted their personal judgment and relied on mental health workers to act as safety net. Conclusion......: The volunteer involvement is meaningful but also challenging. The families value professional support....

  6. Theory of satellite geodesy applications of satellites to geodesy

    CERN Document Server

    Kaula, William M

    2000-01-01

    The main purpose of this classic text is to demonstrate how Newtonian gravitational theory and Euclidean geometry can be used and developed in the earth's environment. The second is to collect and explain some of the mathematical techniques developed for measuring the earth by satellite.Book chapters include discussions of the earth's gravitational field, with special emphasis on spherical harmonies and the potential of the ellipsoid; matrices and orbital geometry; elliptic motion, linear perturbations, resonance, and other aspects of satellite orbit dynamics; the geometry of satellite obser

  7. What Is Mitochondrial DNA?

    Science.gov (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  8. Faulty DNA-polymerase {delta}/{epsilon}-mediated excision-repair in response to gamma-radiation or ultraviolet-light in P53-deficient fibroblast strains from affected members of a cancer-prone family with Li-Fraumeni syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Mirzayans, R.; Enns, L.; Dietrich, K.; Barley, R.D.C.; Paterson, M.C. [Alberta Univ., Edmonton, AB (Canada). Cross Cancer Inst.]|[Alberta Univ., Edmonton, AB (Canada). Dept. of Oncology]|[Alberta Univ., Edmonton, AB (Canada). Dept. of Biological Science

    1996-04-01

    Dermal fibroblast strains cultured from affected members of a cancer-prone family with Li-Fraumeni syndrome (LFS) harbor a point mutation in one allele of the p53 tumor suppressor gene, resulting in loss of normal p53-deficient strains to carry out the long-patch mode of excision repair, mediated by DNA polymerases delta and epsilon, after exposure to Co-60 gamma radiation or far ultraviolet (UV) (chiefly 254 mm) light. Repair was monitored by incubation of the irradiated cultures in the presence of aphidicolin (ape) or 1-beta-D-arabinofuranosylcytosine (araC), each a specific inhibitor of long-patch repair, followed by measurement of drug-induced DNA strand breaks (reflecting non-ligated strand incision events) by alkaline surcrose velocity sedimentation. The LFS strains displayed deficient repair capacity in response to both gamma rays and UV light. The repair anomaly in UV-irradiated LFS cultures was manifested not only in the overall genome, but also in the transcriptionally active, preferentially repaired c-myc gene. Using autoradiography we also assessed unscheduled DNA synthesis (UDS) after UV irradiation and found this conventional measure of repair replication to be deficient in LFS strains. Moreover, both ape and araC decreased the level of UV-induced UDS by similar to 75% in normal cells, but each had only a marginal effect on LFS cells. We further demonstrated that the LFS strains are impaired in the recovery of both RNA and replicative DNA syntheses after UV treatment, two molecular anomalies of the DNA repair deficiency disorders xeroderma pigmentosum and Cockayne`s syndrome. Together these results imply a critical role for wild-type p53 protein in DNA polymerase delta/epsilon-mediated excision repair, both the mechanism operating on the entire genome and that acting on expressed genes. (Author).

  9. Roles and interactions of begomoviruses and satellite DNAs associated with okra leaf curl disease in Mali, West Africa.

    Science.gov (United States)

    Kon, Tatsuya; Rojas, Maria R; Abdourhamane, Issoufou K; Gilbertson, Robert L

    2009-04-01

    Okra leaf curl disease (OLCD) is a major constraint on okra (Abelmoschus esculentus) production in West Africa. Two monopartite begomoviruses (okra virus-1 and okra virus-2), a betasatellite and a DNA1 satellite are associated with OLCD in Mali. Okra virus-1 is an isolate of okra yellow crinkle virus (OYCrV), okra virus-2 is a recombinant isolate of cotton leaf curl Gezira virus (CLCuGV) and the betasatellite is a variant of cotton leaf curl Gezira betasatellite (CLCuGB). Cloned DNA of OYCrV and CLCuGV were infectious and induced leaf curl symptoms in Nicotiana benthamiana plants, but did not induce OLCD in okra. However, when these clones were individually co-inoculated with the cloned CLCuGB DNA, symptom severity and viral DNA levels were increased in N. benthamiana plants and typical OLCD symptoms were induced in okra. The CLCuGB was also replicated by, and increased symptom severity of, three monopartite tomato-infecting begomoviruses, including two from West Africa. The sequence of the DNA1 satellite was highly divergent, indicating that it represents a distinct West African lineage. DNA1 replicated autonomously, and replication required the DNA1-encoded Rep protein. Although DNA1 reduced helper begomovirus DNA levels, symptoms were not attenuated. In the presence of CLCuGB, DNA levels of the helper begomoviruses and DNA1 were substantially increased. Together, these findings establish that OLCD in Mali is caused by a complex of monopartite begomoviruses and a promiscuous betasatellite with an associated parasitic DNA1 satellite. These findings are discussed in terms of the aetiology of OLCD and the evolution of new begomovirus/satellite DNA complexes.

  10. Multi-mission Satellite Management

    Science.gov (United States)

    Jamilkowski, M. L.; Teter, M. A.; Grant, K. D.; Dougherty, B.; Cochran, S.

    2015-12-01

    NOAA's next-generation environmental satellite, the Joint Polar Satellite System (JPSS) replaces the current Polar-orbiting Operational Environmental Satellites (POES). JPSS satellites carry sensors which collect meteorological, oceanographic, climatological, and solar-geophysical observations of the earth, atmosphere, and space. The first JPSS satellite was launched in 2011 and is currently NOAA's primary operational polar satellite. The JPSS ground system is the Common Ground System (CGS), and provides command, control, and communications (C3) and data processing (DP). A multi-mission system, CGS provides combinations of C3/DP for numerous NASA, NOAA, DoD, and international missions. In preparation for the next JPSS satellite, CGS improved its multi-mission capabilities to enhance mission operations for larger constellations of earth observing satellites with the added benefit of streamlining mission operations for other NOAA missions. CGS's multi-mission capabilities allows management all of assets as a single enterprise, more efficiently using ground resources and personnel and consolidating multiple ground systems into one. Sophisticated scheduling algorithms compare mission priorities and constraints across all ground stations, creating an enterprise schedule optimized to mission needs, which CGS executes to acquire the satellite link, uplink commands, downlink and route data to the operations and data processing facilities, and generate the final products for delivery to downstream users. This paper will illustrate the CGS's ability to manage multiple, enterprise-wide polar orbiting missions by demonstrating resource modeling and tasking, production of enterprise contact schedules for NOAA's Fairbanks ground station (using both standing and ad hoc requests), deconflicting resources due to ground outages, and updating resource allocations through dynamic priority definitions.

  11. The future of forensic DNA analysis

    Science.gov (United States)

    Butler, John M.

    2015-01-01

    The author's thoughts and opinions on where the field of forensic DNA testing is headed for the next decade are provided in the context of where the field has come over the past 30 years. Similar to the Olympic motto of ‘faster, higher, stronger’, forensic DNA protocols can be expected to become more rapid and sensitive and provide stronger investigative potential. New short tandem repeat (STR) loci have expanded the core set of genetic markers used for human identification in Europe and the USA. Rapid DNA testing is on the verge of enabling new applications. Next-generation sequencing has the potential to provide greater depth of coverage for information on STR alleles. Familial DNA searching has expanded capabilities of DNA databases in parts of the world where it is allowed. Challenges and opportunities that will impact the future of forensic DNA are explored including the need for education and training to improve interpretation of complex DNA profiles. PMID:26101278

  12. The Canadian mobile satellite system

    Science.gov (United States)

    Bertenyi, Elemer

    1992-07-01

    Plans to upgrade Canadian mobile data services by introducing a full, two way mobile voice and data service, using a large geostationary satellite which is scheduled to be launched in 1994, are reported. This Mobile Satellite (MSAT) will offer customers the ability to communicate, using mobile or transportable terminals, from the most remote parts of the continent, to any other point within North America, and indeed the whole world. Currently planned MSAT services are reviewed, the main features of the overall system are outlined, and the configuration and key performance parameters of the MSAT satellite are presented. The communications subsystem is detailed, and a summary of the spacecraft service module is given.

  13. Progress in satellite tracking cranes

    Science.gov (United States)

    Ellis, D.H.; Smith, D.G.; Olsen, Glenn H.; Fuller, M.R.; Landfried, S.E.; Higuchi, H.; Vermillion, C.H.

    1992-01-01

    We review the history of tracking cranes with satellite telemetry and identify some of the difficulties in designing satellite transmitters and harnesses for cranes. Miniaturization of these transmitters and a plethora of harnessing experiments since 1989 allow us to recommend limited application of this technology to all species of cranes. We are still uncertain, however, if cranes harnessed with satellite telemetry devices are able to reproduce after migration. Because of this uncertainty, we urge caution in the use of this technology, especially with breeding adults in severely endangered populations. This manuscript also describes continuing research needs.

  14. Slitless spectroscopy of geosynchronous satellites

    Science.gov (United States)

    Tippets, Roger D.; Wakefield, Stephen; Young, Shannon; Ferguson, Ian; Earp-Pitkins, Christopher; Chun, Francis K.

    2015-10-01

    A preliminary investigation into the use of slitless spectroscopy for characterization of geosynchronous satellites is described. A 100 line/mm diffraction grating is used as the dispersing device, and the spectral data obtained are compared to a model with good results. A method used to collect and calibrate slitless spectral observations accounting for pixel to wavelength conversion, pixel response as a function of wavelength, and solar features is presented. Observations of several geosynchronous satellites throughout a night reveal reflectance with noticeable and different profiles indicating that slitless spectroscopy offers the potential for another modality for identifying and discriminating satellites.

  15. Satellite communications principles and applications

    CERN Document Server

    Calcutt, David

    1994-01-01

    Satellites are increasingly used for global communications, as well as for radio and television transmissions. With the growth of mobile communications, and of digital technology, the use of satellite systems is set to expand substantially and already all students of electronics or communications engineering must study the subject.This book steers a middle path between offering a basic understanding of the process of communication by satellite and the methodology used; and the extensive mathematical analysis normally adopted in similar texts. It presents the basic concepts, using as mu

  16. Family therapy

    Directory of Open Access Journals (Sweden)

    Shaikh Altamash

    2013-01-01

    Full Text Available Another major force not letting us succeed in the treatment of diabetes remains right inside the patients home, their family members. Hence, it is important to know the perception of the close family members about this simple and strong tool in diabetes, ′insulin′. The drug is nearing its century, it has not fully being accepted gracefully even in todays electronic savvy society. So, we need to strongly discover the reason for its non-acceptance, while trials are out inventing new drugs. One vital thing that can change this attitude is increasing the understanding of this drug, insulin in depth to close people around the patient, the ′family′. Underestimating family′s perception about disease and treatment for diabetes is detrimental to both diseased and the doctor. This consists of a biopsychosocial model; biological, psychological and social factors. Family forms the most important part of it. The strategies in family therapy include psychodynamic, structural, strategic, and cognitive-behavioral component. Diabetes has and will continue to rise, so will be the treatment options. From the clinicians side its to fix fasting first but from patients its fix family first. Family therapy demonstrates the importance of insulin initiation and maintenance in insulin naive patients, and continuation for others. The specific needs of such patients and their impact on family life are met with family therapy. Who needs family therapy? Benefits of family therapy and a case based approach is covered.

  17. Satellite Propellant Pump Research

    Science.gov (United States)

    Schneider, Steven J.; Veres, Joseph P.; Hah, Chunill; Nerone, Anthony L.; Cunningham, Cameron C.; Kraft, Thomas G.; Tavernelli, Paul F.; Fraser, Bryan

    2005-01-01

    NASA Glenn initiated a satellite propellant pump technology demonstration program. The goal was to demonstrate the technologies for a 60 percent efficient pump at 1 gpm flow rate and 500 psia pressure rise. The pump design and analysis used the in-house developed computer codes named PUMPA and HPUMP3D. The requirements lead to a 4-stage impeller type pump design with a tip diameter of 0.54 inches and a rotational speed of 57,000 rpm. Analyses indicated that flow cavitation was not a problem in the design. Since the flow was incompressible, the stages were identical. Only the 2-stage pump was designed, fabricated, assembled, and tested for demonstration. Water was selected as the surrogate fluid for hydrazine in this program. Complete mechanical design including stress and dynamic analyses were conducted. The pump was driven by an electric motor directly coupled to the impellers. Runs up to 57,000 rpm were conducted, where a pressure rise of 200 psia at a flow rate of 0.8 gpm was measured to validate the design effort.

  18. Diversity and phylogeography of begomovirus-associated beta satellites of okra in India

    Directory of Open Access Journals (Sweden)

    Venkataravanappa V

    2011-12-01

    Full Text Available Abstract Background Okra (Abelmoschus esculentus; family Malvaceae is grown in temperate as well as subtropical regions of the world, both for human consumption as a vegetable and for industrial uses. Okra yields are affected by the diseases caused by phyopathogenic viruses. India is the largest producer of okra and in this region a major biotic constraint to production are viruses of the genus Begomovirus. Begomoviruses affecting okra across the Old World are associated with specific, symptom modulating satellites (beta satellites. We describe a comprehensive analysis of the diversity of beta satellites associated with okra in India. Results The full-length sequences of 36 beta satellites, isolated from okra exhibiting typical begomovirus symptoms (leaf curl and yellow vein, were determined. The sequences segregated in to four groups. Two groups correspond to the beta satellites Okra leaf curl beta satellite (OLCuB and Bhendi yellow vein beta satellite (BYVB that have previously been identified in okra from the sub-continent. One sequence was distinct from all other, previously isolated beta satellites and represents a new species for which we propose the name Bhendi yellow vein India beta satellite (BYVIB. This new beta satellite was nevertheless closely related to BYVB and OLCuB. Most surprising was the identification of Croton yellow vein mosaic beta satellite (CroYVMB in okra; a beta satellite not previously identified in a malvaceous plant species. The okra beta satellites were shown to have distinct geographic host ranges with BYVB occurring across India whereas OLCuB was only identified in northwestern India. Okra infections with CroYVMB were only identified across the northern and eastern central regions of India. A more detailed analysis of the sequences showed that OLCuB, BYVB and BYVIB share highest identity with respect βC1 gene. βC1 is the only gene encoded by beta satellites, the product of which is the major pathogenicity

  19. Diversity and phylogeography of Begomovirus-associated beta satellites of Okra in India.

    Science.gov (United States)

    Venkataravanappa, V; Reddy, C N Lakshminarayana; Swaranalatha, P; Jalali, Salil; Briddon, Rob W; Reddy, M Krishna

    2011-12-21

    Okra (Abelmoschus esculentus; family Malvaceae) is grown in temperate as well as subtropical regions of the world, both for human consumption as a vegetable and for industrial uses. Okra yields are affected by the diseases caused by phyopathogenic viruses. India is the largest producer of okra and in this region a major biotic constraint to production are viruses of the genus Begomovirus. Begomoviruses affecting okra across the Old World are associated with specific, symptom modulating satellites (beta satellites). We describe a comprehensive analysis of the diversity of beta satellites associated with okra in India. The full-length sequences of 36 beta satellites, isolated from okra exhibiting typical begomovirus symptoms (leaf curl and yellow vein), were determined. The sequences segregated in to four groups. Two groups correspond to the beta satellites Okra leaf curl beta satellite (OLCuB) and Bhendi yellow vein beta satellite (BYVB) that have previously been identified in okra from the sub-continent. One sequence was distinct from all other, previously isolated beta satellites and represents a new species for which we propose the name Bhendi yellow vein India beta satellite (BYVIB). This new beta satellite was nevertheless closely related to BYVB and OLCuB. Most surprising was the identification of Croton yellow vein mosaic beta satellite (CroYVMB) in okra; a beta satellite not previously identified in a malvaceous plant species. The okra beta satellites were shown to have distinct geographic host ranges with BYVB occurring across India whereas OLCuB was only identified in northwestern India. Okra infections with CroYVMB were only identified across the northern and eastern central regions of India. A more detailed analysis of the sequences showed that OLCuB, BYVB and BYVIB share highest identity with respect βC1 gene. βC1 is the only gene encoded by beta satellites, the product of which is the major pathogenicity determinant of begomovirus-beta satellite

  20. Strumenti d’osservazione per il telerilevamento da satellite

    Directory of Open Access Journals (Sweden)

    Giorgio Perrotta

    2009-03-01

    Full Text Available Earth observation instruments for satellite remote sensingThis article features a brief description of the instrumentation  families commonly used during Earth Observation activities. The optical exploration of our planet, already anticipated more than 50 years ago at the beginning of the exploration era with the first analogic photographic instrumentation, is now complemented by sophisticated instruments that work under the domain of radio  waves in order to produce informations useful fo a wide variety of applications.

  1. Family Polymorphism

    DEFF Research Database (Denmark)

    Ernst, Erik

    2001-01-01

    safety and flexibility at the level of multi-object systems. We are granted the flexibility of using different families of kinds of objects, and we are guaranteed the safety of the combination. This paper highlights the inability of traditional polymorphism to handle multiple objects, and presents family...... polymorphism as a way to overcome this problem. Family polymorphism has been implemented in the programming language gbeta, a generalized version of Beta, and the source code of this implementation is available under GPL....

  2. Sea Turtle Satellite Telemetry Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Sea turtles captured in various fishing gear (pound nets, long haul seines, gill nets) were outfitted with satellite transmitters so that their movements, migratory...

  3. Virtual Satellite Integration Environment Project

    Data.gov (United States)

    National Aeronautics and Space Administration — An integrated environment for rapid design studies of small satellite missions will be developed. This environment will be designed to streamline processes at the...

  4. Virtual Satellite Integration Environment Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Advatech Pacific proposes to develop a Virtual Satellite Integration Environment (VSIE) for the NASA Ames Mission Design Center. The VSIE introduces into NASA...

  5. European global navigation satellite launches

    Science.gov (United States)

    Zielinski, Sarah

    The European Space Agency launched its first Galileo satellite on 28 December 2005.When fully deployed, the Galileo system will provide a European global navigation alternative to the U.S. global positioning system (GPS) and the Russian global navigation satellite system (Glonass).The Galileo system will consist of 30 satellites (27 operational plus three active spare satellites) that are scheduled to be launched and fully operational by the end of 2008.The system will provide real-time positioning within one meter of accuracy and be fully inter-operable with the U.S. and Russian systems. However, unlike GPS and Glonass, Galileo will be under civilian rather than military control.

  6. Taos: A low cost satellite

    Science.gov (United States)

    Jung, P.

    Aerospatiale, under contract to CNES, has studied a new satellite based system with the double mission of mobile tracking and paging. This is called Taos. A constellation of five Taos satellites will allow positioning with an accuracy of 1 km, as well as small message transmission with a maximum time delay of 2 hours. Using a low earth orbit, Taos will have a small power budget, with the attendant gains in dimensions, mass, and eventually cost. The emergence of such class of lightsats has been fostered by the progress of electronics, as well as the new small launchers now being offered. Furthermore, the market is clearly hungry for ever more worldwide data collection. This paper describes the Taos system of satellite and ground segment, for which a primary goal will be a significant reduction of the recurring price. Weighing 152 kg, each satellite will have a power of 270 W.

  7. Satellite Observations of Arctic Change

    Data.gov (United States)

    National Aeronautics and Space Administration — The purpose of this site is to expose NASA satellite data and research on Arctic change in the form of maps that illustrate the changes taking place in the Arctic...

  8. Family literacy

    DEFF Research Database (Denmark)

    Sehested, Caroline

    2012-01-01

    I Projekt familielæsning, der er et samarbejde mellem Nationalt Videncenter for Læsning og Hillerød Bibliotek, arbejder vi med at få kontakt til de familier, som biblioteket ellers aldrig ser som brugere og dermed også de børn, der vokser op i familier, for hvem bøger og oplæsningssituationer ikk...... er en selvfølgelig del af barndommen. Det, vi vil undersøge og ønsker at være med til at udvikle hos disse familier, er det, man kan kalde family literacy....

  9. Biogeography based Satellite Image Classification

    OpenAIRE

    Harish Kundra; Parminder Singh; Navdeep Kaur; V.K. Panchal

    2009-01-01

    Biogeography is the study of the geographical distribution of biological organisms. The mindset of the engineer is that we can learn from nature. Biogeography Based Optimization is a burgeoning nature inspired technique to find the optimal solution of the problem. Satellite image classification is an important task because it is the only way we can know about the land cover map of inaccessible areas. Though satellite images have been classified in past by using various techniques, the researc...

  10. A multipurpose satellite ejection system

    Science.gov (United States)

    Moore, Michael B.

    1987-01-01

    A design is presented for a pneumatic ejection system capable of ejecting a spin stabilized satellite from the cargo bay of space vehicles. This system was orginally designed for use on the Spacelab 6 shuttle mission, but is now being considered for use with expendable rockets for launching satellites. The ejection system was designed to launch a 150 lb satellite at an initial ejection velocity of 32 ft/sec with a spin rate of 30 rev/min. The ejection system consists of a pneumatic cylinder, satellite retaining mechanism, and bearing assembly to allow the satellite to rotate during the spin up phase. As the cylinder is pressurized rapidly causing movement of the actuation piston, the mechanism automatically releases the spinning satellite by retracting a pneumatic locking pin and three spring loaded holddown pins. When the piston reaches the end of its stroke, it encounters a crushable aluminum honeycomb shock absorber which decelerates the piston and retaining mechanism. The assembly is designed for multiple uses except for the crushable shock absorber and pyrotechnic valves. The advantage of the design is discussed and patent no. and date given.

  11. Family Secrets: The Bioethics of Genetic Testing

    Science.gov (United States)

    Markowitz, Dina G.; DuPre, Michael J.; Holt, Susan; Chen, Shaw-Ree; Wischnowski, Michael

    2006-01-01

    This article discusses "Family Secrets," a problem-based learning (PBL) curriculum module that focuses on the bioethical implications of genetic testing. In high school biology classrooms throughout New York State, students are using "Family Secrets" to learn about DNA testing; Huntington's disease (HD); and the ethical, legal,…

  12. [DNA of some regions of constitutive heterochromatin is demethylated and decondensed in MRC5 and A431 cells].

    Science.gov (United States)

    Vaĭsertreĭger, I S R; Podgornaia, O I; Enukashvili, N I

    2007-01-01

    It is believed that satellite DNA is compact and transcriptionally inert during interphase. We determined localization, range of compactization and methylation state of the centromeric and pericentromeric satellite DNA using the method of fluorescence hybridization in situ (FISH) combined with the antibody immunostaining against the methylated DNA. We investigated the tissue cells (the cells of placenta and lymphocytes), primary (MRC5 fibroblasts) and malignant (A431) cell cultures. Centromeric satellite DNA was condensed and stained with antibodies against 5-methylcytosine in all the cases. Pericentromeric satellite 3 of the chromosome 1 was condensed in lymphocytes, placenta cells and young culture of fibroblasts. The unwrapping of satellite 3 of the chromosome 1 has been observed in the senescent MRC5 fibroblasts and in the malignant cell line A431. The compact areas of pericentromeric satellites were stained with antibodies against the methylated DNA, white the decondensed areas were'nt stained. Thus, we observed pericentromeric satellite 3 decondensation in senescent fibroblasts culture MRC5 and in cell line A431. The decondensation was accompanied by the partial demethylation of the satellite DNA, which is believed to belong to constitutive heterochromatin.

  13. This is My Family

    OpenAIRE

    Yeğen, Hale Nur; Çetin, Merve

    2017-01-01

    Me and my family, Families poem, Mother-Father, Brother-Sister, Grandparents, Uncle-Aunt, Cousin, Family, Family handgame, My family tree, Activities (Three In a Family), Digital Games, A family poem, Quiz

  14. Genetic heterogeneity in Pakistani microcephaly families

    DEFF Research Database (Denmark)

    Sajid Hussain, M; Bakhtiar, Syeda Marriam; Farooq, Muhammad

    2013-01-01

    Autosomal recessive primary microcephaly (MCPH) is caused by mutations in at least eight different genes involved either in cell division or DNA repair. Most mutations are identified in consanguine families from Pakistan, Iran and India. To further assess their genetic heterogeneity and mutational...... spectra, we have analyzed 57 consanguine Pakistani MCPH families. In 34 MCPH families, we detected linkage to five out of the eight well-characterized disease loci and identified mutations in 27 families, leaving seven families without mutations in the coding exons of the presumably underlying MCPH genes...

  15. Lopsided Collections of Satellite Galaxies

    Science.gov (United States)

    Kohler, Susanna

    2016-12-01

    You might think that small satellite galaxies would be distributed evenly around their larger galactic hosts but local evidence suggests otherwise. Are satellite distributions lopsided throughout the universe?Satellites in the Local GroupThe distribution of the satellite galaxies orbiting Andromeda, our neighboring galaxy, is puzzling: 21 out of 27 ( 80%) of its satellites are on the side of Andromeda closest to us. In a similar fashion, 4 of the 11 brightest Milky Way satellites are stacked on the side closest to Andromeda.It seems to be the case, then, that satellites around our pair of galaxies preferentially occupy the space between the two galaxies. But is this behavior specific to the Local Group? Or is it commonplace throughout the universe? In a recent study, a team of scientists led by Noam Libeskind (Leibniz Institute for Astrophysics Potsdam, Germany) set out to answer this question.Properties of the galaxies included in the authors sample. Left: redshifts for galaxy pairs. Right: Number of satellite galaxies around hosts. [Adapted from Libeskind et al. 2016]Asymmetry at LargeLibeskind and collaborators tested whether this behavior is common by searching through Sloan Digital Sky Survey observations for galaxy pairs that are similar to the Milky Way/Andromeda pair. The resulting sample consists of 12,210 pairs of galaxies, which have 46,043 potential satellites among them. The team then performed statistical tests on these observations to quantify the anisotropic distribution of the satellites around the host galaxies.Libeskind and collaborators find that roughly 8% more galaxies are seen within a 15 angle facing the other galaxy of a pair than would be expected in a uniform distribution. The odds that this asymmetric behavior is randomly produced, they show, are lower than 1 in 10 million indicating that the lopsidedness of satellites around galaxies in pairs is a real effect and occurs beyond just the Local Group.Caution for ModelingProbability that

  16. Weather Satellite Enterprise Information Chain

    Science.gov (United States)

    Jamilkowski, M. L.; Grant, K. D.; Miller, S. W.; Cochran, S.

    2015-12-01

    NOAA & NASA are acquiring the next-generation civilian operational weather satellite: Joint Polar Satellite System (JPSS). Contributing the afternoon orbit & ground system (GS) to replace current NOAA POES Satellites, its sensors will collect meteorological, oceanographic & climatological data. The JPSS Common Ground System (CGS), consisting of C3 and IDP segments, is developed by Raytheon. It now flies the Suomi National Polar-orbiting Partnership (S-NPP) satellite, transferring data between ground facilities, processing them into environmental products for NOAA weather centers, and expanding to support JPSS-1 in 2017. As a multi-mission system, CGS provides combinations of C3, data processing, and product delivery for numerous NASA, NOAA, DoD and international missions.The CGS provides a wide range of support to a number of missions: Command and control and mission management for the S-NPP mission today, expanding this support to the JPSS-1 satellite mission in 2017 Data acquisition for S-NPP, the JAXA's Global Change Observation Mission - Water (GCOM-W1), POES, and the Defense Meteorological Satellite Program (DMSP) and Coriolis/WindSat for the DoD Data routing over a global fiber network for S-NPP, JPSS-1, GCOM-W1, POES, DMSP, Coriolis/WindSat, NASA EOS missions, MetOp for EUMETSAT and the National Science Foundation Environmental data processing and distribution for S-NPP, GCOM-W1 and JPSS-1 The CGS plays a key role in facilitating the movement and value-added enhancement of data all the way from satellite-based sensor data to delivery to the consumers who generate forecasts and produce watches and warnings. This presentation will discuss the information flow from sensors, through data routing and processing, and finally to product delivery. It will highlight how advances in architecture developed through lessons learned from S-NPP and implemented for JPSS-1 will increase data availability and reduce latency for end user applications.

  17. DNA Methyltransferase Activity Assays: Advances and Challenges.

    Science.gov (United States)

    Poh, Wan Jun; Wee, Cayden Pang Pee; Gao, Zhiqiang

    2016-01-01

    DNA methyltransferases (MTases), a family of enzymes that catalyse the methylation of DNA, have a profound effect on gene regulation. A large body of evidence has indicated that DNA MTase is potentially a predictive biomarker closely associated with genetic disorders and genetic diseases like cancer. Given the attention bestowed onto DNA MTases in molecular biology and medicine, highly sensitive detection of DNA MTase activity is essential in determining gene regulation, epigenetic modification, clinical diagnosis and therapeutics. Conventional techniques such as isotope labelling are effective, but they often require laborious sample preparation, isotope labelling, sophisticated equipment and large amounts of DNA, rendering them unsuitable for uses at point-of-care. Simple, portable, highly sensitive and low-cost assays are urgently needed for DNA MTase activity screening. In most recent technological advances, many alternative DNA MTase activity assays such as fluorescent, electrochemical, colorimetric and chemiluminescent assays have been proposed. In addition, many of them are coupled with nanomaterials and/or enzymes to significantly enhance their sensitivity. Herein we review the progress in the development of DNA MTase activity assays with an emphasis on assay mechanism and performance with some discussion on challenges and perspectives. It is hoped that this article will provide a broad coverage of DNA MTase activity assays and their latest developments and open new perspectives toward the development of DNA MTase activity assays with much improved performance for uses in molecular biology and clinical practice.

  18. Linked Autonomous Interplanetary Satellite Orbit Navigation

    Science.gov (United States)

    Parker, Jeffrey S.; Anderson, Rodney L.; Born, George H.; Leonard, Jason M.; McGranaghan, Ryan M.; Fujimoto, Kohei

    2013-01-01

    A navigation technology known as LiAISON (Linked Autonomous Interplanetary Satellite Orbit Navigation) has been known to produce very impressive navigation results for scenarios involving two or more cooperative satellites near the Moon, such that at least one satellite must be in an orbit significantly perturbed by the Earth, such as a lunar halo orbit. The two (or more) satellites track each other using satellite-to-satellite range and/or range-rate measurements. These relative measurements yield absolute orbit navigation when one of the satellites is in a lunar halo orbit, or the like. The geometry between a lunar halo orbiter and a GEO satellite continuously changes, which dramatically improves the information content of a satellite-to-satellite tracking signal. The geometrical variations include significant out-of-plane shifts, as well as inplane shifts. Further, the GEO satellite is almost continuously in view of a lunar halo orbiter. High-fidelity simulations demonstrate that LiAISON technology improves the navigation of GEO orbiters by an order of magnitude, relative to standard ground tracking. If a GEO satellite is navigated using LiAISON- only tracking measurements, its position is typically known to better than 10 meters. If LiAISON measurements are combined with simple radiometric ground observations, then the satellite s position is typically known to better than 3 meters, which is substantially better than the current state of GEO navigation. There are two features of LiAISON that are novel and advantageous compared with conventional satellite navigation. First, ordinary satellite-to-satellite tracking data only provides relative navigation of each satellite. The novelty is the placement of one navigation satellite in an orbit that is significantly perturbed by both the Earth and the Moon. A navigation satellite can track other satellites elsewhere in the Earth-Moon system and acquire knowledge about both satellites absolute positions and velocities

  19. Graduate Distance Education in Family Relations: A Case Study

    Science.gov (United States)

    Piercy, Kathleen W.; Lee, Thomas R.

    2006-01-01

    This paper discusses graduate distance education in family relations and related disciplines, using a case study approach. Challenges that occur in distance graduate programs are outlined and illustrated by examination of a new master's degree program in Family and Human Development. The program delivers courses by satellite broadcast and…

  20. Family Practice Models for an Army Community. A Demonstration Project.

    Science.gov (United States)

    The report was written with the intent that it could be used as an initial guide or reference by those who are establishing a Family Practice Clinic...appropriate. A satellite study has been done on appointment calendar utilization at the North Fort Ord Family Practice Clinic. Some of the data from that study are presented.

  1. Stream Gauges and Satellite Measurements

    Science.gov (United States)

    Alsdorf, D. E.

    2010-12-01

    Satellite measurements should not be viewed as a replacement for stream gauges. However, occasionally it is suggested that because satellite-based measurements can provide river discharge, a motivation for satellite approaches is an increasing lack of stream gauges. This is an argument for more stream gauges, but not necessarily for satellite measurements. Rather, in-situ and spaceborne methods of estimating discharge are complementary. Stream gauges provide frequent measurements at one point in the river reach whereas satellites have the potential to measure throughout all reaches but at orbital repeat intervals of days to weeks. The Surface Water and Ocean Topography satellite mission (SWOT) is an opportunity to further develop these complements. The motivation for SWOT, and indeed for any satellite based method of estimating discharge, should not be as a replacement for stream gauges. Scientific and application uses should motivate the measurements. For example, understanding floods with their dynamic water surfaces are best sampled from remote platforms that provide water surface elevations throughout the floodwave. As another example, today’s water and energy balance models are giving outputs at increasing spatial resolution and are making use of water surface elevations throughout the modeled basin. These models require a similar resolution in the calibrating and validating observations. We should also be aware of practical limitations. In addition to providing spatially distributed hydrodynamic measurements on rivers, SWOT will be able to measure storage changes in the estimated 30 million lakes in the world that are larger than a hectare. Knowing the storage changes in these lakes is especially important in certain regions such as the Arctic but gauging even a small fraction of these is impractical. Another motivator for satellite methods is that even in the presence of stream gauges, discharge data is not always well shared throughout all countries

  2. Petite Amateur Navy Satellite (PANSAT)

    Science.gov (United States)

    Sakoda, D.; Hiser, J. K.

    1989-01-01

    The Naval Postgraduate School's (NPS) Space Systems Academic Group (SSAG) is designing and developing a small communications satellite for launch aboard the shuttle as a complex autonomous payload (CAP). The objectives of PANSAT are three-fold. First, PANSAT will provide an ideal educational tool for the officer students at NPS supporting Space Systems Engineering and Space Systems Operations with hands-on hardware development. Second, the satellite will provide digital store-and-forward communications, or packet radio, for the amateur radio community. The third objective is to provide a low-cost, space-based platform for small experiments. PANSAT will be launched from the shuttle at a nominal altitude of 200 n.m. and an inclination of at least 37 degrees. The satellite weight is 150 lbs. Since there is no attitude control, eight dipole whip antennas will be used to provide isotropic ground coverage for communications. FM digital communications will be used with up-link and down-link on a single frequency in the amateur band of 437.25 MHz. A maximum 50 kHz of bandwidth is envisioned for the satellite. The expected lifetime of the satellite is 1 1/2 to 2 years before atmospheric reentry. The PANSAT design consists of the following: communications subsystem (COMM); computer, or data processor and sequencer (DP&S); power subsystem; structure subsystem; and experiment payload.

  3. Measurements of Outgassing from Satellites

    Science.gov (United States)

    Cho, Hyokjin; Moon, Guee-Won; Lee, Sang-Hoon; Seo, Hee-Jun

    2004-08-01

    TQCM(Thermoelectric Quartz Crystal Microbalance)s and witness plates were used to measure the molecular contamination for satellites and the outgassing from satellites during vacuum bake-out tests and thermal vacuum tests at KARI(Korea Aerospace Research Institute). First, vacuum bake-out tests were performed several times for the satellite, KAISTSAT-4(KAIST Satellite-4) flight model, and its components under different temperature conditions. Second, thermal vacuum tests for KOMPSAT-2(Korea Multi-Purpose Satellite-2) flight model were done under specific environment conditions. Through the measurements by TQCMs, the mass and the mass deposition rate of a molecular contamination could be traced in a real time. The molecular contamination of witness plates' surfaces could also be measured through an infrared spectrometer, and those results were compared to the TQCMs' results. And the materials from the decontamination plate of the thermal vacuum chamber after the tests were also analyzed using a GC-MS (Gas Chromatograph - Mass Spectrometer).

  4. Dynamics of DNA Mismatch Repair

    Science.gov (United States)

    Coats, Julie; Lin, Yuyen; Rasnik, Ivan

    2009-11-01

    DNA mismatch repair protects the genome from spontaneous mutations by recognizing errors, excising damage, and re-synthesizing DNA in a pathway that is highly conserved. Mismatch recognition is accomplished by the MutS family of proteins which are weak ATPases that bind specifically to damaged DNA, but the specific molecular mechanisms by which these proteins recognize damage and initiate excision are not known. Previous structural investigations have implied that protein-induced conformational changes are central to mismatch recognition. Because damage detection is a highly dynamic process in which conformational changes of the protein-DNA complexes occur on a time scale of a few seconds, it is difficult to obtain meaningful kinetic information with traditional ensemble techniques. In this work, we use single molecule fluorescence resonance energy transfer (smFRET) to study the conformational dynamics of fluorescently labeled DNA substrates in the presence of the mismatch repair protein MutS from E. coli and its human homolog MSH2/MSH6. Our studies allow us to obtain quantitative kinetic information about the rates of binding and dissociation and to determine the conformational states for each protein-DNA complex.

  5. Family History

    Science.gov (United States)

    ... to your relatives about their health. Draw a family tree and add the health information. Having copies of medical records and death certificates is also helpful. Centers for Disease Control and Prevention

  6. Family matters

    DEFF Research Database (Denmark)

    Kieffer-Kristensen, Rikke; Siersma, Volkert Dirk; Teasdale, Thomas William

    2013-01-01

    brain injury participated. Family and brain injury characteristics were reported by the ill and healthy parents. Children self-reported post-traumatic stress symptoms (PSS) using the Child Impact of Events revised (CRIES). Emotional and behavioural problems among the children were also identified...... by the parents using the Achenbach’s Child Behaviour Checklist (CBCL). RESULTS: The family stress variables relating to the healthy spouse in all six comparisons were significant (p... scores for the children. For the adjusted associations, we again found the family stress variables in the healthy spouse to be related to the risk of emotional and behavioral problems in the children. CONCLUSIONS: The present results suggest that in ABI families, the children’s emotional functioning...

  7. Familial hypercholesterolemia

    Science.gov (United States)

    ... high. The condition begins at birth and can cause heart attacks at an early age. Related topics include: Familial ... does not respond well to treatment and may cause an early heart attack. Possible Complications Complications may include: Heart attack at ...

  8. FAMILY RHAGIONIDAE.

    Science.gov (United States)

    Santos, Charles Morphy D; Carmo, Daniel D D

    2016-06-14

    The family Rhagionidae is one of the oldest Brachyeran lineages. Its monophyly is still uncertain. There are four rhagionid genera distributed in Neotropical Region but only three species of Chrysopilus are found in Colombia.

  9. Satellite Data Transmission (SDT) requirement

    Science.gov (United States)

    Chie, C. M.; White, M.; Lindsey, W. C.

    1984-01-01

    An 85 Mb/s modem/codec to operate in a 34 MHz C-band domestic satellite transponder at a system carrier to noise power ratio of 19.5 dB is discussed. Characteristics of a satellite channel and the approach adopted for the satellite data transmission modem/codec selection are discussed. Measured data and simulation results of the existing 50 Mbps link are compared and used to verify the simulation techniques. Various modulation schemes that were screened for the SDT are discussed and the simulated performance of two prime candidates, the 8 PSK and the SMSK/2 are given. The selection process that leads to the candidate codec techniques are documented and the technology of the modem/codec candidates is assessed. Costs of the modems and codecs are estimated.

  10. Landsat—Earth observation satellites

    Science.gov (United States)

    ,

    2015-11-25

    Since 1972, Landsat satellites have continuously acquired space-based images of the Earth’s land surface, providing data that serve as valuable resources for land use/land change research. The data are useful to a number of applications including forestry, agriculture, geology, regional planning, and education. Landsat is a joint effort of the U.S. Geological Survey (USGS) and the National Aeronautics and Space Administration (NASA). NASA develops remote sensing instruments and the spacecraft, then launches and validates the performance of the instruments and satellites. The USGS then assumes ownership and operation of the satellites, in addition to managing all ground reception, data archiving, product generation, and data distribution. The result of this program is an unprecedented continuing record of natural and human-induced changes on the global landscape.

  11. Small satellites and their regulation

    CERN Document Server

    Jakhu, Ram S

    2014-01-01

    Since the launch of UoSat-1 of the University of Surrey (United Kingdom) in 1981, small satellites proved regularly to be useful, beneficial, and cost-effective tools. Typical tasks cover education and workforce development, technology demonstration, verification and validation, scientific and engineering research as well as commercial applications. Today the launch masses range over almost three orders of magnitude starting at less than a kilogram up to a few hundred kilograms, with budgets of less than US$ 100.00 and up to millions within very short timeframes of sometimes less than two years. Therefore each category of small satellites provides specific challenges in design, development and operations. Small satellites offer great potentials to gain responsive, low-cost access to space within a short timeframe for institutions, companies, regions and countries beyond the traditional big players in the space arena. For these reasons (particularly the low cost of construction, launch and operation), small (m...

  12. Satellite Communications Using Commercial Protocols

    Science.gov (United States)

    Ivancic, William D.; Griner, James H.; Dimond, Robert; Frantz, Brian D.; Kachmar, Brian; Shell, Dan

    2000-01-01

    NASA Glenn Research Center has been working with industry, academia, and other government agencies in assessing commercial communications protocols for satellite and space-based applications. In addition, NASA Glenn has been developing and advocating new satellite-friendly modifications to existing communications protocol standards. This paper summarizes recent research into the applicability of various commercial standard protocols for use over satellite and space- based communications networks as well as expectations for future protocol development. It serves as a reference point from which the detailed work can be readily accessed. Areas that will be addressed include asynchronous-transfer-mode quality of service; completed and ongoing work of the Internet Engineering Task Force; data-link-layer protocol development for unidirectional link routing; and protocols for aeronautical applications, including mobile Internet protocol routing for wireless/mobile hosts and the aeronautical telecommunications network protocol.

  13. Reinventing the Solar Power Satellite

    Science.gov (United States)

    Landis, Geoffrey A.

    2004-01-01

    The selling price of electrical power varies with time. The economic viability of space solar power is maximum if the power can be sold at peak power rates, instead of baseline rate. Price and demand of electricity was examined from spot-market data from four example markets: New England, New York City, suburban New York, and California. The data was averaged to show the average price and demand for power as a function of time of day and time of year. Demand varies roughly by a factor of two between the early-morning minimum demand, and the afternoon maximum; both the amount of peak power, and the location of the peak, depends significantly on the location and the weather. The demand curves were compared to the availability curves for solar energy and for tracking and non-tracking satellite solar power systems in order to compare the market value of terrestrial and solar electrical power. In part 2, new designs for a space solar power (SSP) system were analyzed to provide electrical power to Earth for economically competitive rates. The approach was to look at innovative power architectures to more practical approaches to space solar power. A significant barrier is the initial investment required before the first power is returned. Three new concepts for solar power satellites were invented and analyzed: a solar power satellite in the Earth-Sun L2 point, a geosynchronous no-moving parts solar power satellite, and a nontracking geosynchronous solar power satellite with integral phased array. The integral-array satellite had several advantages, including an initial investment cost approximately eight times lower than the conventional design.

  14. Regenerative capacity of old muscle stem cells declines without significant accumulation of DNA damage.

    Directory of Open Access Journals (Sweden)

    Wendy Cousin

    Full Text Available The performance of adult stem cells is crucial for tissue homeostasis but their regenerative capacity declines with age, leading to failure of multiple organs. In skeletal muscle this failure is manifested by the loss of functional tissue, the accumulation of fibrosis, and reduced satellite cell-mediated myogenesis in response to injury. While recent studies have shown that changes in the composition of the satellite cell niche are at least in part responsible for the impaired function observed with aging, little is known about the effects of aging on the intrinsic properties of satellite cells. For instance, their ability to repair DNA damage and the effects of a potential accumulation of DNA double strand breaks (DSBs on their regenerative performance remain unclear. This work demonstrates that old muscle stem cells display no significant accumulation of DNA DSBs when compared to those of young, as assayed after cell isolation and in tissue sections, either in uninjured muscle or at multiple time points after injury. Additionally, there is no significant difference in the expression of DNA DSB repair proteins or globally assayed DNA damage response genes, suggesting that not only DNA DSBs, but also other types of DNA damage, do not significantly mark aged muscle stem cells. Satellite cells from DNA DSB-repair-deficient SCID mice do have an unsurprisingly higher level of innate DNA DSBs and a weakened recovery from gamma-radiation-induced DNA damage. Interestingly, they are as myogenic in vitro and in vivo as satellite cells from young wild type mice, suggesting that the inefficiency in DNA DSB repair does not directly correlate with the ability to regenerate muscle after injury. Overall, our findings suggest that a DNA DSB-repair deficiency is unlikely to be a key factor in the decline in muscle regeneration observed upon aging.

  15. Regulation and function of DNA methylation in plants and animals

    Science.gov (United States)

    He, Xin-Jian; Chen, Taiping; Zhu, Jian-Kang

    2011-01-01

    DNA methylation is an important epigenetic mark involved in diverse biological processes. In plants, DNA methylation can be established through the RNA-directed DNA methylation pathway, an RNA interference pathway for transcriptional gene silencing (TGS), which requires 24-nt small interfering RNAs. In mammals, de novo DNA methylation occurs primarily at two developmental stages: during early embryogenesis and during gametogenesis. While it is not clear whether establishment of DNA methylation patterns in mammals involves RNA interference in general, de novo DNA methylation and suppression of transposons in germ cells require 24-32-nt piwi-interacting small RNAs. DNA methylation status is dynamically regulated by DNA methylation and demethylation reactions. In plants, active DNA demethylation relies on the repressor of silencing 1 family of bifunctional DNA glycosylases, which remove the 5-methylcytosine base and then cleave the DNA backbone at the abasic site, initiating a base excision repair (BER) pathway. In animals, multiple mechanisms of active DNA demethylation have been proposed, including a deaminase- and DNA glycosylase-initiated BER pathway. New information concerning the effects of various histone modifications on the establishment and maintenance of DNA methylation has broadened our understanding of the regulation of DNA methylation. The function of DNA methylation in plants and animals is also discussed in this review. PMID:21321601

  16. Regulation and function of DNA methylation in plants and animals

    KAUST Repository

    He, Xinjian

    2011-02-15

    DNA methylation is an important epigenetic mark involved in diverse biological processes. In plants, DNA methylation can be established through the RNA-directed DNA methylation pathway, an RNA interference pathway for transcriptional gene silencing (TGS), which requires 24-nt small interfering RNAs. In mammals, de novo DNA methylation occurs primarily at two developmental stages: during early embryogenesis and during gametogenesis. While it is not clear whether establishment of DNA methylation patterns in mammals involves RNA interference in general, de novo DNA methylation and suppression of transposons in germ cells require 24-32-nt piwi-interacting small RNAs. DNA methylation status is dynamically regulated by DNA methylation and demethylation reactions. In plants, active DNA demethylation relies on the repressor of silencing 1 family of bifunctional DNA glycosylases, which remove the 5-methylcytosine base and then cleave the DNA backbone at the abasic site, initiating a base excision repair (BER) pathway. In animals, multiple mechanisms of active DNA demethylation have been proposed, including a deaminase- and DNA glycosylase-initiated BER pathway. New information concerning the effects of various histone modifications on the establishment and maintenance of DNA methylation has broadened our understanding of the regulation of DNA methylation. The function of DNA methylation in plants and animals is also discussed in this review. © 2011 IBCB, SIBS, CAS All rights reserved.

  17. Communication Satellites 1958 to 1986

    Science.gov (United States)

    1984-10-01

    Greenland India Libya Mexico Morocco Niger Nigeria Norway Oman Peru Portugal Saudi Arabia Spain Sudan Zaire .C.) Angola Bangladesh Bolivia...34 Paper 13-5, EASCOM 󈨑 Conference Record (September 1977). 748. G. Cheadle, "Philippine Dow» » tic Satellite System," AIAA Paper 74-491, AIAA 5th...Experiment in 1.7f 11.5, and 34.5 GHz with Engineering Tesi Satellite Type II," AIAA Paper 78-623, AIAA 7th Communications Sate!’ite Systems Conference

  18. Big Deployables in Small Satellites

    OpenAIRE

    Davis, Bruce; Francis, William; Goff, Jonathan; Cross, Michael; Copel, Daniel

    2014-01-01

    The concept of utilizing small satellites to perform big mission objectives has grown from a distant idea to a demonstrated reality. One of the challenges in using small-satellite platforms for high-value missions is the packaging of long and large surface-area devices such as antennae, solar arrays and sensor positioning booms. One possible enabling technology is the slit-tube, or a deployable “tape-measure” boom which can be flattened and rolled into a coil achieving a high volumetric packa...

  19. Magnetospheres of the galilean satellites.

    Science.gov (United States)

    Kivelson, M G; Slavin, J A; Southwood, D J

    1979-08-03

    The plasma and field perturbations of magnetospheres that would surround magnetized galilean satellites embedded in the corotating jovian plasma differ from those produced by interaction with an unmagnetized conductor. If the intrinsic satellite dipole is antiparallel to that of Jupiter, the magnetosphere will be open. It is predicted that Io has an internal magnetic field with a dipole moment of 6.5 x 10(22) gauss-cubic centimeters antiparallel to Jupiter's, and Io's special properties can be interpreted on the basis of a reconnecting magnetosphere.

  20. DNA Microarrays

    Science.gov (United States)

    Nguyen, C.; Gidrol, X.

    Genomics has revolutionised biological and biomedical research. This revolution was predictable on the basis of its two driving forces: the ever increasing availability of genome sequences and the development of new technology able to exploit them. Up until now, technical limitations meant that molecular biology could only analyse one or two parameters per experiment, providing relatively little information compared with the great complexity of the systems under investigation. This gene by gene approach is inadequate to understand biological systems containing several thousand genes. It is essential to have an overall view of the DNA, RNA, and relevant proteins. A simple inventory of the genome is not sufficient to understand the functions of the genes, or indeed the way that cells and organisms work. For this purpose, functional studies based on whole genomes are needed. Among these new large-scale methods of molecular analysis, DNA microarrays provide a way of studying the genome and the transcriptome. The idea of integrating a large amount of data derived from a support with very small area has led biologists to call these chips, borrowing the term from the microelectronics industry. At the beginning of the 1990s, the development of DNA chips on nylon membranes [1, 2], then on glass [3] and silicon [4] supports, made it possible for the first time to carry out simultaneous measurements of the equilibrium concentration of all the messenger RNA (mRNA) or transcribed RNA in a cell. These microarrays offer a wide range of applications, in both fundamental and clinical research, providing a method for genome-wide characterisation of changes occurring within a cell or tissue, as for example in polymorphism studies, detection of mutations, and quantitative assays of gene copies. With regard to the transcriptome, it provides a way of characterising differentially expressed genes, profiling given biological states, and identifying regulatory channels.

  1. Removal of a frameshift between the hsdM and hsdS genes of the EcoKI Type IA DNA restriction and modification system produces a new type of system and links the different families of Type I systems.

    Science.gov (United States)

    Roberts, Gareth A; Chen, Kai; Cooper, Laurie P; White, John H; Blakely, Garry W; Dryden, David T F

    2012-11-01

    The EcoKI DNA methyltransferase is a trimeric protein comprised of two modification subunits (M) and one sequence specificity subunit (S). This enzyme forms the core of the EcoKI restriction/modification (RM) enzyme. The 3' end of the gene encoding the M subunit overlaps by 1 nt the start of the gene for the S subunit. Translation from the two different open reading frames is translationally coupled. Mutagenesis to remove the frameshift and fuse the two subunits together produces a functional RM enzyme in vivo with the same properties as the natural EcoKI system. The fusion protein can be purified and forms an active restriction enzyme upon addition of restriction subunits and of additional M subunit. The Type I RM systems are grouped into families, IA to IE, defined by complementation, hybridization and sequence similarity. The fusion protein forms an evolutionary intermediate form lying between the Type IA family of RM enzymes and the Type IB family of RM enzymes which have the frameshift located at a different part of the gene sequence.

  2. Synthetic Nucleotides as Probes of DNA Polymerase Specificity

    Directory of Open Access Journals (Sweden)

    Jason M. Walsh

    2012-01-01

    Full Text Available The genetic code is continuously expanding with new nucleobases designed to suit specific research needs. These synthetic nucleotides are used to study DNA polymerase dynamics and specificity and may even inhibit DNA polymerase activity. The availability of an increasing chemical diversity of nucleotides allows questions of utilization by different DNA polymerases to be addressed. Much of the work in this area deals with the A family DNA polymerases, for example, Escherichia coli DNA polymerase I, which are DNA polymerases involved in replication and whose fidelity is relatively high, but more recent work includes other families of polymerases, including the Y family, whose members are known to be error prone. This paper focuses on the ability of DNA polymerases to utilize nonnatural nucleotides in DNA templates or as the incoming nucleoside triphosphates. Beyond the utility of nonnatural nucleotides as probes of DNA polymerase specificity, such entities can also provide insight into the functions of DNA polymerases when encountering DNA that is damaged by natural agents. Thus, synthetic nucleotides provide insight into how polymerases deal with nonnatural nucleotides as well as into the mutagenic potential of nonnatural nucleotides.

  3. University Satellite Campus Management Models

    Science.gov (United States)

    Fraser, Doug; Stott, Ken

    2015-01-01

    Among the 60 or so university satellite campuses in Australia are many that are probably failing to meet the high expectations of their universities and the communities they were designed to serve. While in some cases this may be due to the demand driven system, it may also be attributable in part to the ways in which they are managed. The…

  4. GOES-R: Satellite Insight

    Science.gov (United States)

    Fitzpatrick, Austin J.; Leon, Nancy J.; Novati, Alexander; Lincoln, Laura K.; Fisher, Diane K.

    2012-01-01

    GOES-R: Satellite Insight seeks to bring awareness of the GOES-R (Geostationary Operational Environmental Satellite -- R Series) satellite currently in development to an audience of all ages on the emerging medium of mobile games. The iPhone app (Satellite Insight) was created for the GOES-R Program. The app describes in simple terms the types of data products that can be produced from GOES-R measurements. The game is easy to learn, yet challenging for all audiences. It includes educational content and a path to further information about GOESR, its technology, and the benefits of the data it collects. The game features action-puzzle game play in which the player must prevent an overflow of data by matching falling blocks that represent different types of GOES-R data. The game adds more different types of data blocks over time, as long as the player can prevent a data overflow condition. Points are awarded for matches, and players can compete with themselves to beat their highest score.

  5. Icy satellites, rings and Pluto

    Science.gov (United States)

    Klinger, J.

    The present state of knowledge on the occurrence of ices on the satellites of Jupiter, Saturn, Uranus and Neptune, on ring particles and on Pluto is briefly reviewed. An overview is given of the role of ices in the geological evolution of the above mentioned bodies.

  6. Audio Satellites: Overhearing Everyday Life

    DEFF Research Database (Denmark)

    Kirkegaard, Jonas Rasmussen; Breinbjerg, M.; Højlund, M. K.

    2017-01-01

    around or displaced arbitrarily in a given landscape. In the web browser, the different sound streams from the individual satellites can be mixed together to form a cooperative soundscape. The project thus allows people to tune into and explore the overheard soundscape of everyday life in a collaborative...

  7. Electric propulsion for small satellites

    Science.gov (United States)

    Keidar, Michael; Zhuang, Taisen; Shashurin, Alexey; Teel, George; Chiu, Dereck; Lukas, Joseph; Haque, Samudra; Brieda, Lubos

    2015-01-01

    Propulsion is required for satellite motion in outer space. The displacement of a satellite in space, orbit transfer and its attitude control are the task of space propulsion, which is carried out by rocket engines. Electric propulsion uses electric energy to energize or accelerate the propellant. The electric propulsion, which uses electrical energy to accelerate propellant in the form of plasma, is known as plasma propulsion. Plasma propulsion utilizes the electric energy to first, ionize the propellant and then, deliver energy to the resulting plasma leading to plasma acceleration. Many types of plasma thrusters have been developed over last 50 years. The variety of these devices can be divided into three main categories dependent on the mechanism of acceleration: (i) electrothermal, (ii) electrostatic and (iii) electromagnetic. Recent trends in space exploration associate with the paradigm shift towards small and efficient satellites, or micro- and nano-satellites. A particular example of microthruster considered in this paper is the micro-cathode arc thruster (µCAT). The µCAT is based on vacuum arc discharge. Thrust is produced when the arc discharge erodes some of the cathode at high velocity and is accelerated out the nozzle by a Lorentz force. The thrust amount is controlled by varying the frequency of pulses with demonstrated range to date of 1-50 Hz producing thrust ranging from 1 µN to 0.05 mN.

  8. Cratering rates on the Galilean satellites.

    Science.gov (United States)

    Zahnle, K; Dones, L; Levison, H F

    1998-12-01

    We exploit recent theoretical advances toward the origin and orbital evolution of comets and asteroids to obtain revised estimates for cratering rates in the jovian system. We find that most, probably more than 90%, of the craters on the Galilean satellites are caused by the impact of Jupiter-family comets (JFCs). These are comets with short periods, in generally low-inclination orbits, whose dynamics are dominated by Jupiter. Nearly isotropic comets (long period and Halley-type) contribute at the 1-10% level. Trojan asteroids might also be important at the 1-10% level; if they are important, they would be especially important for smaller craters. Main belt asteroids are currently unimportant, as each 20-km crater made on Ganymede implies the disruption of a 200-km diameter parental asteroid, a destruction rate far beyond the resources of today's asteroid belt. Twenty-kilometer diameter craters are made by kilometer-size impactors; such events occur on a Galilean satellite about once in a million years. The paucity of 20-km craters on Europa indicates that its surface is of order 10 Ma. Lightly cratered surfaces on Ganymede are nominally of order 0.5-1.0 Ga. The uncertainty in these estimates is about a factor of five. Callisto is old, probably more than 4 Ga. It is too heavily cratered to be accounted for by the current flux of JFCs. The lack of pronounced apex-antapex asymmetries on Ganymede may be compatible with crater equilibrium, but it is more easily understood as evidence for nonsynchronous rotation of an icy carapace. c 1998 Academic Press.

  9. Family Literacy

    Directory of Open Access Journals (Sweden)

    Livija Knaflič

    1999-12-01

    Full Text Available Research in child and adult literacy demonstrates that the achievement and the level of literacy that children attain at school is connected with the social and cultural characteristics and the level of literacy of the child's family. This intergenerational transfer of the level of literacy has motivated the search for different ways of improving the level of literacy.The concept of family literacy is based on the assumption that a higher level of parent literacy means that the children may achieve the same, and it also offers better schooling prospects. Family literacy programmes help fami­lies to develop different activities, in­cluding reading and writing skills, both in their community and in everyday life.

  10. RFP for the italien satellite AGILE

    DEFF Research Database (Denmark)

    Madsen, Peter Buch; Jørgensen, John Leif; Riis, Troels

    1999-01-01

    The document descibes the ASC Star Tracker (performance, functionality, requirements etc.) to the Italian satellite AGILE.......The document descibes the ASC Star Tracker (performance, functionality, requirements etc.) to the Italian satellite AGILE....

  11. Satellite Tags- Guam/CNMI EEZ

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Satellite tagging was implemented in 2013. Satellite tagging is conducted using a Dan Inject air rifle and deployment arrows designed by Wildlife Computers. Two...

  12. Biophysical applications of satellite remote sensing

    CERN Document Server

    Hanes, Jonathan

    2014-01-01

    Including an introduction and historical overview of the field, this comprehensive synthesis of the major biophysical applications of satellite remote sensing includes in-depth discussion of satellite-sourced biophysical metrics such as leaf area index.

  13. New Equipment Training Center-Satellite Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The ARDEC Satellite Facility is a 24-hour on-site military satellite transmission and downlink capability to Southwest Asia and all other military OCONUS and CONUS...

  14. DIORAMA Model of Satellite Body Orientation

    Energy Technology Data Exchange (ETDEWEB)

    Werley, Kenneth Alan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-03-04

    The DIORAMA GPS satellite platform orientation model is described. Satellites need to keep sensors pointed towards the earth and solar panels oriented to face the sun (when not in the earth’s shadow) while they orbit the earth.

  15. Family Structure and Family Processes in Mexican American Families

    OpenAIRE

    Zeiders, Katharine H.; Roosa, Mark W.; Tein, Jenn-Yun

    2011-01-01

    Despite increases in single-parent families among Mexican Americans (MA), few studies have examined the association of family structure and family adjustment. Utilizing a diverse sample of 738 Mexican American families (21.7% single parent), the current study examined differences across family structure on early adolescent outcomes, family functioning, and parent-child relationship variables. Results revealed that early adolescents in single parent families reported greater school misconduct,...

  16. Advanced Extremely High Frequency Satellite (AEHF)

    Science.gov (United States)

    2015-12-01

    resistant communications for high priority military ground, sea, and air assets. The system consists of four satellites in Geosynchronous Earth Orbit that...submarine terminals, and airborne terminals. The mission control segment controls satellites on orbit , monitors satellite health, and provides...Schriever Air Force Base (AFB). Due to the proprietary nature of the AEHF Space Satellite (on- orbit ) Segment, this segment is not considered core and the

  17. Sustained Satellite Missions for Climate Data Records

    Science.gov (United States)

    Halpern, David

    2012-01-01

    Satellite CDRs possess the accuracy, longevity, and stability for sustained moni toring of critical variables to enhance understanding of the global integrated Earth system and predict future conditions. center dot Satellite CDRs are a critical element of a global climate observing system. center dot Satellite CDRs are a difficult challenge and require high - level managerial commitment, extensive intellectual capital, and adequate funding.

  18. Global Navigation Satellite System and Augmentation

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 22; Issue 12 ... Keywords. Global Navigation Satellite System, GPS, Indian Regional Navigation Satellite System, GLONASS, Galileo, Compass, GAGAN. ... The article also covers the Indian RegionalNavigation Satellite System (IRNSS) and its potentials.

  19. Processor Units Reduce Satellite Construction Costs

    Science.gov (United States)

    2014-01-01

    As part of the effort to build the Fast Affordable Science and Technology Satellite (FASTSAT), Marshall Space Flight Center developed a low-cost telemetry unit which is used to facilitate communication between a satellite and its receiving station. Huntsville, Alabama-based Orbital Telemetry Inc. has licensed the NASA technology and is offering to install the cost-cutting units on commercial satellites.

  20. 14 CFR 141.91 - Satellite bases.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 3 2010-01-01 2010-01-01 false Satellite bases. 141.91 Section 141.91... OTHER CERTIFICATED AGENCIES PILOT SCHOOLS Operating Rules § 141.91 Satellite bases. The holder of a... assistant chief instructor is designated for each satellite base, and that assistant chief instructor is...