Diversity of DNA β, a satellite molecule associated with some monopartite begomoviruses

International Nuclear Information System (INIS)

Briddon, Rob W.; Bull, Simon E.; Amin, Imran; Idris, Ali M.; Mansoor, Shahid; Bedford, Ian D.; Dhawan, Poonam; Rishi, Narayan; Siwatch, Surender S.; Abdel-Salam, Aly M.; Brown, Judith K.; Zafar, Yusuf; Markham, Peter G.

2003-01-01

DNA β molecules are symptom-modulating, single-stranded DNA satellites associated with monopartite begomoviruses (family Geminiviridae). Such molecules have thus far been shown to be associated with Ageratum yellow vein virus from Singapore and Cotton leaf curl Multan virus from Pakistan. Here, 26 additional DNA β molecules, associated with diverse plant species obtained from different geographical locations, were cloned and sequenced. These molecules were shown to be widespread in the Old World, where monopartite begomoviruses are known to occur. Analysis of the sequences revealed a highly conserved organization for DNA β molecules consisting of a single conserved open reading frame, an adenine-rich region, and a region of high sequence conservation [the satellite conserved region (SCR)]. The SCR contains a potential hairpin structure with the loop sequence TAA/GTATTAC; similar to the origins of replication of geminiviruses and nanoviruses. Two major groups of DNA β satellites were resolved by phylogenetic analyses. One group originated from hosts within the Malvaceae and the second from a more diverse group of plants within the Solanaceae and Compositae. Within the two clusters, DNA β molecules showed relatedness based both on host and geographic origin. These findings strongly support coadaptation of DNA β molecules with their respective helper begomoviruses

Comparative Analysis of Satellite DNA in the Drosophila melanogaster Species Complex

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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.

Distribution of DTHS3 satellite DNA across 12 bivalve species Eva ...

Indian Academy of Sciences (India)

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In this work, characterization of DTHS3 satellite DNA was further expanded within the Class. Bivalvia. Monomer variants of DTHS3 satDNA were compared in 12 bivalve species belonging to two different Subclasses, Heterodonta and Pteriomorphia. This satDNA, whose age is estimated to a minimum of 516 Ma, ...

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

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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.

Myonuclear transcription is responsive to mechanical load and DNA content but uncoupled from cell size during hypertrophy.

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Kirby, Tyler J; Patel, Rooshil M; McClintock, Timothy S; Dupont-Versteegden, Esther E; Peterson, Charlotte A; McCarthy, John J

2016-03-01

Myofibers increase size and DNA content in response to a hypertrophic stimulus, thus providing a physiological model with which to study how these factors affect global transcription. Using 5-ethynyl uridine (EU) to metabolically label nascent RNA, we measured a sevenfold increase in myofiber transcription during early hypertrophy before a change in cell size and DNA content. The typical increase in myofiber DNA content observed at the later stage of hypertrophy was associated with a significant decrease in the percentage of EU-positive myonuclei; however, when DNA content was held constant by preventing myonuclear accretion via satellite cell depletion, both the number of transcriptionally active myonuclei and the amount of RNA generated by each myonucleus increased. During late hypertrophy, transcription did not scale with cell size, as smaller myofibers (transcriptional activity. Finally, transcription was primarily responsible for changes in the expression of genes known to regulate myofiber size. These findings show that resident myonuclei possess a significant reserve capacity to up-regulate transcription during hypertrophy and that myofiber transcription is responsive to DNA content but uncoupled from cell size during hypertrophy. © 2016 Kirby et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Integration of hepatitis B virus DNA in chromosome-specific satellite sequences

International Nuclear Information System (INIS)

Shaul, Y.; Garcia, P.D.; Schonberg, S.; Rutter, W.J.

1986-01-01

The authors previously reported the cloning and detailed analysis of the integrated hepatitis B virus sequences in a human hepatoma cell line. They report here the integration of at least one of hepatitis B virus at human satellite DNA sequences. The majority of the cellular sequences identified by this satellite were organized as a multimeric composition of a 0.6-kilobase EcoRI fragment. This clone hybridized in situ almost exclusively to the centromeric heterochromatin of chromosomes 1 and 16 and to a lower extent to chromosome 2 and to the heterochromatic region of the Y chromosome. The immediate flanking host sequence appeared as a hierarchy of repeating units which were almost identical to a previously reported human satellite III DNA sequence

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

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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.

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.

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

2013-02-19

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.

Discovery of a Regulatory Motif for Human Satellite DNA Transcription in Response to BATF2 Overexpression.

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Bai, Xuejia; Huang, Wenqiu; Zhang, Chenguang; Niu, Jing; Ding, Wei

2016-03-01

One of the basic leucine zipper transcription factors, BATF2, has been found to suppress cancer growth and migration. However, little is known about the genes downstream of BATF2. HeLa cells were stably transfected with BATF2, then chromatin immunoprecipitation-sequencing was employed to identify the DNA motifs responsive to BATF2. Comprehensive bioinformatics analyses indicated that the most significant motif discovered as TTCCATT[CT]GATTCCATTC[AG]AT was primarily distributed among the chromosome centromere regions and mostly within human type II satellite DNA. Such motifs were able to prime the transcription of type II satellite DNA in a directional and asymmetrical manner. Consistently, satellite II transcription was up-regulated in BATF2-overexpressing cells. The present study provides insight into understanding the role of BATF2 in tumours and the importance of satellite DNA in the maintenance of genomic stability. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

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

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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

Plantago lagopus B Chromosome Is Enriched in 5S rDNA-Derived Satellite DNA

Czech Academy of Sciences Publication Activity Database

Kumke, K.; Macas, Jiří; Fuchs, J.; Altschmied, L.; Kour, J.; Dhar, M.K.; Houben, A.

2016-01-01

Roč. 148, č. 1 (2016), s. 68-73 ISSN 1424-8581 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : Polymorhpic A chromosome segment * Satellite repeat * Supernumerary chromosome * 5S rDNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.354, year: 2016

Rapid DNA analysis for automated processing and interpretation of low DNA content samples.

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Turingan, Rosemary S; Vasantgadkar, Sameer; Palombo, Luke; Hogan, Catherine; Jiang, Hua; Tan, Eugene; Selden, Richard F

2016-01-01

Short tandem repeat (STR) analysis of casework samples with low DNA content include those resulting from the transfer of epithelial cells from the skin to an object (e.g., cells on a water bottle, or brim of a cap), blood spatter stains, and small bone and tissue fragments. Low DNA content (LDC) samples are important in a wide range of settings, including disaster response teams to assist in victim identification and family reunification, military operations to identify friend or foe, criminal forensics to identify suspects and exonerate the innocent, and medical examiner and coroner offices to identify missing persons. Processing LDC samples requires experienced laboratory personnel, isolated workstations, and sophisticated equipment, requires transport time, and involves complex procedures. We present a rapid DNA analysis system designed specifically to generate STR profiles from LDC samples in field-forward settings by non-technical operators. By performing STR in the field, close to the site of collection, rapid DNA analysis has the potential to increase throughput and to provide actionable information in real time. A Low DNA Content BioChipSet (LDC BCS) was developed and manufactured by injection molding. It was designed to function in the fully integrated Accelerated Nuclear DNA Equipment (ANDE) instrument previously designed for analysis of buccal swab and other high DNA content samples (Investigative Genet. 4(1):1-15, 2013). The LDC BCS performs efficient DNA purification followed by microfluidic ultrafiltration of the purified DNA, maximizing the quantity of DNA available for subsequent amplification and electrophoretic separation and detection of amplified fragments. The system demonstrates accuracy, precision, resolution, signal strength, and peak height ratios appropriate for casework analysis. The LDC rapid DNA analysis system is effective for the generation of STR profiles from a wide range of sample types. The technology broadens the range of sample

Blood cell mitochondrial DNA content and premature ovarian aging.

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Marco Bonomi

Full Text Available Primary ovarian insufficiency (POI is a critical fertility defect characterized by an anticipated and silent impairment of the follicular reserve, but its pathogenesis is largely unexplained. The frequent maternal inheritance of POI together with a remarkable dependence of ovarian folliculogenesis upon mitochondrial biogenesis and bioenergetics suggested the possible involvement of a generalized mitochondrial defect. Here, we verified the existence of a significant correlation between blood and ovarian mitochondrial DNA (mtDNA content in a group of women undergoing ovarian hyperstimulation (OH, and then aimed to verify whether mtDNA content was significantly altered in the blood cells of POI women. We recruited 101 women with an impaired ovarian reserve: 59 women with premature ovarian failure (POF and 42 poor responders (PR to OH. A Taqman copy number assay revealed a significant mtDNA depletion (P<0.001 in both POF and PR women in comparison with 43 women of similar age and intact ovarian reserve, or 53 very old women with a previous physiological menopause. No pathogenic variations in the mitochondrial DNA polymerase γ (POLG gene were detected in 57 POF or PR women with low blood mtDNA content. In conclusion, blood cell mtDNA depletion is a frequent finding among women with premature ovarian aging, suggesting that a still undetermined but generalized mitochondrial defect may frequently predispose to POI which could then be considered a form of anticipated aging in which the ovarian defect may represent the first manifestation. The determination of mtDNA content in blood may become an useful tool for the POI risk prediction.

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

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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.

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.

Nuclear DNA contents of Echinchloa crus-galli and its Gaussian relationships with environments

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Li, Dan-Dan; Lu, Yong-Liang; Guo, Shui-Liang; Yin, Li-Ping; Zhou, Ping; Lou, Yu-Xia

2017-02-01

Previous studies on plant nuclear DNA content variation and its relationships with environmental gradients produced conflicting results. We speculated that the relationships between nuclear DNA content of a widely-distributed species and its environmental gradients might be non-linear if it was sampled in a large geographical gradient. Echinochloa crus-galli (L.) P. Beauv. is a worldwide species, but without documents on its intraspecific variation of nuclear DNA content. Our objectives are: 1) to detect intraspecific variation scope of E. crus-galli in its nuclear DNA content, and 2) to testify whether nuclear DNA content of the species changes with environmental gradients following Gaussian models if its populations were sampled in a large geographical gradient. We collected seeds of 36 Chinese populations of E. crus-galli across a wide geographical gradient, and sowed them in a homogeneous field to get their offspring to determine their nuclear DNA content. We analyzed the relationships of nuclear DNA content of these populations with latitude, longitude, and nineteen bioclimatic variables by using Gaussian and linear models. (1) Nuclear DNA content varied from 2.113 to 2.410 pg among 36 Chinese populations of E. crus-galli, with a mean value of 2.256 pg. (2) Gaussian correlations of nuclear DNA content (y) with geographical gradients were detected, with latitude (x) following y = 2.2923*e -(x - 24.9360)2/2*63.79452 (r = 0.546, P correlations of its Nuclear DNA content with geographical and most bioclimatic gradients.

Satellite DNA-based artificial chromosomes for use in gene therapy.

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Hadlaczky, G

2001-04-01

Satellite DNA-based artificial chromosomes (SATACs) can be made by induced de novo chromosome formation in cells of different mammalian species. These artificially generated accessory chromosomes are composed of predictable DNA sequences and they contain defined genetic information. Prototype human SATACs have been successfully constructed in different cell types from 'neutral' endogenous DNA sequences from the short arm of the human chromosome 15. SATACs have already passed a number of hurdles 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.

Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat

Czech Academy of Sciences Publication Activity Database

Koo, D.H.; Tiwari, V.K.; Hřibová, Eva; Doležel, Jaroslav; Friebe, B.; Gill, B.S.

2016-01-01

Roč. 148, č. 4 (2016), s. 314-321 ISSN 1424-8581 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : in-situ hybridization * chromosome addition lines * resistance genes lr57 * repetitive dna * triticum-ovatum * powdery mildew * plant genome * bread wheat * leaf rust * identification * Aegilops geniculata * Chromosome identification * Fluorescence in situ hybridization * Satellite DNA * Wheat Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.354, year: 2016

Cytofluorophotometrical study of the DNA content of the uterine cervical carcinoma and the vaginal epithelium

International Nuclear Information System (INIS)

Tokumoto, Yoshiaki

1987-01-01

The Feulgen DNA content in cells of uterine cervical carcinoma and that of its adjacent vaginal epithelium were measured by microfluorophotometry. The Feulgen DNA content in cells of uterine cervical carcinoma was increased and showed a greater variation of its DNA values compared with diploid cells. The Feulgen DNA content in cells of normal vaginal epithelium adjacent to cervical carcinoma was also increased compared with diploid cells in 6 out of 8 cases. The relativity between the cellular DNA content of cervical carcinoma and that of its adjacent normal vaginal epithelium was found. In 10 out of 14 cases of uterine cervical carcinoma, the mean value of cellular DNA content was increased after by therapuetic irradiation with 10 Gy. Radiation effects on the DNA content of vaginal epithelial cells were similar to those on the DNA content of carcinoma cells. (author)

Reduced mitochondrial DNA content associates with poor prognosis of prostate cancer in African American men.

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Shahriar Koochekpour

Full Text Available Reduction or depletion of mitochondrial DNA (mtDNA has been associated with cancer progression. Although imbalanced mtDNA content is known to occur in prostate cancer, differences in mtDNA content between African American (AA and Caucasian American (CA men are not defined. We provide the first evidence that tumors in AA men possess reduced level of mtDNA compared to CA men. The median tumor mtDNA content was reduced in AA men. mtDNA content was also reduced in normal prostate tissues of AA men compared to CA men, suggesting a possible predisposition to cancer in AA men. mtDNA content was also reduced in benign prostatic hyperplasia (BPH tissue from AA men. Tumor and BPH tissues from patients ≥ 60 years of age possess reduced mtDNA content compared to patients 7 compared to ≤ 7, whereas reduced mtDNA content was observed in tumors of Gleason grade >7 compared to ≤ 7. Together, our data suggest that AA men possess lower mtDNA levels in normal and tumor tissues compared to CA men, which could contribute to higher risk and more aggressive prostate cancer in AA men.

Reduced mitochondrial DNA content associates with poor prognosis of prostate cancer in African American men.

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Koochekpour, Shahriar; Marlowe, Timothy; Singh, Keshav K; Attwood, Kristopher; Chandra, Dhyan

2013-01-01

Reduction or depletion of mitochondrial DNA (mtDNA) has been associated with cancer progression. Although imbalanced mtDNA content is known to occur in prostate cancer, differences in mtDNA content between African American (AA) and Caucasian American (CA) men are not defined. We provide the first evidence that tumors in AA men possess reduced level of mtDNA compared to CA men. The median tumor mtDNA content was reduced in AA men. mtDNA content was also reduced in normal prostate tissues of AA men compared to CA men, suggesting a possible predisposition to cancer in AA men. mtDNA content was also reduced in benign prostatic hyperplasia (BPH) tissue from AA men. Tumor and BPH tissues from patients ≥ 60 years of age possess reduced mtDNA content compared to patients 7 compared to ≤ 7, whereas reduced mtDNA content was observed in tumors of Gleason grade >7 compared to ≤ 7. Together, our data suggest that AA men possess lower mtDNA levels in normal and tumor tissues compared to CA men, which could contribute to higher risk and more aggressive prostate cancer in AA men.

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

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Giuliana Allegrucci

Full Text Available 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.

DNA content variation and its significance in the evolution of the genus Micrasterias (Desmidiales, Streptophyta.

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Aloisie Poulíčková

Full Text Available It is now clear that whole genome duplications have occurred in all eukaryotic evolutionary lineages, and that the vast majority of flowering plants have experienced polyploidisation in their evolutionary history. However, study of genome size variation in microalgae lags behind that of higher plants and seaweeds. In this study, we have addressed the question whether microalgal phylogeny is associated with DNA content variation in order to evaluate the evolutionary significance of polyploidy in the model genus Micrasterias. We applied flow-cytometric techniques of DNA quantification to microalgae and mapped the estimated DNA content along the phylogenetic tree. Correlations between DNA content and cell morphometric parameters were also tested using geometric morphometrics. In total, DNA content was successfully determined for 34 strains of the genus Micrasterias. The estimated absolute 2C nuclear DNA amount ranged from 2.1 to 64.7 pg; intraspecific variation being 17.4-30.7 pg in M. truncata and 32.0-64.7 pg in M. rotata. There were significant differences between DNA contents of related species. We found strong correlation between the absolute nuclear DNA content and chromosome numbers and significant positive correlation between the DNA content and both cell size and number of terminal lobes. Moreover, the results showed the importance of cell/life cycle studies for interpretation of DNA content measurements in microalgae.

DNA content analysis allows discrimination between Trypanosoma cruzi and Trypanosoma rangeli.

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Naves, Lucila Langoni; da Silva, Marcos Vinícius; Fajardo, Emanuella Francisco; da Silva, Raíssa Bernardes; De Vito, Fernanda Bernadelli; Rodrigues, Virmondes; Lages-Silva, Eliane; Ramírez, Luis Eduardo; Pedrosa, André Luiz

2017-01-01

Trypanosoma cruzi, a human protozoan parasite, is the causative agent of Chagas disease. Currently the species is divided into six taxonomic groups. The genome of the CL Brener clone has been estimated to be 106.4-110.7 Mb, and DNA content analyses revealed that it is a diploid hybrid clone. Trypanosoma rangeli is a hemoflagellate that has the same reservoirs and vectors as T. cruzi; however, it is non-pathogenic to vertebrate hosts. The haploid genome of T. rangeli was previously estimated to be 24 Mb. The parasitic strains of T. rangeli are divided into KP1(+) and KP1(-). Thus, the objective of this study was to investigate the DNA content in different strains of T. cruzi and T. rangeli by flow cytometry. All T. cruzi and T. rangeli strains yielded cell cycle profiles with clearly identifiable G1-0 (2n) and G2-M (4n) peaks. T. cruzi and T. rangeli genome sizes were estimated using the clone CL Brener and the Leishmania major CC1 as reference cell lines because their genome sequences have been previously determined. The DNA content of T. cruzi strains ranged from 87,41 to 108,16 Mb, and the DNA content of T. rangeli strains ranged from 63,25 Mb to 68,66 Mb. No differences in DNA content were observed between KP1(+) and KP1(-) T. rangeli strains. Cultures containing mixtures of the epimastigote forms of T. cruzi and T. rangeli strains resulted in cell cycle profiles with distinct G1 peaks for strains of each species. These results demonstrate that DNA content analysis by flow cytometry is a reliable technique for discrimination between T. cruzi and T. rangeli isolated from different hosts.

Decreased mitochondrial DNA content in blood samples of patients with stage I breast cancer

International Nuclear Information System (INIS)

Xia, Peng; An, Han-Xiang; Dang, Cheng-Xue; Radpour, Ramin; Kohler, Corina; Fokas, Emmanouil; Engenhart-Cabillic, Rita; Holzgreve, Wolfgang; Zhong, Xiao Yan

2009-01-01

Alterations of mitochondrial DNA (mtDNA) have been implicated in carcinogenesis. We developed an accurate multiplex quantitative real-time PCR for synchronized determination of mtDNA and nuclear DNA (nDNA). We sought to investigate whether mtDNA content in the peripheral blood of breast cancer patients is associated with clinical and pathological parameters. Peripheral blood samples were collected from 60 patients with breast cancer and 51 age-matched healthy individuals as control. DNA was extracted from peripheral blood for the quantification of mtDNA and nDNA, using a one-step multiplex real-time PCR. A FAM labeled MGB probe and primers were used to amplify the mtDNA sequence of the ATP 8 gene, and a VIC labeled MGB probe and primers were employed to amplify the glyceraldehyde-3-phosphate-dehydrogenase gene. mtDNA content was correlated with tumor stage, menstruation status, and age of patients as well as lymph node status and the expression of estrogen receptor (ER), progesterone receptor (PR) and Her-2/neu protein. The content of mtDNA in stage I breast cancer patients was significantly lower than in other stages (overall P = 0.023). Reduced mtDNA was found often in post menopausal cancer group (P = 0.024). No difference in mtDNA content, in regards to age (p = 0.564), lymph node involvement (p = 0.673), ER (p = 0.877), PR (p = 0.763), and Her-2/neu expression (p = 0.335), was observed. Early detection of breast cancer has proved difficult and current detection methods are inadequate. In the present study, decreased mtDNA content in the peripheral blood of patients with breast cancer was strongly associated with stage I. The use of mtDNA may have diagnostic value and further studies are required to validate it as a potential biomarker for early detection of breast cancer

Deficit in DNA content relative to histones in X-irradiated HeLa cells

International Nuclear Information System (INIS)

Bases, R.; Mendez, F.; Neubort, S.

1976-01-01

The DNA and histone content of HeLa S-3 cell cultures was measured by direct mass assays 21 hours after 1000 rad of X-irradiation, when the cells were arrested in G2 phase. The nuclear DNA content of such cultures was found to be deficient (73 per cent of control values). In contrast, the synthesis of nuclear histones persisted, and the total histone content was close to 100 per cent of control values. When synchronously-growing cultures were irradiated in mid-S phase and examined 3.5 hours later in G2 phase, both DNA and histone content were equal to control values. (author)

Nuclear DNA content of the hybrid plant pathogen Phytophthora andina determined by flow cytometry.

Science.gov (United States)

Wang, Jianan; Presser, Jackson W; Goss, Erica M

2016-09-01

Phytophthora andina is a heterothallic plant pathogen of Andean solanaceous hosts and is an interspecific hybrid of P. infestans and an unknown Phytophthora species. The objective of this study was to estimate the nuclear DNA content of isolates in three clonal lineages of P. andina relative to P. infestans Twelve isolates of P. andina and six isolates of P. infestans were measured for nuclear DNA content by propidium iodide-stained flow cytometry. We found that the DNA content of P. andina was similar but slightly smaller, on average, than that of our sample of P. infestans isolates. This is consistent with P. andina being a homoploid hybrid rather than allopolyploid hybrid. Nuclear DNA content was more variable among a smaller sample of P. infestans isolates, including a putative triploid isolate from Mexico, but small differences in nuclear DNA content were also observed among P. andina isolates. Both species appear to be able to tolerate significant variation in genome size. © 2016 by The Mycological Society of America.

Nuclear DNA content variation in life history phases of the Bonnemasoniaceae (Rhodophyta).

Science.gov (United States)

Salvador Soler, Noemi; Gómez Garreta, Amelia; Ribera Siguan, Ma Antonia; Kapraun, Donald F

2014-01-01

Nuclear DNA content in gametophytes and sporophytes or the prostrate phases of the following species of Bonnemaisoniaceae (Asparagopsis armata, Asparagopsis taxiformis, Bonnemaisonia asparagoides, Bonnemaisonia clavata and Bonnemaisonia hamifera) were estimated by image analysis and static microspectrophotometry using the DNA-localizing fluorochrome DAPI (4', 6-diamidino-2-phenylindole, dilactate) and the chicken erythrocytes standard. These estimates expand on the Kew database of DNA nuclear content. DNA content values for 1C nuclei in the gametophytes (spermatia and vegetative cells) range from 0.5 pg to 0.8 pg, and for 2C nuclei in the sporophytes or the prostrate phases range from 1.15-1.7 pg. Although only the 2C and 4C values were observed in the sporophyte or the prostrate phase, in the vegetative cells of the gametophyte the values oscillated from 1C to 4C, showing the possible start of endopolyploidy. The results confirm the alternation of nuclear phases in these Bonnemaisoniaceae species, in those that have tetrasporogenesis, as well as those that have somatic meiosis. The availability of a consensus phylogenetic tree for Bonnemaisoniaceae has opened the way to determine evolutionary trends in DNA contents. Both the estimated genome sizes and the published chromosome numbers for Bonnemaisoniaceae suggest a narrow range of values consistent with the conservation of an ancestral genome.

Nuclear DNA Content Variation in Life History Phases of the Bonnemasoniaceae (Rhodophyta)

Science.gov (United States)

Salvador Soler, Noemi; Gómez Garreta, Amelia; Ribera Siguan, Mª Antonia; Kapraun, Donald F.

2014-01-01

Nuclear DNA content in gametophytes and sporophytes or the prostrate phases of the following species of Bonnemaisoniaceae (Asparagopsis armata, Asparagopsis taxiformis, Bonnemaisonia asparagoides, Bonnemaisonia clavata and Bonnemaisonia hamifera) were estimated by image analysis and static microspectrophotometry using the DNA-localizing fluorochrome DAPI (4′, 6-diamidino-2-phenylindole, dilactate) and the chicken erythrocytes standard. These estimates expand on the Kew database of DNA nuclear content. DNA content values for 1C nuclei in the gametophytes (spermatia and vegetative cells) range from 0.5 pg to 0.8 pg, and for 2C nuclei in the sporophytes or the prostrate phases range from 1.15–1.7 pg. Although only the 2C and 4C values were observed in the sporophyte or the prostrate phase, in the vegetative cells of the gametophyte the values oscillated from 1C to 4C, showing the possible start of endopolyploidy. The results confirm the alternation of nuclear phases in these Bonnemaisoniaceae species, in those that have tetrasporogenesis, as well as those that have somatic meiosis. The availability of a consensus phylogenetic tree for Bonnemaisoniaceae has opened the way to determine evolutionary trends in DNA contents. Both the estimated genome sizes and the published chromosome numbers for Bonnemaisoniaceae suggest a narrow range of values consistent with the conservation of an ancestral genome. PMID:24465835

Nuclear DNA content in 20 species of Siluriformes (Teleostei: Ostariophysi from the Neotropical region

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Paulo César Fenerich

2004-01-01

Full Text Available In the present study, 20 species of Siluriformes fish were analyzed in order to determine their nuclear DNA content and compare these data with their diploid number. In addition, the extension and importance of the changes that occurred during the process of diversification in the group of Neotropical freshwater catfish were investigated. The only species studied of the family Doradidae, Rhinodoras d'orbignyi (2n = 58, presented 3.46 ± 0.13 pg of DNA. Among the species of the family Heptapteridae, the values of nuclear DNA content and the diploid numbers ranged from 1.13 ± 0.09 pg of DNA in Pimelodella sp. (2n = 46 to 2.38 ± 0.07 pg of DNA in Imparfinis mirini (2n = 58. The family Loricariidae showed the widest variation in diploid number and nuclear DNA content values, ranging from 2n = 52 and 3.96 ± 0.22 pg of DNA in Liposarcus anisitsi to 2n = 76 and 4.90 ± 0.12 pg of DNA in Hypostomus sp. 4. In this group, two local samples of Pimelodus maculatus (Pimelodidae were analyzed, and both exhibited 2n = 56, but different nuclear DNA content values (2.68 ± 0.22 pg and 2.82 ± 0.20 pg, respectively. Among the Pseudopimelodidae species analyzed, Pseudopimelodus mangurus (2n = 54 showed 2.23 ± 0.15 pg and Microglanis cottoides (2n = 54 exhibited 2.50 ± 0.18 pg of DNA. Two species of Trichomycterus (Trichomycteridae also presented the same diploid number, 2n = 54 chromosomes, but, while the species from the Quinta stream presented a DNA content of 2.62 ± 0.19 pg, in the sample from the Capivara river this value was 2.30 ± 0.23 pg. In the analyzed species, the results showed that the changes in DNA content were frequently not followed by changes in the diploid number. This fact permits to suggest that, in addition to structural chromosome rearrangements, other mechanisms, including deletions, duplications and polyploidy, could be involved in the process of species differentiation in the representatives of the fish order Siluriformes.

Prognostic significance of DNA content in stage I adenocarcinoma of the lung

International Nuclear Information System (INIS)

Roberts, Heidi L.; Komaki, Ritsuko; Allen, Pamela; El-Naggar, Adel K.

1998-01-01

Purpose: Up to 30% of lung cancers (Stage I) with the most favorable outcome recur within 5 years after surgery. This study reviews the pattern of failure after surgical resection in early lung cancers and determines whether flow cytometric DNA variables were prognostic indicators for survival, disease-free survival (DFS), or distant metastasis-free survival (DMFS). Methods and Materials: Pathologic specimens from 45 patients at The University of Texas M. D. Anderson Cancer Center who underwent surgical resection and mediastinal nodal dissection for stage I (AJCC) adenocarcinomas of the lung were analyzed by flow cytometry for DNA content. Survival was calculated by the method of Desu and Lee. Chi-square and cross tabulation were used in the analysis. Results: The mean age of the patients was 62 years, and 52.3% were male. All patients were clinical Stage I (T1-2 N0), Karnofsky performance status ≥70, and had a weight loss <10 lbs. Median overall survival (OS) and DFS were 50 months and 33 months, respectively. OS, DFS, and DMFS at 1, 3 and 5 years were 73%, 57%, and 35%; 63%, 53%, and 45%; and 67%, 56%, and 48%, respectively. Analysis of all 45 patients revealed 86% of patients developing brain metastasis had an abnormal DNA content ≥ 30%, whereas 4% of patients with brain metastasis had abnormal DNA content < 30% (p = 0.01). This correlation maintained significance when only pT1/2 lesions were analyzed. There was a significant statistical correlation between abnormal DNA and 5-year OS, with 74% OS for those with abnormal DNA < 30% vs. 42% for ≥ 30% (p = 0.036). The 5-year DFS for pT1/2 patients was significantly correlated with abnormal DNA content: 53% for patients with abnormal DNA < 30% vs. 17% for patients with abnormal DNA ≥ 30%, respectively (p = 0.03). Of those with %S fraction (%S) < 2, 13% failed locally compared to 41% of those with %S ≥ 2. There was a highly significant correlation between DNA index (DNAI) and aneuploid %S: 68% of patients

Beacon satellite studies and modelling of total electron contents of the ionosphere

International Nuclear Information System (INIS)

Tyagi, T.R.

1990-01-01

An attempt is made to highlight some of the beacon satellite studies, particularly those relating to total electron content (TEC) and scintillations, with special attention to Indian subcontinent observations. The modelling of TEC is described. The scope of new experiments for specific problem is indicated. (author). 78 refs., 12 figs

Growth regulators, DNA content and anatomy in vitro -cultivated ...

African Journals Online (AJOL)

Growth regulators, DNA content and anatomy in vitro -cultivated Curcuma longa ... Shoots were inoculated in MS culture medium with the addition of 30 g/L of sucrose ... flow cytometry, utilizing two reference standards, green pea, and tomato.

Different AT-rich satellite DNAs in Cucurbita pepo and Cucurbita maxima.

Science.gov (United States)

Ganal, M; Hemleben, V

1986-11-01

The AT-rich highly repeated satellite DNA of Cucurbita pepo (zucchini) and Cucurbita maxima (pumpkin) were cloned and their DNA structure was investigated. DNA sequencing revealed that the repeat length of satellite DNA in Cucurbita pepo is 349-352 base pairs. The percentage of AT-base pairs is about 61%. This satellite is highly conserved in restriction enzyme pattern and DNA sequence; sequence heterogeneity is about 10%. In contrast, the satellite DNA of Cucurbita maxima has a repeat length of 168-169 base pairs. This satellite is also rich in AT-base pairs (64%), existing in at least three different variants as revealed by restriction enzyme analysis and DNA sequencing. The sequence heterogeneity between these variants is about 15%. The two satellite DNAs showed no cross-hybridization to each other and sequence homology is only limited. Nevertheless, we found in the C. pepo genome a high amount of sequences resembling the satellite of C. maxima. In contrast, the satellite repeat of C. pepo is found in the C. maxima DNA only in a few copies. These observations were discussed with respect to satellite DNA evolution and compared to the data received from monocotyledonous species.

Microstructure and ultrastructure of alfalfa seeds with different moisture contents after satellite carrying

International Nuclear Information System (INIS)

Feng Peng; Li Jian; Zhang Yunwei; Liu Ruohan

2009-01-01

Seeds with different moisture contents (9%, 11%, 13%, 15%, 17%) of Medicago sativa L. cv. Zhongmu No. 1 were boarded on the Shijian-8 satellite and then the microscopic and ultrastructure were observed. The results showed that spongy tissue and leaf palisade of plant after space flight were different to their control. The impact of on spongy cells was more obvious than the palisade cells; greater chloroplasts, empty and crack overflow mitochondria were observed. More starch grain were found at the samples cultured from 15% and 17% moisture content treatment, which was analyzed that starch grains in leaf cell was affected by the moisture content of seeds. (authors)

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

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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.

Nuclear DNA content variation among central European Koeleria taxa

Czech Academy of Sciences Publication Activity Database

Pečinka, A.; Suchánková, Pavla; Lysák, Martin; Trávníček, B.; Doležel, Jaroslav

2006-01-01

Roč. 98, - (2006), s. 117-122 ISSN 0305-7364 R&D Projects: GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : Chromosome number * nuclear DNA content * flow cytometry Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.448, year: 2006

Genetic stock assessment of spawning arctic cisco (Coregonus autumnalis) populations by flow cytometric determination of DNA content.

Science.gov (United States)

Lockwood, S F; Bickham, J W

1991-01-01

Intraspecific variation in cellular DNA content was measured in five Coregonus autumnalis spawning populations from the Mackenzie River drainage, Canada, using flow cytometry. The rivers assayed were the Peel, Arctic Red, Mountain, Carcajou, and Liard rivers. DNA content was determined from whole blood preparations of fish from all rivers except the Carcajou, for which kidney tissue was used. DNA content measurements of kidney and blood preparations of the same fish from the Mountain River revealed statistically indistinguishable results. Mosaicism was found in blood preparations from the Peel, Arctic Red, Mountain, and Liard rivers, but was not observed in kidney tissue preparations from the Mountain or Carcajou rivers. The Liard River sample had significantly elevated mean DNA content relative to the other four samples; all other samples were statistically indistinguishable. Significant differences in mean DNA content among spawning stocks of a single species reinforces the need for adequate sample sizes of both individuals and populations when reporting "C" values for a particular species.

Significance of somatic mutations and content alteration of mitochondrial DNA in esophageal cancer

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Wang Yu-Fen

2006-04-01

Full Text Available Abstract Background The roles of mitochondria in energy metabolism, the generation of ROS, aging, and the initiation of apoptosis have implicated their importance in tumorigenesis. In this study we aim to establish the mutation spectrum and to understand the role of somatic mtDNA mutations in esophageal cancer. Methods The entire mitochondrial genome was screened for somatic mutations in 20 pairs (18 esophageal squamous cell carcinomas, one adenosquamous carcinoma and one adenocarcinoma of tumor/surrounding normal tissue of esophageal cancers, using temporal temperature gradient gel electrophoresis (TTGE, followed by direct DNA sequencing to identify the mutations. Results Fourteen somatic mtDNA mutations were identified in 55% (11/20 of tumors analyzed, including 2 novel missense mutations and a frameshift mutation in ND4L, ATP6 subunit, and ND4 genes respectively. Nine mutations (64% were in the D-loop region. Numerous germline variations were found, at least 10 of them were novel and five were missense mutations, some of them occurred in evolutionarily conserved domains. Using real-time quantitative PCR analysis, the mtDNA content was found to increase in some tumors and decrease in others. Analysis of molecular and other clinicopathological findings does not reveal significant correlation between somatic mtDNA mutations and mtDNA content, or between mtDNA content and metastatic status. Conclusion Our results demonstrate that somatic mtDNA mutations in esophageal cancers are frequent. Some missense and frameshift mutations may play an important role in the tumorigenesis of esophageal carcinoma. More extensive biochemical and molecular studies will be necessary to determine the pathological significance of these somatic mutations.

Characterization of Satellite DNA Sequences from the Commercially Important Marine Rotifers Brachionus rotundiformis and Brachionus plicatilis.

Science.gov (United States)

Boehm; Gibson; Lubzens

2000-01-01

This study was initiated to search for species-specific and strain-specific satellite DNA sequences for which oligonucleotide primers could be designed to differentiate between various commercially important strains of the marine monogonont rotifers Brachionus rotundiformis and Brachionus plicatilis. Two unrelated, highly reiterated satellite sequences were cloned and characterized. The eight sequenced monomers from B. rotundiformis and six from B. plicatilis had low intrarepeat variability and were similar in their overall lengths, A + T compositions, and high degrees of repeated motif substructure. However, hybridizations to 19 representative strains, sequence characterizations, and GenBank searches indicated that these two satellites are morphotype-specific and population-specific, respectively, and share little homology to each other or to other characterized sequences in the database. Primer pairs designed for the B. rotundiformis satellite confirmed hybridization specificities on polymerase chain reaction and could serve as a useful molecular diagnostic tool to identify strains belonging to the SS morphotype, which are gaining widespread usage as first feeds for marine fish in commercial production.

Evaluation of DNA bending models in their capacity to predict electrophoretic migration anomalies of satellite DNA sequences.

Science.gov (United States)

Matyášek, Roman; Fulneček, Jaroslav; Kovařík, Aleš

2013-09-01

DNA containing a sequence that generates a local curvature exhibits a pronounced retardation in electrophoretic mobility. Various theoretical models have been proposed to explain relationship between DNA structural features and migration anomaly. Here, we studied the capacity of 15 static wedge-bending models to predict electrophoretic behavior of 69 satellite monomers derived from four divergent families. All monomers exhibited retarded mobility in PAGE corresponding to retardation factors ranging 1.02-1.54. The curvature varied both within and across the groups and correlated with the number, position, and lengths of A-tracts. Two dinucleotide models provided strong correlation between gel mobility and curvature prediction; two trinucleotide models were satisfactory while remaining dinucleotide models provided intermediate results with reliable prediction for subsets of sequences only. In some cases, similarly shaped molecules exhibited relatively large differences in mobility and vice versa. Generally less accurate predictions were obtained in groups containing less homogeneous sequences possessing distinct structural features. In conclusion, relatively universal theoretical models were identified suitable for the analysis of natural sequences known to harbor relatively moderate curvature. These models could be potentially applied to genome wide studies. However, in silico predictions should be viewed in context of experimental measurement of intrinsic DNA curvature. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SDSS-IV MaNGA: Uncovering the Angular Momentum Content of Central and Satellite Early-type Galaxies

Science.gov (United States)

Greene, J. E.; Leauthaud, A.; Emsellem, E.; Ge, J.; Aragón-Salamanca, A.; Greco, J.; Lin, Y.-T.; Mao, S.; Masters, K.; Merrifield, M.; More, S.; Okabe, N.; Schneider, D. P.; Thomas, D.; Wake, D. A.; Pan, K.; Bizyaev, D.; Oravetz, D.; Simmons, A.; Yan, R.; van den Bosch, F.

2018-01-01

We study 379 central and 159 satellite early-type galaxies with two-dimensional kinematics from the integral-field survey Mapping Nearby Galaxies at APO (MaNGA) to determine how their angular momentum content depends on stellar and halo mass. Using the Yang et al. group catalog, we identify central and satellite galaxies in groups with halo masses in the range {10}12.5 {h}-1 {M}ȯ {10}11 {h}-2 {M}ȯ tend to have very little rotation, while nearly all galaxies at lower mass show some net rotation. The ∼30% of high-mass galaxies that have significant rotation do not stand out in other galaxy properties, except for a higher incidence of ionized gas emission. Our data are consistent with recent simulation results suggesting that major merging and gas accretion have more impact on the rotational support of lower-mass galaxies. When carefully matching the stellar mass distributions, we find no residual differences in angular momentum content between satellite and central galaxies at the 20% level. Similarly, at fixed mass, galaxies have consistent rotation properties across a wide range of halo mass. However, we find that errors in classification of central and satellite galaxies with group finders systematically lower differences between satellite and central galaxies at a level that is comparable to current measurement uncertainties. To improve constraints, the impact of group-finding methods will have to be forward-modeled via mock catalogs.

Karyotype and nuclear DNA content of Trichomycterus areolatus (Siluriformes, Trichomycteridae

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Nelson Colihueque

2006-01-01

Full Text Available Cytogenetic analysis of Trichomycterus areolatus, collected from the Tijeral and Huilma Rivers in southern Chile has shown a diploid chromosome number of 2n = 54, a fundamental number of FN = 106, and a karyotypic formula of 44m + 8sm + 2st. Intra-individual polymorphism of chromosome number (2n = 54, 55 and 56 in specimens from the Huilma River has also been documented, providing further evidence of the occurrence of this phenomenon in Trichomycterus. The karyotype exhibited large chromosome pairs: metacentric pairs 1 (relative length 7.54%, 2 (5.75% and 3 (5.09%, submetacentric pair 23 (5.25%, and subtelocentic pair 27 (5.28%. Nuclear DNA content analysis showed an average value of 5.04 ± 1.09 pg/nucleus. This DNA content is higher than the mean value described for other species in this genus.

Updating the maize karyotype by chromosome DNA sizing

Science.gov (United States)

2018-01-01

The karyotype is a basic concept regarding the genome, fundamentally described by the number and morphological features of all chromosomes. Chromosome class, centromeric index, intra- and interchromosomal asymmetry index, and constriction localization are important in clinical, systematic and evolutionary approaches. In spite of the advances in karyotype characterization made over the last years, new data about the chromosomes can be generated from quantitative methods, such as image cytometry. Therefore, using Zea mays L., this study aimed to update the species’ karyotype by supplementing information on chromosome DNA sizing. After adjustment of the procedures, chromosome morphometry and class as well as knob localization enabled describing the Z. mays karyotype. In addition, applying image cytometry, DNA sizing was unprecedentedly measured for the arms and satellite of all chromosomes. This way, unambiguous identification of the chromosome pairs, and hence the assembly of 51 karyograms, were only possible after the DNA sizing of each chromosome, their arms and satellite portions. These accurate, quantitative and reproducible data also enabled determining the distribution and variation of DNA content in each chromosome. From this, a correlation between DNA amount and total chromosome length evidenced that the mean DNA content of chromosome 9 was higher than that of chromosome 8. The chromosomal DNA sizing updated the Z. mays karyotype, providing insights into its dynamic genome with regards to the organization of the ten chromosomes and their respective portions. Considering the results and the relevance of cytogenetics in the current scenario of comparative sequencing and genomics, chromosomal DNA sizing should be incorporated as an additional parameter for karyotype definition. Based on this study, it can be affirmed that cytogenetic approaches go beyond the simple morphological description of chromosomes. PMID:29293613

Human artificial chromosomes with alpha satellite-based de novo centromeres show increased frequency of nondisjunction and anaphase lag.

Science.gov (United States)

Rudd, M Katharine; Mays, Robert W; Schwartz, Stuart; Willard, Huntington F

2003-11-01

Human artificial chromosomes have been used to model requirements for human chromosome segregation and to explore the nature of sequences competent for centromere function. Normal human centromeres require specialized chromatin that consists of alpha satellite DNA complexed with epigenetically modified histones and centromere-specific proteins. While several types of alpha satellite DNA have been used to assemble de novo centromeres in artificial chromosome assays, the extent to which they fully recapitulate normal centromere function has not been explored. Here, we have used two kinds of alpha satellite DNA, DXZ1 (from the X chromosome) and D17Z1 (from chromosome 17), to generate human artificial chromosomes. Although artificial chromosomes are mitotically stable over many months in culture, when we examined their segregation in individual cell divisions using an anaphase assay, artificial chromosomes exhibited more segregation errors than natural human chromosomes (P artificial chromosomes missegregate over a fivefold range, the data suggest that variable centromeric DNA content and/or epigenetic assembly can influence the mitotic behavior of artificial chromosomes.

Cytological study of DNA content and nuclear morphometric analysis for aid in the diagnosis of high-grade dysplasia within oral leukoplakia.

Science.gov (United States)

Yang, Xi; Xiao, Xuan; Wu, Wenyan; Shen, Xuemin; Zhou, Zengtong; Liu, Wei; Shi, Linjun

2017-09-01

To quantitatively examine the DNA content and nuclear morphometric status of oral leukoplakia (OL) and investigate its association with the degree of dysplasia in a cytologic study. Oral cytobrush biopsy was carried out to obtain exfoliative epithelial cells from lesions before scalpel biopsy at the same location in a blinded series of 70 patients with OL. Analysis of nuclear morphometry and DNA content status using image cytometry was performed with oral smears stained with the Feulgen-thionin method. Nuclear morphometric analysis revealed significant differences in DNA content amount, DNA index, nuclear area, nuclear radius, nuclear intensity, sphericity, entropy, and fractal dimension (all P content analysis identified 34 patients with OL (48.6%) with DNA content abnormality. Nonhomogeneous lesion (P = .018) and high-grade dysplasia (P = .008) were significantly associated with abnormal DNA content. Importantly, the positive correlation between the degree of oral dysplasia and DNA content status was significant (P = .004, correlation coefficient = 0.342). Cytology analysis of DNA content and nuclear morphometric status using image cytometry may support their use as a screening and monitoring tool for OL progression. Copyright © 2017 Elsevier Inc. All rights reserved.

A prototype method for diagnosing high ice water content probability using satellite imager data

Science.gov (United States)

Yost, Christopher R.; Bedka, Kristopher M.; Minnis, Patrick; Nguyen, Louis; Strapp, J. Walter; Palikonda, Rabindra; Khlopenkov, Konstantin; Spangenberg, Douglas; Smith, William L., Jr.; Protat, Alain; Delanoe, Julien

2018-03-01

Recent studies have found that ingestion of high mass concentrations of ice particles in regions of deep convective storms, with radar reflectivity considered safe for aircraft penetration, can adversely impact aircraft engine performance. Previous aviation industry studies have used the term high ice water content (HIWC) to define such conditions. Three airborne field campaigns were conducted in 2014 and 2015 to better understand how HIWC is distributed in deep convection, both as a function of altitude and proximity to convective updraft regions, and to facilitate development of new methods for detecting HIWC conditions, in addition to many other research and regulatory goals. This paper describes a prototype method for detecting HIWC conditions using geostationary (GEO) satellite imager data coupled with in situ total water content (TWC) observations collected during the flight campaigns. Three satellite-derived parameters were determined to be most useful for determining HIWC probability: (1) the horizontal proximity of the aircraft to the nearest overshooting convective updraft or textured anvil cloud, (2) tropopause-relative infrared brightness temperature, and (3) daytime-only cloud optical depth. Statistical fits between collocated TWC and GEO satellite parameters were used to determine the membership functions for the fuzzy logic derivation of HIWC probability. The products were demonstrated using data from several campaign flights and validated using a subset of the satellite-aircraft collocation database. The daytime HIWC probability was found to agree quite well with TWC time trends and identified extreme TWC events with high probability. Discrimination of HIWC was more challenging at night with IR-only information. The products show the greatest capability for discriminating TWC ≥ 0.5 g m-3. Product validation remains challenging due to vertical TWC uncertainties and the typically coarse spatio-temporal resolution of the GEO data.

Differentiation of the guinea pig eye: nuclear ultrastructure, template activity and DNA content

International Nuclear Information System (INIS)

Schmalenberger, B.

1980-01-01

Nuclei of various cell types in the eye of embryonal and adult Guinea pigs were studied by means of electron microscopy, cytophotometry and autoradiography. Striking differences in condensation and arrangement of chromatin were found between the different tissues and cells. Several nuclear types were analyzed quantitatively with regard to their content of condensed and decondensed chromatin by means of electron microscopic morphometry. Structural differences in chromatin organization coincided with different nuclear DNA contents in various cell types of the retina, such as bipolar cells, Mueller cells, rods and cones, and the pigmented epithelium. The differences between DNA-Feulgen means obtained by cytophotometric analysis were highly significant. Template activity as shown by 3 H-uridine incorporation made evident than the rate of RNA synthesis is positively correlated with the quantity of decondensed chromatin. It is speculated that differentiation of the Guinea pig eye involves differential DNA synthesis, and that the extra-DNA could have some ''trigger'' function for the pattern of chromatin condensation and thus the pattern of gene expression. (author)

Nuclear DNA content of the pigeon orchid (Dendrobium crumenatum Sw. with the analysis of flow cytometry

Directory of Open Access Journals (Sweden)

Upatham Meesawat

2008-05-01

Full Text Available Nuclear DNA content for the adult plants grown in a greenhouse and in vitro young plantlets of the pigeon orchid (Dendrobium crumenatum Sw. was analyzed using flow cytometry. The resulting 2C DNA values ranged from 2.30±0.14 pgto 2.43±0.06 pg. However, nuclear DNA ploidy levels of long-term in vitro plantlets were found to be triploid and tetraploid.These ploidy levels were confirmed by chromosome counting. Tetraploid individuals (2n = 4x = 76 had approximately two times DNA content than diploid (2n = 2x = 38 individuals. This variation may be due to prolonged cultivation and thepresence of exogenous plant growth regulators.

Alterations of DNA content in human endometrial stromal cells transfected with a temperature-sensitive SV40: tetraploidization and physiological consequences.

Science.gov (United States)

Rinehart, C A; Mayben, J P; Butler, T D; Haskill, J S; Kaufman, D G

1992-01-01

The normal genomic stability of human cells is reversed during neoplastic transformation. The SV40 large T antigen alters the DNA content in human endometrial stromal cells in a manner that relates to neoplastic progression. Human endometrial stromal cells were transfected with a plasmid containing the A209 temperature-sensitive mutant of SV40 (tsSV40), which is also defective in the viral origin of replication. Ninety-seven clonal transfectants from seven different primary cell strains were isolated. Initial analysis revealed that 20% of the clonal populations (19/97) had an apparent diploid DNA content, 35% (34/97) had an apparent tetraploid DNA content, and the remainder were mixed populations of diploid and tetraploid cells. No aneuploid populations were observed. Diploid tsSV40 transformed cells always give rise to a population of cells with a tetraploid DNA content when continuously cultured at the permissive temperature. The doubling of DNA content can be vastly accelerated by the sudden reintroduction of large T antigen activity following a shift from non-permissive to permissive temperature. Tetraploid tsSV40 transfected cells have a lower capacity for anchorage-independent growth and earlier entry into 'crisis' than diploid cells. These results indicate that during the pre-crisis, extended lifespan phase of growth, the SV40 large T antigen causes a doubling of DNA content. This apparent doubling of DNA content does not confer growth advantage during the extended lifespan that precedes 'crisis'.

Content of DNA in cancerous tumours of the breast before and after large-fractionated irradiation

Energy Technology Data Exchange (ETDEWEB)

Shiukashvili, N N

1976-07-01

The article presents the results of microspectrophotometric investigation of DNA in different cancerous tumors of the breast gland before and after large-fractionated irradiation. The study of quantitative content of DNA in the non-irradiated tumors of the breast of different histological structure showed that parenchymatous cells are characterized by a definite variety in the DNA content with a different level of their polyploidy. This points to the fact that different histological forms of the breast cancer are distinguished by the character of the components differentiation. The comparative assessment of the ploidity of the cancerous cells of irradiated and non-irradiated tumors revealed that under the changed conditions of co-existence in all histological forms of cancer new modal classes of the cells develop and general quantity of the DNA content decreases. This testifies to the fact that the histological forms of the breast cancer are not equal sensitive tumors. A microspectrophotometric study of the breast tumors makes it possible to reveal the injury of the malignant tumor cells in the initial period of irradiation, when it is difficult to discover clear-cut dystrophical changes during histological investigation.

99Tcm-MIBI imaging in diagnosing benign/malign pulmonary disease and analysis of lung cancer DNA content

International Nuclear Information System (INIS)

Feng Yanlin; Tan Jiaju; Yang Jie; Zhu Zheng; Yu Fengwen; He Xiaohong; Huang Kemin; Yuan Baihong; Su Shaodi

2002-01-01

Objective: To evaluate the value of 99 Tc m -methoxyisobutylisonitrile (MIBI) lung imaging in diagnosing benign/malign pulmonary disease and the relation of 99 Tc m -MIBI uptake ratio (UR) with lung cancer DNA content. Methods: Early and delay imaging were performed on 27 cases of benign lung disease and 46 cases of malign lung disease. Visual analysis of the images and T/N uptake ratio measurement were performed on every case. Cancer cell DNA content and DNA index (DI) were measured in 24 cases of malign pulmonary disease. Results: The delay phase UR was 1.13 ± 0.19 in benign disease group, and the delay phase UR was 1.45 ± 0.21 in malign disease group (t6.51, P 99 Tc m -MIBI is not an ideal imaging agent for differentiating pulmonary benign/malign disease. Lung cancer DNA content may be reflected by delay phase UR

Investigations on the influence of radiation with variable linear energy transfer (LET) on the DNA-content and DNA-repair-mechanisms in Vicia faba

International Nuclear Information System (INIS)

Eckl, P.

1981-01-01

This study was initiated to investigate, whether there are any radiation-induced changes in DNA-content and if these changes can be repaired. Seeds of Vicia faba L. were grown in glass culture vessels. After 10 to 20 days the seedings were irradiated using a 1 C1 60 Co gammasource (90mrad/h and 33 rad/h) and a 5 mCi 252 Cf neutronsource (90 mrad/h). Both, neutron and gamma irradiation cause a reduction in nuclear DNA-content even after low doses (1 to 10 rad). The extent of depression is only depending on linear energy transfer. Parallel to the induced minimum in DNA-content, but shifted to higher doses, also the mitotic activity reaches a minimum. Whereas neutron irradiation results in a total stop after doses of 8 rad, gamma-irradiation only induces a depression of 80 %. Whith higher doses the mitotic activity increases again. The neutron-induced changes in DNA-content seem to be restored within 90 minutes after irradiation. No continuous increase could be found after low gamma-doses. Gamma-irradiation with higher dose rates ( 60 Co, 33 rad/h) causes a general decrease over the dose-range studied (100 to 1600 rad). Following doses of 100 rad the mitotic activity increases significantly. With higher doses the decrease is exponential. A dose-dependent mitotic delay could also be observed. As described by many authors, unscheduled DNA-synthesis (UDS) could not be detected in nuclei of Vicia faba. This indicates that an other system, perhaps acting in situ - at the damaged place - is responsible for the repair of radiation-induced thymine-damages. (Author)

Detection of minor and major satellite DNA in cytokinesis-blocked mouse splenocytes by a PRINS tandem labelling approach.

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Russo, A; Tommasi, A M; Renzi, L

1996-11-01

A protocol for the simultaneous visualization of minor and major satellite DNA by primed in situ DNA synthesis (PRINS) was developed in cytokinesis-blocked murine splenocytes. After individuation of optimal experimental conditions, a micronucleus (MN) test was carried out by treating splenocytes in vitro with the clastogenic agent mitomycin C and the aneugenic compound Colcemid. It was found that PRINS gives highly reproducible results, also comparable with the literature on MN results obtained by fluorescent in situ hybridization (FISH). Therefore the PRINS methodology may be proposed as a fast alternative to FISH for the characterization of induced MN.

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.

Histogram score contributes for reliability of DNA content estimatives in Brachiaria spp Notas do histograma contribuem para a confiabilidade das estimativas do conteúdo de DNA de Brachiaria spp

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Ana Luiza de Oliveira Timbó

2012-12-01

Full Text Available Flow cytometry allows to estimate the DNA content of a large number of plants quickly. However, inadequate protocols can compromise the reliability of these estimates leading to variations in the values of DNA content the same species. The objective of this study was to propose an efficient protocol to estimate the DNA content of Brachiaria spp. genotypes with different ploidy levels using flow cytometry. We evaluated four genotypes (B. ruziziensis diploid and artificially tetraploidized; a tetraploid B. brizantha and a natural triploid hybrid, three buffer solutions (MgSO4, Galbraith and Tris-HCl and three species as internal reference standards (Raphanus sativus, Solanum lycopersicum e Pisum sativum. The variables measured were: histogram score (1-5, coefficient of variation and estimation of DNA content. The best combination for the analysis of Brachiaria spp. DNA content was the use of MgSO4 buffer with R. sativus as a internal reference standard. Genome sizes expressed in picograms of DNA are presented for all genotypes and the importance of the histogram score on the results reliability of DNA content analyses were discussed.A citometria de fluxo permite estimar o conteúdo de DNA de um grande número de plantas rapidamente. No entanto, protocolos inadequados podem comprometer a confiabilidade dessas estimativas, levando a variações nos valores de conteúdo de DNA para uma mesma espécie. Neste trabalho, objetivou-se propor um protocolo eficiente para a estimativa do conteúdo de DNA de genótipos de Brachiaria spp. com diferentes níveis de ploidia, utilizando a citometria de fluxo. Foram avaliados quatro genótipos (B. ruziziensis, diploide e tetraploidizada artificialmente; B. brizantha tetraploide e um híbrido natural triploide, 3 soluções tampões (MgSO4, Galbraith e Tris-HCl e três espécies como padrões de referência interno (Raphanus sativus, Solanum lycopersicum e Pisum sativum. As variáveis mensuradas foram: nota do

TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence.

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Fortin, Connor H; Schulze, Katharina V; Babbitt, Gregory A

2015-01-01

It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence logos plots are severely limited in that they convey no explicit information regarding the structural dynamics of DNA backbone, a feature often critical to binding specificity. We present TRX-LOGOS, an R software package and Perl wrapper code that interfaces the JASPAR database for computational regulatory genomics. TRX-LOGOS extends the traditional sequence logo plot to include Shannon information content calculated with regard to the dinucleotide-based BI-BII conformation shifts in phosphate linkages on the DNA backbone, thereby adding a visual measure of intrinsic DNA flexibility that can be critical for many DNA-protein interactions. TRX-LOGOS is available as an R graphics module offered at both SourceForge and as a download supplement at this journal. To demonstrate the general utility of TRX logo plots, we first calculated the information content for 416 Saccharomyces cerevisiae transcription factor binding sites functionally confirmed in the Yeastract database and matched to previously published yeast genomic alignments. We discovered that flanking regions contain significantly elevated information content at phosphate linkages than can be observed at nucleobases. We also examined broader transcription factor classifications defined by the JASPAR database, and discovered that many general signatures of transcription factor binding are locally more information rich at the level of DNA backbone dynamics than nucleobase sequence. We used TRX-logos in combination with MEGA 6.0 software

An association analysis between mitochondrial DNA content, G10398A polymorphism, HPV infection, and the prognosis of cervical cancer in the Chinese Han population.

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Feng, Dali; Xu, Hui; Li, Xin; Wei, Yuehua; Jiang, Huangang; Xu, Hong; Luo, Aihua; Zhou, Fuxiang

2016-04-01

The aim was to analyze quantitative (mitochondrial DNA (mtDNA) content) and qualitative (G10398A polymorphism) mtDNA alterations as well as human papillomavirus (HPV) infection in cervical cancer prognosis. One hundred and twenty-two cases of formalin-fixed paraffin-embedded cervical carcinoma specimens were collected from the Yichang Tumor Hospital and Zhongnan Hospital of Wuhan University in the recent 10 years together with medical records. A quantitative real-time PCR (RT-PCR) was used to determine the copy number of the mitochondrial DNA and HPV expression levels. G10398A polymorphism was determined by PCR-RFLP assay. The overall survival of patients with higher mtDNA content was significantly reduced compared with lower mtDNA content patients (P = 0.029). But there was no difference of prognosis between the mtDNA 10398 A allele and G allele. However, the Kaplan-Meier survival curve illustrated a significantly reduced overall survival in the patients with 10398A plus high mtDNA copy number compared with the other groups (P content compared with 10398G (P content were positively related in the younger subgroup (≤45 years) (correlation coefficient = 0.456, P = 0.022). This study indicated that mtDNA content and HPV infection status are associated with cervical cancer prognosis. High mitochondrial DNA content plus 10398 A may be a marker of poor prognosis in cervical cancer. And mtDNA variation may potentially influence the predisposition to HPV infection and cervical carcinogenesis.

Decreased Mitochondrial DNA Content in Association with Exposure to Polycyclic Aromatic Hydrocarbons in House Dust during Wintertime: From a Population Enquiry to Cell Culture

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Pieters, Nicky; Koppen, Gudrun; Smeets, Karen; Napierska, Dorota; Plusquin, Michelle; De Prins, Sofie; Van De Weghe, Hendrik; Nelen, Vera; Cox, Bianca; Cuypers, Ann; Hoet, Peter; Schoeters, Greet; Nawrot, Tim S.

2013-01-01

Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental pollutants that are formed in combustion processes. At the cellular level, exposure to PAHs causes oxidative stress and/or some of it congeners bind to DNA, which may interact with mitochondrial function. However, the influence of these pollutants on mitochondrial DNA (mtDNA) content remains largely unknown. We determined whether indoor exposure to PAHs is associated with mitochondrial damage as represented by blood mtDNA content. Blood mtDNA content (ratio mitochondrial/nuclear DNA copy number) was determined by real-time qPCR in 46 persons, both in winter and summer. Indoor PAH exposure was estimated by measuring PAHs in sedimented house dust, including 6 volatile PAHs and 8 non-volatile PAHs. Biomarkers of oxidative stress at the level of DNA and lipid peroxidation were measured. In addition to the epidemiologic enquiry, we exposed human TK6 cells during 24 h at various concentrations (range: 0 to 500 µM) of benzo(a)pyrene and determined mtDNA content. Mean blood mtDNA content averaged (±SD) 0.95±0.185. The median PAH content amounted 554.1 ng/g dust (25th–75th percentile: 390.7–767.3) and 1385ng/g dust (25th–75th percentile: 1000–1980) in winter for volatile and non-volatile PAHs respectively. Independent for gender, age, BMI and the consumption of grilled meat or fish, blood mtDNA content decreased by 9.85% (95% CI: −15.16 to −4.2; p = 0.002) for each doubling of non-volatile PAH content in the house dust in winter. The corresponding estimate for volatile PAHs was −7.3% (95% CI: −13.71 to −0.42; p = 0.04). Measurements of oxidative stress were not correlated with PAH exposure. During summer months no association was found between mtDNA content and PAH concentration. The ability of benzo(a)pyrene (range 0 µM to 500 µM) to lower mtDNA content was confirmed in vitro in human TK6 cells. Based on these findings, mtDNA content can be a target of PAH toxicity in humans

Decreased mitochondrial DNA content in association with exposure to polycyclic aromatic hydrocarbons in house dust during wintertime: from a population enquiry to cell culture.

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Nicky Pieters

Full Text Available Polycyclic aromatic hydrocarbons (PAHs are widespread environmental pollutants that are formed in combustion processes. At the cellular level, exposure to PAHs causes oxidative stress and/or some of it congeners bind to DNA, which may interact with mitochondrial function. However, the influence of these pollutants on mitochondrial DNA (mtDNA content remains largely unknown. We determined whether indoor exposure to PAHs is associated with mitochondrial damage as represented by blood mtDNA content. Blood mtDNA content (ratio mitochondrial/nuclear DNA copy number was determined by real-time qPCR in 46 persons, both in winter and summer. Indoor PAH exposure was estimated by measuring PAHs in sedimented house dust, including 6 volatile PAHs and 8 non-volatile PAHs. Biomarkers of oxidative stress at the level of DNA and lipid peroxidation were measured. In addition to the epidemiologic enquiry, we exposed human TK6 cells during 24 h at various concentrations (range: 0 to 500 µM of benzo(apyrene and determined mtDNA content. Mean blood mtDNA content averaged (± SD 0.95 ± 0.185. The median PAH content amounted 554.1 ng/g dust (25(th-75(th percentile: 390.7-767.3 and 1385 ng/g dust (25(th-75(th percentile: 1000-1980 in winter for volatile and non-volatile PAHs respectively. Independent for gender, age, BMI and the consumption of grilled meat or fish, blood mtDNA content decreased by 9.85% (95% CI: -15.16 to -4.2; p = 0.002 for each doubling of non-volatile PAH content in the house dust in winter. The corresponding estimate for volatile PAHs was -7.3% (95% CI: -13.71 to -0.42; p = 0.04. Measurements of oxidative stress were not correlated with PAH exposure. During summer months no association was found between mtDNA content and PAH concentration. The ability of benzo(apyrene (range 0 µM to 500 µM to lower mtDNA content was confirmed in vitro in human TK6 cells. Based on these findings, mtDNA content can be a target of PAH toxicity in humans.

Mitochondrial DNA content in embryo culture medium is significantly associated with human embryo fragmentation.

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Stigliani, S; Anserini, P; Venturini, P L; Scaruffi, P

2013-10-01

Is the amount of cell-free DNA released by human embryos into culture medium correlated with embryo morphological features? The mitochondrial DNA (mtDNA) content of culture medium is significantly associated with the fragmentation rate on Days 2 and 3 of embryo development, whether the oocyte came from women ≤ 35 or >35 years old. Cellular fragmentation is often utilized as one of the morphological parameters for embryo quality assessment. The amount of cellular fragments is considered to be an important morphological parameter for embryo implantation potential. It has been hypothesized that fragments are apoptotic bodies or anuclear cytoplasmatic pieces of blastomeres, although no definitive conclusion has been drawn about their pathogenesis. Human fertilized oocytes were individually cultured from Day 1 to Days 2 and 3. A total of 800 samples (166 spent media from Day 2 and 634 from Day 3) were enrolled into the present study. Double-stranded DNA (dsDNA) was quantified in 800 spent embryo culture media by Pico Green dye fluorescence assay. After DNA purification, genomic DNA (gDNA) and mtDNA were profiled by specific quantitative PCR. Statistical analyses defined correlations among DNA contents, embryo morphology and maternal age. Different independent tests confirmed the presence of DNA into embryo culture medium and, for the first time, we demonstrate that both gDNA and mtDNA are detectable in the secretome. The amount of DNA is larger in embryos with bad quality cleavage compared with high-grade embryos, suggesting that the DNA profile of culture medium is an objective marker for embryo quality assessment. In particular, DNA profiles are significantly associated with fragmentation feature (total dsDNA: P = 0.0010; mtDNA; P = 0.0247) and advanced maternal age. It is necessary to establish whether DNA profiling of spent embryo culture medium is a robust onsite test that can improve the prediction of blastulation, implantation and/or pregnancy rate. The

Comparative Analysis of Repetitive DNA between the Main Vectors of Chagas Disease: Triatoma infestans and Rhodnius prolixus.

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Pita, Sebastián; Mora, Pablo; Vela, Jesús; Palomeque, Teresa; Sánchez, Antonio; Panzera, Francisco; Lorite, Pedro

2018-04-24

Chagas disease or American trypanosomiasis affects six to seven million people worldwide, mostly in Latin America. This disease is transmitted by hematophagous insects known as "kissing bugs" (Hemiptera, Triatominae), with Triatoma infestans and Rhodnius prolixus being the two most important vector species. Despite the fact that both species present the same diploid chromosome number (2 n = 22), they have remarkable differences in their total DNA content, chromosome structure and genome organization. Variations in the DNA genome size are expected to be due to differences in the amount of repetitive DNA sequences. The T. infestans genome-wide analysis revealed the existence of 42 satellite DNA families. BLAST searches of these sequences against the R. prolixus genome assembly revealed that only four of these satellite DNA families are shared between both species, suggesting a great differentiation between the Triatoma and Rhodnius genomes. Fluorescence in situ hybridization (FISH) location of these repetitive DNAs in both species showed that they are dispersed on the euchromatic regions of all autosomes and the X chromosome. Regarding the Y chromosome, these common satellite DNAs are absent in T. infestans but they are present in the R. prolixus Y chromosome. These results support a different origin and/or evolution in the Y chromosome of both species.

Karyotype analysis, DNA content and molecular screening in Lippia alba (Verbenaceae

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Patrícia M.O. Pierre

2011-09-01

Full Text Available Cytogenetic analyses, of pollen viability, nuclear DNA content and RAPD markers were employed to study three chemotypes of Lippia alba (Mill. (Verbenaceae in order to understand the genetic variation among them. Different ploidy levels and mixoploid individuals were observed. This work comprises the first report of different chromosome numbers (cytotypes in L. alba. The chromosome numbers of La2-carvone and La3-linalool chemotypes suggested that they are polyploids. Flow cytometric analysis showed an increase of nuclear DNA content that was not directly proportional to ploidy level variation. A cluster analysis based on RAPD markers revealed that La3-linalool shares genetic markers with La1-citral and La2-carvone. The analysis showed that the majority of genetic variation of La3-linalool could be a consequence of ixoploidy. ur data indicates that sexual reproduction aong those three chemotypes is unlikely and suggests the beginning of reproductive isolation. The results demonstrated that chromosome analysis, nuclear DNA content estimation and RAPD markers constitute excellent tools for detecting genetic variation among L. alba chemotypes.Análises citogenéticas, de viabilidade do pólen, do conteúdo de DNA nuclear e marcadores RAPD foram empregadas no estudo de três quimiotipos de Lippia alba (Mill. (Verbenaceae visando contribuir para o entendimento da variação genética entre os mesmos. Diferentes níveis de ploidia e indivíduos mixoploides foram observados. Este trabalho compreende o primeiro relato de diferentes números cromossômicos (citótipos em L. alba. Os números cromossômicos dos quimiotipos La2-carvona e La3-linalol sugere que eles seja poliploides. A análise da citometria de fluxo mostrou um aumento do conteúdo de DNA nuclear que não foi diretamente proporcional à variação no nível de ploidia. A análise de agrupamento baseada nos marcadores RAPD demonstrou que La3-linalol compartilha marcadores genéticos com La1

Mitochondrial DNA and STR analyses for human DNA from maggots crop contents: a forensic entomology case from central-southern China.

Science.gov (United States)

Li, X; Cai, J F; Guo, Y D; Xiong, F; Zhang, L; Feng, H; Meng, F M; Fu, Y; Li, J B; Chen, Y Q

2011-08-01

Insect larvae and adult insects found on human corpses can provide important forensic evidence however it is useful to be able to prove evidence of association. Without this, it could be claimed that the insect evidence was a contaminant or had been planted on the body. This paper describes how mitochondrial DNA (mtDNA) and STR analysis of the crop contents of larvae of the blowfly Aldrichina grahami collected from separated body parts was used to provide evidence of association.

Prenatal Ambient Air Pollution, Placental Mitochondrial DNA Content, and Birth Weight in the INMA (Spain) and ENVIRONAGE (Belgium) Birth Cohorts

Science.gov (United States)

Clemente, Diana B.P.; Casas, Maribel; Vilahur, Nadia; Begiristain, Haizea; Bustamante, Mariona; Carsin, Anne-Elie; Fernández, Mariana F.; Fierens, Frans; Gyselaers, Wilfried; Iñiguez, Carmen; Janssen, Bram G.; Lefebvre, Wouter; Llop, Sabrina; Olea, Nicolás; Pedersen, Marie; Pieters, Nicky; Santa Marina, Loreto; Souto, Ana; Tardón, Adonina; Vanpoucke, Charlotte; Vrijheid, Martine; Sunyer, Jordi; Nawrot, Tim S.

2015-01-01

Background: Mitochondria are sensitive to environmental toxicants due to their lack of repair capacity. Changes in mitochondrial DNA (mtDNA) content may represent a biologically relevant intermediate outcome in mechanisms linking air pollution and fetal growth restriction. Objective: We investigated whether placental mtDNA content is a possible mediator of the association between prenatal nitrogen dioxide (NO2) exposure and birth weight. Methods: We used data from two independent European cohorts: INMA (n = 376; Spain) and ENVIRONAGE (n = 550; Belgium). Relative placental mtDNA content was determined as the ratio of two mitochondrial genes (MT-ND1 and MTF3212/R3319) to two control genes (RPLP0 and ACTB). Effect estimates for individual cohorts and the pooled data set were calculated using multiple linear regression and mixed models. We also performed a mediation analysis. Results: Pooled estimates indicated that a 10-μg/m3 increment in average NO2 exposure during pregnancy was associated with a 4.9% decrease in placental mtDNA content (95% CI: –9.3, –0.3%) and a 48-g decrease (95% CI: –87, –9 g) in birth weight. However, the association with birth weight was significant for INMA (–66 g; 95% CI: –111, –23 g) but not for ENVIRONAGE (–20 g; 95% CI: –101, 62 g). Placental mtDNA content was associated with significantly higher mean birth weight (pooled analysis, interquartile range increase: 140 g; 95% CI: 43, 237 g). Mediation analysis estimates, which were derived for the INMA cohort only, suggested that 10% (95% CI: 6.6, 13.0 g) of the association between prenatal NO2 and birth weight was mediated by changes in placental mtDNA content. Conclusion: Our results suggest that mtDNA content can be one of the potential mediators of the association between prenatal air pollution exposure and birth weight. Citation: Clemente DB, Casas M, Vilahur N, Begiristain H, Bustamante M, Carsin AE, Fernández MF, Fierens F, Gyselaers W, Iñiguez C, Janssen BG

Cytometric analysis of mammalian sperm for induced morphologic and DNA content errors

International Nuclear Information System (INIS)

Pinkel, D.

1983-01-01

Some flow-cytometric and image analysis procedures under development for quantitative analysis of sperm morphology are reviewed. The results of flow-cytometric DNA-content measurements on sperm from radiation exposed mice are also summarized, the results related to the available cytological information, and their potential dosimetric sensitivity discussed

Raman study of CaDNA films as a function of water content and excess CaCl2 concentration: Stability of the B conformation.

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Schwenker, Megan; Marlowe, Robert; Lee, Scott; Rupprecht, Allan

2006-03-01

Highly oriented, wet-spun films of CaDNA expand in the direction perpendicular to the helical axis as the hydration of the film is increased. CaDNA films with a high CaCl2 content show an unexpected shrinkage at a relative humidity of about 93%. We have performed Raman experiments on CaDNA films as a function of both water content and excess CaCl2 concentration in order to determine if this unexpected shrinkage might be related to a conformational transition of the DNA molecules. We find that the DNA molecules remain in the B conformation for all salt contents down to a relative humidity of 59%.

[A study on the relationship between postmortem interval and the changes of DNA content in the kidney cellule of rat].

Science.gov (United States)

Liu, L; Peng, D B; Liu, Y; Deng, W N; Liu, Y L; Li, J J

2001-05-01

To study changes of DNA content in the kidney cellule of rats and relationship with the postmortem interval. This experiment chose seven parameter of cell nuclear, including the area and integral optical density, determined the changes of DNA content in the kidney cellule of 15 rats at different intervals between 0 and 48 h postmortem with auto-TV-image system. The degradation rate of DNA in nuclear has a certainty relationship to early PMI(in 48 h) of rat, and get binomial regress equation. Determining the quantity of DNA in nuclear should be an objective and exact way to estimate the PMI.

Comparison of mapped and measured total ionospheric electron content using global positioning system and beacon satellite observations

International Nuclear Information System (INIS)

Lanyi, G.E.; Roth, T.

1988-01-01

Total ionospheric electron contents (TEC) were measured by global positioning system (GPS) dual-frequency receivers developed by the Jet Propulsion Laboratory. The measurements included P-code (precise ranging code) and carrier phase data for six GPS satellites during multiple five-hour observing sessions. A set of these GPS TEC measurements were mapped from the GPS lines of sight to the line of sight of a Faraday beacon satellite by statistically fitting the TEC data to a simple model of the ionosphere. The mapped GPS TEC values were compared with the Faraday rotation measurements. Because GPS transmitter offsets are different for each satellite and because some GPS receiver offsets were uncalibrated, the sums of the satellite and receiver offsets were estimated simultaneously with the TEC in a least squares procedure. The accuracy of this estimation procedure is evaluated indicating that the error of the GPS-determined line of sight TEC can be at or below 1 x 10 to the 16th el/sq cm. Consequently, the current level of accuracy is comparable to the Faraday rotation technique; however, GPS provides superior sky coverage. 15 references

Similarity of satellite DNA properties in the order Rodentia

Energy Technology Data Exchange (ETDEWEB)

Mazrimas, J A; Hatch, F T

1977-09-01

We have characterized satellite DNAs from 9 species of kangaroo rat (Dipodomys) and have shown that the HS-..cap alpha.. and HS-..beta.. satellites, where present, are nearly identical in all species as to melting transition midpoint (Tm), and density in neutral CsCl, alkaline CsCl, and Cs/sub 2/SO/sub 4/-Ag/sup +/ gradients. However, the MS satellites exist in two internally similar classes. The satellite DNAs from three other rodents were characterized (densities listed are in neutral CsCl). The pocket gopher, Thomomys bottae, contains Th-..cap alpha.. (1.713 g/ml) and Th-..beta.. (1.703 g/ml). The guinea pig (Cavia porcellus) contains Ca-..cap alpha.., Ca-..beta.., and Ca-..gamma.. at densities of 1.706 g/ml, 1.704 g/ml, and 1.704 g/ml, respectively. The antelope ground squirrel (Ammospermophilus harrisi) contains Am-..cap alpha.., 1.708 g/ml, Am-..beta.., 1.717 g/ml, and Am-..gamma.., 1.707 g/ml. The physical and chemical properties of the alpha-satellites from the above four rodents representing four different families in two suborders of Rodentia were compared. They show nearly identical Tm, nucleoside composition of single strands, and single strand densities in alkaline CsCl. Similar comparisons on the second or third satellite DNAs from these rodents also indicate a close relationship to each other. Thus the high degree of similarity of satellite sequences found in such a diverse group of rodents suggests a cellular function that is subject to natural selection, and implies that these sequences have been conserved over a considerable span of evolutionary time since the divergence of these rodents about 50 million years ago.

Similarity of satellite DNA properties in the order Rodentia

Energy Technology Data Exchange (ETDEWEB)

Mazrimas, J A; Hatch, F T

1977-09-01

Satellite DNAs from 9 species of kangaroo rat (Dipodomys) have been characterized and have shown that the HS-..cap alpha.. and HS-..beta.. satellites, where present, are nearly identical in all species as to melting transition midpoint (Tm), and density in neutral CsCl, alkaline CsCl, and Cs/sub 2/SO/sub 4/-Ag/sup +/ gradients. However, the MS satellites exist in two internally similar classes. The satellite DNAs from three other rodents were characterized (densities listed are in neutral CsCl). The pocket gopher, Thomomys bottae, contains Th-..cap alpha.. (1.713 g/ml) and Th..beta.. (1.703 g/ml). The guinea pig (Cavia porcellus) contains Ca-..cap alpha.., Ca-..beta.. and Ca-..gamma.. at densities of 1.706 g/ml, 1.704 g/ml and 1.704 g/ml, respectively. The antelope ground squirrel (Ammospermophilus harrisi) contains Am-..cap alpha.., 1.708 g/ml, Am-..beta.., 1.717 g/ml, and Am-..gamma.., 1.707 g/ml. The physical and chemical properties of the alpha-satellites from the above four rodents representing four different families in two suborders of Rodentia were compared. They show nearly identical Tm, nucleoside composition of single strands, and single strand densities in alkaline CsCl. Similar comparisons on the second or third satellite DNAs from these rodents also indicate a close relationship to each other. Thus the high degree of similarity of satellite sequences found in such a diverse group of rodents suggests a cellular function that is subject to natural selection, and implies that these sequences have been conserved over a considerable span of evolutionary time since the divergence of these rodents about 50 million years ago.

The Trypanosoma cruzi satellite DNA OligoC-TesT and Trypanosoma cruzi kinetoplast DNA OligoC-TesT for diagnosis of Chagas disease: a multi-cohort comparative evaluation study.

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Koen De Winne

Full Text Available BACKGROUND: The Trypanosoma cruzi satellite DNA (satDNA OligoC-TesT is a standardised PCR format for diagnosis of Chagas disease. The sensitivity of the test is lower for discrete typing unit (DTU TcI than for TcII-VI and the test has not been evaluated in chronic Chagas disease patients. METHODOLOGY/PRINCIPAL FINDINGS: We developed a new prototype of the OligoC-TesT based on kinetoplast DNA (kDNA detection. We evaluated the satDNA and kDNA OligoC-TesTs in a multi-cohort study with 187 chronic Chagas patients and 88 healthy endemic controls recruited in Argentina, Chile and Spain and 26 diseased non-endemic controls from D.R. Congo and Sudan. All specimens were tested in duplicate. The overall specificity in the controls was 99.1% (95% CI 95.2%-99.8% for the satDNA OligoC-TesT and 97.4% (95% CI 92.6%-99.1% for the kDNA OligoC-TesT. The overall sensitivity in the patients was 67.9% (95% CI 60.9%-74.2% for the satDNA OligoC-TesT and 79.1% (95% CI 72.8%-84.4% for the kDNA OligoC-Test. CONCLUSIONS/SIGNIFICANCE: Specificities of the two T. cruzi OligoC-TesT prototypes are high on non-endemic and endemic controls. Sensitivities are moderate but significantly (p = 0.0004 higher for the kDNA OligoC-TesT compared to the satDNA OligoC-TesT.

The Trypanosoma cruzi Satellite DNA OligoC-TesT and Trypanosoma cruzi Kinetoplast DNA OligoC-TesT for Diagnosis of Chagas Disease: A Multi-cohort Comparative Evaluation Study

Science.gov (United States)

De Winne, Koen; Büscher, Philippe; Luquetti, Alejandro O.; Tavares, Suelene B. N.; Oliveira, Rodrigo A.; Solari, Aldo; Zulantay, Ines; Apt, Werner; Diosque, Patricio; Monje Rumi, Mercedes; Gironès, Nuria; Fresno, Manuel; Lopez-Velez, Rogelio; Perez-Molina, José A.; Monge-Maillo, Begoña; Garcia, Lineth; Deborggraeve, Stijn

2014-01-01

Background The Trypanosoma cruzi satellite DNA (satDNA) OligoC-TesT is a standardised PCR format for diagnosis of Chagas disease. The sensitivity of the test is lower for discrete typing unit (DTU) TcI than for TcII-VI and the test has not been evaluated in chronic Chagas disease patients. Methodology/Principal Findings We developed a new prototype of the OligoC-TesT based on kinetoplast DNA (kDNA) detection. We evaluated the satDNA and kDNA OligoC-TesTs in a multi-cohort study with 187 chronic Chagas patients and 88 healthy endemic controls recruited in Argentina, Chile and Spain and 26 diseased non-endemic controls from D.R. Congo and Sudan. All specimens were tested in duplicate. The overall specificity in the controls was 99.1% (95% CI 95.2%–99.8%) for the satDNA OligoC-TesT and 97.4% (95% CI 92.6%–99.1%) for the kDNA OligoC-TesT. The overall sensitivity in the patients was 67.9% (95% CI 60.9%–74.2%) for the satDNA OligoC-TesT and 79.1% (95% CI 72.8%–84.4%) for the kDNA OligoC-Test. Conclusions/Significance Specificities of the two T. cruzi OligoC-TesT prototypes are high on non-endemic and endemic controls. Sensitivities are moderate but significantly (p = 0.0004) higher for the kDNA OligoC-TesT compared to the satDNA OligoC-TesT. PMID:24392177

NSAIDs modulate CDKN2A, TP53, and DNA content risk for progression to esophageal adenocarcinoma.

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Patricia C Galipeau

2007-02-01

Full Text Available Somatic genetic CDKN2A, TP53, and DNA content abnormalities are common in many human cancers and their precursors, including esophageal adenocarcinoma (EA and Barrett's esophagus (BE, conditions for which aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs have been proposed as possible chemopreventive agents; however, little is known about the ability of a biomarker panel to predict progression to cancer nor how NSAID use may modulate progression. We aimed to evaluate somatic genetic abnormalities with NSAIDs as predictors of EA in a prospective cohort study of patients with BE.Esophageal biopsies from 243 patients with BE were evaluated at baseline for TP53 and CDKN2A (p16 alterations, tetraploidy, and aneuploidy using sequencing; loss of heterozygosity (LOH; methylation-specific PCR; and flow cytometry. At 10 y, all abnormalities, except CDKN2A mutation and methylation, contributed to EA risk significantly by univariate analysis, ranging from 17p LOH (relative risk [RR] = 10.6; 95% confidence interval [CI] 5.2-21.3, p < 0.001 to 9p LOH (RR = 2.6; 95% CI 1.1-6.0, p = 0.03. A panel of abnormalities including 17p LOH, DNA content tetraploidy and aneuploidy, and 9p LOH was the best predictor of EA (RR = 38.7; 95% CI 10.8-138.5, p < 0.001. Patients with no baseline abnormality had a 12% 10-y cumulative EA incidence, whereas patients with 17p LOH, DNA content abnormalities, and 9p LOH had at least a 79.1% 10-y EA incidence. In patients with zero, one, two, or three baseline panel abnormalities, there was a significant trend toward EA risk reduction among NSAID users compared to nonusers (p = 0.01. The strongest protective effect was seen in participants with multiple genetic abnormalities, with NSAID nonusers having an observed 10-y EA risk of 79%, compared to 30% for NSAID users (p < 0.001.A combination of 17p LOH, 9p LOH, and DNA content abnormalities provided better EA risk prediction than any single TP53, CDKN2A, or DNA content

rDNA mapping, heterochromatin characterization and AT/GC content of Agapanthus africanus (L. Hoffmanns (Agapanthaceae

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ARYANE C. REIS

2016-01-01

Full Text Available ABSTRACT Agapanthus (Agapanthaceae has 10 species described. However, most taxonomists differ respect to this number because the great phenotypic plasticity of the species. The cytogenetic has been an important tool to aid the plant taxon identification, and to date, all taxa of Agapanthus L'Héritier studied cytologically, presented 2n = 30. Although the species possess large chromosomes, the group is karyologically little explored. This work aimed to increase the cytogenetic knowledge of Agapanthus africanus (L. Hoffmanns by utilization of chromosome banding techniques with DAPI / CMA3 and Fluorescent in situ Hybridization (FISH. In addition, flow cytometry was used for determination of DNA content and the percentage of AT / GC nitrogenous bases. Plants studied showed 2n = 30 chromosomes, ranging from 4.34 - 8.55 µm, with the karyotype formulae (KF = 10m + 5sm. Through FISH, one 45S rDNA signal was observed proximally to centromere of the chromosome 7, while for 5S rDNA sites we observed one signal proximally to centromere of chromosome 9. The 2C DNA content estimated for the species was 2C = 24.4 with 59% of AT and 41% of GC. Our data allowed important upgrade for biology and cytotaxonomy of Agapanthus africanus (L. Hoffmanns.

Determination of Ploidy Level and Nuclear DNA Content in the Droseraceae by Flow Cytometry

Czech Academy of Sciences Publication Activity Database

Hoshi, Y.; Azumatani, M.; Suyama, T.; Adamec, Lubomír

2017-01-01

Roč. 82, č. 3 (2017), s. 321-327 ISSN 0011-4545 Institutional support: RVO:67985939 Keywords : nuclear DNA content * genome size * Droseraceae Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 0.913, year: 2016

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.

New sequence-based data on the relative DNA contents of chromosomes in the normal male and female human diploid genomes for radiation molecular cytogenetics

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Repin Mikhail V

2009-06-01

Full Text Available Abstract Background The objective of this work is to obtain the correct relative DNA contents of chromosomes in the normal male and female human diploid genomes for the use at FISH analysis of radiation-induced chromosome aberrations. Results The relative DNA contents of chromosomes in the male and female human diploid genomes have been calculated from the publicly available international Human Genome Project data. New sequence-based data on the relative DNA contents of human chromosomes were compared with the data recommended by the International Atomic Energy Agency in 2001. The differences in the values of the relative DNA contents of chromosomes obtained by using different approaches for 15 human chromosomes, mainly for large chromosomes, were below 2%. For the chromosomes 13, 17, 20 and 22 the differences were above 5%. Conclusion New sequence-based data on the relative DNA contents of chromosomes in the normal male and female human diploid genomes were obtained. This approach, based on the genome sequence, can be recommended for the use in radiation molecular cytogenetics.

Correlation of DNA content and nucleomorphometric features with World Health Organization grading of meningiomas.

Science.gov (United States)

Grunewald, J P; Röhl, F W; Kirches, E; Dietzmann, K

1998-02-01

Many studies dealing with extracranial cancer showed a strong correlation of DNA ploidy to a poor clinical outcome, recurrence, or malignancy. In brain tumors, analysis of DNA content did not always provided significant diagnostic information. In this study, DNA density and karyometric parameters of 50 meningiomas (26 Grade I, 10 Grade II, 14 Grade III) were quantitatively evaluated by digital cell image analyses of Feulgen-stained nuclei. In particular, the densitometric parameter SEXT, which describes nuclear DNA content, as well as the morphometric values LENG (a computer-assisted measurement of nuclear circumference), AREA (a computer-assisted measurement of nuclear area), FCON (a parameter that describes nuclear roundness), and CONC (a describing nuclear contour), evaluated with the software IMAGE C, were correlated to World Health Organization (WHO) grading using univariate and multivariate methods. AREA and LENG values showed significant differences between tumors of Grades I and III. FCON values were unable to distinguish WHO Grade III from Grade I/II but were useful in clearly separating Grade II from Grade I tumors. CONC values detected differences between WHO Grades II and I/III tumors but not between the latter. SEXT values clearly distinguished Grade III from Grade I/II tumors. The 1c, 2c, 2.5c, and 5c exceeding rates showed no predictive values. Only the 6c exceeding rate showed a significant difference between Grades I and III. These results outline the characteristic features of the atypical (Grade II) meningiomas, which make them a recognizable tumor entity distinct from benign and anaplastic meningiomas. The combination of DNA densitometric and morphometric findings seems to be a powerful addition to the histopathologic classification of meningiomas, as suggested by the WHO.

Nuclear DNA content and base composition in 28 taxa of Musa.

Science.gov (United States)

Kamaté, K; Brown, S; Durand, P; Bureau, J M; De Nay, D; Trinh, T H

2001-08-01

The nuclear DNA content of 28 taxa of Musa was assessed by flow cytometry, using line PxPC6 of Petunia hybrida as an internal standard. The 2C DNA value of Musa balbisiana (BB genome) was 1.16 pg, whereas Musa acuminata (AA genome) had an average 2C DNA value of 1.27 pg, with a difference of 11% between its subspecies. The two haploid (IC) genomes, A and B, comprising most of the edible bananas, are therefore of similar size, 0.63 pg (610 million bp) and 0.58 pg (560 million bp), respectively. The genome of diploid Musa is thus threefold that of Arabidopsis thaliana. The genome sizes in a set of triploid Musa cultivars or clones were quite different, with 2C DNA values ranging from 1.61 to 2.23 pg. Likewise, the genome sizes of tetraploid cultivars ranged from 1.94 to 2.37 pg (2C). Apparently, tetraploids (for instance, accession I.C.2) can have a genome size that falls within the range of triploid genome sizes, and vice versa (as in the case of accession Simili Radjah). The 2C values estimated for organs such as leaf, leaf sheath, rhizome, and flower were consistent, whereas root material gave atypical results, owing to browning. The genomic base composition of these Musa taxa had a median value of 40.8% GC (SD = 0.43%).

Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus.

Science.gov (United States)

Sanford, J; Forrester, L; Chapman, V; Chandley, A; Hastie, N

1984-03-26

The major and the minor satellite sequences of Mus musculus were undermethylated in both sperm and oocyte DNAs relative to the amount of undermethylation observed in adult somatic tissue DNA. This hypomethylation was specific for satellite sequences in sperm DNA. Dispersed repetitive and low copy sequences show a high degree of methylation in sperm DNA; however, a dispersed repetitive sequence was undermethylated in oocyte DNA. This finding suggests a difference in the amount of total genomic DNA methylation between sperm and oocyte DNA. The methylation levels of the minor satellite sequences did not change during spermiogenesis, and were not associated with the onset of meiosis or a specific stage in sperm development.

Chromosome numbers and DNA content in some species of Mecardonia (Gratiolae, Plantaginaceae)

Science.gov (United States)

Sosa, María M.; Angulo, María B.; Greppi, Julián A.; Bugallo, Verónica

2016-01-01

Abstract Cytogenetic characterization and determination of DNA content by flow cytometry of five species of Mecardonia Ruiz et Pavon, 1798 (Gratiolae, Plantaginaceae) was performed. This is the first study of nuclear DNA content carried out in the genus. Mitotic analysis revealed a base chromosome number x = 11 for all entities and different ploidy levels, ranging from diploid (2n = 2x = 22) to hexaploid (2n = 6x = 66). The results include the first report of the chromosome numbers for Mecardonia flagellaris (Chamisso & Schlechtendal, 1827) (2n = 22), Mecardonia grandiflora (Bentham) Pennell, 1946 (2n = 22), Mecardonia kamogawae Greppi & Hagiwara, 2011 (2n = 66), and Mecardonia sp. (2n = 44). The three ploidy levels here reported suggest that polyploidy is common in Mecardonia and appear to be an important factor in the evolution of this genus. The 2C- and 1Cx-values were also estimated in all the species. The 2C-values ranged from 1.91 to 5.29 pg. The 1Cx-values ranged from 0.88 to 1.03 pg. The general tendency indicated a decrease in the 1Cx-value with increasing ploidy level. The significance of the results is discussed in relation to taxonomy of the genus. PMID:28123693

Targeting and tracing of specific DNA sequences with dTALEs in living cells

Science.gov (United States)

Thanisch, Katharina; Schneider, Katrin; Morbitzer, Robert; Solovei, Irina; Lahaye, Thomas; Bultmann, Sebastian; Leonhardt, Heinrich

2014-01-01

Epigenetic regulation of gene expression involves, besides DNA and histone modifications, the relative positioning of DNA sequences within the nucleus. To trace specific DNA sequences in living cells, we used programmable sequence-specific DNA binding of designer transcription activator-like effectors (dTALEs). We designed a recombinant dTALE (msTALE) with variable repeat domains to specifically bind a 19-bp target sequence of major satellite DNA. The msTALE was fused with green fluorescent protein (GFP) and stably expressed in mouse embryonic stem cells. Hybridization with a major satellite probe (3D-fluorescent in situ hybridization) and co-staining for known cellular structures confirmed in vivo binding of the GFP-msTALE to major satellite DNA present at nuclear chromocenters. Dual tracing of major satellite DNA and the replication machinery throughout S-phase showed co-localization during mid to late S-phase, directly demonstrating the late replication timing of major satellite DNA. Fluorescence bleaching experiments indicated a relatively stable but still dynamic binding, with mean residence times in the range of minutes. Fluorescently labeled dTALEs open new perspectives to target and trace DNA sequences and to monitor dynamic changes in subnuclear positioning as well as interactions with functional nuclear structures during cell cycle progression and cellular differentiation. PMID:24371265

Targeting and tracing of specific DNA sequences with dTALEs in living cells.

Science.gov (United States)

Thanisch, Katharina; Schneider, Katrin; Morbitzer, Robert; Solovei, Irina; Lahaye, Thomas; Bultmann, Sebastian; Leonhardt, Heinrich

2014-04-01

Epigenetic regulation of gene expression involves, besides DNA and histone modifications, the relative positioning of DNA sequences within the nucleus. To trace specific DNA sequences in living cells, we used programmable sequence-specific DNA binding of designer transcription activator-like effectors (dTALEs). We designed a recombinant dTALE (msTALE) with variable repeat domains to specifically bind a 19-bp target sequence of major satellite DNA. The msTALE was fused with green fluorescent protein (GFP) and stably expressed in mouse embryonic stem cells. Hybridization with a major satellite probe (3D-fluorescent in situ hybridization) and co-staining for known cellular structures confirmed in vivo binding of the GFP-msTALE to major satellite DNA present at nuclear chromocenters. Dual tracing of major satellite DNA and the replication machinery throughout S-phase showed co-localization during mid to late S-phase, directly demonstrating the late replication timing of major satellite DNA. Fluorescence bleaching experiments indicated a relatively stable but still dynamic binding, with mean residence times in the range of minutes. Fluorescently labeled dTALEs open new perspectives to target and trace DNA sequences and to monitor dynamic changes in subnuclear positioning as well as interactions with functional nuclear structures during cell cycle progression and cellular differentiation.

The Emerging Trends in Satellite and Wireless Communications ...

Indian Academy of Sciences (India)

Table of contents. The Emerging Trends in Satellite and Wireless Communications Technologies · Satellite Communications · Communications Satellites for Global Coverage · Satellite Transponders · The Four Generations Of Commercial Communication Geo-Sat · PowerPoint Presentation · An Indian Scenario INSAT ...

Joint estimation of vertical total electron content (VTEC) and satellite differential code biases (SDCBs) using low-cost receivers

Science.gov (United States)

Zhang, Baocheng; Teunissen, Peter J. G.; Yuan, Yunbin; Zhang, Hongxing; Li, Min

2018-04-01

Vertical total electron content (VTEC) parameters estimated using global navigation satellite system (GNSS) data are of great interest for ionosphere sensing. Satellite differential code biases (SDCBs) account for one source of error which, if left uncorrected, can deteriorate performance of positioning, timing and other applications. The customary approach to estimate VTEC along with SDCBs from dual-frequency GNSS data, hereinafter referred to as DF approach, consists of two sequential steps. The first step seeks to retrieve ionospheric observables through the carrier-to-code leveling technique. This observable, related to the slant total electron content (STEC) along the satellite-receiver line-of-sight, is biased also by the SDCBs and the receiver differential code biases (RDCBs). By means of thin-layer ionospheric model, in the second step one is able to isolate the VTEC, the SDCBs and the RDCBs from the ionospheric observables. In this work, we present a single-frequency (SF) approach, enabling the joint estimation of VTEC and SDCBs using low-cost receivers; this approach is also based on two steps and it differs from the DF approach only in the first step, where we turn to the precise point positioning technique to retrieve from the single-frequency GNSS data the ionospheric observables, interpreted as the combination of the STEC, the SDCBs and the biased receiver clocks at the pivot epoch. Our numerical analyses clarify how SF approach performs when being applied to GPS L1 data collected by a single receiver under both calm and disturbed ionospheric conditions. The daily time series of zenith VTEC estimates has an accuracy ranging from a few tenths of a TEC unit (TECU) to approximately 2 TECU. For 73-96% of GPS satellites in view, the daily estimates of SDCBs do not deviate, in absolute value, more than 1 ns from their ground truth values published by the Centre for Orbit Determination in Europe.

Diet Assessment Based on Rumen Contents: A Comparison between DNA Metabarcoding and Macroscopy.

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Ruth V Nichols

Full Text Available Dietary choices are central to our understanding of ecology and evolution. Still, many aspects of food choice have been hampered by time consuming procedures and methodological problems. Faster and cheaper methods, such as DNA metabarcoding, have therefore been widely adopted. However, there is still very little empirical support that this new method is better and more accurate compared to the classic methods. Here, we compare DNA metabarcoding to macroscopic identifications of rumen contents in two species of wild free-ranging ungulates: roe deer and fallow deer. We found that the methods were comparable, but they did not completely overlap. Sometimes the DNA method failed to identify food items that were found macroscopically, and the opposite was also true. However, the total number of taxa identified increased using DNA compared to the macroscopic analysis. Moreover, the taxonomic precision of metabarcoding was substantially higher, with on average 90% of DNA-sequences being identified to genus or species level compared to 75% of plant fragments using macroscopy. In niche overlap analyses, presence/absence data showed that both methods came to very similar conclusions. When using the sequence count data and macroscopic weight, niche overlap was lower than when using presence-absence data yet tended to increase when using DNA compared to macroscopy. Nevertheless, the significant positive correlation between macroscopic quantity and number of DNA sequences counted from the same plant group give support for the use of metabarcoding to quantify plants in the rumen. This study thus shows that there is much to be gained by using metabarcoding to quantitatively assess diet composition compared to macroscopic analysis, including higher taxonomic precision, sensitivity and cost efficiency.

New insights into Trypanosoma cruzi evolution, genotyping and molecular diagnostics from satellite DNA sequence analysis.

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Juan C Ramírez

2017-12-01

Full Text Available Trypanosoma cruzi has been subdivided into seven Discrete Typing Units (DTUs, TcI-TcVI and Tcbat. Two major evolutionary models have been proposed to explain the origin of hybrid lineages, but while it is widely accepted that TcV and TcVI are the result of genetic exchange between TcII and TcIII strains, the origin of TcIII and TcIV is still a matter of debate. T. cruzi satellite DNA (SatDNA, comprised of 195 bp units organized in tandem repeats, from both TcV and TcVI stocks were found to have SatDNA copies type TcI and TcII; whereas contradictory results were observed for TcIII stocks and no TcIV sequence has been analyzed yet. Herein, we have gone deeper into this matter analyzing 335 distinct SatDNA sequences from 19 T. cruzi stocks representative of DTUs TcI-TcVI for phylogenetic inference. Bayesian phylogenetic tree showed that all sequences were grouped in three major clusters, which corresponded to sequences from DTUs TcI/III, TcII and TcIV; whereas TcV and TcVI stocks had two sets of sequences distributed into TcI/III and TcII clusters. As expected, the lowest genetic distances were found between TcI and TcIII, and between TcV and TcVI sequences; whereas the highest ones were observed between TcII and TcI/III, and among TcIV sequences and those from the remaining DTUs. In addition, signature patterns associated to specific T. cruzi lineages were identified and new primers that improved SatDNA-based qPCR sensitivity were designed. Our findings support the theory that TcIII is not the result of a hybridization event between TcI and TcII, and that TcIV had an independent origin from the other DTUs, contributing to clarifying the evolutionary history of T. cruzi lineages. Moreover, this work opens the possibility of typing samples from Chagas disease patients with low parasitic loads and improving molecular diagnostic methods of T. cruzi infection based on SatDNA sequence amplification.

New insights into Trypanosoma cruzi evolution, genotyping and molecular diagnostics from satellite DNA sequence analysis.

Science.gov (United States)

Ramírez, Juan C; Torres, Carolina; Curto, María de Los A; Schijman, Alejandro G

2017-12-01

Trypanosoma cruzi has been subdivided into seven Discrete Typing Units (DTUs), TcI-TcVI and Tcbat. Two major evolutionary models have been proposed to explain the origin of hybrid lineages, but while it is widely accepted that TcV and TcVI are the result of genetic exchange between TcII and TcIII strains, the origin of TcIII and TcIV is still a matter of debate. T. cruzi satellite DNA (SatDNA), comprised of 195 bp units organized in tandem repeats, from both TcV and TcVI stocks were found to have SatDNA copies type TcI and TcII; whereas contradictory results were observed for TcIII stocks and no TcIV sequence has been analyzed yet. Herein, we have gone deeper into this matter analyzing 335 distinct SatDNA sequences from 19 T. cruzi stocks representative of DTUs TcI-TcVI for phylogenetic inference. Bayesian phylogenetic tree showed that all sequences were grouped in three major clusters, which corresponded to sequences from DTUs TcI/III, TcII and TcIV; whereas TcV and TcVI stocks had two sets of sequences distributed into TcI/III and TcII clusters. As expected, the lowest genetic distances were found between TcI and TcIII, and between TcV and TcVI sequences; whereas the highest ones were observed between TcII and TcI/III, and among TcIV sequences and those from the remaining DTUs. In addition, signature patterns associated to specific T. cruzi lineages were identified and new primers that improved SatDNA-based qPCR sensitivity were designed. Our findings support the theory that TcIII is not the result of a hybridization event between TcI and TcII, and that TcIV had an independent origin from the other DTUs, contributing to clarifying the evolutionary history of T. cruzi lineages. Moreover, this work opens the possibility of typing samples from Chagas disease patients with low parasitic loads and improving molecular diagnostic methods of T. cruzi infection based on SatDNA sequence amplification.

Effect of gamma rays on nucleic acids content (RNA and DNA) of the cotton leaf worm Spodoptera Littoralis (BOISD). Vol. 4

International Nuclear Information System (INIS)

Sallam, H.A.; El-Shall, S.A.; Sobeiha, A.K.; El-Bamby, M.A.

1996-01-01

Full grown pupae of the cotton leaf worm Spodoptera Littoralis (Boisd) were exposed to exposed to sub sterilizing doses of 100, 200 and 300 Gy gamma radiation. The changes in nucleic acids content (RNA and DNA) of irradiated pupae, after 24 hours from irradiation, and also in 3 days old adults resulting from irradiated pupae were investigated. The total nucleic acids content in either pupae or adults was progressively reduced as the dose was increased. The reduction of both RNA and DNA in females was greater than in males. DNA was more radiosensitive than RNA. The destructive action of irradiation on nucleic acids was more pronounced in adult stage. Irradiation increased the RNA/DNA ratio than control at all treatments for female pupae at 200 Gy. 2 tabs

Effect of gamma rays on nucleic acids content (RNA and DNA) of the cotton leaf worm Spodoptera Littoralis (BOISD). Vol. 4.

Energy Technology Data Exchange (ETDEWEB)

Sallam, H A; El-Shall, S A [Biological Applications Department, Nuclear Research Center, Atomic Energy Authority, Cairo (Egypt); Sobeiha, A K; El-Bamby, M A [Plant Protection Department, Faculty of Agriculture, Ain Shams University, Cairo (Egypt)

1996-03-01

Full grown pupae of the cotton leaf worm Spodoptera Littoralis (Boisd) were exposed to exposed to sub sterilizing doses of 100, 200 and 300 Gy gamma radiation. The changes in nucleic acids content (RNA and DNA) of irradiated pupae, after 24 hours from irradiation, and also in 3 days old adults resulting from irradiated pupae were investigated. The total nucleic acids content in either pupae or adults was progressively reduced as the dose was increased. The reduction of both RNA and DNA in females was greater than in males. DNA was more radiosensitive than RNA. The destructive action of irradiation on nucleic acids was more pronounced in adult stage. Irradiation increased the RNA/DNA ratio than control at all treatments for female pupae at 200 Gy. 2 tabs.

Influence of exercise contraction mode and protein supplementation on human skeletal muscle satellite cell content and muscle fiber growth

DEFF Research Database (Denmark)

Farup, Jean; Rahbek, Stine Klejs; Riis, Simon

2014-01-01

-specific association between emergence of satellite cells (SCs), muscle growth, and remodeling in response to 12 wk unilateral resistance training performed as eccentric (Ecc) or concentric (Conc) resistance training ± whey protein (Whey, 19.5 g protein + 19.5 g glucose) or placebo (Placebo, 39 g glucose......Skeletal muscle satellite cells (SCs) are involved in remodeling and hypertrophy processes of skeletal muscle. However, little knowledge exists on extrinsic factors that influence the content of SCs in skeletal muscle. In a comparative human study, we investigated the muscle fiber type......) supplementation. Muscle biopsies (vastus lateralis) were analyzed for fiber type-specific SCs, myonuclei, and fiber cross-sectional area (CSA). Following training, SCs increased with Conc in both type I and type II fibers (P

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.

Transcription of tandemly repetitive DNA: functional roles.

Science.gov (United States)

Biscotti, Maria Assunta; Canapa, Adriana; Forconi, Mariko; Olmo, Ettore; Barucca, Marco

2015-09-01

A considerable fraction of the eukaryotic genome is made up of satellite DNA constituted of tandemly repeated sequences. These elements are mainly located at centromeres, pericentromeres, and telomeres and are major components of constitutive heterochromatin. Although originally satellite DNA was thought silent and inert, an increasing number of studies are providing evidence on its transcriptional activity supporting, on the contrary, an unexpected dynamicity. This review summarizes the multiple structural roles of satellite noncoding RNAs at chromosome level. Indeed, satellite noncoding RNAs play a role in the establishment of a heterochromatic state at centromere and telomere. These highly condensed structures are indispensable to preserve chromosome integrity and genome stability, preventing recombination events, and ensuring the correct chromosome pairing and segregation. Moreover, these RNA molecules seem to be involved also in maintaining centromere identity and in elongation, capping, and replication of telomere. Finally, the abnormal variation of centromeric and pericentromeric DNA transcription across major eukaryotic lineages in stress condition and disease has evidenced the critical role that these transcripts may play and the potentially dire consequences for the organism.

Screening for Methylated Poly(⌊-histidine with Various Dimethylimidazolium/Methylimidazole/Imidazole Contents as DNA Carrier

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Shoichiro Asayama

2015-08-01

Full Text Available Methylated poly(l-histidine (PLH-Me, our original polypeptide, has controlled the contents of dimethylimidazolium, τ/π-methylimidazole and imidazole groups for efficient gene delivery. The screening for the PLH-Me as DNA carrier has been carried out by use of the PLH with 25 mol% (τ-methyl, 16 mol%; π-methyl, 17 mol%; deprotonated imidazole, 41 mol%, 68 mol% (τ-methyl, 16 mol%; π-methyl, 8 mol%; deprotonated imidazole, 8 mol% and 87 mol% (τ-methyl, 7 mol%; π-methyl, 4 mol%; deprotonated imidazole, 2 mol% dimethylimidazolium groups, that is, PLH-Me(25, PLH-Me(68 and PLH-Me(87, respectively. The screening of the chemical structure of PLH-Me has been carried out for DNA carrier properties, which are the stability of its DNA polyion complexes and gene expression. The DNA complexes with the 25 mol% and 68 mol% dimethylated PLH-Me possessed almost same ability to retain DNA, as compared with the 87 mol% dimethylated PLH-Me, which was examined by competitive exchange with dextran sulfate. From the gene transfection experiment against HepG2 cells, human hepatoma cell line, the PLH-Me(25/DNA complex was revealed to mediate highest gene expression. These results suggest that the dimethyl-imidazolium/methylimidazole/imidazole balance of the PLH-Me is important for DNA carrier design.

Stability in chromosome number and DNA content in synthetic tetraploids of Lolium multiflorum after two generations of selection

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Roselaine Cristina Pereira

Full Text Available ABSTRACT: Chromosome doubling of Italian ryegrass genotypes ( Lolium multiflorum Lam. adapted to the brazilian edaphoclimatic conditions is an important strategy used by breeders and aims to obtain more vigorous genotypes with better forage quality and disease resistance. The effectiveness of chromosome doubling can be measured by genetic stability and fertility rates of plants over generations. However, a common problem in the polyploidization process is the regeneration of mixoploid plants that have impaired fertility and genetic stability. The objective of this study was to verify if progenies of recently tetraploidized plants remain stable regarding DNA content and chromosome number, over two generations. Progenies of L. multiflorum plants artificially tetraploidized with colchicine treatment were evaluated. Chromosome counting and estimates of the DNA content were used to evaluate the genetic stability. The percentage of tetraploid plants (4X increased over generations (18%, 34% and 91% in cycle 0, 1 and 2, respectively. All progenies identified as tetraploid by flow citometry showed variation in chromosome number (mixoploidy, but produced viable seeds. Results showed that stabilization in chromosome number and DNA content in tetraploidized plant progenies requires time and that the success of this procedure depends on a continuous and accurate screening and selection.

Reduced Dnmt3a increases Gdf5 expression with suppressed satellite cell differentiation and impaired skeletal muscle regeneration.

Science.gov (United States)

Hatazawa, Yukino; Ono, Yusuke; Hirose, Yuma; Kanai, Sayaka; Fujii, Nobuharu L; Machida, Shuichi; Nishino, Ichizo; Shimizu, Takahiko; Okano, Masaki; Kamei, Yasutomi; Ogawa, Yoshihiro

2018-03-01

DNA methylation is an epigenetic mechanism regulating gene expression. In this study, we observed that DNA methyltransferase 3a (Dnmt3a) expression is decreased after muscle atrophy. We made skeletal muscle-specific Dnmt3a-knockout (Dnmt3a-KO) mice. The regeneration capacity after muscle injury was markedly decreased in Dnmt3a-KO mice. Diminished mRNA and protein expression of Dnmt3a were observed in skeletal muscles as well as in satellite cells, which are important for muscle regeneration, in Dnmt3a-KO mice. Dnmt3a-KO satellite cell showed smaller in size (length/area), suggesting suppressed myotube differentiation. Microarray analysis of satellite cells showed that expression of growth differentiation factor 5 (Gdf5) mRNA was markedly increased in Dnmt3a-KO mice. The DNA methylation level of the Gdf5 promoter was markedly decreased in Dnmt3a-KO satellite cells. In addition, DNA methylation inhibitor azacytidine treatment increased Gdf5 expression in wild-type satellite cells, suggesting Gdf5 expression is regulated by DNA methylation. Also, we observed increased inhibitor of differentiation (a target of Gdf5) mRNA expression in Dnmt3a-KO satellite cells. Thus, Dnmt3a appears to regulate satellite cell differentiation via DNA methylation. This mechanism may play a role in the decreased regeneration capacity during atrophy such as in aged sarcopenia.-Hatazawa, Y., Ono, Y., Hirose, Y., Kanai, S., Fujii, N. L., Machida, S., Nishino, I., Shimizu, T., Okano, M., Kamei, Y., Ogawa, Y. Reduced Dnmt3a increases Gdf5 expression with suppressed satellite cell differentiation and impaired skeletal muscle regeneration.

DNA Methylation at a Bovine Alpha Satellite I Repeat CpG Site during Development following Fertilization and Somatic Cell Nuclear Transfer

OpenAIRE

Couldrey, Christine; Wells, David N.

2013-01-01

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 bla...

Observation of total electron content and irregularities in electron density using GHz band radiowaves emitted from satellite

International Nuclear Information System (INIS)

Ogawa, Tadahiko; Fujita, Masaharu; Awaka, Jun.

1978-01-01

The experiments to investigate the influence of troposphere on millimeter and sub-millimeter wave propagation were carried out, using the engineering test satellite -- 2 (ETS-2) which became the Japanese first stationary satellite and carries the transmitter emitting beacon waves of 1.7, 11.5 and 34.5 GHz coherent each other. By these experiments, it was found that the waves of 1.7 and 11.5 GHz were affected by the ionosphere. The measurement of total electron content using GHz band waves was the first trial in the world, and is capable of grasping its change with higher accuracy than conventional methods. Scintillation of 1.7 GHz is mainly the phenomenon during night, and it was revealed that it has a peak at 22.30 local time and occurred through the radiowave scattering owing to the irregularities of the ionosphere. It is also suggested that some plasma instability is generated in the place where electron density gradient in the ionosphere is large, and the irregularities of fine scale are produced, assuming from GHz band scintillations at the time of magnetic storm. The relations among wave number spectrum, scintillation frequency spectrum and S4 index (statistical quantity to give estimate for scintillation amplitude) can be derived by the weak scattering theory (Simple scattering theory). As seen above, the diagnosis of plasma disturbances in the ionosphere is feasible by the simultaneous observations of total electron content and scintillation. (Wakatsuki, Y.)

Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus.

OpenAIRE

Sanford, J; Forrester, L; Chapman, V; Chandley, A; Hastie, N

1984-01-01

The major and the minor satellite sequences of Mus musculus were undermethylated in both sperm and oocyte DNAs relative to the amount of undermethylation observed in adult somatic tissue DNA. This hypomethylation was specific for satellite sequences in sperm DNA. Dispersed repetitive and low copy sequences show a high degree of methylation in sperm DNA; however, a dispersed repetitive sequence was undermethylated in oocyte DNA. This finding suggests a difference in the amount of total genomic...

Evaluation of cell number and DNA content in mouse embryos cultivated with uranium

International Nuclear Information System (INIS)

Kundt, Mirian S.; Cabrini, Romulo L.

2000-01-01

The evaluation of the degree of development, the number of cells and the DNA content, were used to evaluate the embryotoxicity of uranium. Embryos at a one cell stage were cultured with uranyl nitrate hexahydrate (UN) at a final concentration of uranium (U) of 26, 52 and 104 μgU/ml. At 24 hs of culture, the embryos at the 2 cell stage, were put in new wells with the same concentrations of U as the previous day, until the end of the period of incubation at 72 hs. At 72 hs of culture, 87% of the original one cell embryos were at morula stage, and in those cultivated with uranium, the percentage decreased significantly to 77; 63.24 and 40.79% respectively for the different U concentrations. Those embryos that exhibited a normal morphology, were selected and fixed on slides. The number of cells per embryo was evaluated in Giemsa stained preparations. The DNA content was evaluated cytophotometrically in Feulgen stained nuclei. The number of cells decreased significantly from 20,3 ± 5.6 in the control to 19 ± 6; 14 ± 3 and 13.9 ± 5.6 for the different concentrations. All the embryos evaluated showed one easy recognizable polar body, which was used a haploid indicator (n). The content of DNA was measured in a total of 20 control embryos and 16 embryos cultivated with UN. In control embryos, 92,7% of the nuclei presented a normal ploidy from 2n to 4n, 2,9% nuclei were hypoploid and 4,4% were hyperploid. The percentage of hypoploid nuclei rose in a dose-dependent fashion to 3.45; 44.45 and 50.34% respectively for the embryos cultured at the different U concentrations. The results indicate that U is embryotoxic, that its effects are dose dependent at the concentrations used in this study and that even those embryos that show a normal morphology, can be genetically affected. We show that the model employed is extremely sensitive. It is possible to use the preimplantation embryos, as a model to test the effect of possibly mutagenic agents of the nuclear industry. (author)

Cytometric analysis of shape and DNA content in mammalian sperm

Energy Technology Data Exchange (ETDEWEB)

Gledhill, B.L.

1983-10-10

Male germ cells respond dramatically to a variety of insults and are important reproductive dosimeters. Semen analyses are very useful in studies on the effects of drugs, chemicals, and environmental hazards on testicular function, male fertility and heritable germinal mutations. Sperm were analyzed by flow cytometry and slit-scan flow analysis for injury following the exposure of testes to mutagens. The utility of flow cytometry in genotoxin screening and monitoring of occupational exposure was evaluated. The technique proved valuable in separation of X- and Y-chromosome bearing sperm and the potential applicability of this technique in artificial insemination and a solution, of accurately assessing the DNA content of sperm were evaluated-with reference to determination of X- and Y-chromosome bearing sperm.

Cytometric analysis of shape and DNA content in mammalian sperm

International Nuclear Information System (INIS)

Gledhill, B.L.

1983-01-01

Male germ cells respond dramatically to a variety of insults and are important reproductive dosimeters. Semen analyses are very useful in studies on the effects of drugs, chemicals, and environmental hazards on testicular function, male fertility and heritable germinal mutations. Sperm were analyzed by flow cytometry and slit-scan flow analysis for injury following the exposure of testes to mutagens. The utility of flow cytometry in genotoxin screening and monitoring of occupational exposure was evaluated. The technique proved valuable in separation of X- and Y-chromosome bearing sperm and the potential applicability of this technique in artificial insemination and a solution, of accurately assessing the DNA content of sperm were evaluated-with reference to determination of X- and Y-chromosome bearing sperm

A method for the determination of bacterial spore DNA content based on isotopic labelling, spore germination and diphenylamine assay; ploidy of spores of several Bacillus species

International Nuclear Information System (INIS)

Hauser, P.M.; Karamata, D.

1992-01-01

A reliable method for measuring the spore DNA content, based on radioactive DNA labelling, spore germination in absence of DNA replication and diphenylamine assay, was developed. The accuracy of the method, within 10 - 15%, is adequate for determining the number of chromosomes per spore, provided that the genome size is known. B subtilis spores were shown to be invariably monogenomic, while those of larger bacilli Bacillus megaterium, Bacillus cereus and Bacillus thuringiensis, often, if not invariably, contain two genomes. Attempts to modify the spore DNA content of B subtilis by altering the richness of the sporulation medium, the sporulation conditions (liquid or solid medium), or by mutation, were apparently unsuccessful. An increase of spore size with medium richness, not accompanied by an increase in DNA content, was observed. The implication of the apparently species-specific spore ploidy and the influence of the sporulation conditions on spore size and shape are discussed

Using Sentinel-1 and Landsat 8 satellite images to estimate surface soil moisture content.

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Mexis, Philippos-Dimitrios; Alexakis, Dimitrios D.; Daliakopoulos, Ioannis N.; Tsanis, Ioannis K.

2016-04-01

Nowadays, the potential for more accurate assessment of Soil Moisture (SM) content exploiting Earth Observation (EO) technology, by exploring the use of synergistic approaches among a variety of EO instruments has emerged. This study is the first to investigate the potential of Synthetic Aperture Radar (SAR) (Sentinel-1) and optical (Landsat 8) images in combination with ground measurements to estimate volumetric SM content in support of water management and agricultural practices. SAR and optical data are downloaded and corrected in terms of atmospheric, geometric and radiometric corrections. SAR images are also corrected in terms of roughness and vegetation with the synergistic use of Oh and Topp models using a dataset consisting of backscattering coefficients and corresponding direct measurements of ground parameters (moisture, roughness). Following, various vegetation indices (NDVI, SAVI, MSAVI, EVI, etc.) are estimated to record diachronically the vegetation regime within the study area and as auxiliary data in the final modeling. Furthermore, thermal images from optical data are corrected and incorporated to the overall approach. The basic principle of Thermal InfraRed (TIR) method is that Land Surface Temperature (LST) is sensitive to surface SM content due to its impact on surface heating process (heat capacity and thermal conductivity) under bare soil or sparse vegetation cover conditions. Ground truth data are collected from a Time-domain reflectometer (TRD) gauge network established in western Crete, Greece, during 2015. Sophisticated algorithms based on Artificial Neural Networks (ANNs) and Multiple Linear Regression (MLR) approaches are used to explore the statistical relationship between backscattering measurements and SM content. Results highlight the potential of SAR and optical satellite images to contribute to effective SM content detection in support of water resources management and precision agriculture. Keywords: Sentinel-1, Landsat 8, Soil

Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts.

Science.gov (United States)

Trofimova, Irina; Krasikova, Alla

2016-12-01

Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.

Compensatory lung growth: protein, DNA and RNA lung contents in undernourished trilobectomized rats Crescimento pulmonar compensatório: conteúdos pulmonares de proteína, DNA e RNA em ratos subnutridos trilobectomizados

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Raul Lopes Ruiz Júnior

2005-06-01

Full Text Available PURPOSE: To demonstrate compensatory lung growth (CLG by lung contents of proteins, DNA, and RNA in undernourished young adult rats, submitted to pulmonary trilobectomy. METHODS: We used 137 male Wistar rats, randomly distributed into 9 groups; they were submitted to three treatments (control, thoracotomy, and trilobectomy, and sacrificed at three different times (7, 30, and 90 days. In trilobectomy we removed the right median, accessory, and caudal lobes. We studied lung proteins, DNA, and RNA contents. RESULTS: In the cranial lobe and left lung, protein content was higher in trilobectomized rats however there was insufficient CLG to make up for the loss. The increase of DNA in the cranial lobe and left lung of trilobectomized rats was sufficient to compensate for this loss, resulting in a similar content to controls. RNA content in trilobectomized rats, was higher in the cranial lobe and left lung, more efficient in the cranial lobe, but less than in the other groups. CONCLUSION: CLG occurred in trilobectomized rats, probably with cell hyperplasia and little hypertrophy, due to the large DNA compensation and small RNA compensation. This was markedly different to well-nourished animals, who had pronounced hypertrophy.OBJETIVO: demonstrar se ocorre crescimento pulmonar compensatório (CPC representado pelos conteúdos de proteínas, DNA e RNA no rato adulto jovem, subnutrido, submetido à trilobectomia pulmonar. MÉTODOS: Utilizamos 137 ratos "Wistar", machos, distribuídos por sorteio, em 9 grupos, submetidos a três tratamentos (controle, toracotomia, trilobectomia, sacrificados em três momentos (7, 30 e 90 dias. Na trilobectomia foram extirpados os lobos médio, acessório e caudal direitos. Variáveis estudadas: conteúdos pulmonares de proteínas, DNA e RNA. RESULTADOS: No lobo cranial e pulmão esquerdo o conteúdo protéico foi maior nos trilobectomizados. Ocorreu CPC insuficiente para suprir a perda desta variável, sendo menor nos pulm

DNA-content in isolated nuclei of postembryonic stages of progeny from normal and irradiated males of Tetranychus urticae (Acari Tetranychidoe)

International Nuclear Information System (INIS)

Tempelaar, M.J.

1980-01-01

The lC DNA-content of isolated nuclei of postembryonic stages of Tetranychus urticae stained with the classic and a modified Schiff's reagent was cytophotometrically estimated as 0.1 pg, a low value in animals. For many tissues of this arrhenotokus species the ploidy ratio between males and females is 1:2, indicating the absence of sex-related differences in ploidy. In addition, DNA measurements were performed to evaluate irradiation-experiments, starting with X-irradiation of mature sperm in males with doses known from previous work to induce chromosomal fragments that are subject to loss and missegregation in the embryonic mitotic stages of the female progeny despite the presumed holokinetic nature of the chromosomes. The DNA-content of the nuclei of the surviving postembryonic preadult stages did not indicate the occurrence of nuclei with in-between male/female values, ruling out loss and missegregation of fragments as important factors in postembryonic lethality. Abnormally low DNA-values in some adult females could be attributed to development of embryos before oviposition caused by radiation-induced effects. (orig.) [de

Quantification of Rain Induced Artifacts on Digital Satellite Television ...

African Journals Online (AJOL)

The presence of artifacts on the high definition television (TV) content and the eventual loss of the digital TV signals to rain is still a major concern to satellite operators, digital satellite television (DSTV) and terrestrial television content providers. In this paper, the artifacts present in a typical DSTV signal is examined on a ...

Increase of mitochondrial DNA content and transcripts in early bovine embryogenesis associated with upregulation of mtTFA and NRF1 transcription factors

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Heyman Yvan

2005-11-01

Full Text Available Abstract Background Recent work has shown that mitochondrial biogenesis and mitochondrial functions are critical determinants of embryonic development. However, the expression of the factors controlling mitochondrial biogenesis in early embryogenesis has received little attention so far. Methods We used real-time quantitative PCR to quantify mitochondrial DNA (mtDNA in bovine oocytes and in various stages of in vitro produced embryos. To investigate the molecular mechanisms responsible for the replication and the transcriptional activation of mtDNA, we quantified the mRNA corresponding to the mtDNA-encoded cytochrome oxidase 1 (COX1, and two nuclear-encoded factors, i.e. the Nuclear Respiratory Factor 1 (NRF1, and the nuclear-encoded Mitochondrial Transcription Factor A (mtTFA. Results Unlike findings reported in mouse embryos, the mtDNA content was not constant during early bovine embryogenesis. We found a sharp, 60% decrease in mtDNA content between the 2-cell and the 4/8-cell stages. COX1 mRNA was constant until the morula stage after which it increased dramatically. mtTFA mRNA was undetectable in oocytes and remained so until the 8/16-cell stage; it began to appear only at the morula stage, suggesting de novo synthesis. In contrast, NRF1 mRNA was detectable in oocytes and the quantity remained constant until the morula stage. Conclusion Our results revealed a reduction of mtDNA content in early bovine embryos suggesting an active process of mitochondrial DNA degradation. In addition, de novo mtTFA expression associated with mitochondrial biogenesis activation and high levels of NRF1 mRNA from the oocyte stage onwards argue for the essential function of these factors during the first steps of bovine embryogenesis.

Heat, hydrogen peroxide, and UV resistance of Bacillus subtilis spores with increased core water content and with or without major DNA-binding proteins

International Nuclear Information System (INIS)

Popham, D.L.; Sengupta, S.; Setlow, P.

1995-01-01

Spores of a Bacillus subtilis strain with an insertion mutation in the dacB gene, which codes for an enzyme involved in spore cortex biosynthesis, have a higher core water content than wild-type spores. Spores lacking the two major α/β-type small, acid-soluble proteins (SASP) (termed a α - β - spores) have the same core water content as do wild-type spores, but α - β - dacB spores had more core water than did dacB spores. The resistance of α - β - , α - β - dacB, dacB, and wild-type spores to dry and moist heat, hydrogen peroxide, and UV radiation has been determined, as has the role of DNA damage in spore killing by moist heat and hydrogen peroxide. These data (1) suggest that core water content has little if any role in spore UV resistance and are consistent with binding of α/β-type SASP to DNA being the major mechanism providing protection to spores from UV radiation; (2) suggest that binding of αβ-type SASP to DNA is the major mechanism unique to spores providing protection from dry heat; (3) suggest that spore resistance to moist heat and hydrogen peroxide is affected to a large degree by the core water content, as increased core water resulted in large decreases in spore resistance to these agents; and (4) indicate that since this decreased resistance (i.e., in dacB spores) is not associated with increased spore killing by DNA damage, spore DNA must normally be extremely well protected against such damage, presumably by the saturation of spore DNA by α/β-type SASP. 19 refs., 2 figs., 5 tabs

Regenerative capacity of old muscle stem cells declines without significant accumulation of DNA damage.

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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.

The Effects of Low LET Radiation and Aging on DNA Content in Rats Hepatocytes

International Nuclear Information System (INIS)

Ekhtiar, A. M.

2004-01-01

It has been shown that the polyploidization levels in rat's hepatocytes increased with aging. The high LET ionizing radiation also induce cell polyploidization by two different means: cells and nuclei fusion, and mitosis restriction after DNA replication. The purpose of the present study was to determine the kinetic of rat's hepatocytes polyploidization with aging, and the late effects of low doses of gamma irradiation on polyploidization. Two groups of rats were used. Each group composed of 150 four weeks old animals. The first group was served as a control, and the second was irradiated with 4 Gy of gamma irradiation at the age of one month. Of each group, 7-8 animals were monthly scarified (for two years), and their liver tissues were used to obtain cell suspensions which were further fixed in gradual series concentrations of ethanol. After staining with Propidum Iodide PI (10 6 cells per ml of PI used at 10 - 5 M final concentration), the cells were analyzed on a FACS Vantage Flow Cytometer (Becton Dickinson). With the control group, the results showed: 1) A decrease of cell fraction that contained normal diploid until steady level. 2) Biphasic changes of fraction tetraploidy cells (increase until age of 4 month followed by decrease). 3) The fraction of octaploidy cells appeared at age of 3-4 month and increased continuously by the aging. In regard to life-span reductions of irradiated animals, the DNA contents were similar to those in control groups in addition to some variation due to a programmed cell death (Apoptosis) induced by irradiation and regenerations. These variations persisted till the age of 7 month. It was concluded that the level of DNA content might be used to determine the rat's age, and the low LET radiation had no effect on the phenomenon of polyploidization. (author)

DNA biosynthesis content and intensiveness in mice thymus at early periods following fast neutron irradiation with different energy rate

International Nuclear Information System (INIS)

Indyk, V.M.; Antonenko, G.I.; Parnovskaya, N.V.

1988-01-01

Biosynthesis of dna of the thymic glands of animals irradiated by fast neutrons with different energy values in the early post-irradiation period is investigated. It is shown that the rate of mass recovery in organs, their cellular nature, dna content and indices of their specific activity have the dose and time dependences, as well as they considerably differ at different neutron energies and different quality radiation. With the increase of neutron energy value their biological effectiveness decreases

NOAA Satellite and Information Service's International and Interagency

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: To meet the challenge of understanding and predicting changes in climate, weather, oceans, and coasts Affaris Division Skip to main content NOAA HOME NESDIS HOME WEATHER OCEANS & COASTS FISHERIES CHARTING SATELLITES CLIMATE RESEARCH CAREERS Satellite and Data Policy Developing Partnerships

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.

Effect of serotonin on the expression of antigens and DNA levels in Yersinia pestis cells with different plasmid content

Science.gov (United States)

Klueva, Svetlana N.; Korsukov, Vladimir N.; Schukovskaya, Tatyana N.; Kravtsov, Alexander L.

2004-08-01

Using flow cytometry (FCM) the influence of exogenous serotonin on culture growth, DNA content and fluorescence intensity of cells binding FITC-labelled plague polyclonal immunoglobulins was studied in Yersinia pestis EV (pFra+, pCad+, pPst+), Yersinia pestis KM218 (pFra-, pCad-, pPst-), Yersinia pestis KM 216 (pFra-, pCad-, pPst+). The results have been obtained by FCM showed serotonin accelerated Yersinia pestis EV (pFra+, pCad+, pPst+), Yersinia pestis KM218 (pFra-, pCad-, pPst-) culture growth during cultivation in Hottinger broth pH 7.2 at 28°C at concentration of 10-5 M. The presence of 10-5 M serotonin in nutrient broth could modulate DNA content in 37°C growing population of plague microbe independently of their plasmid content. Serotonin have been an impact on the distribution pattern of the cells according to their phenotypical characteristics, which was reflected in the levels of population heterogeneity in the intensity of specific immunofluorescence determined by FMC.

Aerosol Retrievals from Proposed Satellite Bistatic Lidar Observations: Algorithm and Information Content

Science.gov (United States)

Alexandrov, M. D.; Mishchenko, M. I.

2017-12-01

Accurate aerosol retrievals from space remain quite challenging and typically involve solving a severely ill-posed inverse scattering problem. We suggested to address this ill-posedness by flying a bistatic lidar system. Such a system would consist of formation flying constellation of a primary satellite equipped with a conventional monostatic (backscattering) lidar and an additional platform hosting a receiver of the scattered laser light. If successfully implemented, this concept would combine the measurement capabilities of a passive multi-angle multi-spectral polarimeter with the vertical profiling capability of a lidar. Thus, bistatic lidar observations will be free of deficiencies affecting both monostatic lidar measurements (caused by the highly limited information content) and passive photopolarimetric measurements (caused by vertical integration and surface reflection).We present a preliminary aerosol retrieval algorithm for a bistatic lidar system consisting of a high spectral resolution lidar (HSRL) and an additional receiver flown in formation with it at a scattering angle of 165 degrees. This algorithm was applied to synthetic data generated using Mie-theory computations. The model/retrieval parameters in our tests were the effective radius and variance of the aerosol size distribution, complex refractive index of the particles, and their number concentration. Both mono- and bimodal aerosol mixtures were considered. Our algorithm allowed for definitive evaluation of error propagation from measurements to retrievals using a Monte Carlo technique, which involves random distortion of the observations and statistical characterization of the resulting retrieval errors. Our tests demonstrated that supplementing a conventional monostatic HSRL with an additional receiver dramatically increases the information content of the measurements and allows for a sufficiently accurate characterization of tropospheric aerosols.

Cell type-specific characterization of nuclear DNA contents within complex tissues and organs

Directory of Open Access Journals (Sweden)

Lambert Georgina M

2005-10-01

Full Text Available Abstract Background Eukaryotic organisms are defined by the presence of a nucleus, which encloses the chromosomal DNA, and is characterized by its DNA content (C-value. Complex eukaryotic organisms contain organs and tissues that comprise interspersions of different cell types, within which polysomaty, endoreduplication, and cell cycle arrest is frequently observed. Little is known about the distribution of C-values across different cell types within these organs and tissues. Results We have developed, and describe here, a method to precisely define the C-value status within any specific cell type within complex organs and tissues of plants. We illustrate the application of this method to Arabidopsis thaliana, specifically focusing on the different cell types found within the root. Conclusion The method accurately and conveniently charts C-value within specific cell types, and provides novel insight into developmental processes. The method is, in principle, applicable to any transformable organism, including mammals, within which cell type specificity of regulation of endoreduplication, of polysomaty, and of cell cycle arrest is suspected.

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.

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 levels...

Characterization of a chromosome-specific chimpanzee alpha satellite subset: Evolutionary relationship to subsets on human chromosomes

Energy Technology Data Exchange (ETDEWEB)

Warburton, P.E.; Gosden, J.; Lawson, D. [Western General Hospital, Edinburgh (United Kingdom)] [and others

1996-04-15

Alpha satellite DNA is a tandemly repeated DNA family found at the centromeres of all primate chromosomes examined. The fundamental repeat units of alpha satellite DNA are diverged 169- to 172-bp monomers, often found to be organized in chromosome-specific higher-order repeat units. The chromosomes of human (Homo sapiens (HSA)), chimpanzee (Pan troglodytes (PTR) and Pan paniscus), and gorilla (Gorilla gorilla) share a remarkable similarity and synteny. It is of interest to ask if alpha satellite arrays at centromeres of homologous chromosomes between these species are closely related (evolving in an orthologous manner) or if the evolutionary processes that homogenize and spread these arrays within and between chromosomes result in nonorthologous evolution of arrays. By using PCR primers specific for human chromosome 17-specific alpha satellite DNA, we have amplified, cloned, and characterized a chromosome-specific subset from the PTR chimpanzee genome. Hybridization both on Southern blots and in situ as well as sequence analysis show that this subset is most closely related, as expected, to sequences on HSA 17. However, in situ hybridization reveals that this subset is not found on the homologous chromosome in chimpanzee (PTR 19), but instead on PTR 12, which is homologous to HSA 2p. 40 refs., 3 figs.

Altered mitochondrial genome content signals worse pathology and prognosis in prostate cancer.

Science.gov (United States)

Kalsbeek, Anton M F; Chan, Eva K F; Grogan, Judith; Petersen, Desiree C; Jaratlerdsiri, Weerachai; Gupta, Ruta; Lyons, Ruth J; Haynes, Anne-Maree; Horvath, Lisa G; Kench, James G; Stricker, Phillip D; Hayes, Vanessa M

2018-01-01

Mitochondrial genome (mtDNA) content is depleted in many cancers. In prostate cancer, there is intra-glandular as well as inter-patient mtDNA copy number variation. In this study, we determine if mtDNA content can be used as a predictor for prostate cancer staging and outcomes. Fresh prostate cancer biopsies from 115 patients were obtained at time of surgery. All cores underwent pathological review, followed by isolation of cancer and normal tissue. DNA was extracted and qPCR performed to quantify the total amount of mtDNA as a ratio to genomic DNA. Differences in mtDNA content were compared for prostate cancer pathology features and disease outcomes. We showed a significantly reduced mtDNA content in prostate cancer compared with normal adjacent prostate tissue (mean difference 1.73-fold, P-value Prostate cancer with increased mtDNA content showed unfavorable pathologic characteristics including, higher disease stage (PT2 vs PT3 P-value = 0.018), extracapsular extension (P-value = 0.02) and a trend toward an increased Gleason score (P-value = 0.064). No significant association was observed between changes in mtDNA content and biochemical recurrence (median follow up of 107 months). Contrary to other cancer types, prostate cancer tissue shows no universally depleted mtDNA content. Rather, the change in mtDNA content is highly variable, mirroring known prostate cancer genome heterogeneity. Patients with high mtDNA content have an unfavorable pathology, while a high mtDNA content in normal adjacent prostate tissue is associated with worse prognosis. © 2017 Wiley Periodicals, Inc.

RETRIEVAL OF AEROSOL MICROPHYSICAL PROPERTIES BASED ON THE OPTIMAL ESTIMATION METHOD: INFORMATION CONTENT ANALYSIS FOR SATELLITE POLARIMETRIC REMOTE SENSING MEASUREMENTS

Directory of Open Access Journals (Sweden)

W. Z. Hou

2018-04-01

Full Text Available This paper evaluates the information content for the retrieval of key aerosol microphysical and surface properties for multispectral single-viewing satellite polarimetric measurements cantered at 410, 443, 555, 670, 865, 1610 and 2250 nm over bright land. To conduct the information content analysis, the synthetic data are simulated by the Unified Linearized Vector Radiative Transfer Model (UNLVTM with the intensity and polarization together over bare soil surface for various scenarios. Following the optimal estimation theory, a principal component analysis method is employed to reconstruct the multispectral surface reflectance from 410 nm to 2250 nm, and then integrated with a linear one-parametric BPDF model to represent the contribution of polarized surface reflectance, thus further to decouple the surface-atmosphere contribution from the TOA measurements. Focusing on two different aerosol models with the aerosol optical depth equal to 0.8 at 550 nm, the total DFS and DFS component of each retrieval aerosol and surface parameter are analysed. The DFS results show that the key aerosol microphysical properties, such as the fine- and coarse-mode columnar volume concentration, the effective radius and the real part of complex refractive index at 550 nm, could be well retrieved with the surface parameters simultaneously over bare soil surface type. The findings of this study can provide the guidance to the inversion algorithm development over bright surface land by taking full use of the single-viewing satellite polarimetric measurements.

Retrieval of Aerosol Microphysical Properties Based on the Optimal Estimation Method: Information Content Analysis for Satellite Polarimetric Remote Sensing Measurements

Science.gov (United States)

Hou, W. Z.; Li, Z. Q.; Zheng, F. X.; Qie, L. L.

2018-04-01

This paper evaluates the information content for the retrieval of key aerosol microphysical and surface properties for multispectral single-viewing satellite polarimetric measurements cantered at 410, 443, 555, 670, 865, 1610 and 2250 nm over bright land. To conduct the information content analysis, the synthetic data are simulated by the Unified Linearized Vector Radiative Transfer Model (UNLVTM) with the intensity and polarization together over bare soil surface for various scenarios. Following the optimal estimation theory, a principal component analysis method is employed to reconstruct the multispectral surface reflectance from 410 nm to 2250 nm, and then integrated with a linear one-parametric BPDF model to represent the contribution of polarized surface reflectance, thus further to decouple the surface-atmosphere contribution from the TOA measurements. Focusing on two different aerosol models with the aerosol optical depth equal to 0.8 at 550 nm, the total DFS and DFS component of each retrieval aerosol and surface parameter are analysed. The DFS results show that the key aerosol microphysical properties, such as the fine- and coarse-mode columnar volume concentration, the effective radius and the real part of complex refractive index at 550 nm, could be well retrieved with the surface parameters simultaneously over bare soil surface type. The findings of this study can provide the guidance to the inversion algorithm development over bright surface land by taking full use of the single-viewing satellite polarimetric measurements.

A novel automatic quantification method for high-content screening analysis of DNA double strand-break response.

Science.gov (United States)

Feng, Jingwen; Lin, Jie; Zhang, Pengquan; Yang, Songnan; Sa, Yu; Feng, Yuanming

2017-08-29

High-content screening is commonly used in studies of the DNA damage response. The double-strand break (DSB) is one of the most harmful types of DNA damage lesions. The conventional method used to quantify DSBs is γH2AX foci counting, which requires manual adjustment and preset parameters and is usually regarded as imprecise, time-consuming, poorly reproducible, and inaccurate. Therefore, a robust automatic alternative method is highly desired. In this manuscript, we present a new method for quantifying DSBs which involves automatic image cropping, automatic foci-segmentation and fluorescent intensity measurement. Furthermore, an additional function was added for standardizing the measurement of DSB response inhibition based on co-localization analysis. We tested the method with a well-known inhibitor of DSB response. The new method requires only one preset parameter, which effectively minimizes operator-dependent variations. Compared with conventional methods, the new method detected a higher percentage difference of foci formation between different cells, which can improve measurement accuracy. The effects of the inhibitor on DSB response were successfully quantified with the new method (p = 0.000). The advantages of this method in terms of reliability, automation and simplicity show its potential in quantitative fluorescence imaging studies and high-content screening for compounds and factors involved in DSB response.

Flow cytometric and microscopic analysis of the effect of tannic acid on plant nuclei and estimation of DNA content

Czech Academy of Sciences Publication Activity Database

Loureiro, J.; Rodriguez, E.; Doležel, Jaroslav; Santos, C.

2006-01-01

Roč. 98, - (2006), s. 515-527 ISSN 0305-7364 R&D Projects: GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : genome size * flow cytometry * nuclear DNA content Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.448, year: 2006

Cell cycle phase of nondividing cells in aging human cell cultures determined by DNA content and chromosomal constitution

International Nuclear Information System (INIS)

Yanishevsky, R.M.

1975-01-01

Human diploid cell cultures, strain WI-38, have a finite proliferative capacity and have been proposed as a model of biological aging. To identify the cell cycle phase of the nondividing cells, cultures of various ages were exposed to 3 Hdt for 48 hours to label dividing cells, then the cycle phase was identified for individual cells by one of two methods, and finally, the proliferative status of the same cells was scored by autoradiographic evidence of 3 HdT uptake. The methods to identify the cycle phase were: determination of DNA strain content by Feulgen scanning cytophotometry, and determination of chromosome constitution by the technique of premature chromosome condensation (PCC). Preliminary experiments showed the effect of continuous exposure to various levels of 3 HdT on cell growth. High levels of 3 HdT inhibited cell cycle traverse: the cell number and labeling index curves reached a plateau; the cell volume increased; the cells accumulated with 4C DNA contents and it appeared that they blocked in G 2 phase. This pattern is consistent with a radiation effect. (U.S.)

Interspersion of highly repetitive DNA with single copy DNA in the genome of the red crab, Geryon quinquedens

Energy Technology Data Exchange (ETDEWEB)

Christie, N.T. (Univ. of Tennessee, Oak Ridge); Skinner, D.M.

1979-02-01

Kinetic analysis of the reassociation of 420 nucleotide (NT) long fragments has shown that essentially all of the repetitive sequences of the DNA of the red crab Geryon quinquedens are highly repetitive. There are negligible amounts of low and intermediate repetitive DNAs. Though atypical of most eukaryotes, this pattern has been observed in al other brachyurans (true crabs) studied. The major repetitive component is subdivided into short runs of 300 NT and longer runs of greater than 1200 NT while the minor component has an average sequence length of 400 NT. Both components reassociate at rates commonly observed for satellite DNAs. Unique among eukaryotes the organization of the genome includes single copy DNA contiguous to short runs (300 NT) of both repetitive components. Although patent satellites are not present, subsets of the repetitive DNA have been isolated by either restriction endonuclease digestion or by centrifugation in Ag/sup +/ or Hg/sup 2 +//Cs/sub 2/SO/sub 4/ density gradients.

More efficient repair of DNA double-strand breaks in skeletal muscle stem cells compared to their committed progeny

Directory of Open Access Journals (Sweden)

Leyla Vahidi Ferdousi

2014-11-01

Full Text Available The loss of genome integrity in adult stem cells results in accelerated tissue aging and is possibly cancerogenic. Adult stem cells in different tissues appear to react robustly to DNA damage. We report that adult skeletal stem (satellite cells do not primarily respond to radiation-induced DNA double-strand breaks (DSBs via differentiation and exhibit less apoptosis compared to other myogenic cells. Satellite cells repair these DNA lesions more efficiently than their committed progeny. Importantly, non-proliferating satellite cells and post-mitotic nuclei in the fiber exhibit dramatically distinct repair efficiencies. Altogether, reduction of the repair capacity appears to be more a function of differentiation than of the proliferation status of the muscle cell. Notably, satellite cells retain a high efficiency of DSB repair also when isolated from the natural niche. Finally, we show that repair of DSB substrates is not only very efficient but, surprisingly, also very accurate in satellite cells and that accurate repair depends on the key non-homologous end-joining factor DNA-PKcs.

More efficient repair of DNA double-strand breaks in skeletal muscle stem cells compared to their committed progeny.

Science.gov (United States)

Vahidi Ferdousi, Leyla; Rocheteau, Pierre; Chayot, Romain; Montagne, Benjamin; Chaker, Zayna; Flamant, Patricia; Tajbakhsh, Shahragim; Ricchetti, Miria

2014-11-01

The loss of genome integrity in adult stem cells results in accelerated tissue aging and is possibly cancerogenic. Adult stem cells in different tissues appear to react robustly to DNA damage. We report that adult skeletal stem (satellite) cells do not primarily respond to radiation-induced DNA double-strand breaks (DSBs) via differentiation and exhibit less apoptosis compared to other myogenic cells. Satellite cells repair these DNA lesions more efficiently than their committed progeny. Importantly, non-proliferating satellite cells and post-mitotic nuclei in the fiber exhibit dramatically distinct repair efficiencies. Altogether, reduction of the repair capacity appears to be more a function of differentiation than of the proliferation status of the muscle cell. Notably, satellite cells retain a high efficiency of DSB repair also when isolated from the natural niche. Finally, we show that repair of DSB substrates is not only very efficient but, surprisingly, also very accurate in satellite cells and that accurate repair depends on the key non-homologous end-joining factor DNA-PKcs. Copyright © 2014. Published by Elsevier B.V.

Human Artificial Chromosomes with Alpha Satellite-Based De Novo Centromeres Show Increased Frequency of Nondisjunction and Anaphase Lag

OpenAIRE

Rudd, M. Katharine; Mays, Robert W.; Schwartz, Stuart; Willard, Huntington F.

2003-01-01

Human artificial chromosomes have been used to model requirements for human chromosome segregation and to explore the nature of sequences competent for centromere function. Normal human centromeres require specialized chromatin that consists of alpha satellite DNA complexed with epigenetically modified histones and centromere-specific proteins. While several types of alpha satellite DNA have been used to assemble de novo centromeres in artificial chromosome assays, the extent to which they fu...

Early- and later-phases satellite cell responses and myonuclear content with resistance training in young men.

Science.gov (United States)

Damas, Felipe; Libardi, Cleiton A; Ugrinowitsch, Carlos; Vechin, Felipe C; Lixandrão, Manoel E; Snijders, Tim; Nederveen, Joshua P; Bacurau, Aline V; Brum, Patricia; Tricoli, Valmor; Roschel, Hamilton; Parise, Gianni; Phillips, Stuart M

2018-01-01

Satellite cells (SC) are associated with skeletal muscle remodelling after muscle damage and/or extensive hypertrophy resulting from resistance training (RT). We recently reported that early increases in muscle protein synthesis (MPS) during RT appear to be directed toward muscle damage repair, but MPS contributes to hypertrophy with progressive muscle damage attenuation. However, modulations in acute-chronic SC content with RT during the initial (1st-wk: high damage), early (3rd-wk: attenuated damage), and later (10th-wk: no damage) stages is not well characterized. Ten young men (27 ± 1 y, 23.6 ± 1.0 kg·m-2) underwent 10-wks of RT and muscle biopsies (vastus-lateralis) were taken before (Pre) and post (48h) the 1st (T1), 5th (T2) and final (T3) RT sessions to evaluate fibre type specific SC content, cross-sectional area (fCSA) and myonuclear number by immunohistochemistry. We observed RT-induced hypertrophy after 10-wks of RT (fCSA increased ~16% in type II, P phase of RT than muscle hypertrophy resulted from 10-wks RT in young men. Chronic elevated SC pool size with RT is important providing proper environment for future stresses or larger fCSA increases.

Gastric lymphomas in Turkey. Analysis of prognostic factors with special emphasis on flow cytometric DNA content.

Science.gov (United States)

Aydin, Z D; Barista, I; Canpinar, H; Sungur, A; Tekuzman, G

2000-07-01

In contrast to DNA ploidy, to the authors' knowledge the prognostic significance of S-phase fraction (SPF) in gastric lymphomas has not been determined. In the current study, the prognostic significance of various parameters including SPF and DNA aneuploidy were analyzed and some distinct epidemiologic and biologic features of gastric lymphomas in Turkey were found. A series of 78 gastric lymphoma patients followed at Hacettepe University is reported. DNA flow cytometry was performed for 34 patients. The influence of various parameters on survival was investigated with the log rank test. The Cox proportional hazards model was fitted to identify independent prognostic factors. The median age of the patients was 50 years. There was no correlation between patient age and tumor grade. DNA content analysis revealed 4 of the 34 cases to be aneuploid with DNA index values < 1.0. The mean SPF was 33.5%. In the univariate analysis, surgical resection of the tumor, modified Ann Arbor stage, performance status, response to first-line chemotherapy, lactate dehydrogenase (LDH) level, and SPF were important prognostic factors for disease free survival (DFS). The same parameters, excluding LDH level, were important for determining overall survival (OS). In the multivariate analysis, surgical resection of the tumor, disease stage, performance status, and age were found to be important prognostic factors for OS. To the authors' knowledge the current study is the first to demonstrate the prognostic significance of SPF in gastric lymphomas. The distinguishing features of Turkish gastric lymphoma patients are 1) DNA indices of aneuploid cases that all are < 1.0, which is a unique feature; 2) a lower percentage of aneuploid cases; 3) a higher SPF; 4) a younger age distribution; and 5) lack of an age-grade correlation. The authors conclude that gastric lymphomas in Turkey have distinct biologic and epidemiologic characteristics. Copyright 2000 American Cancer Society.

Analysis of pyrimidine dimer content of isolated DNA by nuclease digestion

International Nuclear Information System (INIS)

Farland, W.H.; Sutherland, B.M.

1980-01-01

Isolated DNA is highly susceptible to degradation by exogenous nucleases. Complete digestion is possible with a number of well-characterized enzymes from a variety of sources. Treatment of DNA with a battery of enzymes including both phosphodiesterase and phosphatase activities yields a mixture of nucleosides and inorganic phosphate (P/sub i/) as a final product. Unlike native DNA, ultraviolet-irradiated DNA is resistant to complete digestion. Setlow et al. demonstrated that the structural changes in the DNA responsible for the nuclease resistance were the formation of cyclobutyl pyrimidine dimers, the major photoproduct in UV-irradiated DNA. Using venom phosphodiesterase, they demonstrated that UV irradiation of DNA affected both the rate and extent of enzymatic hydrolysis. In addition, it was demonstrated that the major nuclease-resistant product of this hydrolysis was an oligonucleotide containing dimerized pyrimidines. Treatment of the DNA to split the dimers, either photochemically or photoenzymatically, rendered the polymer more susceptible to hydrolysis by the phosphodiesterase. The specificity of photoreactivating enzyme for pyrimidine dimers lends support to the role of these structures in conferring nuclease resistance to UV-irradiated DNA. The nuclease resistance of DNA containing dimers has been the basis of several assays for the measurement of these photoproducts. Sutherland and Chamberlin reported the development of a rapid and sensitive assay for dimers in 32 P-labeled DNA

Influence of serum HBV-DNA content on the expression of TGF-β1 and TNF-α in patients with chronic hepatitis B

International Nuclear Information System (INIS)

Gao Yujie; Nan Chunhong; Yan Lijuan; Yue Zhijun; Yang Zhicai

2004-01-01

Objective: To study the relationship between the serum HBV-DNA content and levels of transforming growth factor β1 (TGF-β1), tumor necrosis factor-α (TNF-α) as well as the degree of hepatic fibrosis in patients with chronic hepatitis B. Methods: Serum HBV-DNA content quantification was determined with PCR-real time fluorescence method; TGF-β1 and TNF-α with ELISA and the hepatic fibrosis indicators HA, LN, IV-C, P-III with RIA. Altogether 89 patients with clinical chronic hepatitis B of various degrees (mild 25, moderate 35, advanced 29) were tested. Results: With the progress of hepatic injury, the serum contents of HBV-DNA, TGF-β1, TNF-α were correspondingly increased with significant differences among the patients groups (p<0.01). The TGF-β1, TNF-α, HA, IV-C, PC III, levels were positively correlated to the degree of hepatic injury with r=0.9561, 0.8123, 0.8561, 0.7723, 0.7150 respectively and p<0.01; for LN it was r=0.542 and p<0.05. Conclusion: In patients with chronic hepatitis B, hepatic fibrosis is the fundamental process in the pathogenesis of liver cirrhosis. High concentration of HBV is the crucial factor for development of hepatic fibrosis, which works synergically with many cytokines especially TGF-β1 and TNF-α

Evaluation of DNA bending models in their capacity to predict electrophoretic migration anomalies of satellite DNA sequences

Czech Academy of Sciences Publication Activity Database

Matyášek, Roman; Fulneček, Jaroslav; Kovařík, Aleš

2013-01-01

Roč. 34, č. 17 (2013), s. 2511-2521 ISSN 0173-0835 R&D Projects: GA ČR(CZ) GA206/09/1751; GA ČR(CZ) GAP501/10/0208; GA ČR(CZ) GA13-10057S Institutional research plan: CEZ:AV0Z50040702 Institutional support: RVO:68081707 Keywords : HIGHLY REPETITIVE DNA * DOUBLE-HELICAL DNA * CURVED DNA Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 3.161, year: 2013

qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

International Nuclear Information System (INIS)

Jackson, Christopher B.; Gallati, Sabina; Schaller, André

2012-01-01

Highlights: ► Serial qPCR accurately determines fragmentation state of any given DNA sample. ► Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. ► Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. ► Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze–thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA (λ nDNA ) and mtDNA (λ mtDNA ) we present an approach to possibly correct measurements in degraded samples in the future. To our knowledge this is the first time different degradation impact of the two

qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

Energy Technology Data Exchange (ETDEWEB)

Jackson, Christopher B., E-mail: Christopher.jackson@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland); Gallati, Sabina, E-mail: sabina.gallati@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland); Schaller, Andre, E-mail: andre.schaller@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland)

2012-07-06

Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA ({lambda}{sub nDNA}) and mtDNA ({lambda}{sub mtDNA}) we present an approach to possibly correct measurements in

Arginine-rich cross-linking peptides with different SV40 nuclear localization signal content as vectors for intranuclear DNA delivery.

Science.gov (United States)

Bogacheva, Mariia; Egorova, Anna; Slita, Anna; Maretina, Marianna; Baranov, Vladislav; Kiselev, Anton

2017-11-01

The major barriers for intracellular DNA transportation by cationic polymers are their toxicity, poor endosomal escape and inefficient nuclear uptake. Therefore, we designed novel modular peptide-based carriers modified with SV40 nuclear localization signal (NLS). Core peptide consists of arginine, histidine and cysteine residues for DNA condensation, endosomal escape promotion and interpeptide cross-linking, respectively. We investigated three polyplexes with different NLS content (10 mol%, 50 mol% and 90 mol% of SV40 NLS) as vectors for intranuclear DNA delivery. All carriers tested were able to condense DNA, to protect it from DNAase I and were not toxic to the cells. We observed that cell cycle arrest by hydroxyurea did not affect transfection efficacy of NLS-modified carriers which we confirmed using quantitative confocal microscopy analysis. Overall, peptide carrier modified with 90 mol% of SV40 NLS provided efficient transfection and nuclear uptake in non-dividing cells. Thus, incorporation of NLS into arginine-rich cross-linking peptides is an adequate approach to the development of efficient intranuclear gene delivery vehicles. Copyright © 2017 Elsevier Ltd. All rights reserved.

G+C content dominates intrinsic nucleosome occupancy

Directory of Open Access Journals (Sweden)

Hughes Timothy R

2009-12-01

Full Text Available Abstract Background The relative preference of nucleosomes to form on individual DNA sequences plays a major role in genome packaging. A wide variety of DNA sequence features are believed to influence nucleosome formation, including periodic dinucleotide signals, poly-A stretches and other short motifs, and sequence properties that influence DNA structure, including base content. It was recently shown by Kaplan et al. that a probabilistic model using composition of all 5-mers within a nucleosome-sized tiling window accurately predicts intrinsic nucleosome occupancy across an entire genome in vitro. However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences. Results We find that a simple linear combination of only 14 simple DNA sequence attributes (G+C content, two transformations of dinucleotide composition, and the frequency of eleven 4-bp sequences explains nucleosome occupancy in vitro and in vivo in a manner comparable to the Kaplan model. G+C content and frequency of AAAA are the most important features. G+C content is dominant, alone explaining ~50% of the variation in nucleosome occupancy in vitro. Conclusions Our findings provide a dramatically simplified means to predict and understand intrinsic nucleosome occupancy. G+C content may dominate because it both reduces frequency of poly-A-like stretches and correlates with many other DNA structural characteristics. Since G+C content is enriched or depleted at many types of features in diverse eukaryotic genomes, our results suggest that variation in nucleotide composition may have a widespread and direct influence on chromatin structure.

More efficient repair of DNA double-strand breaks in skeletal muscle stem cells compared to their committed progeny

OpenAIRE

Leyla Vahidi Ferdousi; Pierre Rocheteau; Romain Chayot; Benjamin Montagne; Zayna Chaker; Patricia Flamant; Shahragim Tajbakhsh; Miria Ricchetti

2014-01-01

International audience; The loss of genome integrity in adult stem cells results in accelerated tissue aging and is possibly cancerogenic. Adult stem cells in different tissues appear to react robustly to DNA damage. We report that adult skeletal stem (satellite) cells do not primarily respond to radiation-induced DNA double-strand breaks (DSBs) via differentiation and exhibit less apoptosis compared to other myogenic cells. Satellite cells repair these DNA lesions more efficiently than their...

Dissociation between insulin secretion and DNA synthesis in cultured pancreatic islets

DEFF Research Database (Denmark)

Nielsen, Jens Høiriis

1985-01-01

-Tdr incorporation. However, long-term exposure to IBMX did not result in increased DNA content of the islets. Inhibition of the DNA synthesis by 5 mM hydroxyurea resulted in a marked reduction in DNA content of the islets but no decrease in either insulin release or insulin content when expressed per ng DNA...

Nuclear and mitochondrial DNA quantification of various forensic materials.

Science.gov (United States)

Andréasson, H; Nilsson, M; Budowle, B; Lundberg, H; Allen, M

2006-12-01

Due to the different types and quality of forensic evidence materials, their DNA content can vary substantially, and particularly low quantities can impact the results in an identification analysis. In this study, the quantity of mitochondrial and nuclear DNA was determined in a variety of materials using a previously described real-time PCR method. DNA quantification in the roots and distal sections of plucked and shed head hairs revealed large variations in DNA content particularly between the root and the shaft of plucked hairs. Also large intra- and inter-individual variations were found among hairs. In addition, DNA content was estimated in samples collected from fingerprints and accessories. The quantification of DNA on various items also displayed large variations, with some materials containing large amounts of nuclear DNA while no detectable nuclear DNA and only limited amounts of mitochondrial DNA were seen in others. Using this sensitive real-time PCR quantification assay, a better understanding was obtained regarding DNA content and variation in commonly analysed forensic evidence materials and this may guide the forensic scientist as to the best molecular biology approach for analysing various forensic evidence materials.

Satellite spectrophotometer for research of the atmospheric ozone

International Nuclear Information System (INIS)

Getzov, P.; Mardirossian, G.; Stoyanov, S.

2014-01-01

The measurement of atmospheric ozone and its influence upon climate and life on Earth is undoubtedly one of the most pressing issues of present time. A mathematical model of an optical tract of a spectrophotometer has been designed. The paper presents the functional scheme of a satellite optoelectronic spectrophotometer for measuring the total content of atmospheric ozone and other gas components of the atmosphere, which has increased precision, smaller weight and energy consumption, increased space and time resolution, quickness of reaction and increased volume of useful information. The object of the paper is the design of an appliance which ensures research of ozone content in atmosphere from the board of a satellite

DNA content of cells with generalized chromosome shattering induced by ultraviolet light plus caffeine

International Nuclear Information System (INIS)

Cremer, C.; Gray, J.W.

1982-01-01

Asynchronously growing Chinese hamster cells (M3-1) were UV-irradiated (lambda = 254 nm) and then incubated with/without caffeine (2 mM) for 20 h. Microscopic evaluation of metaphase spreads revealed that after UV-irradiation alone (5.0 J/m 2 ) and caffeine treatment alone, the percentage of cells with condensed chromatin appearing fragmented and/or pulverized ('GCS-like' cells; GCS, Generalized Chromosome Shattering) was very low while it was high following the combined treatment. Cytogenetic and flow cytometric analysis of cells obtained by mechanical shaking cultures treated with UV and caffeine indicated that 'GCS-like' cells have the same DNA content as untreated cells in G2 phase and mitosis. (orig.)

GPS-based satellite tracking system for precise positioning

Science.gov (United States)

Yunck, T. P.; Melbourne, W. G.; Thornton, C. L.

1985-01-01

NASA is developing a Global Positioning System (GPS) based measurement system to provide precise determination of earth satellite orbits, geodetic baselines, ionospheric electron content, and clock offsets between worldwide tracking sites. The system will employ variations on the differential GPS observing technique and will use a network of nine fixed ground terminals. Satellite applications will require either a GPS flight receiver or an on-board GPS beacon. Operation of the system for all but satellite tracking will begin by 1988. The first major satellite application will be a demonstration of decimeter accuracy in determining the altitude of TOPEX in the early 1990's. By then the system is expected to yield long-baseline accuracies of a few centimeters and instantaneous time synchronization to 1 ns.

Boom-Bust Turnovers of Megabase-Sized Centromeric DNA in Solanum Species: Rapid Evolution of DNA Sequences Associated with Centromeres

Czech Academy of Sciences Publication Activity Database

Zhang, H.Q.; Koblížková, Andrea; Wang, K.; Gong, Z.Y.; Oliveira, L.; Torres, G.A.; Wu, Y.; Zhang, W.; Novák, Petr; Buell, C.R.; Macas, Jiří; Jiang, J.

2014-01-01

Roč. 26, č. 4 (2014), s. 1436-1447 ISSN 1040-4651 Institutional support: RVO:60077344 Keywords : Alpha-satellite DNA * repetitive sequences * rice centromeres Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.338, year: 2014

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.

Fluorescence Microscopy of Nanochannel-Confined DNA.

Science.gov (United States)

Westerlund, Fredrik; Persson, Fredrik; Fritzsche, Joachim; Beech, Jason P; Tegenfeldt, Jonas O

2018-01-01

Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level and both the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments and analyze the data.

High-resolution DNA content analysis of microbiopsy samples in oral lichen planus.

Science.gov (United States)

Pentenero, M; Monticone, M; Marino, R; Aiello, C; Marchitto, G; Malacarne, D; Giaretti, W; Gandolfo, S; Castagnola, P

2017-04-01

DNA aneuploidy has been reported to be a predictor of poor prognosis in both premalignant and malignant lesions. In oral lichen planus (OLP), this hypothesis remains to be proved. This study aimed to determine the rate of occurrence of DNA aneuploidy in patients with OLP by high-resolution DNA flow cytometry. Patients with OLP were consecutively enrolled. Tissue samples were subdivided for formalin fixation and routine histological assessment and for immediate storage at -20°C for later DNA ploidy analysis, which was performed by DAPI staining of the extracted nuclei and excitation with a UV lamp. The DNA aneuploid sublines were characterized by the DNA Index. A DNA aneuploid status was observed in two of 77 patients with OLP (2.6%). When considering the clinical aspect of the OLP lesions, both DNA aneuploid cases had a reticular clinical aspect. DNA aneuploidy is an uncommon event in OLP and less frequent compared to other non-dysplastic and non-OLP oral potentially malignant disorders. The extremely low rate of DNA aneuploidy could represent an occasional finding or reflect the low rate of malignant transformation observed in patients with OLP even if the real prognostic value of DNA ploidy analysis in patients with OLP remains to be confirmed. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Role of oxidative DNA damage in genome instability and cancer

International Nuclear Information System (INIS)

Bignami, M.; Kunkel, T.

2009-01-01

Inactivation of mismatch repair (MMR) is associated with a dramatic genomic instability that is observed experimentally as a mutator phenotype and micro satellite instability (MSI). It has been implicit that the massive genetic instability in MMR defective cells simply reflects the accumulation of spontaneous DNA polymerase errors during DNA replication. We recently identified oxidation damage, a common threat to DNA integrity to which purines are very susceptible, as an important cofactor in this genetic instability

Satellites

International Nuclear Information System (INIS)

Burns, J.A.; Matthews, M.S.

1986-01-01

The present work is based on a conference: Natural Satellites, Colloquium 77 of the IAU, held at Cornell University from July 5 to 9, 1983. Attention is given to the background and origins of satellites, protosatellite swarms, the tectonics of icy satellites, the physical characteristics of satellite surfaces, and the interactions of planetary magnetospheres with icy satellite surfaces. Other topics include the surface composition of natural satellites, the cratering of planetary satellites, the moon, Io, and Europa. Consideration is also given to Ganymede and Callisto, the satellites of Saturn, small satellites, satellites of Uranus and Neptune, and the Pluto-Charon system

Application of Remote Sensing for Mapping Soil Organic Matter Content

Directory of Open Access Journals (Sweden)

Bangun Muljo Sukojo

2010-10-01

Full Text Available Information organic content is important in monitoring and managing the environment as well as doing agricultural production activities. This research tried to map soil organic content in Malang using remote sensing technology. The research uses 6 bands of data captured by Landsat TM (Thematic Mapper satellite (band 1, 2, 3, 4, 5, 7. The research focuses on pixels having Normalized Difference Soil Index (NDSI more than 0.3. Ground-truth data were collected by analysing organic content of soil samples using Black-Walkey method. The result of analysis shows that digital number of original satellite image can be used to predict soil organic matter content. The implementation of regression equation in predicting soil organic content shows that 63.18% of research area contains of organic in a moderate category.

Quantifying quality in DNA self-assembly

Science.gov (United States)

Wagenbauer, Klaus F.; Wachauf, Christian H.; Dietz, Hendrik

2014-01-01

Molecular self-assembly with DNA is an attractive route for building nanoscale devices. The development of sophisticated and precise objects with this technique requires detailed experimental feedback on the structure and composition of assembled objects. Here we report a sensitive assay for the quality of assembly. The method relies on measuring the content of unpaired DNA bases in self-assembled DNA objects using a fluorescent de-Bruijn probe for three-base ‘codons’, which enables a comparison with the designed content of unpaired DNA. We use the assay to measure the quality of assembly of several multilayer DNA origami objects and illustrate the use of the assay for the rational refinement of assembly protocols. Our data suggests that large and complex objects like multilayer DNA origami can be made with high strand integration quality up to 99%. Beyond DNA nanotechnology, we speculate that the ability to discriminate unpaired from paired nucleic acids in the same macromolecule may also be useful for analysing cellular nucleic acids. PMID:24751596

DNA methylation dynamics in muscle development and disease

Directory of Open Access Journals (Sweden)

Elvira eCarrio

2015-03-01

Full Text Available DNA methylation is an essential epigenetic modification for mammalian development and is crucial for the establishment and maintenance of cellular identity. Traditionally, DNA methylation has been considered as a permanent repressive epigenetic mark. However, the application of genome-wide approaches has allowed the analysis of DNA methylation in different genomic contexts revealing a more dynamic regulation than originally thought, since active DNA methylation and demethylation occur during cellular differentiation and tissue specification. Satellite cells are the primary stem cells in adult skeletal muscle and are responsible for postnatal muscle growth, hypertrophy, and muscle regeneration. This review outlines the published data regarding DNA methylation changes along the skeletal muscle program, in both physiological and pathological conditions, to better understand the epigenetic mechanisms that control myogenesis

A SERS-active sensor based on heterogeneous gold nanostar core-silver nanoparticle satellite assemblies for ultrasensitive detection of aflatoxinB1.

Science.gov (United States)

Li, Aike; Tang, Lijuan; Song, Dan; Song, Shanshan; Ma, Wei; Xu, Liguang; Kuang, Hua; Wu, Xiaoling; Liu, Liqiang; Chen, Xin; Xu, Chuanlai

2016-01-28

A surface-enhanced Raman scattering (SERS) sensor based on gold nanostar (Au NS) core-silver nanoparticle (Ag NP) satellites was fabricated for the first time to detect aflatoxinB1 (AFB1). We constructed the SERS sensor using AFB1 aptamer (DNA1)-modified Ag satellites and a complementary sequence (DNA2)-modified Au NS core. The Raman label (ATP) was modified on the surface of Ag satellites. The SERS signal was enhanced when the satellite NP was attached to the Au core NS. The AFB1 aptamer on the surface of Ag satellites would bind to the targets when AFB1 was present in the system, Ag satellites were then removed and the SERS signal decreased. This SERS sensor showed superior specificity for AFB1 and the linear detection range was from 1 to 1000 pg mL(-1) with the limit of detection (LOD) of 0.48 pg mL(-1). The excellent recovery experiment using peanut milk demonstrated that the sensor could be applied in food and environmental detection.

Measurement of total electron content of midlatitude ionosphere and protonosphere via Faraday rotation and group relay techniques using transmission from geostationary satellites ATS-3 and ATS-6

Science.gov (United States)

Paul, M. P.

1982-01-01

Measurement of integrated columnar electron content and total electron content for the local ionosphere and the overlying protonosphere via Faraday rotation and group delay techniques has proven very useful. A field station was established having the geographic location of 31.5 deg N latitude and 91.06 deg W longitude to accomplish these objectives. A polarimeter receiving system was set up in the beginning to measure the Faraday rotation of 137.35 MHz radio signal from geostationary satellite ATS 3 to yield the integrated columnar electron content of the local ionosphere. The measurement was continued regularly, and the analysis of the data thus collected provided a synopsis of the statistical variation of the ionosphere along with the transient variations that occurred during the periods of geomagnetic and other disturbances.

Blood extracellular DNA after irradiation

International Nuclear Information System (INIS)

Vladimirov, V.G.; Tishchenko, L.I.; Surkova, E.A.; Vasil'eva, I.N.

1993-01-01

It has been shown that blood extracellular DNA of irradiated rats largely consists of the low-molecular DNA and its oligomers. Molecular masses of oligomers are multiple to molecular mass of monomer fragment with nucleosome size. The low-molecular DNA has linear form. The average content of GC-pairs in low-molecular DNA is higher than in total rat's DNA (48.5% against 41.5%). The low-molecular DNA is a part of complex containing RNA, acidic proteins and lipids. It is assumed that the formation of low-molecular DNA is a result of Ca/Mg - dependent nuclear endonuclease action

Fluorescence quantitative PCR in detection of HBV DNA

International Nuclear Information System (INIS)

Shen Zheng; Li Ming; Shen Xia

2003-01-01

Objective: To study the relationship between the serum content of HBV-DNA and expression of serological markers with HBV infection patients. Methods: Serum samples from 375 hepatitis B patients with different clinical status and 70 normal persons were quantitated for HBV-DNA by FQ-PCR. Results: The average of HBV-DNA contents in the patient in the groups of HBsAg (+) and of HBeAg(+) were significantly higher than those in the group of HBsAg(-) and of HBeAg(-). Even in the group of HBeAg negative, high HBV-DNA contents might still be present in both the HBeAg(+) and HBeAg(-) groups. Conclusion: FQ-PCR can be used to monitor the real state of HBV infection, replication and the course of disease

Remote sensing of the ionosphere using satellite radio beacons

International Nuclear Information System (INIS)

Davies, Kenneth

1991-01-01

Since the launch of Sputnik I in 1957, satellite radio beacons have been used to measure the total electron content of the ionosphere. A review of the role of satellite beacons in studies of the vertical and spatial structure of the total electron content and on the occurrence of plasma irregularities, both of which affect transionospheric radio signals, is presented. Measurements of Faraday rotation and time of flight give information on the topside of the ionosphere and on the protonosphere. Morphological studies show that the slab thickness of the ionosphere depends on the solar index but is approximately independent of geographical location. Scintillation of amplitude, phase, polarization, and angle provide information on plasma irregularity occurrence in space and time. (author). 23 refs., 16 figs ., 4 tabs

Application of Near-Infrared Spectroscopy to Quantitatively Determine Relative Content of Puccnia striiformis f. sp. tritici DNA in Wheat Leaves in Incubation Period

Directory of Open Access Journals (Sweden)

Yaqiong Zhao

2017-01-01

Full Text Available Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst is a devastating wheat disease worldwide. Potential application of near-infrared spectroscopy (NIRS in detection of pathogen amounts in latently Pst-infected wheat leaves was investigated for disease prediction and control. A total of 300 near-infrared spectra were acquired from the Pst-infected leaf samples in an incubation period, and relative contents of Pst DNA in the samples were obtained using duplex TaqMan real-time PCR arrays. Determination models of the relative contents of Pst DNA in the samples were built using quantitative partial least squares (QPLS, support vector regression (SVR, and a method integrated with QPLS and SVR. The results showed that the kQPLS-SVR model built with a ratio of training set to testing set equal to 3 : 1 based on the original spectra, when the number of the randomly selected wavelength points was 700, the number of principal components was 8, and the number of the built QPLS models was 5, was the best. The results indicated that quantitative detection of Pst DNA in leaves in the incubation period could be implemented using NIRS. A novel method for determination of latent infection levels of Pst and early detection of stripe rust was provided.

Biomarkers of mitochondrial content in skeletal muscle of healthy young human subjects

DEFF Research Database (Denmark)

Larsen, Steen; Nielsen, Joachim; Hansen, Christina Neigaard

2012-01-01

Key points  Several biochemical measures of mitochondrial components are used as biomarkers of mitochondrial content and muscle oxidative capacity. However, no studies have validated these surrogates against a morphological measure of mitochondrial content in human subjects.  The most commonly used...... markers (citrate synthase activity, cardiolipin content, mitochondrial DNA content (mtDNA), complex I-V protein, and complex I-IV activity) were correlated with a measure of mitochondrial content (transmission electron microscopy) and muscle oxidative capacity (respiration in permeabilized fibres......).  Cardiolipin content followed by citrate synthase activity and complex I activity were the biomarkers showing the strongest association with mitochondrial content.  mtDNA was found to be a poor biomarker of mitochondrial content.  Complex IV activity was closely associated with mitochondrial oxidative...

Quantification of meat proportions by measuring DNA contents in raw and boiled sausages using matrix-adapted calibrators and multiplex real-time PCR.

Science.gov (United States)

Köppel, René; Eugster, Albert; Ruf, Jürg; Rentsch, Jürg

2012-01-01

The quantification of meat proportions in raw and boiled sausage according to the recipe was evaluated using three different calibrators. To measure the DNA contents from beef, pork, sheep (mutton), and horse, a tetraplex real-time PCR method was applied. Nineteen laboratories analyzed four meat products each made of different proportions of beef, pork, sheep, and horse meat. Three kinds of calibrators were used: raw and boiled sausages of known proportions ranging from 1 to 55% of meat, and a dilution series of DNA from muscle tissue. In general, results generated using calibration sausages were more accurate than those resulting from the use of DNA from muscle tissue, and exhibited smaller measurement uncertainties. Although differences between uses of raw and boiled calibration sausages were small, the most precise and accurate results were obtained by calibration with fine-textured boiled reference sausages.

Application of flow cytometry for exploring the evolution of Geosmithia fungi living in association with bark beetles: the role of conidial DNA content

Czech Academy of Sciences Publication Activity Database

Veselská, Tereza; Kolařík, Miroslav

2015-01-01

Roč. 13, FEB 2015 (2015), s. 83-92 ISSN 1754-5048 R&D Projects: GA ČR(CZ) GAP506/11/2302 Institutional support: RVO:61388971 Keywords : Ambrosia fungi * Bark beetles * Conidial DNA content Subject RIV: EE - Microbiology, Virology Impact factor: 2.631, year: 2015

DNA probes

International Nuclear Information System (INIS)

Castelino, J.

1992-01-01

The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

Effect of UV-irradiation on DNA-membrane complex of Bacillus subtilis

International Nuclear Information System (INIS)

Chefranova, O.A.; Gaziev, A.I.

1979-01-01

The UV radiation effect on DNA membrane complex of Bacillus subtilis has been studied. Increase of DNA content in the DNA membrane complex in two strains of 168 and recA - and its decrease in the polA - strain are shown. The above effect in the first two stamms is suppressed with caffeine and correlates with the change in protein content in the DNA membrane complex, determined by a radioactive label, but not lipids in other words, fixation of DNA and membrane goes through proteins. Capability of DNA content increase in the DNA membrane complex after UV irradiation and subsequent bacteria incubation in a total medium correlates with the relative sensitivity of stamm UV sensitivity. It is suggested, that the reparation synthesis goes in cells on the membrane and that binding of DNA and the membrane is necessary for the normal DNA reparation process

Image cytometry: nuclear and chromosomal DNA quantification.

Science.gov (United States)

Carvalho, Carlos Roberto; Clarindo, Wellington Ronildo; Abreu, Isabella Santiago

2011-01-01

Image cytometry (ICM) associates microscopy, digital image and software technologies, and has been particularly useful in spatial and densitometric cytological analyses, such as DNA ploidy and DNA content measurements. Basically, ICM integrates methodologies of optical microscopy calibration, standard density filters, digital CCD camera, and image analysis softwares for quantitative applications. Apart from all system calibration and setup, cytological protocols must provide good slide preparations for efficient and reliable ICM analysis. In this chapter, procedures for ICM applications employed in our laboratory are described. Protocols shown here for human DNA ploidy determination and quantification of nuclear and chromosomal DNA content in plants could be used as described, or adapted for other studies.

Evaluation of cell number and DNA content in mouse embryos cultivated with uranium; Evaluacion del numero de celulas y el contenido de DNA en embriones murinos cultivados con uranio

Energy Technology Data Exchange (ETDEWEB)

Kundt, Mirian S; Cabrini, Romulo L [Comision Nacional de Energia Atomica, General San Martin (Argentina). Dept. de Radiobiologia

2000-07-01

The evaluation of the degree of development, the number of cells and the DNA content, were used to evaluate the embryotoxicity of uranium. Embryos at a one cell stage were cultured with uranyl nitrate hexahydrate (UN) at a final concentration of uranium (U) of 26, 52 and 104 {mu}gU/ml. At 24 hs of culture, the embryos at the 2 cell stage, were put in new wells with the same concentrations of U as the previous day, until the end of the period of incubation at 72 hs. At 72 hs of culture, 87% of the original one cell embryos were at morula stage, and in those cultivated with uranium, the percentage decreased significantly to 77; 63.24 and 40.79% respectively for the different U concentrations. Those embryos that exhibited a normal morphology, were selected and fixed on slides. The number of cells per embryo was evaluated in Giemsa stained preparations. The DNA content was evaluated cytophotometrically in Feulgen stained nuclei. The number of cells decreased significantly from 20,3 {+-} 5.6 in the control to 19 {+-} 6; 14 {+-} 3 and 13.9 {+-} 5.6 for the different concentrations. All the embryos evaluated showed one easy recognizable polar body, which was used a haploid indicator (n). The content of DNA was measured in a total of 20 control embryos and 16 embryos cultivated with UN. In control embryos, 92,7% of the nuclei presented a normal ploidy from 2n to 4n, 2,9% nuclei were hypoploid and 4,4% were hyperploid. The percentage of hypoploid nuclei rose in a dose-dependent fashion to 3.45; 44.45 and 50.34% respectively for the embryos cultured at the different U concentrations. The results indicate that U is embryotoxic, that its effects are dose dependent at the concentrations used in this study and that even those embryos that show a normal morphology, can be genetically affected. We show that the model employed is extremely sensitive. It is possible to use the preimplantation embryos, as a model to test the effect of possibly mutagenic agents of the nuclear industry

Molecular characterization and chromosomal distribution of a species-specific transcribed centromeric satellite repeat from the olive fruit fly, Bactrocera oleae.

Directory of Open Access Journals (Sweden)

Konstantina T Tsoumani

Full Text Available Satellite repetitive sequences that accumulate in the heterochromatin consist a large fraction of a genome and due to their properties are suggested to be implicated in centromere function. Current knowledge of heterochromatic regions of Bactrocera oleae genome, the major pest of the olive tree, is practically nonexistent. In our effort to explore the repetitive DNA portion of B. oleae genome, a novel satellite sequence designated BoR300 was isolated and cloned. The present study describes the genomic organization, abundance and chromosomal distribution of BoR300 which is organized in tandem, forming arrays of 298 bp-long monomers. Sequence analysis showed an AT content of 60.4%, a CENP-B like-motif and a high curvature value based on predictive models. Comparative analysis among randomly selected monomers demonstrated a high degree of sequence homogeneity (88%-97% of BoR300 repeats, which are present at approximately 3,000 copies per haploid genome accounting for about 0.28% of the total genomic DNA, based on two independent qPCR approaches. In addition, expression of the repeat was also confirmed through RT-PCR, by which BoR300 transcripts were detected in both sexes. Fluorescence in situ hybridization (FISH of BoR300 on mitotic metaphases and polytene chromosomes revealed signals to the centromeres of two out of the six chromosomes which indicated a chromosome-specific centromeric localization. Moreover, BoR300 is not conserved in the closely related Bactrocera species tested and it is also absent in other dipterans, but it's rather restricted to the B. oleae genome. This feature of species-specificity attributed to BoR300 satellite makes it a good candidate as an identification probe of the insect among its relatives at early development stages.

[The development of pollen grains and formation of pollen tubes in higher plants : I. Quantitative measurements of the DNA-content of generative and vegetative nuclei in the pollen grain and pollen tube of Petunia hybrida mutants].

Science.gov (United States)

Hesemann, C U

1971-01-01

The DNA-content of generative and vegetative nuclei in mature pollen grains of four Petunia hybrida mutants was determined by cytophotometry. In addition the DNA-content of generative and vegetative nuclei in the pollen tube of two of these four mutants (virescens-2 n and ustulata-2 n) was cytophotometrically measured.The DNA-values found in the generative nuclei indicate that the DNA-replication continues in the mature pollen grain and comes to an end only after the migration of the nuclei into the pollen tube. These data are in disagreement with the results of DNA-measurements described for a limited number of other species which all show completion of DNA-synthesis during the maturation stage of the pollen grains.The vegetative nuclei of the four Petunia mutants studied show significant differences in the onset of the degenerative phase. Extreme variation is manifested in the ustulata-2 n mutant in which the degeneration of nuclei may reach the final stage in the maturing pollen grain. However in this mutant vegetative nuclei with an unaltered DNA-content may also be demonstrated in the pollen tube. Some of the vegetative nuclei in the pollen tube of ustulata-2 n exhibit an increased amount of DNA which could be the result of differential DNA-replication in the vegetative nuclei. The decrease of the DNA-content in a certain fraction of the vegetative nuclei in the maturing pollen grain does not agree with observations made in other species by several authors who report DNA constancy until the pollen grain is fully mature.The data obtained from the analysis of the four Petunia hybrida mutants point to an important role of the vegetative nucleus in the development of the pollen tube. The Petunia hybrida mutants may be regarded as especially favourable material for investigations concerning the function of the vegetative cell in the development of the pollen grain and pollen tube.

Engineering satellite-based navigation and timing global navigation satellite systems, signals, and receivers

CERN Document Server

Betz, J

2016-01-01

This book describes the design and performance analysis of satnav systems, signals, and receivers. It also provides succinct descriptions and comparisons of all the world’s satnav systems. Its comprehensive and logical structure addresses all satnav signals and systems in operation and being developed. Engineering Satellite-Based Navigation and Timing: Global Navigation Satellite Systems, Signals, and Receivers provides the technical foundation for designing and analyzing satnav signals, systems, and receivers. Its contents and structure address all satnav systems and signals: legacy, modernized, and new. It combines qualitative information with detailed techniques and analyses, providing a comprehensive set of insights and engineering tools for this complex multidisciplinary field. Part I describes system and signal engineering including orbital mechanics and constellation design, signal design principles and underlying considerations, link budgets, qua tifying receiver performance in interference, and e...

cDNA sequence quality data - Budding yeast cDNA sequencing project | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us Budding yeast cDNA sequencing project cDNA sequence quality data Data detail Data name cDNA sequence quality... data DOI 10.18908/lsdba.nbdc00838-003 Description of data contents Phred's quality score. P...tion Download License Update History of This Database Site Policy | Contact Us cDNA sequence quality

Changes in distribution of cell cycle phases and DNA content in HeLa S3 cell after irradiation

International Nuclear Information System (INIS)

Wang Shunbao

1992-01-01

The effects of irradiation and hyperthermia on the distribution in various phases and DNA content of HeLa S 3 cells were analyzed by flow cytometry and an image analysis instrument. A marked increase in DNA content from 6.718 to 9.614(AU) in HeLa S 3 cells after 6 Gy irradiation was seen to correspond with the changes in the distribution of various phases in G 2 + M, from 22% to 52%. Meanwhile, the surviving fraction of HeLa S 3 cells after 6 Gy irradiation was less than 1%. However, after heating at 44 deg C for 10 min, the amount of cells in G 2 + M increased from 22.5% to 52.5% and the surviving fraction after hyperthermia was less than 2.65%. The changes in distribution of various phases after Ir-192 irradiation were similar to those seen after X-ray irradiation. The delay of G 2 + M phase after treatment with 8 Gy plus heating at 44 deg C for 7 min in HeLa S 3 cells was similar to that seen in the case of treatment with 8 Gy alone. As the surviving fraction accompanying the G 2 + M delay after irradiation plus heat treatment was very low, we suggest that the changes of distribution in various phases of HeLa S 3 cells after treatment might be used as a rapid indicator of serious injury

Effect of cellular glutathione content on the induction of DNA double strand breaks by 25 MeV electrons

Energy Technology Data Exchange (ETDEWEB)

Frankenberg, D.; Kistler, M.; Eckhardt-Schupp, F.

1987-08-01

The effect of endogenous glutathione (GSH) on the induction of DNA double strand breaks (dsb) by 25 MeV electrons was investigated using stationary haploid yeast cells defective in ..gamma..-glutamyl-cysteine-synthetase (gsh 1) containing less than 5 per cent of the normal GSH content. In gsh 1 cells the induction of dsb is increased by a factor of 1.5 under oxic and 1.8 under anoxic irradiation conditions whereas the oxygen enhancement ratio was only slightly decreased (1.9) compared to wild-type cells (2.4).

Effect of cellular glutathione content on the induction of DNA double strand breaks by 25 MeV electrons

International Nuclear Information System (INIS)

Frankenberg, D.; Kistler, M.; Eckhardt-Schupp, F.

1987-01-01

The effect of endogenous glutathione (GSH) on the induction of DNA double strand breaks (dsb) by 25 MeV electrons was investigated using stationary haploid yeast cells defective in γ-glutamyl-cysteine-synthetase (gsh 1) containing less than 5 per cent of the normal GSH content. In gsh 1 cells the induction of dsb is increased by a factor of 1.5 under oxic and 1.8 under anoxic irradiation conditions whereas the oxygen enhancement ratio was only slightly decreased (1.9) compared to wild-type cells (2.4). (author)

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).

Effect of Electromagnetic Radiation Exposure on Histology and DNA Content of the Brain Cortex and Hypothalamus of Young and Adult Male Albino Rats

International Nuclear Information System (INIS)

Othman, A.I.; Othman, A.I.

2012-01-01

Concerns have been raised regarding the potential adverse effects of exposure to electromagnetic radiation (EMR) arising from mobile phone. The present study investigates the effect of the daily exposure of adult and young rats to EMR for 1 hour (at a frequency of 900 MHz, a power density of 0.02 mW/cm 2 and an average specific absorption rate of 1.165 W/kg) on the DNA content and tissue architecture of the cortex and hypothalamus of the rat brain. Both young and adult rats were sacrificed at two intervals, after 4 months of daily EMR exposure and after 1 month of stopping the exposure. The present results showed a significant increase in the DNA intensity of young and adult rats in both areas after 4 months of daily EMR exposure. However, decreased DNA content around the normal level was observed after one month of stopping the exposure. Light microscopic examination of irradiated rats revealed edema, vacuolation, necrosis and proliferated glial cells. Stopping EMR exposure showed mild amelioration in the structural damage of the cerebral cortex of young animals, however, most drastic changes still persisted in the other animals. In conclusion, these data may confirm the neurotoxic risks arising from the extensive use of mobile phones that may alter the brain histology and impair its function

DNA probes

Energy Technology Data Exchange (ETDEWEB)

Castelino, J

1993-12-31

The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

Radiation-induced changes in DNA methylation of repetitive elements in the mouse heart

Energy Technology Data Exchange (ETDEWEB)

Koturbash, Igor, E-mail: ikoturbash@uams.edu [Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Miousse, Isabelle R. [Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Sridharan, Vijayalakshmi [Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Nzabarushimana, Etienne; Skinner, Charles M. [Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Melnyk, Stepan B.; Pavliv, Oleksandra [Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Hauer-Jensen, Martin [Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Surgical Service, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205 (United States); Nelson, Gregory A. [Departments of Basic Sciences and Radiation Medicine, Loma Linda University, Loma Linda, CA 92354 (United States); Boerma, Marjan [Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States)

2016-05-15

Highlights: • Radiation-induced dynamic changes in cardiac DNA methylation were detected. • Early LINE-1 hypomethylation was followed by hypermethylation at a later time-point. • Radiation affected one-carbon metabolism in the heart tissue. • Irradiation resulted in accumulation of satellite DNA mRNA transcripts. - Abstract: DNA methylation is a key epigenetic mechanism, needed for proper control over the expression of genetic information and silencing of repetitive elements. Exposure to ionizing radiation, aside from its strong genotoxic potential, may also affect the methylation of DNA, within the repetitive elements, in particular. In this study, we exposed C57BL/6J male mice to low absorbed mean doses of two types of space radiation—proton (0.1 Gy, 150 MeV, dose rate 0.53 ± 0.08 Gy/min), and heavy iron ions ({sup 56}Fe) (0.5 Gy, 600 MeV/n, dose rate 0.38 ± 0.06 Gy/min). Radiation-induced changes in cardiac DNA methylation associated with repetitive elements were detected. Specifically, modest hypomethylation of retrotransposon LINE-1 was observed at day 7 after irradiation with either protons or {sup 56}Fe. This was followed by LINE-1, and other retrotransposons, ERV2 and SINE B1, as well as major satellite DNA hypermethylation at day 90 after irradiation with {sup 56}Fe. These changes in DNA methylation were accompanied by alterations in the expression of DNA methylation machinery and affected the one-carbon metabolism pathway. Furthermore, loss of transposable elements expression was detected in the cardiac tissue at the 90-day time-point, paralleled by substantial accumulation of mRNA transcripts, associated with major satellites. Given that the one-carbon metabolism pathway can be modulated by dietary modifications, these findings suggest a potential strategy for the mitigation and, possibly, prevention of the negative effects exerted by ionizing radiation on the cardiovascular system. Additionally, we show that the methylation status and

Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species.

Science.gov (United States)

Kuhn, G C S; Teo, C H; Schwarzacher, T; Heslop-Harrison, J S

2009-05-01

Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the fine-scale organization of unrelated satDNAs residing at the same chromosome location, and the sequence structure and dynamics of satDNA junctions. We studied the organization and sequence junctions of two nonhomologous satDNAs, pBuM and DBC-150, in three species from the neotropical Drosophila buzzatii cluster (repleta group). In situ hybridization to microchromosomes, interphase nuclei and extended DNA fibers showed frequent interspersion of the two satellites in D. gouveai, D. antonietae and, to a lesser extent, D. seriema. We isolated by PCR six pBuM x DBC-150 junctions: four are exclusive to D. gouveai and two are exclusive to D. antonietae. The six junction breakpoints occur at different positions within monomers, suggesting independent origin. Four junctions showed abrupt transitions between the two satellites, whereas two junctions showed a distinct 10 bp tandem duplication before the junction. Unlike pBuM, DBC-150 junction repeats are more variable than randomly cloned monomers and showed diagnostic features in common to a 3-monomer higher-order repeat seen in the sister species D. serido. The high levels of interspersion between pBuM and DBC-150 repeats suggest extensive rearrangements between the two satellites, maybe favored by specific features of the microchromosomes. Our interpretation is that the junctions evolved by multiples events of illegitimate recombination between nonhomologous satDNA repeats, with subsequent rounds of unequal crossing-over expanding the copy number of some of the junctions.

The X-linked 1.688 Satellite in Drosophila melanogaster Promotes Specific Targeting by Painting of Fourth.

Science.gov (United States)

Kim, Maria; Ekhteraei-Tousi, Samaneh; Lewerentz, Jacob; Larsson, Jan

2018-02-01

Repetitive DNA, represented by transposons and satellite DNA, constitutes a large portion of eukaryotic genomes, being the major component of constitutive heterochromatin. There is a growing body of evidence that it regulates several nuclear functions including chromatin state and the proper functioning of centromeres and telomeres. The 1.688 satellite is one of the most abundant repetitive sequences in Drosophila melanogaster , with the longest array being located in the pericentromeric region of the X-chromosome. Short arrays of 1.688 repeats are widespread within the euchromatic part of the X-chromosome, and these arrays were recently suggested to assist in recognition of the X-chromosome by the dosage compensation male-specific lethal complex. We discovered that a short array of 1.688 satellite repeats is essential for recruitment of the protein POF to a previously described site on the X-chromosome ( PoX2 ) and to various transgenic constructs. On an isolated target, i.e. , an autosomic transgene consisting of a gene upstream of 1.688 satellite repeats, POF is recruited to the transgene in both males and females. The sequence of the satellite, as well as its length and position within the recruitment element, are the major determinants of targeting. Moreover, the 1.688 array promotes POF targeting to the roX1 -proximal PoX1 site in trans Finally, binding of POF to the 1.688-related satellite-enriched sequences is conserved in evolution. We hypothesize that the 1.688 satellite functioned in an ancient dosage compensation system involving POF targeting to the X-chromosome. Copyright © 2018 by the Genetics Society of America.

Protein Supplementation Augments Muscle Fiber Hypertrophy but Does Not Modulate Satellite Cell Content During Prolonged Resistance-Type Exercise Training in Frail Elderly.

Science.gov (United States)

Dirks, Marlou L; Tieland, Michael; Verdijk, Lex B; Losen, Mario; Nilwik, Rachel; Mensink, Marco; de Groot, Lisette C P G M; van Loon, Luc J C

2017-07-01

Protein supplementation increases gains in lean body mass following prolonged resistance-type exercise training in frail older adults. We assessed whether the greater increase in lean body mass can be attributed to muscle fiber type specific hypertrophy with concomitant changes in satellite cell (SC) content. A total of 34 frail elderly individuals (77 ± 1 years, n = 12 male adults) participated in this randomized, double-blind, placebo-controlled trial with 2 arms in parallel. Participants performed 24 weeks of progressive resistance-type exercise training (2 sessions per week) during which they were supplemented twice-daily with milk protein (2 × 15 g) or a placebo. Muscle biopsies were taken at baseline, and after 12 and 24 weeks of intervention, to determine type I and type II muscle fiber specific cross-sectional area (CSA), SC content, and myocellular characteristics. In the placebo group, a trend for a 20% ± 11% increase in muscle fiber CSA was observed in type II fibers only (P = .051), with no increase in type I muscle fiber CSA. In the protein group, type I and II muscle fiber CSA increased by 23% ± 7% and 34% ± 10% following 6 months of training, respectively (P  .05). No changes in myonuclear content and SC contents were observed over time in either group (both P > .05). Regression analysis showed that changes in myonuclear content and domain size are predictive of muscle fiber hypertrophy. Protein supplementation augments muscle fiber hypertrophy following prolonged resistance-type exercise training in frail older people, without changes in myonuclear and SC content. Copyright © 2017 AMDA – The Society for Post-Acute and Long-Term Care Medicine. Published by Elsevier Inc. All rights reserved.

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.

Simultaneous ground-satellite observations of daytime traveling ionospheric disturbances over Japan using the GPS-TEC network and the CHAMP satellite

Science.gov (United States)

Moral, A. C.; Shiokawa, K.; Otsuka, Y.; Liu, H.; Nishioka, M.; Tsugawa, T.

2017-12-01

We report results of simultaneous ground-satellite measurements of daytime travelling ionospheric disturbances (TIDs) over Japan by using the GEONET GPS receiver network and the CHAMP satellite. For the two years of 2002 and 2008, we examined GPS measurements of TEC (Total Electron Content) and neutral and electron densities measured by CHAMP satellite. Total of fifteen TID events with clear southward moving structures in the GPS-TEC measurements are found by simultaneous ground-satellite measurements. On 2002, simultaneous events are only observed in January (1 event) and February (4 events). On 2008, ten events are observed around winter months (January (3 events), February (5), March (1), and October (1)). Neutral and electron densities measured by CHAMP show quasi-periodic fluctuations throughout the passages for all events. The CHAMP satellite crossed at least one clear TID phase front for all the events. We fitted a sinusoidal function to both ground and satellite data to obtain the frequencies and phase of the observed variations. We calculated the corresponding phase relationships between TEC variations and neutral and electron densities measured by CHAMP to categorize the events. In the presentations we report correspondence of these TID structures seen in the simultaneous ground-satellite observations by GPS-TEC and CHAMP, and discuss their phase relationship to identify the source of the daytime TIDs and specify how much of the observed variations are showing clear frequencies/or not in the nature at middle latitudes.

Chromosome-specific DNA Repeat Probes

Energy Technology Data Exchange (ETDEWEB)

Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.

2006-03-16

In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

Theory and Application of DNA Histogram Analysis.

Science.gov (United States)

Bagwell, Charles Bruce

The underlying principles and assumptions associated with DNA histograms are discussed along with the characteristics of fluorescent probes. Information theory was described and used to calculate the information content of a DNA histogram. Two major types of DNA histogram analyses are proposed: parametric and nonparametric analysis. Three levels…

DNA Microarray Technology

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Skip to main content DNA Microarray Technology Enter Search Term(s): Español Research Funding An Overview Bioinformatics Current Grants Education and Training Funding Extramural Research News Features Funding Divisions Funding ...

Characterization of muntjac DNA

International Nuclear Information System (INIS)

Davis, R.C.

1981-01-01

Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange

Characterization of muntjac DNA

Energy Technology Data Exchange (ETDEWEB)

Davis, R.C.

1981-05-27

Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange.

Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.

Directory of Open Access Journals (Sweden)

Can Alkan

2007-09-01

Full Text Available The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%-5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.

Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.

Science.gov (United States)

Alkan, Can; Ventura, Mario; Archidiacono, Nicoletta; Rocchi, Mariano; Sahinalp, S Cenk; Eichler, Evan E

2007-09-01

The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%-5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.

Sulfhydryl group content of chicken progesterone receptor: effect of oxidation on DNA binding activity

International Nuclear Information System (INIS)

Peleg, S.; Schrader, W.T.; O'Malley, B.W.

1988-01-01

DNA binding activity of chicken progesterone receptor B form (PRB) and A form (PRA) has been examined. This activity is strongly dependent upon the presence of thiols in the buffer. Stability studies showed that PRB was more sensitive to oxidation that was PRA. Receptor preparations were fractionated by DNA-cellulose chromatography to DNA-positive and DNA-negative subpopulations, and sulfhydryl groups were quantified on immunopurified receptor by labeling with [ 3 H]-N-ethylmaleimide. Labeling of DNA-negative receptors with [ 3 H]-N-ethylmaleimide showed 21-23 sulfhydryl groups on either PRA or PRB form when the proteins were reduced and denatured. A similar number was seen without reduction if denatured DNA-positive receptor species were tested. In contrast, the DNA-negative PRB had only 10-12 sulfhydryl groups detectable without reduction. A similar number (12-13 sulfhydryl groups) was found for PRA species that lost DNA binding activity after exposure to a nonreducing environment in vitro. The authors conclude that the naturally occurring receptor forms unable to bind to DNA, as well as receptor forms that have lost DNA binding activity due to exposure to nonreducing environment in vitro, contain 10-12 oxidized cysteine residues, likely present as disulfide bonds. Since they were unable to reduce the disulfide bonds when the native DNA-negative receptor proteins were treated with dithiothreitol (DTT), they speculate that irreversible loss of DNA binding activity of receptor in vitro is due to oxidation of cysteine residues that are not accessible to DTT in the native state

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.

A mutant Pfu DNA polymerase designed for advanced uracil-excision DNA engineering.

Science.gov (United States)

Nørholm, Morten H H

2010-03-16

The combined use of restriction enzymes with PCR has revolutionized molecular cloning, but is inherently restricted by the content of the manipulated DNA sequences. Uracil-excision based cloning is ligase and sequence independent and allows seamless fusion of multiple DNA sequences in simple one-tube reactions, with higher accuracy than overlapping PCR. Here, the addition of a highly efficient DNA polymerase and a low-background-, large-insertion- compatible site-directed mutagenesis protocol is described, largely expanding the versatility of uracil-excision DNA engineering. The different uracil-excision based molecular tools that have been developed in an open-source fashion, constitute a comprehensive, yet simple and inexpensive toolkit for any need in molecular cloning.

Efficient replication of the in vitro transcripts from cloned cDNA of tomato black ring virus satellite RNA requires the 48K satellite RNA-encoded protein.

Science.gov (United States)

Hemmer, O; Oncino, C; Fritsch, C

1993-06-01

Tomato black ring virus isolate L supports the multiplication of a large satellite RNA of 1376 nt which has no common features with the two genomic RNAs except for the terminal motif 5' VPg UUGAAAA and a 3' poly(A) tail. The TBRV sat-RNA contains an ORF for a protein of 48K which is translated both in vitro and in vivo. To determine the function of the 48K protein we have studied the effect of different mutations introduced in the ORF of the cDNA clone on the capacity of transcripts to multiply in Chenopodium quinoa plants or protoplasts when inoculated along with the genomic RNAs. Transcripts in which nucleotides have been substituted within the 5' proximal region of the ORF multiplied poorly even when the modification conserved the 48K protein sequence, suggesting that this portion of the ORF contains cis-acting RNA sequences. Transcripts with alterations in the internal region of the ORF retained their multiplication capacity provided the mutation did not destroy the ORF or modify the length of the protein expressed. The absence of multiplication in plants of transcripts unable to express the 48K protein and their inability to replicate in protoplasts suggest strongly that the sat-RNA translation product itself is implicated in the replication of sat-RNA.

Nicotiana small RNA sequences support a host genome origin of cucumber mosaic virus satellite RNA.

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Kiran Zahid

2015-01-01

Full Text Available Satellite RNAs (satRNAs are small noncoding subviral RNA pathogens in plants that depend on helper viruses for replication and spread. Despite many decades of research, the origin of satRNAs remains unknown. In this study we show that a β-glucuronidase (GUS transgene fused with a Cucumber mosaic virus (CMV Y satellite RNA (Y-Sat sequence (35S-GUS:Sat was transcriptionally repressed in N. tabacum in comparison to a 35S-GUS transgene that did not contain the Y-Sat sequence. This repression was not due to DNA methylation at the 35S promoter, but was associated with specific DNA methylation at the Y-Sat sequence. Both northern blot hybridization and small RNA deep sequencing detected 24-nt siRNAs in wild-type Nicotiana plants with sequence homology to Y-Sat, suggesting that the N. tabacum genome contains Y-Sat-like sequences that give rise to 24-nt sRNAs capable of guiding RNA-directed DNA methylation (RdDM to the Y-Sat sequence in the 35S-GUS:Sat transgene. Consistent with this, Southern blot hybridization detected multiple DNA bands in Nicotiana plants that had sequence homology to Y-Sat, suggesting that Y-Sat-like sequences exist in the Nicotiana genome as repetitive DNA, a DNA feature associated with 24-nt sRNAs. Our results point to a host genome origin for CMV satRNAs, and suggest novel approach of using small RNA sequences for finding the origin of other satRNAs.

W-enriched satellite sequence in the Indian meal moth, Plodia interpunctella (Lepidoptera, Pyralidae).

Science.gov (United States)

Dalíková, Martina; Zrzavá, Magda; Kubíčková, Svatava; Marec, František

2017-10-01

The W chromosome of most lepidopteran species represents the largest heterochromatin entity in the female genome. Although satellite DNA is a typical component of constitutive heterochromatin, there are only a few known satellite DNAs (satDNAs) located on the W chromosome in moths and butterflies. In this study, we isolated and characterized new satDNA (PiSAT1) from microdissected W chromosomes of the Indian meal moth, Plodia interpunctella. Even though the PiSAT1 is mainly localized near the female-specific segment of the W chromosome, short arrays of this satDNA also occur on autosomes and/or the Z chromosome. Probably due to the predominant location in the non-recombining part of the genome, PiSAT1 exhibits a relatively large nucleotide variability in its monomers. However, at least a part of all predicted functional motifs is located in conserved regions. Moreover, we detected polyadenylated transcripts of PiSAT1 in all developmental stages and in both sexes (female and male larvae, pupae and adults). Our results suggest a potential structural and functional role of PiSAT1 in the P. interpunctella genome, which is consistent with accumulating evidence for the important role of satDNAs in eukaryotic genomes.

Primena satelitskih snimaka za dopunu sadržaja topografskih karata / An application of satellite images for improving the content of topographic maps

Directory of Open Access Journals (Sweden)

Miodrag D. Regodić

2010-10-01

Full Text Available Neažurnost sadržaja topografskih karata (TK, uslovljena ponajviše stvarnim ekonomskim teškoćama pri izradi novih i dopuni postojećih izdanja, kao i nedovoljnost i sve teže stanje pri izradi ostalih geotopografskih materijala (GTM, u velikoj meri otežavaju geotopografsko obezbeđenje (GTOb vojske u miru, kao i u svim periodima pripreme i vođenja ratnih dejstava. Rešenje ovog problema je u iznalaženju adekvatnog načina upotrebe proizvoda svih vrsta daljinskih snimanja, a naročito u obradi kvalitetnih satelitskih snimaka. Kao najbolji pokazatelj velikih mogućnosti daljinske detekcije, korišćenjem satelitskih snimaka, u kartografskoj praksi primenom kvalitetnih softverskih rešenja, u radu je predstavljena dopuna topografske karte nedostajućim topografskim sadržajem. / Lack of updated content of topographic maps (TMs, mainly due to economic issues regarding the publishing of existing or revised TMs, substantially affects geo-topographic supply (GTS of the Army both in peace and warfare time, as well as shortage of other geo-topographic materials (GTMs. The solution to this problem is in finding an appropriate method of using products of all types of remote sensing, high quality satellite images in particular. Having shown the best possibilities of remote sensing while using satellite images in mapping through the quality software solutions, the author presents an addition to topographic maps based on missing topographic data. Introduction Numerous natural and social phenomena are constantly observed, surveyed, registered and analyzed. Permanent or periodical satellite surveillance and recording for different purposes are growing in importance. The purposes can range from meteorological issues, through study of large water surfaces to military intelligence, etc. These recording can be used in making topographic, thematic and working maps as well as other geo-topographic material. Processing and analyzing of ikonos2 satellite images

Soviet satellite communications science and technology

Energy Technology Data Exchange (ETDEWEB)

Birch, J.N.; Campanella, S.J.; Gordon, G.D.; McElroy, D.R.; Pritchard, W.L.; Stamminger, R.

1991-08-01

This is a report by six US scientists and engineers concerning the current state of the art and projections of future Soviet satellite communications technologies. The panel members are experts in satellite stabilization, spacecraft environments, space power generation, launch systems, spacecraft communications sciences and technologies, onboard processing, ground stations, and other technologies that impact communications. The panel assessed the Soviet ability to support high-data-rate space missions at 128 Mbps by evaluating current and projected Soviet satellite communications technologies. A variety of space missions were considered, including Earth-to-Earth communications via satellites in geostationary or highly elliptical orbits, those missions that require space-to-Earth communications via a direct path and those missions that require space-to-Earth communications via a relay satellite. Soviet satellite communications capability, in most cases, is 10 years behind that of the United States and other industrialized nations. However, based upon an analysis of communications links needed to support these missions using current Soviet capabilities, it is well within the current Soviet technology to support certain space missions outlined above at rates of 128 Mbps or higher, although published literature clearly shows that the Soviet Union has not exceeded 60 Mbps in its current space system. These analyses are necessary but not sufficient to determine mission data rates, and other technologies such as onboard processing and storage could limit the mission data rate well below that which could actually be supported via the communications links. Presently, the Soviet Union appears to be content with data rates in the low-Earth-orbit relay via geostationary mode of 12 Mbps. This limit is a direct result of power amplifier limits, spacecraft antenna size, and the utilization of K{sub u}-band frequencies. 91 refs., 16 figs., 15 tabs.

New Satellite Estimates of Mixed-Phase Cloud Properties: A Synergistic Approach for Application to Global Satellite Imager Data

Science.gov (United States)

Smith, W. L., Jr.; Spangenberg, D.; Fleeger, C.; Sun-Mack, S.; Chen, Y.; Minnis, P.

2016-12-01

Determining accurate cloud properties horizontally and vertically over a full range of time and space scales is currently next to impossible using data from either active or passive remote sensors or from modeling systems. Passive satellite imagers provide horizontal and temporal resolution of clouds, but little direct information on vertical structure. Active sensors provide vertical resolution but limited spatial and temporal coverage. Cloud models embedded in NWP can produce realistic clouds but often not at the right time or location. Thus, empirical techniques that integrate information from multiple observing and modeling systems are needed to more accurately characterize clouds and their impacts. Such a strategy is employed here in a new cloud water content profiling technique developed for application to satellite imager cloud retrievals based on VIS, IR and NIR radiances. Parameterizations are developed to relate imager retrievals of cloud top phase, optical depth, effective radius and temperature to ice and liquid water content profiles. The vertical structure information contained in the parameterizations is characterized climatologically from cloud model analyses, aircraft observations, ground-based remote sensing data, and from CloudSat and CALIPSO. Thus, realistic cloud-type dependent vertical structure information (including guidance on cloud phase partitioning) circumvents poor assumptions regarding vertical homogeneity that plague current passive satellite retrievals. This paper addresses mixed phase cloud conditions for clouds with glaciated tops including those associated with convection and mid-latitude storm systems. Novel outcomes of our approach include (1) simultaneous retrievals of ice and liquid water content and path, which are validated with active sensor, microwave and in-situ data, and yield improved global cloud climatologies, and (2) new estimates of super-cooled LWC, which are demonstrated in aviation safety applications and

Saturn satellites

International Nuclear Information System (INIS)

Ruskol, E.L.

1981-01-01

The characteristics of the Saturn satellites are discussed. The satellites close to Saturn - Janus, Mimas, Enceladus, Tethys, Dione and Rhea - rotate along the circular orbits. High reflectivity is attributed to them, and the density of the satellites is 1 g/cm 3 . Titan is one of the biggest Saturn satellites. Titan has atmosphere many times more powerful than that of Mars. The Titan atmosphere is a peculiar medium with a unique methane and hydrogen distribution in the whole Solar system. The external satellites - Hyperion, Japetus and Phoebe - are poorly investigated. Neither satellite substance density, nor their composition are known. The experimental data on the Saturn rings obtained on the ''Pioneer-11'' and ''Voyager-1'' satellites are presented [ru

Precision Viticulture from Multitemporal, Multispectral Very High Resolution Satellite Data

Science.gov (United States)

Kandylakis, Z.; Karantzalos, K.

2016-06-01

In order to exploit efficiently very high resolution satellite multispectral data for precision agriculture applications, validated methodologies should be established which link the observed reflectance spectra with certain crop/plant/fruit biophysical and biochemical quality parameters. To this end, based on concurrent satellite and field campaigns during the veraison period, satellite and in-situ data were collected, along with several grape samples, at specific locations during the harvesting period. These data were collected for a period of three years in two viticultural areas in Northern Greece. After the required data pre-processing, canopy reflectance observations, through the combination of several vegetation indices were correlated with the quantitative results from the grape/must analysis of grape sampling. Results appear quite promising, indicating that certain key quality parameters (like brix levels, total phenolic content, brix to total acidity, anthocyanin levels) which describe the oenological potential, phenolic composition and chromatic characteristics can be efficiently estimated from the satellite data.

Qualitative and quantitative assessment of DNA quality of frozen beef based on DNA yield, gel electrophoresis and PCR amplification and their correlations to beef quality.

Science.gov (United States)

Zhao, Jing; Zhang, Ting; Liu, Yongfeng; Wang, Xingyu; Zhang, Lan; Ku, Ting; Quek, Siew Young

2018-09-15

Freezing is a practical method for meat preservation but the quality of frozen meat can deteriorate with storage time. This research investigated the effect of frozen storage time (up to 66 months) on changes in DNA yield, purity and integrity in beef, and further analyzed the correlation between beef quality (moisture content, protein content, TVB-N value and pH value) and DNA quality in an attempt to establish a reliable, high-throughput method for meat quality control. Results showed that frozen storage time influenced the yield and integrity of DNA significantly (p quality degraded dramatically with the increased storage time based on gel electrophoresis results. Polymerase chain reaction (PCR) products from both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) were observed in all frozen beef samples. Using real-time PCR for quantitative assessment of DNA and meat quality revealed that correlations could be established successfully with mathematical models to evaluate frozen beef quality. Copyright © 2018 Elsevier Ltd. All rights reserved.

Some measurements of total electron content made with the ATS-6 radio beacon

International Nuclear Information System (INIS)

Davies, K.; Degenhardt, W.; Hartmann, G.K.

1978-01-01

The paper deals with some measurements made with the radio beacon on board the ATS-6 satellite in the American and European sectors. Measurements of the slant electron content, the Faraday content, and the plasmaspheric (or residual) content, made under different geographic and geomagnetic conditions, are discussed and compared

Detecting the effects of hydrocarbon pollution in the Amazon forest using hyperspectral satellite images

International Nuclear Information System (INIS)

Arellano, Paul; Tansey, Kevin; Balzter, Heiko; Boyd, Doreen S.

2015-01-01

The global demand for fossil energy is triggering oil exploration and production projects in remote areas of the world. During the last few decades hydrocarbon production has caused pollution in the Amazon forest inflicting considerable environmental impact. Until now it is not clear how hydrocarbon pollution affects the health of the tropical forest flora. During a field campaign in polluted and pristine forest, more than 1100 leaf samples were collected and analysed for biophysical and biochemical parameters. The results revealed that tropical forests exposed to hydrocarbon pollution show reduced levels of chlorophyll content, higher levels of foliar water content and leaf structural changes. In order to map this impact over wider geographical areas, vegetation indices were applied to hyperspectral Hyperion satellite imagery. Three vegetation indices (SR, NDVI and NDVI 705 ) were found to be the most appropriate indices to detect the effects of petroleum pollution in the Amazon forest. - Highlights: • Leaf biochemical alterations in the rainforest are caused by petroleum pollution. • Lower levels of chlorophyll content are symptom of vegetation stress in polluted sites. • Increased foliar water content was found in vegetation near polluted sites. • Vegetation stress was detected by using vegetation indices from satellite images. • Polluted sites and hydrocarbon seepages in rainforest can be identified from space. - Hydrocarbon pollution in the Amazon forest is observed for first time from satellite data

PCR-Free Enrichment of Mitochondrial DNA from Human Blood and Cell Lines for High Quality Next-Generation DNA Sequencing.

Directory of Open Access Journals (Sweden)

Meetha P Gould

Full Text Available Recent advances in sequencing technology allow for accurate detection of mitochondrial sequence variants, even those in low abundance at heteroplasmic sites. Considerable sequencing cost savings can be achieved by enriching samples for mitochondrial (relative to nuclear DNA. Reduction in nuclear DNA (nDNA content can also help to avoid false positive variants resulting from nuclear mitochondrial sequences (numts. We isolate intact mitochondrial organelles from both human cell lines and blood components using two separate methods: a magnetic bead binding protocol and differential centrifugation. DNA is extracted and further enriched for mitochondrial DNA (mtDNA by an enzyme digest. Only 1 ng of the purified DNA is necessary for library preparation and next generation sequence (NGS analysis. Enrichment methods are assessed and compared using mtDNA (versus nDNA content as a metric, measured by using real-time quantitative PCR and NGS read analysis. Among the various strategies examined, the optimal is differential centrifugation isolation followed by exonuclease digest. This strategy yields >35% mtDNA reads in blood and cell lines, which corresponds to hundreds-fold enrichment over baseline. The strategy also avoids false variant calls that, as we show, can be induced by the long-range PCR approaches that are the current standard in enrichment procedures. This optimization procedure allows mtDNA enrichment for efficient and accurate massively parallel sequencing, enabling NGS from samples with small amounts of starting material. This will decrease costs by increasing the number of samples that may be multiplexed, ultimately facilitating efforts to better understand mitochondria-related diseases.

Characterizing SPDY over High Latency Satellite Channels

Directory of Open Access Journals (Sweden)

Luca Caviglione

2014-12-01

Full Text Available The increasing complexity ofWeb contents and the growing diffusion of mobile terminals, which use wireless and satellite links to get access to the Internet, impose the adoption of more specialized protocols. In particular, we focus on SPDY, a novel protocol introduced by Google to optimize the retrieval of complex webpages, to manage large Round Trip Times and high packet losses channels. In this perspective, the paper characterizes SPDY over high latency satellite links, especially with the goal of understanding whether it could be an efficient solution to cope with performance degradations typically affecting Web 2.0 services. To this aim, we implemented an experimental set-up, composed of an ad-hoc proxy, a wireless link emulator, and an instrumented Web browser. The results clearly indicate that SPDY can enhance the performances in terms of loading times, and reduce the traffic fragmentation. Moreover, owing to its connection multiplexing architecture, SPDY can also mitigate the transport layer complexity, which is critical when in presence of Performance Enhancing Proxies usually deployed to isolate satellite trunks.

The nucleotide sequence of satellite RNA in grapevine fanleaf virus, strain F13.

Science.gov (United States)

Fuchs, M; Pinck, M; Serghini, M A; Ravelonandro, M; Walter, B; Pinck, L

1989-04-01

The nucleotide sequence of cDNA copies of grapevine fanleaf virus (strain F13) satellite RNA has been determined. The primary structure obtained was 1114 nucleotides in length, excluding the poly(A) tail, and contained only one long open reading frame encoding a 341 residue, highly hydrophilic polypeptide of Mr37275. The coding sequence was bordered by a leader of 14 nucleotides and a 3'-terminal non-coding region of 74 nucleotides. No homology has been found with small satellite RNAs associated with other nepoviruses. Two limited homologies of eight nucleotides have been detected between the satellite RNA in grapevine fanleaf virus and those in tomato black ring virus, and a consensus sequence U.G/UGAAAAU/AU/AU/A at the 5' end of nepovirus RNAs is reported. A less extended consensus exists in this region in comovirus and picornavirus RNA.

Plasmaspheric-ionospheric contents deduced from ATS-6 measurements over Lannion

International Nuclear Information System (INIS)

Fleury, R.

1978-01-01

The present paper deals with ATS-6 radio beacon measurements at the Lannion Station, of the total columnar electron content between transmitter and receiver and the ionospheric columnar content along the ray path between the receiver and the satellite. The main equations of the method of analysis proposed by Davies et al. (1975) are summarized

Comparing land surface phenology derived from satellite and GPS network microwave remote sensing.

Science.gov (United States)

Jones, Matthew O; Kimball, John S; Small, Eric E; Larson, Kristine M

2014-08-01

The land surface phenology (LSP) start of season (SOS) metric signals the seasonal onset of vegetation activity, including canopy growth and associated increases in land-atmosphere water, energy and carbon (CO2) exchanges influencing weather and climate variability. The vegetation optical depth (VOD) parameter determined from satellite passive microwave remote sensing provides for global LSP monitoring that is sensitive to changes in vegetation canopy water content and biomass, and insensitive to atmosphere and solar illumination constraints. Direct field measures of canopy water content and biomass changes desired for LSP validation are generally lacking due to the prohibitive costs of maintaining regional monitoring networks. Alternatively, a normalized microwave reflectance index (NMRI) derived from GPS base station measurements is sensitive to daily vegetation water content changes and may provide for effective microwave LSP validation. We compared multiyear (2007-2011) NMRI and satellite VOD records at over 300 GPS sites in North America, and their derived SOS metrics for a subset of 24 homogenous land cover sites to investigate VOD and NMRI correspondence, and potential NMRI utility for LSP validation. Significant correlations (P<0.05) were found at 276 of 305 sites (90.5 %), with generally favorable correspondence in the resulting SOS metrics (r (2)=0.73, P<0.001, RMSE=36.8 days). This study is the first attempt to compare satellite microwave LSP metrics to a GPS network derived reflectance index and highlights both the utility and limitations of the NMRI data for LSP validation, including spatial scale discrepancies between local NMRI measurements and relatively coarse satellite VOD retrievals.

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

Science.gov (United States)

Alkan, Can; Cardone, Maria Francesca; Catacchio, Claudia Rita; Antonacci, Francesca; O'Brien, Stephen J; Ryder, Oliver A; Purgato, Stefania; Zoli, Monica; Della Valle, Giuliano; Eichler, Evan E; Ventura, Mario

2011-01-01

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

Network clustering coefficient approach to DNA sequence analysis

Energy Technology Data Exchange (ETDEWEB)

Gerhardt, Guenther J.L. [Universidade Federal do Rio Grande do Sul-Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos 2350/sala 2040/90035-003 Porto Alegre (Brazil); Departamento de Fisica e Quimica da Universidade de Caxias do Sul, Rua Francisco Getulio Vargas 1130, 95001-970 Caxias do Sul (Brazil); Lemke, Ney [Programa Interdisciplinar em Computacao Aplicada, Unisinos, Av. Unisinos, 950, 93022-000 Sao Leopoldo, RS (Brazil); Corso, Gilberto [Departamento de Biofisica e Farmacologia, Centro de Biociencias, Universidade Federal do Rio Grande do Norte, Campus Universitario, 59072 970 Natal, RN (Brazil)]. E-mail: corso@dfte.ufrn.br

2006-05-15

In this work we propose an alternative DNA sequence analysis tool based on graph theoretical concepts. The methodology investigates the path topology of an organism genome through a triplet network. In this network, triplets in DNA sequence are vertices and two vertices are connected if they occur juxtaposed on the genome. We characterize this network topology by measuring the clustering coefficient. We test our methodology against two main bias: the guanine-cytosine (GC) content and 3-bp (base pairs) periodicity of DNA sequence. We perform the test constructing random networks with variable GC content and imposed 3-bp periodicity. A test group of some organisms is constructed and we investigate the methodology in the light of the constructed random networks. We conclude that the clustering coefficient is a valuable tool since it gives information that is not trivially contained in 3-bp periodicity neither in the variable GC content.

Satellite Earth observation data to identify climate and anthropogenic pressures on Bucharest periurban forests

Energy Technology Data Exchange (ETDEWEB)

Zoran, Maria; Savastru, Roxana; Savastru, Dan [National Institute of R& D for Optoelectronics, MG5 Bucharest-Magurele, 077125 Romania (Romania); Dida, Adrian [University Transylvania of Brasov, Brasov (Romania)

2016-03-25

Satellite Earth observation data in the visible and near-infrared (VNIR) wavelengths represent a useful source of information for forest systems monitoring through derived biogeophysical parameters (vegetation index, leaf area index, canopy cover, fraction of absorbed photosynthetically active radiation, chlorophyll content, net primary production, canopy water stress, etc.). Use of satellite remote sensing data to assess forest spatio-temporal changes due to climatic or anthropogenic stressors is an excellent example of the value of multispectral and multitemporal observations. Fusion technique was applied to time-series multispectral and multitemporal satellite imagery (NOAA AVHRR, MODIS Terra/Aqua, Landsat ETM and IKONOS satellite data) for periurban forest areas Cernica-Branesti, placed in the neighboring of Bucharest town, Romania, over 2002-2014 period.

Satellite Earth observation data to identify climate and anthropogenic pressures on Bucharest periurban forests

International Nuclear Information System (INIS)

Zoran, Maria; Savastru, Roxana; Savastru, Dan; Dida, Adrian

2016-01-01

Satellite Earth observation data in the visible and near-infrared (VNIR) wavelengths represent a useful source of information for forest systems monitoring through derived biogeophysical parameters (vegetation index, leaf area index, canopy cover, fraction of absorbed photosynthetically active radiation, chlorophyll content, net primary production, canopy water stress, etc.). Use of satellite remote sensing data to assess forest spatio-temporal changes due to climatic or anthropogenic stressors is an excellent example of the value of multispectral and multitemporal observations. Fusion technique was applied to time-series multispectral and multitemporal satellite imagery (NOAA AVHRR, MODIS Terra/Aqua, Landsat ETM and IKONOS satellite data) for periurban forest areas Cernica-Branesti, placed in the neighboring of Bucharest town, Romania, over 2002-2014 period.

Homologous alpha satellite sequences on human acrocentric chromosomes with selectivity for chromosomes 13, 14, and 21: implications for recombination between nonhomologues and Robertsonian translocations

Energy Technology Data Exchange (ETDEWEB)

Choo, K H; Vissel, B; Brown, R; Filby, R G; Earle, E

1988-02-25

The authors report a new subfamily of alpha satellite DNA (pTRA-2) which is found on all the human acrocentric chromosomes. The alphoid nature of the cloned DNA was established by partial sequencing. Southern analysis of restriction enzyme-digested DNA fragments from mouse/human hybrid cells containing only human chromosome 21 showed that the predominant higher-order repeating unit for pTRA-2 is a 3.9 kb structure. Analysis of a consensus in situ hybridization profile derived from 13 normal individuals revealed the localization of 73% of all centromeric autoradiographic grains over the five acrocentric chromosomes, with the following distribution: 20.4%, 21.5%, 17.1%, 7.3% and 6.5% on chromosomes 13, 14, 21, 15 and 22 respectively. An average of 1.4% of grains was found on the centromere of each of the remaining 19 nonacrocentric chromosomes. These results indicate the presence of a common subfamily of alpha satellite DNA on the five acrocentric chromosomes and suggest an evolutionary process consistent with recombination exchange of sequences between the nonhomologues. The results further suggests that such exchanges are more selective for chromosomes 13, 14 and 21 than for chromosomes 15 and 22. The possible role of centromeric alpha satellite DNA in the aetiology of 13q14q and 14q21q Robertsonian translocation involving the common and nonrandom association of chromosomes 13 and 14, and 14 and 21 is discussed.

Fat Content and Nitrite-Curing Influence the Formation of Oxidation Products and NOC-Specific DNA Adducts during In Vitro Digestion of Meat

Science.gov (United States)

Van Hecke, Thomas; Vossen, Els; Vanden Bussche, Julie; Raes, Katleen; Vanhaecke, Lynn; De Smet, Stefaan

2014-01-01

The effects of fat content and nitrite-curing of pork were investigated on the formation of cytotoxic and genotoxic lipid oxidation products (malondialdehyde, 4-hydroxy-2-nonenal, volatile simple aldehydes), protein oxidation products (protein carbonyl compounds) and NOC-specific DNA adducts (O6-carboxy-methylguanine) during in vitro digestion. The formation of these products during digestion is suggested to be responsible for the association between red meat and processed meat consumption and colorectal cancer risk. Digestion of uncured pork to which fat was added (total fat content 5 or 20%), resulted in significantly higher lipid and protein oxidation in the mimicked duodenal and colonic fluids, compared to digestion of pork without added fat (1% fat). A higher fat content also significantly favored the formation of O6-carboxy-methylguanine in the colon. Nitrite-curing of meat resulted in significantly lower lipid and protein oxidation before and after digestion, while an inconsistent effect on the formation of O6-carboxy-methylguanine was observed. The presented results demonstrate that haem-Fe is not solely responsible for oxidation and nitrosation reactions throughout an in vitro digestion approach but its effect is promoted by a higher fat content in meat. PMID:24978825

Fat content and nitrite-curing influence the formation of oxidation products and NOC-specific DNA adducts during in vitro digestion of meat.

Science.gov (United States)

Van Hecke, Thomas; Vossen, Els; Vanden Bussche, Julie; Raes, Katleen; Vanhaecke, Lynn; De Smet, Stefaan

2014-01-01

The effects of fat content and nitrite-curing of pork were investigated on the formation of cytotoxic and genotoxic lipid oxidation products (malondialdehyde, 4-hydroxy-2-nonenal, volatile simple aldehydes), protein oxidation products (protein carbonyl compounds) and NOC-specific DNA adducts (O6-carboxy-methylguanine) during in vitro digestion. The formation of these products during digestion is suggested to be responsible for the association between red meat and processed meat consumption and colorectal cancer risk. Digestion of uncured pork to which fat was added (total fat content 5 or 20%), resulted in significantly higher lipid and protein oxidation in the mimicked duodenal and colonic fluids, compared to digestion of pork without added fat (1% fat). A higher fat content also significantly favored the formation of O6-carboxy-methylguanine in the colon. Nitrite-curing of meat resulted in significantly lower lipid and protein oxidation before and after digestion, while an inconsistent effect on the formation of O6-carboxy-methylguanine was observed. The presented results demonstrate that haem-Fe is not solely responsible for oxidation and nitrosation reactions throughout an in vitro digestion approach but its effect is promoted by a higher fat content in meat.

Fat content and nitrite-curing influence the formation of oxidation products and NOC-specific DNA adducts during in vitro digestion of meat.

Directory of Open Access Journals (Sweden)

Thomas Van Hecke

Full Text Available The effects of fat content and nitrite-curing of pork were investigated on the formation of cytotoxic and genotoxic lipid oxidation products (malondialdehyde, 4-hydroxy-2-nonenal, volatile simple aldehydes, protein oxidation products (protein carbonyl compounds and NOC-specific DNA adducts (O6-carboxy-methylguanine during in vitro digestion. The formation of these products during digestion is suggested to be responsible for the association between red meat and processed meat consumption and colorectal cancer risk. Digestion of uncured pork to which fat was added (total fat content 5 or 20%, resulted in significantly higher lipid and protein oxidation in the mimicked duodenal and colonic fluids, compared to digestion of pork without added fat (1% fat. A higher fat content also significantly favored the formation of O6-carboxy-methylguanine in the colon. Nitrite-curing of meat resulted in significantly lower lipid and protein oxidation before and after digestion, while an inconsistent effect on the formation of O6-carboxy-methylguanine was observed. The presented results demonstrate that haem-Fe is not solely responsible for oxidation and nitrosation reactions throughout an in vitro digestion approach but its effect is promoted by a higher fat content in meat.

Replication of DNA during barley endosperm development

DEFF Research Database (Denmark)

Giese, H.

1992-01-01

The incorporation of [6-H-3]-thymidine into DNA of developing barley end sperm was examined by autoradiography of cross sections of seeds and DNA analysis. The majority of nuclear divisions took place in the very young endosperm, but as late as 25 days after anthesis there was evidence for DNA...... replication. The DNA content of the endosperm increases during development and in response to nitrogen application in parallel to the storage protein synthesis profile. The hordein genes were hypersensitive to DNase I treatment throughout development....

DNA quantification of basidiomycetous fungi during storage of logging residues

Directory of Open Access Journals (Sweden)

Isabella Børja

2015-04-01

Full Text Available The demand for bioenergy caused an increased use of logging residues, branches and treetops that were previously left on the ground after harvesting. Residues are stored outdoors in piles and it is unclear to what extent fungi transform this material. Our objective was to quantify the amount of wood degrading fungi during storage using quantitative real-time PCR (qPCR to detect basidiomycetous DNA in logging residues, a novel approach in this field. We found that the qPCR method was accurate in quantifying the fungal DNA during storage. As the moisture content of the piled logging residues decreased during the storage period, the fungal DNA content also decreased. Scots pine residues contained more fungal DNA than residues from Norway spruce. Loose piles had generally more fungal DNA than bundled ones.

DGGE and 16S rDNA sequencing analysis of bacterial communities in colon content and feces of pigs fed whole crop rice.

Science.gov (United States)

Wang, Hai-Feng; Zhu, Wei-Yun; Yao, Wen; Liu, Jian-Xin

2007-01-01

The effect of feeding whole crop rice (WCR) to growing-finishing pigs at three levels 0 (Control), 10% and 20% on bacterial communities in colon content and feces was analyzed using 16S rDNA-based techniques. Amplicons of the V6-V8 variable regions of bacterial 16S rDNA were analyzed by denaturing gradient gel electrophoresis (DGGE), cloning and sequencing. The total number of DGGE bands and Shannon index of diversity for feces samples were higher in the pigs fed WCR-containing diets compared with the control, while a decrease trend was observed in these two parameters for colon content samples with the inclusion of WCR in the diets, although statistical differences were not significant. In general, the intestinal bacterial communities were prone to form the cluster for pig fed the same diet. Feeding of WCR induced the presence of special DGGE band with the sequence showing 99% similarity to that of Lactobacillus reuteri (DSM 20016T). The sequences of seven amplicons in total nine clones showed less than 97% similarity with those of previously identified or unidentified bacteria, suggesting that most bacteria in gastrointestinal tracts have not been cultured or identified. The results suggest that the diet containing WCR did not affect the major groups of bacteria, but stimulated the growth of L. reuteri-like species.

Tritium content in some organs and the DNA of rat liver cells following short term administration of tritiated food, tritiated protein or tritiated water

International Nuclear Information System (INIS)

Rochalska, M.; Szot, Z.

1979-01-01

Male Wistar rats were given equivalent doses of various tritium compounds, namely tritiated food (TF), tritiated protein (TP) or tritiated water (TW) for 5 days. On the 6th day of the experiment tritium radioactivity of dry tissues and the DNA of liver cells was determined. DNA of liver cells of animals given TP contained 13-23 times more tritium than that of rats receiving TW. Incorporation of tritium from TF into the examined tissues was found to be higher than that from TP or TW, with the exception of the brain which revealed the highest tritium content after TP. Tritium concentration in lungs, small intestine, muscle, skin and femur of animals given TF or TP did not differ significantly. (author)

CpSAT-1, a transcribed satellite sequence from the codling moth, Cydia pomonella

Czech Academy of Sciences Publication Activity Database

Věchtová, Pavlína; Dalíková, Martina; Sýkorová, Miroslava; Žurovcová, Martina; Füssy, Zoltán; Zrzavá, Magda

2016-01-01

Roč. 144, č. 4 (2016), s. 385-395 ISSN 0016-6707 R&D Projects: GA ČR GA523/09/2106; GA ČR(CZ) GA14-22765S Institutional support: RVO:60077344 Keywords : Cydia pomonella * satellite DNA * holokinetic chromosomes * sex chromosomes * Lepidoptera Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.207, year: 2016

Determination of chromium combined with DNA, RNA and protein in chromium-rich brewer's yeast

International Nuclear Information System (INIS)

Ding Wenjun; Qian Qinfang; Hou Xiaolin; Feng Weiyue; Chai Zhifang

2000-01-01

The contents of chromium in the DNA, RNA and protein fractions separated from chromium-rich and normal brewer's yeast were determined with the neutron activation analysis in order to study the combination of Cr with DNA, RNA and protein in chromium-rich brewer's yeast. The results showed that the extracting rats and concentrations of DNA, RNA and protein had no significant difference in two types of yeast, but the chromium contents of DNA, RNA and protein in the chromium-rich yeast were significantly higher than those in the normal. In addition, the content of chromium in DNA was much higher than that in RNA and protein, which indicated that the inorganic chromium compounds entered into the yeast cell, during the yeast cultivation in the culture medium containing chromium were converted into organic chromium compounds combined with DNA, RNA and protein

Mitochondrial DNA differentiates Alzheimer's disease from Creutzfeldt-Jakob disease.

Science.gov (United States)

Podlesniy, Petar; Llorens, Franc; Golanska, Ewa; Sikorska, Beata; Liberski, Pawel; Zerr, Inga; Trullas, Ramon

2016-05-01

Low content of cell-free mitochondrial DNA (mtDNA) in cerebrospinal fluid (CSF) is a biomarker of early stage Alzheimer's disease (AD), but whether mtDNA is altered in a rapid neurodegenerative dementia such as Creutzfeldt-Jakob disease is unknown. CSF mtDNA was measured using digital polymerase chain reaction (dPCR) in two independent cohorts comprising a total of 112 patients diagnosed with sporadic Creutzfeldt-Jakob disease (sCJD), probable AD, or non-Alzheimer's type dementia. Patients with AD exhibit low mtDNA content in CSF compared with patients diagnosed with sCJD or with non-Alzheimer's type dementias. The CSF concentration of mtDNA does not correlate with Aβ, t-tau, p-tau, and 14-3-3 protein levels in CSF. Low-CSF mtDNA is not a consequence of brain damage and allows the differential diagnosis of AD from sCJD and other dementias. These results support the hypothesis that mtDNA in CSF is a pathophysiological biomarker of AD. Copyright © 2015 Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

GC-Rich Extracellular DNA Induces Oxidative Stress, Double-Strand DNA Breaks, and DNA Damage Response in Human Adipose-Derived Mesenchymal Stem Cells.

Science.gov (United States)

Kostyuk, Svetlana; Smirnova, Tatiana; Kameneva, Larisa; Porokhovnik, Lev; Speranskij, Anatolij; Ershova, Elizaveta; Stukalov, Sergey; Izevskaya, Vera; Veiko, Natalia

2015-01-01

Cell free DNA (cfDNA) circulates throughout the bloodstream of both healthy people and patients with various diseases. CfDNA is substantially enriched in its GC-content as compared with human genomic DNA. Exposure of haMSCs to GC-DNA induces short-term oxidative stress (determined with H2DCFH-DA) and results in both single- and double-strand DNA breaks (comet assay and γH2AX, foci). As a result in the cells significantly increases the expression of repair genes (BRCA1 (RT-PCR), PCNA (FACS)) and antiapoptotic genes (BCL2 (RT-PCR and FACS), BCL2A1, BCL2L1, BIRC3, and BIRC2 (RT-PCR)). Under the action of GC-DNA the potential of mitochondria was increased. Here we show that GC-rich extracellular DNA stimulates adipocyte differentiation of human adipose-derived mesenchymal stem cells (haMSCs). Exposure to GC-DNA leads to an increase in the level of RNAPPARG2 and LPL (RT-PCR), in the level of fatty acid binding protein FABP4 (FACS analysis) and in the level of fat (Oil Red O). GC-rich fragments in the pool of cfDNA can potentially induce oxidative stress and DNA damage response and affect the direction of mesenchymal stem cells differentiation in human adipose-derived mesenchymal stem cells. Such a response may be one of the causes of obesity or osteoporosis.

DNA endoreplication level in endosperm during seed development in three monocotyledonous species

Directory of Open Access Journals (Sweden)

Kazimierz Marciniak

2014-01-01

Full Text Available The DNA content after the Feulgen reaction in the endosperm of three monocotyledonous plant species (Asparagus officinalis, Muscari comosom, Haemanthus kurharinae differing in their 2C DNA content, was cytophotometrically measured. During endosperm development 1-6 endoreplication cycles take place, depending on the species. Differences in nuclear DNA endoreplication dynamics in the tested species are similar to those occurring in root parenchyma, but the endoreplication level in the endosperm is higher.

Genetic Diversity and Population Structure of a Threatened African Tree Species, Milicia excelsa, Using Nuclear Micro satellites DNA Markers

International Nuclear Information System (INIS)

Ouinsavi, Ch.; Sokpon, N.; Ouinsavi, Ch.; Khasa, D.P.

2009-01-01

To accurately estimate the genetic diversity and population structure for improved conservation planning of Milicia excelsa tree, 212 individuals from twelve population samples covering the species' range in Benin were surveyed at seven specific micro satellite DNA loci. All loci were variable, with the mean number of alleles per locus ranging from 5.86 to 7.69. Considerable genetic variability was detected for all populations at the seven loci (AR=4.60; HE=0.811). Moderate but statistically significant genetic differentiation was found among populations considering both FST (0.112) and RST (0.342). All of the populations showed heterozygosity deficits in test of Hardy-Weinberg Equilibrium and significantly positive FIS values due to inbreeding occurring in the species. Pairwise FST values were positively and significantly correlated with geographical distances (r=0.432; P=.007, Mantel's test) indicating that populations are differentiated by isolation by distance. Bayesian analysis of population structure showed division of the genetic variation into four clusters revealing the existence of heterogeneity in population genetic structure. Altogether, these results indicate that genetic variation in Milicia excelsa is geographically structured. Information gained from this study also emphasized the need for in situ conservation of the relict populations and establishment of gene flow corridors through agroforestry systems for interconnecting these remnant populations.

Effect of Ionosphere on Geostationary Communication Satellite Signals

Science.gov (United States)

Erdem, Esra; Arikan, Feza; Gulgonul, Senol

2016-07-01

ionosphere using IRI-Plas-G software. One of the outstanding features of IONOLAB-RAY is the opportunity of Global Ionospheric Map-Total Electron Content (GIM-TEC) assimilation. This feature enables more realistic representation of ionosphere, especially for the times when ionosphere deviates from the generalized models, such as during geomagnetic storms. This feature is critical to examine the effect of ionosphere on satellite signals under ionospheric storm conditions. In this study TURKSAT satellite data is used to compare the results of IONOLAB-RAY and evaluate the effect of ionosphere. TURKSAT is one of the world's leading companies providing all sorts of satellite communications through the satellites of TURKSAT as well as the other satellites. Providing services for voice, data, internet, TV, and radio broadcasting through the satellites across a wide area extending from Europe to Asia. The latest satellite of TURKSAT, namely Turksat 4B was launched on October 2015, before that various versions of TURKSAT satellites are launched since 1994. In the future enlargement of broadcasting area towards equatorial region is aimed, where the ionospheric anomalies and storms are highly expected. In the future this study can be applied to the satellite signals in equatorial regions and effects of ionosphere especially under storm conditions can be discussed. This study is supported by TUBITAK 114E541, 115E915 and Joint TUBITAK 114E092 and AS CR 14/001 projects.

Decreased weight, DNA, RNA and protein content of the brain after neutron irradiation of the 18-day mouse embryo

International Nuclear Information System (INIS)

Antal, S.; Fonagy, A.; Hidvegi, E.J.; Fueloep, Z.; Vogel, H.H. Jr.

1984-01-01

Pregnant mice were irradiated with 0.5 Gy fission neutrons on the eighteenth day of gestation. Average litter size at birth was unchanged but mortality increased 5-6 fold in the first 3 days. Irradiated mice were the same weight as control mice at birth but showed a progressively increasing weight deficiency up to at least 36 days compared to controls. Brain weight was 37, 45 and 25% less in 2-, 3- and 52-week old irradiated animals; the ratio of brain weight to body weight was 25, 27 and 13% less. The concentrations of DNA, RNA and protein (mg/g wet tissue) were the same in irradiated and control mice in brain and liver at all three ages. Total DNA, RNA and protein contents of whole brain after irradiation were 56-75% of control levels. No definite decrease was observed in liver. Histological study at 6 hours after irradiation showed nuclear pyknosis in the central nervous system from definite to very severe according to the part examined. It is concluded that damage to the central nervous system of the 18-day mouse foetus is mainly due to killing and/or inhibition of the differentiation of neuroblasts. (author)

EFFECTS OF VOLUNTARY WHEEL RUNNING ON SATELLITE CELLS IN THE RAT PLANTARIS MUSCLE

Directory of Open Access Journals (Sweden)

Atsushi Kojima

2009-03-01

Full Text Available This study investigated the effects of voluntary wheel running on satellite cells in the rat plantaris muscle. Seventeen 5-week-old male Wistar rats were assigned to a control (n = 5 or training (n = 12 group. Each rat in the training group ran voluntarily in a running-wheel cage for 8 weeks. After the training period, the animals were anesthetized, and the plantaris muscles were removed, weighed, and analyzed immunohistochemically and biochemically. Although there were no significant differences in muscle weight or fiber area between the groups, the numbers of satellite cells and myonuclei per muscle fiber, percentage of satellite cells, and citrate synthase activity were significantly higher in the training group compared with the control group (p < 0.05. The percentage of satellite cells was also positively correlated with distance run in the training group (r = 0.61, p < 0.05. Voluntary running can induce an increase in the number of satellite cells without changing the mean fiber area in the rat plantaris muscle; this increase in satellite cell content is a function of distance run

ATS-6 radio beacon electron content measurements at Ootacamund, India, October 1975-July 1976

International Nuclear Information System (INIS)

Bouwer, S.D.; Davies, K.; Donnelly, R.F.; Grubb, R.N.; Jones, J.E.

1980-03-01

An atlas of total slant-path columnar electron content data measured between the ATS-6 satellite and Ootacamund, India, a site near the magnetic Equator is presented. Although these measurements were taken during a solar minimum, the general level of flare and geomagnetic activity that occurred during the observation period is summarized. These total content (N(T)) data were derived from the modulation phase (group delay) of a carrier signal transmitted from the geostationary satellite's Radio Beacon Experiment. This atlas contains two data sets: (1) N(T) as 2-min subsamples digitally recorded between 2 October 1975 and 28 January 1976 corrected for ATS-6 pitch maneuvers and (2) N(T) as 15-min subsamples chart recorded between 21 October 1975 and 22 July 1976 but uncorrected for changes in satellite orientation

Higher 5-hydroxymethylcytosine identifies immortal DNA strand chromosomes in asymmetrically self-renewing distributed stem cells.

Science.gov (United States)

Huh, Yang Hoon; Cohen, Justin; Sherley, James L

2013-10-15

Immortal strands are the targeted chromosomal DNA strands of nonrandom sister chromatid segregation, a mitotic chromosome segregation pattern unique to asymmetrically self-renewing distributed stem cells (DSCs). By nonrandom segregation, immortal DNA strands become the oldest DNA strands in asymmetrically self-renewing DSCs. Nonrandom segregation of immortal DNA strands may limit DSC mutagenesis, preserve DSC fate, and contribute to DSC aging. The mechanisms responsible for specification and maintenance of immortal DNA strands are unknown. To discover clues to these mechanisms, we investigated the 5-methylcytosine and 5-hydroxymethylcytosine (5hmC) content on chromosomes in mouse hair follicle DSCs during nonrandom segregation. Although 5-methylcytosine content did not differ significantly, the relative content of 5hmC was significantly higher in chromosomes containing immortal DNA strands than in opposed mitotic chromosomes containing younger mortal DNA strands. The difference in relative 5hmC content was caused by the loss of 5hmC from mortal chromosomes. These findings implicate higher 5hmC as a specific molecular determinant of immortal DNA strand chromosomes. Because 5hmC is an intermediate during DNA demethylation, we propose a ten-eleven translocase enzyme mechanism for both the specification and maintenance of nonrandomly segregated immortal DNA strands. The proposed mechanism reveals a means by which DSCs "know" the generational age of immortal DNA strands. The mechanism is supported by molecular expression data and accounts for the selection of newly replicated DNA strands when nonrandom segregation is initiated. These mechanistic insights also provide a possible basis for another characteristic property of immortal DNA strands, their guanine ribonucleotide dependency.

Testing General Relativistic Predictions with the LAGEOS Satellites

International Nuclear Information System (INIS)

Peron, Roberto

2014-01-01

The spacetime around Earth is a good environment in order to perform tests of gravitational theories. According to Einstein’s view of gravitational phenomena, the Earth mass-energy content curves the surrounding spacetime in a peculiar way. This (relatively) quiet dynamical environment enables a good reconstruction of geodetic satellites (test masses) orbit, provided that high-quality tracking data are available. This is the case of the LAGEOS satellites, built and launched mainly for geodetic and geodynamical purposes, but equally good for fundamental physics studies. A review of these studies is presented, focusing on data, models, and analysis strategies. Some recent and less recent results are presented. All of them indicate general relativity theory as a very good description of gravitational phenomena, at least in the studied environment.

DNA preservation in silk.

Science.gov (United States)

Liu, Yawen; Zheng, Zhaozhu; Gong, He; Liu, Meng; Guo, Shaozhe; Li, Gang; Wang, Xiaoqin; Kaplan, David L

2017-06-27

The structure of DNA is susceptible to alterations at high temperature and on changing pH, irradiation and exposure to DNase. Options to protect and preserve DNA during storage are important for applications in genetic diagnosis, identity authentication, drug development and bioresearch. In the present study, the stability of total DNA purified from human dermal fibroblast cells, as well as that of plasmid DNA, was studied in silk protein materials. The DNA/silk mixtures were stabilized on filter paper (silk/DNA + filter) or filter paper pre-coated with silk and treated with methanol (silk/DNA + PT-filter) as a route to practical utility. After air-drying and water extraction, 50-70% of the DNA and silk could be retrieved and showed a single band on electrophoretic gels. 6% silk/DNA + PT-filter samples provided improved stability in comparison with 3% silk/DNA + filter samples and DNA + filter samples for DNA preservation, with ∼40% of the band intensity remaining at 37 °C after 40 days and ∼10% after exposure to UV light for 10 hours. Quantitative analysis using the PicoGreen assay confirmed the results. The use of Tris/borate/EDTA (TBE) buffer enhanced the preservation and/or extraction of the DNA. The DNA extracted after storage maintained integrity and function based on serving as a functional template for PCR amplification of the gene for zinc finger protein 750 (ZNF750) and for transgene expression of red fluorescence protein (dsRed) in HEK293 cells. The high molecular weight and high content of a crystalline beta-sheet structure formed on the coated surfaces likely accounted for the preservation effects observed for the silk/DNA + PT-filter samples. Although similar preservation effects were also obtained for lyophilized silk/DNA samples, the rapid and simple processing available with the silk-DNA-filter membrane system makes it appealing for future applications.

Determining the Cost Effectiveness of Nano-Satellites

Science.gov (United States)

2014-09-01

purchased as little as $7,500 ( Pumpkin 2014) for academic focused missions. Traditional satellites often cost hundreds of millions of dollars. For...and was not easily modified. The costs for the six-year scenario were only spread over five years. If the cost model were updated to spread the...files/national_space_policy_6-28-10.pdf. Pumpkin . “ Pumpkin Price List.” Pumpkin . May 23, 2014. http://www.pumpkininc.com/content/doc/forms

The demise of chloroplast DNA in Arabidopsis.

Science.gov (United States)

Rowan, Beth A; Oldenburg, Delene J; Bendich, Arnold J

2004-09-01

Although it might be expected that chloroplast DNA (cpDNA) would be stably maintained in mature leaves, we report the surprising observation that cpDNA levels decline during plastid development in Arabidopsis thaliana (Col.) until most of the leaves contain little or no DNA long before the onset of senescence. We measured the cpDNA content in developing cotyledons, rosette leaves, and cauline leaves. The amount of cpDNA per chloroplast decreases as the chloroplasts develop, reaching undetectable levels in mature leaves. In young cauline leaves, most individual molecules of cpDNA are found in complex, branched forms. In expanded cauline leaves, cpDNA is present in smaller branched forms only at the base of the leaf and is virtually absent in the distal part of the leaf. We conclude that photosynthetic activity may persist long after the demise of the cpDNA. Copyright 2004 Springer-Verlag

Vesicle fusion observed by content transfer across a tethered lipid bilayer.

Science.gov (United States)

Rawle, Robert J; van Lengerich, Bettina; Chung, Minsub; Bendix, Poul Martin; Boxer, Steven G

2011-10-19

Synaptic transmission is achieved by exocytosis of small, synaptic vesicles containing neurotransmitters across the plasma membrane. Here, we use a DNA-tethered freestanding bilayer as a target architecture that allows observation of content transfer of individual vesicles across the tethered planar bilayer. Tethering and fusion are mediated by hybridization of complementary DNA-lipid conjugates inserted into the two membranes, and content transfer is monitored by the dequenching of an aqueous content dye. By analyzing the diffusion profile of the aqueous dye after vesicle fusion, we are able to distinguish content transfer across the tethered bilayer patch from vesicle leakage above the patch. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

GC-Rich Extracellular DNA Induces Oxidative Stress, Double-Strand DNA Breaks, and DNA Damage Response in Human Adipose-Derived Mesenchymal Stem Cells

Directory of Open Access Journals (Sweden)

Svetlana Kostyuk

2015-01-01

Full Text Available Background. Cell free DNA (cfDNA circulates throughout the bloodstream of both healthy people and patients with various diseases. CfDNA is substantially enriched in its GC-content as compared with human genomic DNA. Principal Findings. Exposure of haMSCs to GC-DNA induces short-term oxidative stress (determined with H2DCFH-DA and results in both single- and double-strand DNA breaks (comet assay and γH2AX, foci. As a result in the cells significantly increases the expression of repair genes (BRCA1 (RT-PCR, PCNA (FACS and antiapoptotic genes (BCL2 (RT-PCR and FACS, BCL2A1, BCL2L1, BIRC3, and BIRC2 (RT-PCR. Under the action of GC-DNA the potential of mitochondria was increased. Here we show that GC-rich extracellular DNA stimulates adipocyte differentiation of human adipose-derived mesenchymal stem cells (haMSCs. Exposure to GC-DNA leads to an increase in the level of RNAPPARG2 and LPL (RT-PCR, in the level of fatty acid binding protein FABP4 (FACS analysis and in the level of fat (Oil Red O. Conclusions. GC-rich fragments in the pool of cfDNA can potentially induce oxidative stress and DNA damage response and affect the direction of mesenchymal stem cells differentiation in human adipose—derived mesenchymal stem cells. Such a response may be one of the causes of obesity or osteoporosis.

Use of a D17Z1 oligonucleotide probe for human DNA quantitation prior to PCR analysis of polymorphic DNA markers

Energy Technology Data Exchange (ETDEWEB)

Walsh, S.; Alavaren, M.; Varlaro, J. [Roche Molecular Systems, Alameda, CA (United States)] [and others

1994-09-01

The alpha-satellite DNA locus D17Z1 contains primate-specific sequences which are repeated several hundred times per chromosome 17. A probe that was designed to hybridize to a subset of the D17Z1 sequence can be used for very sensitive and specific quantitation of human DNA. Sample human genomic DNA is immobilized on nylon membrane using a slot blot apparatus, and then hybridized with a biotinylated D17Z1 oligonucleotide probe. The subsequent binding of streptavidin-horseradish peroxidase to the bound probe allows for either calorimetric (TMB) or chemiluminescent (ECL) detection. Signals obtained for sample DNAs are then compared to the signals obtained for a series of human DNA standards. For either detection method, forty samples can be quantitated in less than two hours, with a sensitivity of 150 pg. As little as 20 pg of DNA can be quantitated when using chemiluminescent detection with longer film exposures. PCR analysis of several VNTR and STR markers has indicated that optimal typing results are generally obtained within a relatively narrow range of input DNA quantities. Too much input DNA can lead to PCR artifacts such as preferential amplification of smaller alleles, non-specific amplification products, and exaggeration of the DNA synthesis slippage products that are seen with STR markers. Careful quantitation of human genomic DNA prior to PCR can avoid or minimize these problems and ultimately give cleaner, more unambiguous PCR results.

Comparison of Six DNA Extraction Procedures and the Application of Plastid DNA Enrichment Methods in Selected Non-photosynthetic Plants

Directory of Open Access Journals (Sweden)

Shin-Yi Shyu

2013-12-01

Full Text Available Genomic DNA was isolated using three DNA extraction commercial kits and three CTAB-based methods for two non-photosynthetic plants, Balanophora japonica and Mitrastemon kanehirai. The quality of the isolated DNA was evaluated and subjected to following restriction enzyme digestions. All six procedures yielded DNA of sufficient quality for PCR, and the method described by Barnwell et al. (1998 performed well in isolating DNA from both species for restriction enzyme digestion. In addition, we succeeded to enrich plastid DNA content by using the methods depending on a high salt buffer to deplete nuclear material. The ‘high salt’ methods based on protocol presented by Milligan (1989 were able to increase plastid DNA effectively and significantly reduce nuclear DNA from M. kanehirai. The plastid DNA enrichment protocols are inexpensive and not time-consuming, and may be applicable to other non-photosynthetic plants.

High-Throughput Block Optical DNA Sequence Identification.

Science.gov (United States)

Sagar, Dodderi Manjunatha; Korshoj, Lee Erik; Hanson, Katrina Bethany; Chowdhury, Partha Pratim; Otoupal, Peter Britton; Chatterjee, Anushree; Nagpal, Prashant

2018-01-01

Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm -1 . Here, surface-enhanced Raman spectroscopy is used to demonstrate label-free identification of DNA nucleobases with multiplexed 3D plasmonic nanofocusing. While nanometer-scale mode volumes prevent identification of single nucleobases within a DNA sequence, the block optical technique can identify A, T, G, and C content in DNA k-mers. The content of each nucleotide in a DNA block can be a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single-letter sequencing. Additionally, coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization. These results pave the way for developing a novel, high-throughput block optical sequencing method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of boarding return satellite on antioxidant enzyme activities during germination of hot pepper seed

International Nuclear Information System (INIS)

Li Shuifeng; Wang Bingliang; Guan Xueyu; Zhang Yan

2006-01-01

The effect of boarding return satellite on antioxidant enzyme activities during germination of hot pepper seed was studied. The results showed that the germination potentiality and germination rate of hot pepper seed after boarding return satellite were increased by 3.5% and 5.3%, respectively. During seed germination, soluble protein and MDA contents decreased, however, the SOD activities increased. SOD activity of treated seeds was higher than that of the control especially during the initial period of germination, while the content of soluble and MDA contents were much lower than those of control. The activities of SOD, G-POD, APX and CAT in 13d seedlings of treated seeds were increased by 14.29%, 25.23%, 1.84% and 21.52%, respectively. It was concluded that space flight enhanced antioxidant enzyme activities of seeds and seedlings, which were very important to prevent membrane lipid superoxide. (authors)

Saw palmetto alters nuclear measurements reflecting DNA content in men with symptomatic BPH: evidence for a possible molecular mechanism.

Science.gov (United States)

Veltri, Robert W; Marks, Leonard S; Miller, M Craig; Bales, Wes D; Fan, John; Macairan, Maria Luz; Epstein, Jonathan I; Partin, Alan W

2002-10-01

To examine the nuclear chromatin characteristics of epithelial cells, looking for an SPHB-mediated effect on nuclear DNA structure and organization. Saw palmetto herbal blend (SPHB) causes contraction of prostate epithelial cells and suppression of tissue dihydrotestosterone levels in men with symptomatic benign prostatic hyperplasia, but a fundamental mechanism remains unknown. A 6-month randomized trial, comparing prostatic tissue of men treated with SPHB (n = 20) or placebo (n = 20), was performed. At baseline, the two groups were similar in age (65 versus 64 years), symptoms (International Prostate Symptom Score 18 versus 17), uroflow (maximal urinary flow rate 10 versus 11 mL/s), prostate volume (59 versus 58 cm(3)), prostate-specific antigen (4.2 versus 2.7 ng/mL), and percentage of epithelium (17% versus 16%). Prostatic tissue was obtained by sextant biopsy before and after treatment. Five-micron sections were Feulgen stained and quantitatively analyzed using the AutoCyte QUIC-DNA imaging system. Images were captured from 200 randomly selected epithelial cell nuclei, and 60 nuclear morphometric descriptors (NMDs) (eg, size, shape, DNA content, and textural features) were determined for each nucleus. Logistic regression analysis was used to assess the differences in the variances of the NMDs between the treated and untreated prostate epithelial cells. At baseline, the SPHB and placebo groups had similar NMD values. After 6 months of placebo, no significant change from baseline was found in the NMDs. However, after 6 months of SPHB, 25 of the 60 NMDs were significantly different compared with baseline, and a multivariate model for predicting treatment effect using 4 of the 25 was created (P <0.001). The multivariate model had an area under the receiver operating characteristic curve of 94% and an accuracy of 85%. Six months of SPHB treatment appears to alter the DNA chromatin structure and organization in prostate epithelial cells. Thus, a possible molecular

Effect of DNA extraction and sample preservation method on rumen bacterial population.

Science.gov (United States)

Fliegerova, Katerina; Tapio, Ilma; Bonin, Aurelie; Mrazek, Jakub; Callegari, Maria Luisa; Bani, Paolo; Bayat, Alireza; Vilkki, Johanna; Kopečný, Jan; Shingfield, Kevin J; Boyer, Frederic; Coissac, Eric; Taberlet, Pierre; Wallace, R John

2014-10-01

The comparison of the bacterial profile of intracellular (iDNA) and extracellular DNA (eDNA) isolated from cow rumen content stored under different conditions was conducted. The influence of rumen fluid treatment (cheesecloth squeezed, centrifuged, filtered), storage temperature (RT, -80 °C) and cryoprotectants (PBS-glycerol, ethanol) on quality and quantity parameters of extracted DNA was evaluated by bacterial DGGE analysis, real-time PCR quantification and metabarcoding approach using high-throughput sequencing. Samples clustered according to the type of extracted DNA due to considerable differences between iDNA and eDNA bacterial profiles, while storage temperature and cryoprotectants additives had little effect on sample clustering. The numbers of Firmicutes and Bacteroidetes were lower (P rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at -80 °C was found as the optimal method to study ruminal bacterial profile. Copyright © 2013 Elsevier Ltd. All rights reserved.

Increased DNA-repair in spleen cells of M. Hodgkin

International Nuclear Information System (INIS)

Frischauf, H.; Neumann, E.; Howanietz, L.; Dolejs, I.; Tuschl, H.; Altmann, H.

1974-11-01

In spleen cells of control patients and cells of Morbus Hodgkin, DNA-repair after gamma- and UV-irradiation was determined measuring the incorporated 3H-thymidine activity in the DNA. Additionally, the ratio of labeled cells compared to non-labeled cells and the grains per cell were evaluated by autoradiographic investigations. DNA-content per cell was measured using pulsecytophotometry. A significant increase of DNA-repair capacity after gamma-irradiation was found by density gradient centrifugation in alkaline sucrose. The same trend could be shown by investigations of unscheduled DNA-synthesis using autoradiographic method. (author)

Leveraging the NPS Femto Satellite for Alternative Satellite Communication Networks

Science.gov (United States)

2017-09-01

programmed for eventual integration with the Iridium Network , which is then tested. C. THESIS ORGANIZATION The thesis addresses these questions...NPS FEMTO SATELLITE FOR ALTERNATIVE SATELLITE COMMUNICATION NETWORKS by Faisal S. Alshaya September 2017 Co-Advisors: Steven J. Iatrou...TYPE AND DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE LEVERAGING THE NPS FEMTO SATELLITE FOR ALTERNATIVE SATELLITE COMMUNICATION NETWORKS 5

Carbon ion induced DNA double-strand breaks in melanophore B16

International Nuclear Information System (INIS)

Wei Zengquan; Zhou Guangming; Wang Jufang; He Jing; Li Qiang; Li Wenjian; Xie Hongmei; Cai Xichen; Tao Huang; Dang Bingrong; Han Guangwu

1997-01-01

DNA double-strand breaks (DSBs) in melanophore B 16 induced by plateau and extended Bragg peak of 75 MeV/u 12 C 6+ ions were studied by using a technique of inverse pulsed-field gel electrophoresis (PIGE). DNA fragment lengths were distributed in two ranges: the larger in 1.4 Mbp-3.2 Mbp and the smaller in less than 1.2 Mbp. It indicates that distribution of DNA fragments induced by heavy ion irradiation is not stochastic and there probably are sensitive sites to heavy ions in DNA molecules of B 16 . Percentage of DNA released from plug (PR) increased and trended towards a quasi-plateau ∝85% as dose increased. Content of the larger fragments decreased and flattened with increasing dose while content of the smaller ones increased and trended towards saturation. (orig.)

Condensing Massive Satellite Datasets For Rapid Interactive Analysis

Science.gov (United States)

Grant, G.; Gallaher, D. W.; Lv, Q.; Campbell, G. G.; Fowler, C.; LIU, Q.; Chen, C.; Klucik, R.; McAllister, R. A.

2015-12-01

Our goal is to enable users to interactively analyze massive satellite datasets, identifying anomalous data or values that fall outside of thresholds. To achieve this, the project seeks to create a derived database containing only the most relevant information, accelerating the analysis process. The database is designed to be an ancillary tool for the researcher, not an archival database to replace the original data. This approach is aimed at improving performance by reducing the overall size by way of condensing the data. The primary challenges of the project include: - The nature of the research question(s) may not be known ahead of time. - The thresholds for determining anomalies may be uncertain. - Problems associated with processing cloudy, missing, or noisy satellite imagery. - The contents and method of creation of the condensed dataset must be easily explainable to users. The architecture of the database will reorganize spatially-oriented satellite imagery into temporally-oriented columns of data (a.k.a., "data rods") to facilitate time-series analysis. The database itself is an open-source parallel database, designed to make full use of clustered server technologies. A demonstration of the system capabilities will be shown. Applications for this technology include quick-look views of the data, as well as the potential for on-board satellite processing of essential information, with the goal of reducing data latency.

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.

GNSS, Satellite Altimetry and Formosat-3/COSMIC for Determination of Ionosphere Parameters

Science.gov (United States)

Mahdi Alizadeh Elizei, M.; Schuh, Harald; Schmidt, Michael; Todorova, Sonya

The dispersion of ionosphere with respect to the microwave signals allows gaining information about the parameters of this medium in terms of the electron density (Ne), or the Total Elec-tron Content (TEC). In the last decade space geodetic techniques, such as Global Navigation Satellite System (GNSS), satellite altimetry missions, and Low Earth Orbiting (LEO) satel-lites have turned into a promising tool for remote sensing the ionosphere. The dual-frequency GNSS observations provide the main input data for development of Global Ionosphere Maps (GIM). However, the GNSS stations are heterogeneously distributed, with large gaps particu-larly over the sea surface, which lowers the precision of the GIM over these areas. Conversely, dual-frequency satellite altimetry missions provide information about the ionosphere precisely above the sea surface. In addition, LEO satellites such as Formosat-3/COSMIC (F-3/C) pro-vide well-distributed information of ionosphere around the world. In this study we developed GIMs of VTEC from combination of GNSS, satellite altimetry and F-3/C data with temporal resolution of 2 hours and spatial resolution of 5 degree in longitude and 2.5 degree in latitude. The combined GIMs provide a more homogeneous global coverage and higher precision and reliability than results of each individual technique.

Karyotype and nucleic acid content in Zantedeschia aethiopica Spr ...

African Journals Online (AJOL)

DR. NJ TONUKARI

2012-07-03

Jul 3, 2012 ... Analysis of karyotype, nucleic deoxyribonucleic acid (DNA) content and sodium dodecyl sulfate polyacrylamide ... base pairs) for Z. aethiopica and 1144.26 ± 0.05 picograms (equivalent to 1144.26 mega base pairs) for Z. elliottiana. ... ml ice-cold nuclei-isolation buffer A of the Partec high resolution. DNA kit ...

Genome Sizes in Hepatica Mill: (Ranunculaceae Show a Loss of DNA, Not a Gain, in Polyploids

Directory of Open Access Journals (Sweden)

B. J. M. Zonneveld

2010-01-01

, and a possible pentaploid. The somatic nuclear DNA contents (2C-value, as measured by flow cytometry with propidium iodide, were shown to range from 33 to 80 pg. The Asiatic and American species, often considered subspecies of H. nobilis, could be clearly distinguished from European H. nobilis. DNA content confirmed the close relationships in the Asiatic species, and these are here considered as subspecies of H. asiatica. Parents for the allotetraploid species could be suggested based on their nuclear DNA content. Contrary to the increase in genome size suggested earlier for Hepatica, a significant (6%–14% loss of nuclear DNA in the natural allopolyploids was found.

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.

An Estimate of the Total DNA in the Biosphere.

Science.gov (United States)

Landenmark, Hanna K E; Forgan, Duncan H; Cockell, Charles S

2015-06-01

Modern whole-organism genome analysis, in combination with biomass estimates, allows us to estimate a lower bound on the total information content in the biosphere: 5.3 × 1031 (±3.6 × 1031) megabases (Mb) of DNA. Given conservative estimates regarding DNA transcription rates, this information content suggests biosphere processing speeds exceeding yottaNOPS values (1024 Nucleotide Operations Per Second). Although prokaryotes evolved at least 3 billion years before plants and animals, we find that the information content of prokaryotes is similar to plants and animals at the present day. This information-based approach offers a new way to quantify anthropogenic and natural processes in the biosphere and its information diversity over time.

An isolated Hda-clamp complex is functional in the regulatory inactivation of DnaA and DNA replication.

Science.gov (United States)

Kawakami, Hironori; Su'etsugu, Masayuki; Katayama, Tsutomu

2006-10-01

In Escherichia coli, a complex consisting of Hda and the DNA-loaded clamp-subunit of the DNA polymerase III holoenzyme promotes hydrolysis of DnaA-ATP. The resultant ADP-DnaA is inactive for initiation of chromosomal DNA replication, thereby repressing excessive initiations. As the cellular content of the clamp is 10-100 times higher than that of Hda, most Hda molecules might be complexed with the clamp in vivo. Although Hda predominantly forms irregular aggregates when overexpressed, in the present study we found that co-overexpression of the clamp with Hda enhances Hda solubility dramatically and we efficiently isolated the Hda-clamp complex. A single molecule of the complex appears to consist of two Hda molecules and a single clamp. The complex is competent in DnaA-ATP hydrolysis and DNA replication in the presence of DNA and the clamp deficient subassembly of the DNA polymerase III holoenzyme (pol III*). These findings indicate that the clamp contained in the complex is loaded onto DNA through an interaction with the pol III* and that the Hda activity is preserved in these processes. The complex consisting of Hda and the DNA-unloaded clamp may play a specific role in a process proceeding to the DnaA-ATP hydrolysis in vivo.

Differential amplification of satellite PaB6 in chromosomally hypervariable Prospero autumnale complex (Hyacinthaceae)

Czech Academy of Sciences Publication Activity Database

Emadzade, K.; Jang, T.S.; Macas, Jiří; Kovařík, Aleš; Novák, Petr; Parker, J.; Weiß-Schneeweiss, H.

2014-01-01

Roč. 114, č. 8 (2014), s. 1597-1608 ISSN 0305-7364 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 ; RVO:68081707 Keywords : Hyacinthaceae * PaB6 * pericentric satellite DNA * next-generation sequencing * Prospero autumnale Subject RIV: EB - Genetics ; Molecular Biology; EB - Genetics ; Molecular Biology (BFU-R) Impact factor: 3.654, year: 2014

Satellite cell response to erythropoietin treatment and endurance training in healthy young men

DEFF Research Database (Denmark)

Hoedt, Andrea; Christensen, Britt; Nellemann, Birgitte

2016-01-01

KEY POINT: Erythropoietin (Epo) treatment may induce myogenic differentiation factor (MyoD) expression and prevent apoptosis in satellite cells (SCs) in murine and in vitro models. Endurance training stimulates SC proliferation in vivo in murine and human skeletal muscle. In the present study, we......-receptor interaction. Moreover, endurance training, but not Epo treatment, increases the SC content in type II myofibres, as well as the content of MyoD(+) SCs. Collectively, our results suggest that Epo treatment can regulate human SCs in vivo, supported by Epo receptor mRNA expression in human SCs. In effect, long......-term Epo treatment during disease conditions involving anaemia may impact SCs and warrants further investigation. Satellite cell (SC) proliferation is observed following erythropoitin treatment in vitro in murine myoblasts and endurance training in vivo in human skeletal muscle. The present study aimed...

DNA content of rodent brains during maturation and aging, and autoradiography of postnatal DNA synthesis in monkey brain

International Nuclear Information System (INIS)

Howard, E.

1973-01-01

[ 3 H]Thymidine is taken up by cells synthesizing DNA prepatory to cell division and remains incorporated in the DNA molecules as a lasting radioactive cell marker unless diluted out by repeated cell divisions. With the mouse and rat, histological studies after [ 3 H]thymidine injections have demonstrated that the cells of the external granular layer of the cerebellum proliferate abundantly during the first 2 weeks of postnatal life. Development of the primate brain is a gradual process extending over a much longer time than is required in the rodent. Despite the relative histological maturity of the monkey cerebellum at birth, the cells of the external granular layer are still actively synthesizing DNA at this time. Two monkeys were given [ 3 H]thymidine at birth and killed within 4 hours. Intense radioactivity was present in the cells of the external granular layer. Cells near the Prukinje perikarya were rather frequently labelled in this monkey, as described by Miale and Sidman in the mouse. In the molecular layer and in the body of the granular layer, relatively few cells were labelled. The labelling was present throughout the cerebellum, although the number of cells labelled varied from one microscopic field to another

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.

Characterizing the DNA Damage Response by Cell Tracking Algorithms and Cell Features Classification Using High-Content Time-Lapse Analysis.

Directory of Open Access Journals (Sweden)

Walter Georgescu

Full Text Available Traditionally, the kinetics of DNA repair have been estimated using immunocytochemistry by labeling proteins involved in the DNA damage response (DDR with fluorescent markers in a fixed cell assay. However, detailed knowledge of DDR dynamics across multiple cell generations cannot be obtained using a limited number of fixed cell time-points. Here we report on the dynamics of 53BP1 radiation induced foci (RIF across multiple cell generations using live cell imaging of non-malignant human mammary epithelial cells (MCF10A expressing histone H2B-GFP and the DNA repair protein 53BP1-mCherry. Using automatic extraction of RIF imaging features and linear programming techniques, we were able to characterize detailed RIF kinetics for 24 hours before and 24 hours after exposure to low and high doses of ionizing radiation. High-content-analysis at the single cell level over hundreds of cells allows us to quantify precisely the dose dependence of 53BP1 protein production, RIF nuclear localization and RIF movement after exposure to X-ray. Using elastic registration techniques based on the nuclear pattern of individual cells, we could describe the motion of individual RIF precisely within the nucleus. We show that DNA repair occurs in a limited number of large domains, within which multiple small RIFs form, merge and/or resolve with random motion following normal diffusion law. Large foci formation is shown to be mainly happening through the merging of smaller RIF rather than through growth of an individual focus. We estimate repair domain sizes of 7.5 to 11 µm2 with a maximum number of ~15 domains per MCF10A cell. This work also highlights DDR which are specific to doses larger than 1 Gy such as rapid 53BP1 protein increase in the nucleus and foci diffusion rates that are significantly faster than for spontaneous foci movement. We hypothesize that RIF merging reflects a "stressed" DNA repair process that has been taken outside physiological conditions when

Absence of ribosomal DNA amplification in the meroistic (telotrophic) ovary of the large milkweed bug Oncopeltus fasciatus (Dallas) (Hemiptera: Lygaeidae)

Science.gov (United States)

1975-01-01

In the typical meroistic insect ovary, the oocyte nucleus synthesizes little if any RNA. Nurse cells or trophocytes actively synthesize ribosomes which are transported to and accumulated by the oocyte. In the telotrophic ovary a morphological separation exists, the nurse cells being localized at the apical end of each ovariole and communicating with the ooocytes via nutritive cords. In order to determine whether the genes coding for ribosomal RNA (rRNA) are amplified in the telotrophic ovary of the milkweed bug Oncopeltus fasciatus, the percentages of the genome coding for ribosomal RNA in somatic cells, spermatogenic cells, ovarian follicles, and nurse cells were compared. The oocytes and most of the nurse cells of O. fasciatus are uninucleolate. DNA hybridizing with ribosomal RNA is localized in a satellite DNA, the density of which is 1.712 g/cm(-3). The density of main-band DNA is 1.694 g/cm(-3). The ribosomal DNA satellite accounts for approximately 0.2% of the DNA in somatic and gametogenic tissues of both males and females. RNA-DNA hybridization analysis demonstrates that approximately 0.03% of the DNA in somatic tissues, testis, ovarian follicles, and isolated nurse cells hybridizes with ribosomal RNA. The fact that the percentage of DNA hybridizing with rRNA is the same in somatic and in male and female gametogenic tissues indicates that amplification of ribosomal DNA does not occur in nurse cells and that if it occurs in oocytes, it represents less than a 50- fold increase in ribosomal DNA. An increase in total genome DNA accounted by polyploidization appears to provide for increasing the amount of ribosomal DNA in the nurse cells. PMID:1158969

Downscaling Satellite Data for Predicting Catchment-scale Root Zone Soil Moisture with Ground-based Sensors and an Ensemble Kalman Filter

Science.gov (United States)

Lin, H.; Baldwin, D. C.; Smithwick, E. A. H.

2015-12-01

Predicting root zone (0-100 cm) soil moisture (RZSM) content at a catchment-scale is essential for drought and flood predictions, irrigation planning, weather forecasting, and many other applications. Satellites, such as the NASA Soil Moisture Active Passive (SMAP), can estimate near-surface (0-5 cm) soil moisture content globally at coarse spatial resolutions. We develop a hierarchical Ensemble Kalman Filter (EnKF) data assimilation modeling system to downscale satellite-based near-surface soil moisture and to estimate RZSM content across the Shale Hills Critical Zone Observatory at a 1-m resolution in combination with ground-based soil moisture sensor data. In this example, a simple infiltration model within the EnKF-model has been parameterized for 6 soil-terrain units to forecast daily RZSM content in the catchment from 2009 - 2012 based on AMSRE. LiDAR-derived terrain variables define intra-unit RZSM variability using a novel covariance localization technique. This method also allows the mapping of uncertainty with our RZSM estimates for each time-step. A catchment-wide satellite-to-surface downscaling parameter, which nudges the satellite measurement closer to in situ near-surface data, is also calculated for each time-step. We find significant differences in predicted root zone moisture storage for different terrain units across the experimental time-period. Root mean square error from a cross-validation analysis of RZSM predictions using an independent dataset of catchment-wide in situ Time-Domain Reflectometry (TDR) measurements ranges from 0.060-0.096 cm3 cm-3, and the RZSM predictions are significantly (p < 0.05) correlated with TDR measurements [r = 0.47-0.68]. The predictive skill of this data assimilation system is similar to the Penn State Integrated Hydrologic Modeling (PIHM) system. Uncertainty estimates are significantly (p < 0.05) correlated to cross validation error during wet and dry conditions, but more so in dry summer seasons. Developing an

Centriolar satellites

DEFF Research Database (Denmark)

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

2015-01-01

Centriolar satellites are small, microscopically visible granules that cluster around centrosomes. These structures, which contain numerous proteins directly involved in centrosome maintenance, ciliogenesis, and neurogenesis, have traditionally been viewed as vehicles for protein trafficking...... 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....

Effects of voluntary wheel running on satellite cells in the rat plantaris muscle.

Science.gov (United States)

Kurosaka, Mitsutoshi; Naito, Hisashi; Ogura, Yuji; Kojima, Atsushi; Goto, Katsumasa; Katamoto, Shizuo

2009-01-01

This study investigated the effects of voluntary wheel running on satellite cells in the rat plantaris muscle. Seventeen 5-week-old male Wistar rats were assigned to a control (n = 5) or training (n = 12) group. Each rat in the training group ran voluntarily in a running-wheel cage for 8 weeks. After the training period, the animals were anesthetized, and the plantaris muscles were removed, weighed, and analyzed immunohistochemically and biochemically. Although there were no significant differences in muscle weight or fiber area between the groups, the numbers of satellite cells and myonuclei per muscle fiber, percentage of satellite cells, and citrate synthase activity were significantly higher in the training group compared with the control group (p run in the training group (r = 0.61, p running can induce an increase in the number of satellite cells without changing the mean fiber area in the rat plantaris muscle; this increase in satellite cell content is a function of distance run. Key pointsThere is no study about the effect of voluntary running on satellite cells in the rat plantaris muscle.Voluntary running training causes an increase of citrate synthase activity in the rat plantaris muscle but does not affect muscle weight and mean fiber area in the rat plantaris muscle.Voluntary running can induce an increase in the number of satellite cells without hypertrophy of the rat plantaris muscle.

Carbon ion induced DNA double-strand breaks in melanophore B{sub 16}

Energy Technology Data Exchange (ETDEWEB)

Zengquan, Wei; Guangming, Zhou; Jufang, Wang; Jing, He; Qiang, Li; Wenjian, Li; Hongmei, Xie; Xichen, Cai; Huang, Tao; Bingrong, Dang; Guangwu, Han [Chinese Academy of Sciences, Lanzhou (China). Inst. of Modern Physics; Qingxiang, Gao [Lanzhou Univ. (China)

1997-09-01

DNA double-strand breaks (DSBs) in melanophore B{sub 16} induced by plateau and extended Bragg peak of 75 MeV/u {sup 12}C{sup 6+} ions were studied by using a technique of inverse pulsed-field gel electrophoresis (PIGE). DNA fragment lengths were distributed in two ranges: the larger in 1.4 Mbp-3.2 Mbp and the smaller in less than 1.2 Mbp. It indicates that distribution of DNA fragments induced by heavy ion irradiation is not stochastic and there probably are sensitive sites to heavy ions in DNA molecules of B{sub 16}. Percentage of DNA released from plug (PR) increased and trended towards a quasi-plateau {proportional_to}85% as dose increased. Content of the larger fragments decreased and flattened with increasing dose while content of the smaller ones increased and trended towards saturation. (orig.)

Cellular content and biosynthesis of polyamines during rooster spermatogenesis.

Science.gov (United States)

Oliva, R; Vidal, S; Mezquita, C

1982-01-01

The natural polyamines spermine and spermidine, and the diamine putrescine, were extracted from rooster testis cells separated by sedimentation at unit gravity, and from vas-deferens spermatozoa. The ratios spermine/DNA and spermidine/DNA were kept relatively constant throughout spermatogenesis, whereas the ratio putrescine/DNA rose in elongated spermatids. The cellular content of spermine, spermidine and putrescine decreased markedly in mature spermatozoa. Two rate-limiting enzymes in the biosynthetic pathway of polyamines, ornithine decarboxylase and S-adenosyl-L-methionine decarboxylase, showed their highest activities at the end of spermiogenesis and were not detectable in vas-deferens spermatozoa. A marked reduction in cell volume during spermiogenesis without a parallel decrease in the cellular content of polyamines suggests the possibility that the marked changes in chromatin composition and structure occurring in rooster late spermatids could take place in an ambience of high polyamine concentration. Images PLATE 1 PMID:7159401

Raman spectroscopy for DNA quantification in cell nucleus.

Science.gov (United States)

Okotrub, K A; Surovtsev, N V; Semeshin, V F; Omelyanchuk, L V

2015-01-01

Here we demonstrate the feasibility of a novel approach to quantify DNA in cell nuclei. This approach is based on spectroscopy analysis of Raman light scattering, and avoids the problem of nonstoichiometric binding of dyes to DNA, as it directly measures the signal from DNA. Quantitative analysis of nuclear DNA contribution to Raman spectrum could be reliably performed using intensity of a phosphate mode at 1096 cm(-1) . When compared to the known DNA standards from cells of different animals, our results matched those values at error of 10%. We therefore suggest that this approach will be useful to expand the list of DNA standards, to properly adjust the duration of hydrolysis in Feulgen staining, to assay the applicability of fuchsines for DNA quantification, as well as to measure DNA content in cells with complex hydrolysis patterns, when Feulgen densitometry is inappropriate. © 2014 International Society for Advancement of Cytometry.

Nuclear DNA content in Galaxias maculatus (Teleostei: Osmeriformes: Galaxiidae Contenido de ADN nuclear en Galaxias maculatus (Teleostei: Osmeriformes: Galaxiidae

Directory of Open Access Journals (Sweden)

Pedro Jara-Seguel

2008-01-01

Full Text Available The nuclear DNA content (2C value was determined in the commercial fish Galaxias maculatus (Galaxiidae was determined by microdensitometry of erythrocyte nuclei after Feulgen staining; rainbow trout erythrocytes with a known 2C value were used as a standard. The 2C value of G. maculatus was 2.21 ± 0.12 pg and its C value was equivalent to 1.105 pg (1,082.9 Mbp. This C value is within the range recorded for other osmeriform species (0.62-3.2 pg. The average sperm head diameter of G. maculatus is lower than the average sperm head diameter of rainbow trout (used as a standard, which coincides with the differences observed in the nuclear DNA content of both species. This information increases the genome data available for G. maculatus and might be useful in future programs dealing with its genetic manipulation.El contenido de ADN nuclear (valor 2C fue determinado en el pez comercial Galaxias maculatus (Galaxiidae usando microdensitometría de núcleos de eritrocitos sometidos a tinción de Feulgen, utilizando como estándar eritrocitos de trucha arco iris con un valor 2C conocido. El valor 2C de G. maculatus fue 2,21 ± 0,12 pg y su valor C es equivalente a 1,105 pg (1.082,9 pMb. Este valor C está dentro del rango registrado para otras especies de osmeriformes (0,62-3,2 pg. El diámetro promedio de la cabeza del espermatozoide de G. maculatus es menor al promedio descrito para la trucha arco iris utilizado como estándar, lo que coincide con las diferencias observadas en el contenido de ADN nuclear entre ambas especies. Estos datos contribuyen a ampliar los antecedentes genómicos disponibles para G. maculatus y podrían ser útiles en futuros programas tendientes a su manipulación genética.

Optimizing cationic and neutral lipids for efficient gene delivery at high serum content.

Science.gov (United States)

Chan, Chia-Ling; Ewert, Kai K; Majzoub, Ramsey N; Hwu, Yeu-Kuang; Liang, Keng S; Leal, Cecília; Safinya, Cyrus R

2014-01-01

Cationic liposome (CL)-DNA complexes are promising gene delivery vectors with potential application in gene therapy. A key challenge in creating CL-DNA complexes for application is that their transfection efficiency (TE) is adversely affected by serum. In particular, little is known about the effects of a high serum content on TE, even though this may provide design guidelines for application in vivo. We prepared CL-DNA complexes in which we varied the neutral lipid [1,2-dioleoyl-sn-glycerophosphatidylcholine, glycerol-monooleate (GMO), cholesterol], the headgroup charge and chemical structure of the cationic lipid, and the ratio of neutral to cationic lipid; we then measured the TE of these complexes as a function of serum content and assessed their cytotoxicity. We tested selected formulations in two human cancer cell lines (M21/melanoma and PC-3/prostate cancer). In the absence of serum, all CL-DNA complexes of custom-synthesized multivalent lipids show high TE. Certain combinations of multivalent lipids and neutral lipids, such as MVL5(5+)/GMO-DNA complexes or complexes based on the dendritic-headgroup lipid TMVLG3(8+) exhibited high TE both in the absence and presence of serum. Although their TE still dropped to a small extent in the presence of serum, it reached or surpassed that of benchmark commercial transfection reagents, particularly at a high serum content. Two-component vectors (one multivalent cationic lipid and one neutral lipid) can rival or surpass benchmark reagents at low and high serum contents (up to 50%, v/v). We propose guidelines for optimizing the serum resistance of CL-DNA complexes based on a given cationic lipid. Copyright © 2014 John Wiley & Sons, Ltd.

Charge transport through DNA based electronic barriers

Science.gov (United States)

Patil, Sunil R.; Chawda, Vivek; Qi, Jianqing; Anantram, M. P.; Sinha, Niraj

2018-05-01

We report charge transport in electronic 'barriers' constructed by sequence engineering in DNA. Considering the ionization potentials of Thymine-Adenine (AT) and Guanine-Cytosine (GC) base pairs, we treat AT as 'barriers'. The effect of DNA conformation (A and B form) on charge transport is also investigated. Particularly, the effect of width of 'barriers' on hole transport is investigated. Density functional theory (DFT) calculations are performed on energy minimized DNA structures to obtain the electronic Hamiltonian. The quantum transport calculations are performed using the Landauer-Buttiker framework. Our main findings are contrary to previous studies. We find that a longer A-DNA with more AT base pairs can conduct better than shorter A-DNA with a smaller number of AT base pairs. We also find that some sequences of A-DNA can conduct better than a corresponding B-DNA with the same sequence. The counterions mediated charge transport and long range interactions are speculated to be responsible for counter-intuitive length and AT content dependence of conductance of A-DNA.

Generalized Encoding CRDSA: Maximizing Throughput in Enhanced Random Access Schemes for Satellite

Directory of Open Access Journals (Sweden)

Manlio Bacco

2014-12-01

Full Text Available This work starts from the analysis of the literature about the Random Access protocols with contention resolution, such as Contention Resolution Diversity Slotted Aloha (CRDSA, and introduces a possible enhancement, named Generalized Encoding Contention Resolution Diversity Slotted Aloha (GE-CRDSA. The GE-CRDSA aims at improving the aggregated throughput when the system load is less than 50%, playing on the opportunity of transmitting an optimal combination of information and parity packets frame by frame. This paper shows the improvement in terms of throughput, by performing traffic estimation and adaptive choice of information and parity rates, when a satellite network undergoes a variable traffic load profile.

Report on workshop "Study of the polar atmosphere and cryosphere using satellite data with surface validation observations including unmanned one"

Directory of Open Access Journals (Sweden)

Hiroshi Kanzawa

1993-07-01

Full Text Available The workshop was organized to discuss algorithms to derive parameters of the polar atmosphere and cryosphere using satellite data received mainly at Syowa Station (69°S, 40°E, Antarctica, i.e., the data from NOAA, MOS (Marine Observation Satellite-1,ERS (European Remote Sensing Satellite-1,JERS (Japanese Earth Resources Satellite-1 with validation data at the surface. It was held on 16 March 1993 at the National Institute of Polar Research (NIPR, total number of participants being about 40. The contents of the workshop are as follows : The present status of receipt and utilization of the satellite data of NOAA, MOS-1,ERS-1,JERS-1; The Atmosphere; Sea ice; The Cryosphere; Introduction to the satellite data analysis system at the Information Science Center at NIPR.

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.

A rapid and quantitative method to determine the tritium content in DNA from small tissue sampes

International Nuclear Information System (INIS)

Kasche, V.; Zoellner, R.

1979-01-01

A rapid and quantitative two-step procedure to isolate double-strand DNA from small (10-100 mg) animal tissue samples is presented. The method is developed for investigations to evaluate the relative importance of organically bound tritium for the dose factors used to calculate dose commitments due to this nuclide. In the first step the proteins in the homogenized sample are hydrolysed, at a high pH (9.0) and ionic strength (1.5) to dissociate protein from DNA, using immobilized Proteinase K as a proteolytic enzyme. The DNA is then absorbed to hydroxylapatite and separated from impurities by step-wise elution with buffers of increasing ionic strength. More than 90% of the DNA in the samples could be isolated in double-strand form by this procedure. The method has been applied to determine pool-sizes and biological half-life times of tritium in DNA from various animal (mouse) tissues. It has also been shown to be suitable in other radiobiological studies where effects on DNA are investigated. (author)

Communication satellite applications

Science.gov (United States)

Pelton, Joseph N.

The status and future of the technologies, numbers and services provided by communications satellites worldwide are explored. The evolution of Intelsat satellites and the associated earth terminals toward high-rate all-digital telephony, data, facsimile, videophone, videoconferencing and DBS capabilities are described. The capabilities, services and usage of the Intersputnik, Eutelsat, Arabsat and Palapa systems are also outlined. Domestic satellite communications by means of the Molniya, ANIK, Olympus, Intelsat and Palapa spacecraft are outlined, noting the fast growth of the market and the growing number of different satellite manufacturers. The technical, economic and service definition issues surrounding DBS systems are discussed, along with presently operating and planned maritime and aeronautical communications and positioning systems. Features of search and rescue and tracking, data, and relay satellite systems are summarized, and services offered or which will be offered by every existing or planned communication satellite worldwide are tabulated.

Isolation of the human anionic glutathione S-transferase cDNA and the relation of its gene expression to estrogen-receptor content in primary breast cancer

International Nuclear Information System (INIS)

Moscow, J.A.; Townsend, A.J.; Goldsmith, M.E.; Whang-Peng, J.; Vickers, P.J.; Poisson, R.; Legault-Poisson, S.; Myers, C.E.; Cowan, K.H.

1988-01-01

The development of multidrug resistance in MCF7 human breast cancer cells is associated with overexpression of P-glycoprotein, changes in activities of several detoxication enzymes, and loss of hormone sensitivity and estrogen receptors (ERs). The authors have cloned the cDNA for one of the drug-detoxifying enzymes overexpressed in multidrug-resistant MCF7 cells (Adr R MCF7), the anionic isozyme of glutathione S-transferase (GSTπ). Hybridization with this GSTπ cDNA, GSTπ-1, demonstrated that increased GSTπ activity in Adr R MCF7 cells is associated with overexpression but not with amplification of the gene. They mapped the GSTπ gene to human chromosome 11q13 by in situ hybridization. Since multidrug resistance and GSTπ overexpression are associated with the loss of ERs in Adr R MCF7 cells, they examined several other breast cancer cell lines that were not selected for drug resistance. In each of these cell lines they found an inverse association between GSTπ expression and ER content. They also examined RNA from 21 primary breast cancers and found a similar association between GSTπ expression and ER content in vivo. The finding of similar patterns of expression of a drug-detoxifying enzyme and of ERs in vitro as well as in vivo suggests that ER-negative breast cancer cells may have greater protection against antineoplastic agents conferred by GSTπ than ER-positive tumors

Observations of inner plasmasphere irregularities with a satellite-beacon radio-interferometer array

International Nuclear Information System (INIS)

Jacobson, A.R.; Hoogeveen, G.; Carlos, R.C.; Wu, G.; Fejer, B.G.; Kelley, M.C.

1996-01-01

A radio-interferometer array illuminated by 136-MHz beacons of several geosynchronous satellites has been used to study small (≥10 13 m -2 ) transient disturbances in the total electron content along the lines of sight to the satellites. High-frequency (f>3 mHz) electron content oscillations are persistently observed, particularly during night and particularly during geomagnetically disturbed periods. The oscillations move across the array plane at speeds in the range 200 endash 2000 m/s, with propagation azimuths that are strongly peaked in lobes toward the western half-plane. Detailed analysis of this azimuth behavior, involving comparison between observations on various satellite positions, indicates compellingly that the phase oscillations originate in radio refraction due to geomagnetically aligned plasma density perturbations in the inner plasmasphere. The motion of the phase perturbations across the array plane is caused by EXB drift of the plasma medium in which the irregularities are embedded. We review the statistics of 2.5 years of around-the-clock data on the local time, magnetic disturbance, seasonal, and line-of-sight variations of these observed irregularities. We compare the irregularities close-quote inferred electrodynamic drifts to what is known about midlatitude plasma drift from incoherent scatter. Finally, we show in detail how the observation of these irregularities provides a unique and complementary monitor of inner plasmasphere irregularity incidence and zonal drift.copyright 1996 American Geophysical Union

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

Science.gov (United States)

Adalsteinsson, Viktor A; Ha, Gavin; Freeman, Samuel S; Choudhury, Atish D; Stover, Daniel G; Parsons, Heather A; Gydush, Gregory; Reed, Sarah C; Rotem, Denisse; Rhoades, Justin; Loginov, Denis; Livitz, Dimitri; Rosebrock, Daniel; Leshchiner, Ignaty; Kim, Jaegil; Stewart, Chip; Rosenberg, Mara; Francis, Joshua M; Zhang, Cheng-Zhong; Cohen, Ofir; Oh, Coyin; Ding, Huiming; Polak, Paz; Lloyd, Max; Mahmud, Sairah; Helvie, Karla; Merrill, Margaret S; Santiago, Rebecca A; O'Connor, Edward P; Jeong, Seong H; Leeson, Rachel; Barry, Rachel M; Kramkowski, Joseph F; Zhang, Zhenwei; Polacek, Laura; Lohr, Jens G; Schleicher, Molly; Lipscomb, Emily; Saltzman, Andrea; Oliver, Nelly M; Marini, Lori; Waks, Adrienne G; Harshman, Lauren C; Tolaney, Sara M; Van Allen, Eliezer M; Winer, Eric P; Lin, Nancy U; Nakabayashi, Mari; Taplin, Mary-Ellen; Johannessen, Cory M; Garraway, Levi A; Golub, Todd R; Boehm, Jesse S; Wagle, Nikhil; Getz, Gad; Love, J Christopher; Meyerson, Matthew

2017-11-06

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.

Pharmacy student engagement, performance, and perception in a flipped satellite classroom.

Science.gov (United States)

McLaughlin, Jacqueline E; Griffin, LaToya M; Esserman, Denise A; Davidson, Christopher A; Glatt, Dylan M; Roth, Mary T; Gharkholonarehe, Nastaran; Mumper, Russell J

2013-11-12

To determine whether "flipping" a traditional basic pharmaceutics course delivered synchronously to 2 satellite campuses would improve student academic performance, engagement, and perception. In 2012, the basic pharmaceutics course was flipped and delivered to 22 satellite students on 2 different campuses. Twenty-five condensed, recorded course lectures were placed on the course Web site for students to watch prior to class. Scheduled class periods were dedicated to participating in active-learning exercises. Students also completed 2 course projects, 3 midterm examinations, 8 graded quizzes, and a cumulative and comprehensive final examination. Results of a survey administered at the beginning and end of the flipped course in 2012 revealed an increase in students' support for learning content prior to class and using class time for more applied learning (p=0.01) and in the belief that learning key foundational content prior to coming to class greatly enhanced in-class learning (p=0.001). Significantly more students preferred the flipped classroom format after completing the course (89.5%) than before completing the course (34.6%). Course evaluation responses and final examination performance did not differ significantly for 2011 when the course was taught using a traditional format and the 2012 flipped-course format. Qualitative findings suggested that the flipped classroom promoted student empowerment, development, and engagement. The flipped pharmacy classroom can enhance the quality of satellite students' experiences in a basic pharmaceutics course through thoughtful course design, enriched dialogue, and promotion of learner autonomy.

Multilocus DNA fingerprints in gallinaceous birds: general approach and problems.

Science.gov (United States)

Hanotte, O; Bruford, M W; Burke, T

1992-06-01

Multilocus profiles were investigated in five different species of Galliformes (ring-necked pheasant Phasianus colchicus, Indian peafowl Pavo cristatus, Japanese quail Coturnix coturnix japonica, domestic chicken Gallus gallus, and red grouse Lagopus lagopus scoticus) using two human multilocus probes (33.6 and 33.15) in combination with each of four restriction enzymes (AluI, DdeI, HaeIII or HinfI). All the species show a DNA fingerprint-like pattern using at least one restriction enzyme in combination with each multilocus probe. The number of bands detected and the value of the index of similarity for each species differ significantly between the profiles obtained with each multilocus probe. Some enzyme/probe combinations reveal strong cross-hybridization of the multilocus probes with satellite or satellite-like DNA sequences in pheasant, peacock, quail and chicken, which partially or completely prevented scoring of the profile. The choice of restriction enzyme was found to influence the number of bands, the value of the index of similarity and the probability of obtaining an identical fingerprint between unrelated individuals. The Mendelian inheritance and independent segregation of the fragments detected using AluI was investigated in three species (ring-necked pheasant, Indian peafowl and red grouse). Some bands were shown to be tightly linked. An extreme case was encountered in the red grouse, where 12 of the 15 bands scored in one parent represented only two, apparently allelic, haplotypes and so derived from a single locus. However, fingerprint patterns will often be adequate for use in paternity analyses, such as in behavioural studies, despite the occurrence of haplotypic sets of bands. Identical DNA multilocus profiles were sometimes observed between captive-bred siblings in one species. These results emphasize the desirability of determining, in each new species, the optimal experimental conditions as a preliminary to any behavioural or population

Systematic biases in DNA copy number originate from isolation procedures

NARCIS (Netherlands)

van Heesch, S.; Mokry, M.; Boskova, V.; Junker, W.; Mehon, R.; Toonen, P.; de Bruijn, E.; Shull, J.D.; Aitman, T.J.; Cuppen, E.; Guryev, V.

2013-01-01

BACKGROUND: The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal. RESULTS: While GC content has been used to correct

History of Satellite TV Broadcasting and Satellite Broadcasting Market in Turkey

Directory of Open Access Journals (Sweden)

Mihalis KUYUCU

2015-09-01

Full Text Available The present study analyses the satellite broadcasting that is the first important development that emerged as a result of digitalization in communication technologies and its reflections in Turkey. As the first milestone in the globalization of television broadcasting, satellite broadcasting provided substantial contribution towards the development of the media. Satellite bro adcasting both increased the broadcasting quality and geographical coverage of the television media. A conceptual study was carried out in the first part of the study in connection with the history of satellite broadcasting in Turkey and across the world. In the research part of the study, an analysis was performed on 160 television channels that broadcast in Turkey via Turksat Satellite. Economic structure of the television channels broadcasting in Turkey via satellite was studied and an analysis was perfo rmed on the operational structure of the channels. As a result of the study, it was emphasized that the television channels broadcasting via satellite platform also use other platforms for the purpose of spreading their broadcasts and television channel ow ners make investments in different branches of the media, too. Capital owners invest in different business areas other than the media although television channels broadcasting via Turksat mostly focus on thematic broadcasting and make effort to generate ec onomic income from advertisements. Delays are encountered in the course of the convergence between the new media and television channels that broadcast only from the satellite platform and such television channels experience more economic problems than the other channels. New media and many TV broadcasting platforms emerged as a result of the developments in the communication technologies. In television broadcasting, satellite platform is not an effective platform on its own. Channels make effort to reach t o more people by using other platforms in addition to

Associations of mitochondrial haplogroups and mitochondrial DNA copy numbers with end-stage renal disease in a Han population.

Science.gov (United States)

Zhang, Yuheng; Zhao, Ying; Wen, Shuzhen; Yan, Rengna; Yang, Qinglan; Chen, Huimei

2017-09-01

Mitochondrial DNA (mtDNA) is closely related to mitochondrion function, and variations have been suggested to be involved in pathogenesis of complex diseases. The present study sought to elucidate mitochondrial haplogroups and mtDNA copy number in end-stage renal disease (ESRD) in a Han population. First, the mitochondrial haplogroups of 37 ESRD patients were clustered into several haplogroups, and haplogroup A & D were taken as the candidate risk haplogroups for ESRD. Second, the frequencies of A and D were assessed in 344 ESRD patients and 438 healthy controls, respectively. Haplogroup D was found to be risk maker for ESRD in young subjects (numbers were evaluated with quantitative-PCR. The ESRD patients exhibited greater cell-free mtDNA contents than the healthy controls but less intracellular mtDNA. Haplogroup D exhibited a further increase in cell-free mtDNA content and a decrease in intracellular mtDNA content among the ESRDs patients. Our findings suggest that mtNDA haplogroup D may contributes to pathogenesis of early-onset ESRD through alterations of mtDNA copy numbers.

37 CFR 360.12 - Form and content of claims.

Science.gov (United States)

2010-07-01

... SUBMISSION OF ROYALTY CLAIMS FILING OF CLAIMS TO ROYALTY FEES COLLECTED UNDER COMPULSORY LICENSE Satellite Claims § 360.12 Form and content of claims. (a) Forms. (1) Each claim to compulsory license royalty fees... owner entitled to claim the royalty fees. (ii) A general statement of the nature of the copyright owner...

Relative tracking control of constellation satellites considering inter-satellite link

Science.gov (United States)

Fakoor, M.; Amozegary, F.; Bakhtiari, M.; Daneshjou, K.

2017-11-01

In this article, two main issues related to the large-scale relative motion of satellites in the constellation are investigated to establish the Inter Satellite Link (ISL) which means the dynamic and control problems. In the section related to dynamic problems, a detailed and effective analytical solution is initially provided for the problem of satellite relative motion considering perturbations. The direct geometric method utilizing spherical coordinates is employed to achieve this solution. The evaluation of simulation shows that the solution obtained from the geometric method calculates the relative motion of the satellite with high accuracy. Thus, the proposed analytical solution will be applicable and effective. In the section related to control problems, the relative tracking control system between two satellites will be designed in order to establish a communication link between the satellites utilizing analytical solution for relative motion of satellites with respect to the reference trajectory. Sliding mode control approach is employed to develop the relative tracking control system for body to body and payload to payload tracking control. Efficiency of sliding mode control approach is compared with PID and LQR controllers. Two types of payload to payload tracking control considering with and without payload degree of freedom are designed and suitable one for practical ISL applications is introduced. Also, Fuzzy controller is utilized to eliminate the control input in the sliding mode controller.

Mobile satellite service communications tests using a NASA satellite

Science.gov (United States)

Chambers, Katherine H.; Koschmeder, Louis A.; Hollansworth, James E.; ONeill, Jack; Jones, Robert E.; Gibbons, Richard C.

1995-01-01

Emerging applications of commercial mobile satellite communications include satellite delivery of compact disc (CD) quality radio to car drivers who can select their favorite programming as they drive any distance; transmission of current air traffic data to aircraft; and handheld communication of data and images from any remote corner of the world. Experiments with the enabling technologies and tests and demonstrations of these concepts are being conducted before the first satellite is launched by utilizing an existing NASA spacecraft.

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....

DNA interactions with a Methylene Blue redox indicator depend on the DNA length and are sequence specific.

Science.gov (United States)

Farjami, Elaheh; Clima, Lilia; Gothelf, Kurt V; Ferapontova, Elena E

2010-06-01

A DNA molecular beacon approach was used for the analysis of interactions between DNA and Methylene Blue (MB) as a redox indicator of a hybridization event. DNA hairpin structures of different length and guanine (G) content were immobilized onto gold electrodes in their folded states through the alkanethiol linker at the 5'-end. Binding of MB to the folded hairpin DNA was electrochemically studied and compared with binding to the duplex structure formed by hybridization of the hairpin DNA to a complementary DNA strand. Variation of the electrochemical signal from the DNA-MB complex was shown to depend primarily on the DNA length and sequence used: the G-C base pairs were the preferential sites of MB binding in the duplex. For short 20 nts long DNA sequences, the increased electrochemical response from MB bound to the duplex structure was consistent with the increased amount of bound and electrochemically readable MB molecules (i.e. MB molecules that are available for the electron transfer (ET) reaction with the electrode). With longer DNA sequences, the balance between the amounts of the electrochemically readable MB molecules bound to the hairpin DNA and to the hybrid was opposite: a part of the MB molecules bound to the long-sequence DNA duplex seem to be electrochemically mute due to long ET distance. The increasing electrochemical response from MB bound to the short-length DNA hybrid contrasts with the decreasing signal from MB bound to the long-length DNA hybrid and allows an "off"-"on" genosensor development.

Extraction of DNA from Forensic Biological Samples for Genotyping.

Science.gov (United States)

Stray, J E; Liu, J Y; Brevnov, M G; Shewale, J G

2010-07-01

Biological forensic samples constitute evidence with probative organic matter. Evidence believed to contain DNA is typically processed for extraction and purification of its nucleic acid content. Forensic DNA samples are composed of two things, a tissue and the substrate it resides on. Compositionally, a sample may contain almost anything and for each, the type, integrity, and content of both tissue and substrate will vary, as will the contaminant levels. This fact makes the success of extraction one of the most unpredictable steps in genotypic analysis. The development of robust genotyping systems and analysis platforms for short tandem repeat (STR) and mitochondrial DNA sequencing and the acceptance of results generated by these methods in the court system, resulted in a high demand for DNA testing. The increasing variety of sample submissions created a need to isolate DNA from forensic samples that may be compromised or contain low levels of biological material. In the past decade, several robust chemistries and isolation methods have been developed to safely and reliably recover DNA from a wide array of sample types in high yield and free of PCR inhibitors. In addition, high-throughput automated workflows have been developed to meet the demand for processing increasing numbers of samples. This review summarizes a number of the most widely adopted methods and the best practices for DNA isolation from forensic biological samples, including manual, semiautomated, and fully automated platforms. Copyright © 2010 Central Police University.

Respiration-to-DNA ratio reflects physiological state of microorganisms in root-free and rhizosphere soil

Science.gov (United States)

Blagodatskaya, E.; Blagodatsky, S.; Kuzyakov, Y.

2009-04-01

The double-stranded DNA (dsDNA) content in soil can serve as a measure of microbial biomass under near steady-state conditions and quantitatively reflect the exponential microbial growth initiated by substrate addition. The yield of respired CO2 per microbial biomass unit (expressed as DNA content) could be a valuable physiological indicator reflecting state of soil microbial community. Therefore, investigations combining both analyses of DNA content and respiration of soil microorganisms under steady-state and during periods of rapid growth are needed. We studied the relationship between CO2 evolution and microbial dsDNA content in native and glucose-amended samples of root-free and rhizosphere soil under Beta vulgaris (Cambisol, loamy sand from the field experiment of the Institute of Agroecology FAL, Braunschweig, Germany). Quantity of dsDNA was determined by direct DNA isolation from soil with mechanic and enzymatic disruption of microbial cell walls with following spectrofluorimetric detection with PicoGreen (Blagodatskaya et al., 2003). Microbial biomass and the kinetic parameters of microbial growth were estimated by dynamics of the CO2 emission from soil amended with glucose and nutrients (Blagodatsky et al., 2000). The CO2 production rate was measured hourly at 22оС using an automated infrared-gas analyzer system. The overall increase in microbial biomass, DNA content, maximal specific growth rate and therefore, in the fraction of microorganisms with r-strategy were observed in rhizosphere as compared to bulk soil. The rhizosphere effect for microbial respiration, biomass and specific growth rate was more pronounced for plots with half-rate of N fertilizer compared to full N addition. The DNA content was significantly lower in bulk compared to rhizosphere soil both before and during microbial growth initiated by glucose amendment. Addition of glucose to the soil strongly increased the amount of CO2 respired per DNA unit. Without substrate addition the

Source of Global Scale Variations in the Midday Vertical Content of Ionospheric Metal Ions

Science.gov (United States)

Joiner, J.; Grebowsky, J. M.; Pesnell, W. D.; Aikin, A. C.; Goldberg, Richard A.

1999-01-01

An analysis of long baseline NIMBUS 7 SBUV (Solar Backscatter UV Spectrometer) observations of the latitudinal variation of the noontime vertical Mg' content above approx. 70 km have revealed seasonal, solar activity and magnetic activity dependencies in the Mg+ content. The distributions were categorized in terms of magnetic coordinates partially because transport processes lifting metallic ions from the main meteor ionization layer below 100 km up into the F- region and down again are controlled by electrodynamical processes. Alternatively, the Nimbus Mg+ distributions may simply be a result of ion/neutral chemistry changes resulting from atmospheric changes and not dynamics. In such a case magnetic control would not dominate the distributions. Using in situ satellite measurements of metal ions from the Atmosphere Explorer satellites in the region above the main meteor layer and published sounding rocket measurements of the main metallic ion layers, the effects of the dynamics on the vertical content are delineated. The consequences of atmospheric changes on the vertical content are explored by separating the Nimbus measurements in a geodetic frame of reference.

The maternal nucleolus plays a key role in centromere satellite maintenance during the oocyte to embryo transition.

Science.gov (United States)

Fulka, Helena; Langerova, Alena

2014-04-01

The oocyte (maternal) nucleolus is essential for early embryonic development and embryos originating from enucleolated oocytes arrest at the 2-cell stage. The reason for this is unclear. Surprisingly, RNA polymerase I activity in nucleolus-less mouse embryos, as manifested by pre-rRNA synthesis, and pre-rRNA processing are not affected, indicating an unusual role of the nucleolus. We report here that the maternal nucleolus is indispensable for the regulation of major and minor satellite repeats soon after fertilisation. During the first embryonic cell cycle, absence of the nucleolus causes a significant reduction in major and minor satellite DNA by 12% and 18%, respectively. The expression of satellite transcripts is also affected, being reduced by more than half. Moreover, extensive chromosome bridging of the major and minor satellite sequences was observed during the first mitosis. Finally, we show that the absence of the maternal nucleolus alters S-phase dynamics and causes abnormal deposition of the H3.3 histone chaperone DAXX in pronuclei of nucleolus-less zygotes.

Data Collection Satellite Application in Precision Agriculture

Science.gov (United States)

Durào, O.

2002-01-01

's over Brazilian territory. There were 25 platforms when SCD-1 was launched. However this number is growing rapidly to 400 platforms, at first for measurements of water reservoir levels as well as other hydrology applications (The Brazilian Electricity Regulatory Agency - ANEEL is the customer), and for many other different applications such as meteorology, oceanography, environmental monitoring sciences, and people and animal tracking. The clear feeling is that users are discovering a satellite system whose benefits were not previously well understood when launched and being able to propose and come up with different and useful applications. A new field in the country that has a great potential to benefit from this system is agriculture. Per se, this is a very important sector of the Brazilian economy and its international trade. Combining it with space technology may justify the investment of new and low cost dedicated satellites. This paper describes a new proposal for use of the SCD-1,2,CBERS-1 satellite system for precision agriculture. New PCD's would be developed for measurements of chemical content of the soil, such as, for example, Nitrogen and others, beyond humidity and solar incidence. This can lead to a more efficient fertilization, harvesting and even the spray of chemical defensives, with the consequence of environment protection. The PCD's ground network so established, along with the information network already available, combined with the space segment of such a system may, as previously said, be able to justify the investment in low cost satellites with this sole purpose.

Radiation-induced energy migration within solid DNA: The role of misonidazole as an electron trap

International Nuclear Information System (INIS)

Al-Kazwini, A.T.; O'Neill, P.; Adams, G.E.; Fielden, E.M.

1990-01-01

The in-pulse luminescence emission from solid DNA produced upon irradiation with electron pulses of energy below 260 keV has been investigated in vacuo at 293 K to gain an insight into the existence of radiation-induced charge/energy migration within DNA. The DNA samples contained misonidazole in the range 3 to 330 base pairs per misonidazole molecule. Under these conditions greater than 90% of the total energy is deposited in the DNA. The in-pulse radiation-induced luminescence spectrum of DNA was found to be critically dependent upon the misonidazole content of DNA. The luminescence intensity from the mixtures decreases with increasing content of misonidazole, and at the highest concentration, the intensity at 550 nm is reduced to 50% of that from DNA only. In the presence of 1 atm of oxygen, the observed emission intensity from DNA in the wavelength region 350-575 was reduced by 35-40% compared to that from DNA in vacuo. It is concluded that electron migration can occur in solid mixtures of DNA over a distance of up to about 100 base pairs

Interim Service ISDN Satellite (ISIS) simulator development for advanced satellite designs and experiments

Science.gov (United States)

Pepin, Gerard R.

1992-01-01

The simulation development associated with the network models of both the Interim Service Integrated Services Digital Network (ISDN) Satellite (ISIS) and the Full Service ISDN Satellite (FSIS) architectures is documented. The ISIS Network Model design represents satellite systems like the Advanced Communications Technology Satellite (ACTS) orbiting switch. The FSIS architecture, the ultimate aim of this element of the Satellite Communications Applications Research (SCAR) Program, moves all control and switching functions on-board the next generation ISDN communications satellite. The technical and operational parameters for the advanced ISDN communications satellite design will be obtained from the simulation of ISIS and FSIS engineering software models for their major subsystems. Discrete event simulation experiments will be performed with these models using various traffic scenarios, design parameters, and operational procedures. The data from these simulations will be used to determine the engineering parameters for the advanced ISDN communications satellite.

The phytochemical 3,3'-diindolylmethane decreases expression of AR-controlled DNA damage repair genes through repressive chromatin modifications and is associated with DNA damage in prostate cancer cells.

Science.gov (United States)

Palomera-Sanchez, Zoraya; Watson, Gregory W; Wong, Carmen P; Beaver, Laura M; Williams, David E; Dashwood, Roderick H; Ho, Emily

2017-09-01

Androgen receptor (AR) is a transcription factor involved in normal prostate physiology and prostate cancer (PCa) development. 3,3'-Diindolylmethane (DIM) is a promising phytochemical agent against PCa that affects AR activity and epigenetic regulators in PCa cells. However, whether DIM suppresses PCa via epigenetic regulation of AR target genes is unknown. We assessed epigenetic regulation of AR target genes in LNCaP PCa cells and showed that DIM treatment led to epigenetic suppression of AR target genes involved in DNA repair (PARP1, MRE11, DNA-PK). Decreased expression of these genes was accompanied by an increase in repressive chromatin marks, loss of AR occupancy and EZH2 recruitment to their regulatory regions. Decreased DNA repair gene expression was associated with an increase in DNA damage (γH2Ax) and up-regulation of genomic repeat elements LINE1 and α-satellite. Our results suggest that DIM suppresses AR-dependent gene transcription through epigenetic modulation, leading to DNA damage and genome instability in PCa cells. Published by Elsevier Inc.

Ionospheric/protonospheric electron content studies using ATS-6

International Nuclear Information System (INIS)

Hajeb-Hosseinieh, H.; Kersley, L.; Edwards, K.J.

1978-01-01

Measurements of ionospheric and protonospheric contents obtained at Aberystwyth from observations of the ATS-6 satellite radio beacon are reported. The monthly median diurnal behavior shows protonospheric contributions of approximately 15 to 20% to the total content along the ray path by day, rising to a predawn maximum of 35% in summer and more than 40% in winter. The protonospheric results are shown to be typical of those expected from other European stations and differences from earlier American measurements are explained in terms of ionospheric interactions in the conjugate hemisphere. The temporal gradients of protonospheric content provide information on the net integrated ionospheric/protonospheric plasma fluxes and the results obtained indicate the importance of plasma exchange with both local and conjugate ionospheres

ZOMG - III. The effect of halo assembly on the satellite population

Science.gov (United States)

Garaldi, Enrico; Romano-Díaz, Emilio; Borzyszkowski, Mikolaj; Porciani, Cristiano

2018-01-01

We use zoom hydrodynamical simulations to investigate the properties of satellites within galaxy-sized dark-matter haloes with different assembly histories. We consider two classes of haloes at redshift z = 0: 'stalled' haloes that assembled at z > 1 and 'accreting' ones that are still forming nowadays. Previously, we showed that the stalled haloes are embedded within thick filaments of the cosmic web, while the accreting ones lie where multiple thin filaments converge. We find that satellites in the two classes have both similar and different properties. Their mass spectra, radial count profiles, baryonic and stellar content, and the amount of material they shed are indistinguishable. However, the mass fraction locked in satellites is substantially larger for the accreting haloes as they experience more mergers at late times. The largest difference is found in the satellite kinematics. Substructures fall towards the accreting haloes along quasi-radial trajectories whereas an important tangential velocity component is developed, before accretion, while orbiting the filament that surrounds the stalled haloes. Thus, the velocity anisotropy parameter of the satellites (β) is positive for the accreting haloes and negative for the stalled ones. This signature enables us to tentatively categorize the Milky Way halo as stalled based on a recent measurement of β. Half of our haloes contain clusters of satellites with aligned orbital angular momenta corresponding to flattened structures in space. These features are not driven by baryonic physics and are only found in haloes hosting grand-design spiral galaxies, independently of their assembly history.

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

The merits of DNA content and cell kinetic parameters for the assessment of intrinsic cellular radiosensitivity to photon and high-LET neutron irradiation

International Nuclear Information System (INIS)

Theron, C.S.; Serafin, A.; Bohm, L.; Slabbert, J.P.

1997-01-01

Differences of the intrinsic cellular radiosensitivity between tumours make the selection of patients for specific radiation schedules very difficult. The reasons for these variations are still unclear, but are thought to be due to genomic and cellular characteristics. Radiosensitivities vary between cell cycle stages, with S-phase cells being most radioresistant and G2/M phase cells most radiosensitive. It is also well established that most tumour cells have an abnormal ploidy. DNA content and cellular proliferation kinetics therefore could influence the intrinsic radiosensitivity. This prompted us to assess the merits of these parameters as predictors of radiation response. (authors)

Statistics of DNA Markers - RGP gmap | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us RGP gmap Statistics of DNA Markers Data detail Data name Statistics of DNA Markers DOI 10.18...908/lsdba.nbdc00318-01-001 Description of data contents Statistics of DNA markers that were used to create t...iption Download License Update History of This Database Site Policy | Contact Us Statistics of DNA Markers - RGP gmap | LSDB Archive ...

Mixed lactate and caffeine compound increases satellite cell activity and anabolic signals for muscle hypertrophy.

Science.gov (United States)

Oishi, Yoshimi; Tsukamoto, Hayato; Yokokawa, Takumi; Hirotsu, Keisuke; Shimazu, Mariko; Uchida, Kenji; Tomi, Hironori; Higashida, Kazuhiko; Iwanaka, Nobumasa; Hashimoto, Takeshi

2015-03-15

We examined whether a mixed lactate and caffeine compound (LC) could effectively elicit proliferation and differentiation of satellite cells or activate anabolic signals in skeletal muscles. We cultured C2C12 cells with either lactate or LC for 6 h. We found that lactate significantly increased myogenin and follistatin protein levels and phosphorylation of P70S6K while decreasing the levels of myostatin relative to the control. LC significantly increased protein levels of Pax7, MyoD, and Ki67 in addition to myogenin, relative to control. LC also significantly increased follistatin expression relative to control and stimulated phosphorylation of mTOR and P70S6K. In an in vivo study, male F344/DuCrlCrlj rats were assigned to control (Sed, n = 10), exercise (Ex, n = 12), and LC supplementation (LCEx, n = 13) groups. LC was orally administered daily. The LCEx and Ex groups were exercised on a treadmill, running for 30 min at low intensity every other day for 4 wk. The LCEx group experienced a significant increase in the mass of the gastrocnemius (GA) and tibialis anterior (TA) relative to both the Sed and Ex groups. Furthermore, the LCEx group showed a significant increase in the total DNA content of TA compared with the Sed group. The LCEx group experienced a significant increase in myogenin and follistatin expression of GA relative to the Ex group. These results suggest that administration of LC can effectively increase muscle mass concomitant with elevated numbers of myonuclei, even with low-intensity exercise training, via activated satellite cells and anabolic signals. Copyright © 2015 the American Physiological Society.

Total electron content measurements at Gauhati using 140 MHz ATS-6 transmissions

International Nuclear Information System (INIS)

Tyagi, T.R.; Singh, L.; Minakshi Devi; Barbara, A.K.

1977-01-01

The amplitude and phase of 140 MHz transmissions from geostationary satellite ATS-6 (0 0 N, 35 0 E) have been recorded at Gauhati (26.16 0 N; 91.75 0 E) for the period Nov. 1975 to Aug. 1976. The calibration technique for geostationary satellite Faraday rotation measurements suggested by Checcacci and Giorgeo has been improved and generalized. It is then utilized to remove the n ambiguity in Faraday rotation values and also to estimate the correct value of diurnal minimum Faraday rotation angle so that the recorded Faraday rotation values can be converted into electron content values. Typical diurnal variation curves have been obtained for all the months except for equinoxes when the satellite transmission was off very often due to ecliptic conditions and hence no complete diurnal curves could be obtained for these months. It has been found that though December and January behave like typical winter months, the month of November is more like an equinoctial month. Similarly, though June and July behave like typical summer months, the month of May is more or less similar to equinoxes. The characteristic features of the diurnal and seasonal behaviour of the electron content have been discussed. (author)

Human circulating plasma DNA significantly decreases while lymphocyte DNA damage increases under chronic occupational exposure to low-dose gamma-neutron and tritium β-radiation.

Science.gov (United States)

Korzeneva, Inna B; Kostuyk, Svetlana V; Ershova, Liza S; Osipov, Andrian N; Zhuravleva, Veronika F; Pankratova, Galina V; Porokhovnik, Lev N; Veiko, Natalia N

2015-09-01

The blood plasma of healthy people contains cell-fee (circulating) DNA (cfDNA). Apoptotic cells are the main source of the cfDNA. The cfDNA concentration increases in case of the organism's cell death rate increase, for example in case of exposure to high-dose ionizing radiation (IR). The objects of the present research are the blood plasma and blood lymphocytes of people, who contacted occupationally with the sources of external gamma/neutron radiation or internal β-radiation of tritium N = 176). As the controls (references), blood samples of people, who had never been occupationally subjected to the IR sources, were used (N = 109). With respect to the plasma samples of each donor there were defined: the cfDNA concentration (the cfDNA index), DNase1 activity (the DNase1 index) and titre of antibodies to DNA (the Ab DNA index). The general DNA damage in the cells was defined (using the Comet assay, the tail moment (TM) index). A chronic effect of the low-dose ionizing radiation on a human being is accompanied by the enhancement of the DNA damage in lymphocytes along with a considerable cfDNA content reduction, while the DNase1 content and concentration of antibodies to DNA (Ab DNA) increase. All the aforementioned changes were also observed in people, who had not worked with the IR sources for more than a year. The ratio cfDNA/(DNase1×Ab DNA × TM) is proposed to be used as a marker of the chronic exposure of a person to the external low-dose IR. It was formulated the assumption that the joint analysis of the cfDNA, DNase1, Ab DNA and TM values may provide the information about the human organism's cell resistivity to chronic exposure to the low-dose IR and about the development of the adaptive response in the organism that is aimed, firstly, at the effective cfDNA elimination from the blood circulation, and, secondly - at survival of the cells, including the cells with the damaged DNA. Copyright © 2015. Published by Elsevier B.V.

TIME COURSE ALTERATIONS OF SATELLITE CELL EVENTS IN RESPONSE TO LIGHT MODERATE ENDURANCE TRAINING IN WHITE GASTROCNEMIUS MUSCLE OF THE RAT

Directory of Open Access Journals (Sweden)

Zong-Yan Cai

2012-01-01

Full Text Available This study investigated satellite cells and their related molecular events adapted to light moderate endurance training in the white gastrocnemius muscle of the rat. The white gastrocnemius muscle of male Sprague-Dawley rats that had been trained for 4 weeks and 8 weeks, with control rats being analysed alongside them, was selected for analysis (n=3 per group. The training protocol consisted of treadmill running at 20 m · min-1 for 30 min on a 0% grade, for 3 days · week-1. Immunohistochemical staining coupled with image analysis was used for quantification. To provide deeper insight into the cell layer, 40 sections per rat, corresponding to 120 values per group, were obtained as a mean value for statistical comparison. The results indicated that at week 4, training effects increased the vascular endothelial growth factor (VEGF content and c-met positive satellite cell numbers. At week 8, the training effect was attenuated for VEGF and c-met satellite cell numbers, but it increased in the muscle fibre area. Additionally, c-met positive satellite cell numbers correlated with VEGF content (r = 0.79, p<0.05. In conclusion, this study suggests that light moderate endurance training could stimulate satellite cell activation that might be related to VEGF signalling. Additionally, the satellite cells activated by moderate endurance training might contribute to slight growth in myocytes.

Results of investigation of trace element content in nucleic acids and histones, isolated from human leucaemic cells

International Nuclear Information System (INIS)

Andronikashvili, Eh.L.; Mosulishvili, L.M.; Belokobyl'skij, A.I.; Kharabadze, N.E.; Desai, A.S.; Foley, G.E.; Harvard Cancer Commission, Boston, MA

1977-01-01

Trace metals in purified nucleic acids and histones, extracted from lymphocyte cell culture of patients with acute lymphocytic leukemia or infections mononucleosis and healthy donors were determined with the activation analysis method. In the lymphocyte DNA of patients with infections mononucleosis and healthy donors the content of Co ++ , Sb ++ , Fe +++ , Zn ++ , turned out to be high, while in the lymphoblast DNA of patients with acute lymphocytic leukemia lower concentrations of these metals were detected, with the exception of Co ++ , the content of which is 20 times higher than in the DNA, extracted from the lymphocytes of healthy donors. In the general histone of the leukemic cells the content of the most of trace metals is higher than in the general lymphocyte histone of healthy donors. The exception is Zn ++ , the content of which is lower

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.

Satellite image collection optimization

Science.gov (United States)

Martin, William

2002-09-01

Imaging satellite systems represent a high capital cost. Optimizing the collection of images is critical for both satisfying customer orders and building a sustainable satellite operations business. We describe the functions of an operational, multivariable, time dynamic optimization system that maximizes the daily collection of satellite images. A graphical user interface allows the operator to quickly see the results of what if adjustments to an image collection plan. Used for both long range planning and daily collection scheduling of Space Imaging's IKONOS satellite, the satellite control and tasking (SCT) software allows collection commands to be altered up to 10 min before upload to the satellite.

Evaluation of the immunomodulatory and DNA protective activities of the shoots of Cynodon dactylon.

Science.gov (United States)

Mangathayaru, K; Umadevi, M; Reddy, C Umamaheswara

2009-05-04

Fresh juice of Cyanodon dactylon known as 'durva' grass is employed in India as a rejuvenator and for wound healing. To validate the traditional use of the herb through evaluation of DNA protective activity in vitro and immunomodulatory activity in vivo. Fresh juice of the grass was prepared as indicated for use in traditional medicine and standardized for solid content. Its total phenol content was estimated by Folin-Ciocalteau method. Freshly prepared juice was investigated for its effect on doxorubicin-induced DNA damage in vitro. Its immunomodulatory activity was tested on balb/c mice by the humoral antibody response which was determined by haemagglutination antibody titer and spleen cell assay. Fresh juice of Cyanodon dactylon of 1.46% (w/w) solid content had a phenolic content of 47+/-0.33 mg/kg GAE. At doses equivalent to 50, 100 and 200mg total solids/kg body weight the juice protected human DNA against doxorubicin-induced DNA damage as demonstrated in DNA spectral studies, where the ratio of absorbance of DNA at 260 and 280 nm in samples pretreated with the juice was 1.66, 1.53 and 1.63 respectively, while it was 1.37 for DNA treated with doxorubicin only. This indicates nucleic acid purity in the Cynodon dactylon treated samples. Oral administration of the juice at 250 and 500 mg/kg in balb/c mice increased humoral antibody response upon antigen challenge, as evidenced by a dose-dependent, statistically significant increase in antibody titer in the haemagglutination antibody assay and plaque forming cell assay. The present report demonstrated the DNA protective activity and immunomodulatory property of the fresh juice of Cynodon dactylon validating the traditional use of the herb as a 'rasayana' in ayurvedic system of medicine.

Necessity of purification during bacterial DNA extraction with environmental soils

Directory of Open Access Journals (Sweden)

Hyun Jeong Lim

2017-08-01

Full Text Available Complexity and heterogeneity of soil samples have often implied the inclusion of purification steps in conventional DNA extraction for polymerase chain reaction (PCR assays. Unfortunately the purification steps are also time and labor intensive. Therefore the necessity of DNA purification was re-visited and investigated for a variety of environmental soil samples that contained various amounts of PCR inhibitors. Bead beating and centrifugation was used as the baseline (without purification method for DNA extraction. Its performance was compared with that of conventional DNA extraction kit (with purification. The necessity criteria for DNA purification were established with environmental soil samples. Using lysis conditions at 3000 rpm for 3 minutes with 0.1 mm glass beads, centrifugation time of 10 minutes and 1:10 dilution ratio, the baseline method outperformed conventional DNA extraction on cell seeded sand samples. Further investigation with PCR inhibitors (i.e., humic acids, clay, and magnesium [Mg] showed that sand samples containing less than 10 μg/g humic acids and 70% clay may not require purifications. Interestingly, the inhibition pattern of Mg ion was different from other inhibitors due to the complexation interaction of Mg ion with DNA fragments. It was concluded that DNA extraction method without purification is suitable for soil samples that have less than 10 μg/g of humic acids, less than 70% clay content and less than 0.01% Mg ion content.

Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

Science.gov (United States)

Zagoskin, Maxim V.; Lazareva, Valentina I.; Grishanin, Andrey K.; Mukha, Dmitry V.

2014-01-01

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals. PMID:25215300

cDNA library Table - KAIKOcDNA | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available c00951-005 Description of data contents List of Bombyx mori cDNA libraries. Data file File name: kaiko_cdna_...library.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kaiko-cdna/LATEST/kaiko_cdna_library.zip File size:... 4.8 KB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/kaiko_cdna_l

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

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

Content Delivery in Future Mobile Communication Networks

Science.gov (United States)

Jonas, Karl; Raber, Sergey

2003-07-01

With the fast progress in the deployment of wireless networks during the last few years, the global communication market requires the development of new methods for content delivery towards mobile users. It is currently characterised by the introduction of the 3rd generation of terrestrial mobile networks based on 3GPP's UMTS standard. It is expected that this will eventually lead to integrated all-IP-based infrastructures supporting a variety of radio access technologies (so-called beyond-3G-networks or 4th Generation networks). The integration of mobility support, security and accounting and provisioning of differentiated qualities of service are among the issues which are currently researched in the 4G framework.Since it is not possible to change network protocols and infrastructure at once in order to optimize them for mobile services, it is very important to find an appropriate way for the migration from the current infrastructure towards an integrated architecture, where fixed and mobile networks coexist and interoperate in the most effective and flexible way.The integration of satellite communication networks into the terrestrial mobile communication environment is the focus of R&D activities at the Competence Centre for Advanced Satellite Communication of the FhG FOKUS institute. These activities are presented in this article, with a focus on the CoDeSat Content Delivery over Satellite project.In the remainder of this article we first summarize services and service requirements as they are considered in our work. We then discuss the challenges derived from these requirements with respect to current network and protocol architectures. Finally, we describe our approach, and the current status of our prototype implementation.

Micromechanics of base pair unzipping in the DNA duplex

International Nuclear Information System (INIS)

Volkov, Sergey N; Paramonova, Ekaterina V; Yakubovich, Alexander V; Solov’yov, Andrey V

2012-01-01

All-atom molecular dynamics (MD) simulations of DNA duplex unzipping in a water environment were performed. The investigated DNA double helix consists of a Drew-Dickerson dodecamer sequence and a hairpin (AAG) attached to the end of the double-helix chain. The considered system is used to examine the process of DNA strand separation under the action of an external force. This process occurs in vivo and now is being intensively investigated in experiments with single molecules. The DNA dodecamer duplex is consequently unzipped pair by pair by means of the steered MD. The unzipping trajectories turn out to be similar for the duplex parts with G⋅C content and rather distinct for the parts with A⋅T content. It is shown that during the unzipping each pair experiences two types of motion: relatively quick rotation together with all the duplex and slower motion in the frame of the unzipping fork. In the course of opening, the complementary pair passes through several distinct states: (i) the closed state in the double helix, (ii) the metastable preopened state in the unzipping fork and (iii) the unbound state. The performed simulations show that water molecules participate in the stabilization of the metastable states of the preopened base pairs in the DNA unzipping fork. (paper)

Soil sail content estimation in the yellow river delta with satellite hyperspectral data

Science.gov (United States)

Weng, Yongling; Gong, Peng; Zhu, Zhi-Liang

2008-01-01

Soil salinization is one of the most common land degradation processes and is a severe environmental hazard. The primary objective of this study is to investigate the potential of predicting salt content in soils with hyperspectral data acquired with EO-1 Hyperion. Both partial least-squares regression (PLSR) and conventional multiple linear regression (MLR), such as stepwise regression (SWR), were tested as the prediction model. PLSR is commonly used to overcome the problem caused by high-dimensional and correlated predictors. Chemical analysis of 95 samples collected from the top layer of soils in the Yellow River delta area shows that salt content was high on average, and the dominant chemicals in the saline soil were NaCl and MgCl2. Multivariate models were established between soil contents and hyperspectral data. Our results indicate that the PLSR technique with laboratory spectral data has a strong prediction capacity. Spectral bands at 1487-1527, 1971-1991, 2032-2092, and 2163-2355 nm possessed large absolute values of regression coefficients, with the largest coefficient at 2203 nm. We obtained a root mean squared error (RMSE) for calibration (with 61 samples) of RMSEC = 0.753 (R2 = 0.893) and a root mean squared error for validation (with 30 samples) of RMSEV = 0.574. The prediction model was applied on a pixel-by-pixel basis to a Hyperion reflectance image to yield a quantitative surface distribution map of soil salt content. The result was validated successfully from 38 sampling points. We obtained an RMSE estimate of 1.037 (R2 = 0.784) for the soil salt content map derived by the PLSR model. The salinity map derived from the SWR model shows that the predicted value is higher than the true value. These results demonstrate that the PLSR method is a more suitable technique than stepwise regression for quantitative estimation of soil salt content in a large area. ?? 2008 CASI.

Non-random alkylation of DNA sequences induced in vivo by chemical mutagens

Energy Technology Data Exchange (ETDEWEB)

Durante, M.; Geri, C.; Bonatti, S.; Parenti, R. (Universita di Pisa (Italy))

1989-08-01

Previous studies of the interaction of alkylating agents on the eukaryotic genome support the idea that induction of DNA adducts is at specific genomic sites. Here we show molecular and cytological evidence that alkylation is rather specific. Mammalian cell cultures were exposed to different doses of mutagens and the DNA was analyzed by density gradient ultracentrifugation, hydroxylapatite fractionation, and by restriction enzyme analysis. Studies with the labelled mutagens N-ethyl-N-nitrosourea and N-methyl-N'-nitro-N-nitrosoguanidine show that there is a non-random distribution of the adducts. The adducts are found more frequently in A-T, G-C rich satellite DNA and highly repetitive sequences. Analysis with restriction enzymes shows that both methyl and ethyl groups influence the restriction patterns of the enzymes HpaII and MspI that recognize specific endogenous DNA methylation. These data suggest, as a subsequent mechanism, a modification in the pattern of the normal endogenous methylation of 5-methylcytosine.

Change of the high-latitude ionosphere during heating by a powerful short radio wave of the EISCAT/Heating complex according to signals of the GLONASS satellite and the incoherent scattering radar

Directory of Open Access Journals (Sweden)

Tereshchenko E. D.

2018-03-01

Full Text Available Results of observations of variations of temperature, electron concentration and total electron content of the high-latitude region of the ionosphere during its modification by powerful short radio waves of the heating complex EISCAT/Heating (Tromsø, Norway according to signals of the GLONASS satellites and the incoherent scattering UHF EISCAT radar (Tromsø, Norway have been provided. The geometry of passes of the GLONASS and GPS satellites for operating conditions of the heating complex in Tromsø has been considered. It has been shown that during the experiments on the EISCAT/Heating complex for the study of the modified structure of the high-latitude ionosphere it is more convenient to use the GLONASS satellites. Parameters of orbits of these satellites allow researching changes of total electron content in the direction along the geomagnetic field line at the place of observation. It has been shown that during heating of the ionosphere by powerful short radio waves its structure is becoming an irregular one. Operation of the heating complex in the mode "switched on – switched off" has caused appearance of wavy variations of total electron content with the periods close to the heating period. The main features of behavior of the total electron content in the case of the continuous heating of the ionosphere in the direction of the magnetic zenith according to the GLONASS satellite are: reduction of total electron content in the central zone of the antenna diagram, i. e. in the direction of the magnetic zenith, and presence of the increased values of total electron content at the edges of the heating zone. According to the incoherent scattering radar the heating of the ionosphere by the powerful short radio wave has created the region of the increased electron temperature and electron concentration along the direction of the magnetic zenith. The behavior of total electron content according to the GLONASS satellite and the radar of

In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases.

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Julia Arand

2012-06-01

Full Text Available The enzymatic control of the setting and maintenance of symmetric and non-symmetric DNA methylation patterns in a particular genome context is not well understood. Here, we describe a comprehensive analysis of DNA methylation patterns generated by high resolution sequencing of hairpin-bisulfite amplicons of selected single copy genes and repetitive elements (LINE1, B1, IAP-LTR-retrotransposons, and major satellites. The analysis unambiguously identifies a substantial amount of regional incomplete methylation maintenance, i.e. hemimethylated CpG positions, with variant degrees among cell types. Moreover, non-CpG cytosine methylation is confined to ESCs and exclusively catalysed by Dnmt3a and Dnmt3b. This sequence position-, cell type-, and region-dependent non-CpG methylation is strongly linked to neighboring CpG methylation and requires the presence of Dnmt3L. The generation of a comprehensive data set of 146,000 CpG dyads was used to apply and develop parameter estimated hidden Markov models (HMM to calculate the relative contribution of DNA methyltransferases (Dnmts for de novo and maintenance DNA methylation. The comparative modelling included wild-type ESCs and mutant ESCs deficient for Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3a/3b, respectively. The HMM analysis identifies a considerable de novo methylation activity for Dnmt1 at certain repetitive elements and single copy sequences. Dnmt3a and Dnmt3b contribute de novo function. However, both enzymes are also essential to maintain symmetrical CpG methylation at distinct repetitive and single copy sequences in ESCs.

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'

Dietary Berries and Ellagic Acid Prevent Oxidative DNA Damage and Modulate Expression of DNA Repair Genes

Directory of Open Access Journals (Sweden)

Ramesh C. Gupta

2008-03-01

Full Text Available DNA damage is a pre-requisite for the initiation of cancer and agents that reduce this damage are useful in cancer prevention. In this study, we evaluated the ability of whole berries and berry phytochemical, ellagic acid to reduce endogenous oxidative DNA damage. Ellagic acid was selected based on > 95% inhibition of 8-oxodeoxyguosine (8-oxodG and other unidentified oxidative DNA adducts induced by 4-hydroxy-17B;-estradiol and CuCl2 in vitro. Inhibition of the latter occurred at lower concentrations (10 u(microM than that for 8-oxodG (100 u(microM. In the in vivo study, female CD-1 mice (n=6 were fed either a control diet or diet supplemented with ellagic acid (400 ppm and dehydrated berries (5% w/w with varying ellagic acid contents -- blueberry (low, strawberry (medium and red raspberry (high, for 3 weeks. Blueberry and strawberry diets showed moderate reductions in endogenous DNA adducts (25%. However, both red raspberry and ellagic acid diets showed a significant reduction of 59% (p < 0.001 and 48% (p < 0.01, respectively. Both diets also resulted in a 3-8 fold over-expression of genes involved in DNA repair such as xeroderma pigmentosum group A complementing protein (XPA, DNA excision repair protein (ERCC5 and DNA ligase III (DNL3. These results suggest that red raspberry and ellagic acid reduce endogenous oxidative DNA damage by mechanisms which may involve increase in DNA repair.

Growth and DNA Methylation Level of Triticum Aestivum Seedlings Treated with 5-Azacytidine

International Nuclear Information System (INIS)

Yingduan, H.; Liu, W. X.; Li, J. Y.; Ding, W. K.; Zhu, Y.; Wang, H.; Jiang, L. N. A.; Zhou, Y. Q.

2016-01-01

In this study, two wheat varieties were used to study effects of DNA methylation inhibitor 5-azacytidine on wheat seedling growth, and found that the high concentration of 5-azacytidine (over 100 meu m) significantly affected growth of wheat seedling root, especially for wheat AK58. When the concentration of 5-azacytidine was between 50 to 250 meu m, plant height of wheat AK58 significantly reduced, and the minimum dwarf phenotype was obtained when treated by 250 meu m 5-azacytidine. Different with wheat AK58, plant height of wheat XM13 increased after being treated by 5-azacytidine. In addition, leaf area and chlorophyll content of two wheat varieties both increased under low concentration of 5-azacytidine (10-50 meu m), and the increase magnitude of wheat AK58 was far more compared with wheat XM13, indicating that moderate methylation could promote development of wheat leaf and photosynthesis, and photosynthesis of wheat AK58 might be closely related with methylation status of genomic DNA. This study also found that proline content of wheat AK58 and soluble sugar content of two wheat varieties increased after being treated by 5-azacytidine, and showed a concentration-dependent increase, further more, soluble sugar content of wheat AK58 was far higher than that of wheat XM13 under normal conditions, thus 5-azacytidine might be conducive to accumulation of soluble sugar in wheat and could obviously influence osmotic adjustment ability of wheat AK58. Further analysis showed that DNA methylation level of wheat AK58 was higher compared with wheat XM13, and was both lower in leaf genomic DNA of two wheat varieties than that in root genomic DNA. Although 5-azacytidine significantly reduced DNA methylation level of leaf and root genome, the decrease amplitude of leaf was more obvious. Collectively, these results suggest that there are some differences in seedling growth, physiological characteristics and DNA methylation level of two wheat varieties, furthermore, DNA

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...

The effect of gamma irradiation on the nucleic acids content of the mediterranean fruit fly ceratitis capitata (Wied)

International Nuclear Information System (INIS)

Fadel, A.M.; Amin, T.R.; Al-Elimi, M.H.

1999-01-01

This work was carried out study the effect of gamma irradiation on the deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) content in the whole body homogenate of the mediterranean fruit fly, ceratitis capitata (Wied.) pupae were gamma irradiated with different doses (o, 50, 70, 90 and 110 Gy) at two different pupal ages (2 and 4 days before adult emergence ) to estimate the nucleic acids in pupae and adult males, and females. Experimental results showed that gamma irradiation of pupae reduced RNA content, and this reduction was proportional with the applied dose and more pronounced in the younger pupae. However, DNA content was reduced only when the highest dose was applied to pupae irradiated 2 days before adult emergence (older pupae). Concerning adult insects which were gamma irradiated as pupae, the results revealed, generally, that males and females which were irradiated 2 days before adult emergence were more affected than those irradiated 4 days before adult emergence. The male DNA content and the female RNA content showed high degrees of reduction which, more or less, increased with increasing the dose used. On the other hand, female DNA and male RNA contents were slightly, changed. The significant importance of the results and some statistical interrelations were discussed

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...

Space Solar Power Satellite Systems, Modern Small Satellites, and Space Rectenna

Science.gov (United States)

Bergsrud, Corey Alexis Marvin

Space solar power satellite (SSPS) systems is the concept of placing large satellite into geostationary Earth orbit (GEO) to harvest and convert massive amounts of solar energy into microwave energy, and to transmit the microwaves to a rectifying antenna (rectenna) array on Earth. The rectenna array captures and converts the microwave power into usable power that is injected into the terrestrial electric grid for use. This work approached the microwave power beam as an additional source of power (with solar) for lower orbiting satellites. Assuming the concept of retrodirectivity, a GEO-SSPS antenna array system tracks and delivers microwave power to lower orbiting satellites. The lower orbiting satellites are equipped with a stacked photovoltaic (PV)/rectenna array hybrid power generation unit (HPGU) in order to harvest solar and/or microwave energy for on-board use during orbit. The area, and mass of the PV array part of the HPGU was reduced at about 32% beginning-of-life power in order to achieve the spacecraft power requirements. The HPGU proved to offer a mass decrease in the PGU, and an increase in mission life due to longer living component life of the rectenna array. Moreover, greater mission flexibility is achieved through a track and power delivery concept. To validate the potential advantages offered by a HPGU, a mission concept was presented that utilizes modern small satellites as technology demonstrators. During launch, a smaller power receiving "daughter" satellite sits inside a larger power transmitting "mother" satellite. Once separated from the launch vehicle the daughter satellite is ejected away from the mother satellite, and each satellite deploys its respective power transmitting or power receiving hardware's for experimentation. The concept of close proximity mission operations between the satellites is considered. To validate the technology of the space rectenna array part of the HPGU, six milestones were completed in the design. The first

SatelliteDL: a Toolkit for Analysis of Heterogeneous Satellite Datasets

Science.gov (United States)

Galloy, M. D.; Fillmore, D.

2014-12-01

SatelliteDL is an IDL toolkit for the analysis of satellite Earth observations from a diverse set of platforms and sensors. The core function of the toolkit is the spatial and temporal alignment of satellite swath and geostationary data. The design features an abstraction layer that allows for easy inclusion of new datasets in a modular way. Our overarching objective is to create utilities that automate the mundane aspects of satellite data analysis, are extensible and maintainable, and do not place limitations on the analysis itself. IDL has a powerful suite of statistical and visualization tools that can be used in conjunction with SatelliteDL. Toward this end we have constructed SatelliteDL to include (1) HTML and LaTeX API document generation,(2) a unit test framework,(3) automatic message and error logs,(4) HTML and LaTeX plot and table generation, and(5) several real world examples with bundled datasets available for download. For ease of use, datasets, variables and optional workflows may be specified in a flexible format configuration file. Configuration statements may specify, for example, a region and date range, and the creation of images, plots and statistical summary tables for a long list of variables. SatelliteDL enforces data provenance; all data should be traceable and reproducible. The output NetCDF file metadata holds a complete history of the original datasets and their transformations, and a method exists to reconstruct a configuration file from this information. Release 0.1.0 distributes with ingest methods for GOES, MODIS, VIIRS and CERES radiance data (L1) as well as select 2D atmosphere products (L2) such as aerosol and cloud (MODIS and VIIRS) and radiant flux (CERES). Future releases will provide ingest methods for ocean and land surface products, gridded and time averaged datasets (L3 Daily, Monthly and Yearly), and support for 3D products such as temperature and water vapor profiles. Emphasis will be on NPP Sensor, Environmental and

Interim Service ISDN Satellite (ISIS) network model for advanced satellite designs and experiments

Science.gov (United States)

Pepin, Gerard R.; Hager, E. Paul

1991-01-01

The Interim Service Integrated Services Digital Network (ISDN) Satellite (ISIS) Network Model for Advanced Satellite Designs and Experiments describes a model suitable for discrete event simulations. A top-down model design uses the Advanced Communications Technology Satellite (ACTS) as its basis. The ISDN modeling abstractions are added to permit the determination and performance for the NASA Satellite Communications Research (SCAR) Program.

DNA nanoparticles with core-shell morphology.

Science.gov (United States)

Chandran, Preethi L; Dimitriadis, Emilios K; Lisziewicz, Julianna; Speransky, Vlad; Horkay, Ferenc

2014-10-14

Mannobiose-modified polyethylenimines (PEI) are used in gene therapy to generate nanoparticles of DNA that can be targeted to the antigen-presenting cells of the immune system. We report that the sugar modification alters the DNA organization within the nanoparticles from homogenous to shell-like packing. The depth-dependent packing of DNA within the nanoparticles was probed using AFM nano-indentation. Unmodified PEI-DNA nanoparticles display linear elastic properties and depth-independent mechanics, characteristic of homogenous materials. Mannobiose-modified nanoparticles, however, showed distinct force regimes that were dependent on indentation depth, with 'buckling'-like response that is reproducible and not due to particle failure. By comparison with theoretical studies of spherical shell mechanics, the structure of mannobiosylated particles was deduced to be a thin shell with wall thickness in the order of few nanometers, and a fluid-filled core. The shell-core structure is also consistent with observations of nanoparticle denting in altered solution conditions, with measurements of nanoparticle water content from AFM images, and with images of DNA distribution in Transmission Electron Microscopy.

Human circulating plasma DNA significantly decreases while lymphocyte DNA damage increases under chronic occupational exposure to low-dose gamma-neutron and tritium β-radiation

Energy Technology Data Exchange (ETDEWEB)

Korzeneva, Inna B., E-mail: inna.korzeneva@molgen.vniief.ru [Russian Federal Nuclear Center – All-Russian Research Institute of Experimental Physics (RFNC-VNIIEF) 607190, Sarov, 37 Mira ave., Nizhniy Novgorod Region (Russian Federation); Kostuyk, Svetlana V.; Ershova, Liza S. [Research Centre for Medical Genetics, Russian Academy of Medical Sciences, 115478 Moscow, 1 Moskvorechye str. (Russian Federation); Osipov, Andrian N. [Federal Medial and Biological Center named after Burnazyan of the Federal Medical and Biological Agency (FMBTz named after Burnazyan of FMBA), Moscow (Russian Federation); State Research Center - Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Zhivopisnaya, 46, Moscow, 123098 (Russian Federation); Zhuravleva, Veronika F.; Pankratova, Galina V. [Russian Federal Nuclear Center – All-Russian Research Institute of Experimental Physics (RFNC-VNIIEF) 607190, Sarov, 37 Mira ave., Nizhniy Novgorod Region (Russian Federation); Porokhovnik, Lev N.; Veiko, Natalia N. [Research Centre for Medical Genetics, Russian Academy of Medical Sciences, 115478 Moscow, 1 Moskvorechye str. (Russian Federation)

2015-09-15

Highlights: • The chronic exposure to low-dose IR induces DSBs in human lymphocytes (TM index). • Exposure to IR decreases the level of human circulating DNA (cfDNA index). • IR induces an increase of DNase1 activity (DNase1 index) in plasma. • IR induces an increase of the level of antibodies to DNA (Ab DNA index) in plasma. • The ratio cfDNA/(DNase 1 × Ab DNA × TM) is a potential marker of human exposure to IR. - Abstract: The blood plasma of healthy people contains cell-fee (circulating) DNA (cfDNA). Apoptotic cells are the main source of the cfDNA. The cfDNA concentration increases in case of the organism’s cell death rate increase, for example in case of exposure to high-dose ionizing radiation (IR). The objects of the present research are the blood plasma and blood lymphocytes of people, who contacted occupationally with the sources of external gamma/neutron radiation or internal β-radiation of tritium N = 176). As the controls (references), blood samples of people, who had never been occupationally subjected to the IR sources, were used (N = 109). With respect to the plasma samples of each donor there were defined: the cfDNA concentration (the cfDNA index), DNase1 activity (the DNase1 index) and titre of antibodies to DNA (the Ab DNA index). The general DNA damage in the cells was defined (using the Comet assay, the tail moment (TM) index). A chronic effect of the low-dose ionizing radiation on a human being is accompanied by the enhancement of the DNA damage in lymphocytes along with a considerable cfDNA content reduction, while the DNase1 content and concentration of antibodies to DNA (Ab DNA) increase. All the aforementioned changes were also observed in people, who had not worked with the IR sources for more than a year. The ratio cfDNA/(DNase1 × Ab DNA × TM) is proposed to be used as a marker of the chronic exposure of a person to the external low-dose IR. It was formulated the assumption that the joint analysis of the cfDNA, DNase1, Ab

The Total Electron Content From InSAR and GNSS: A Midlatitude Study

DEFF Research Database (Denmark)

Musico, Elvira; Cesaroni, Claudio; Spogli, Luca

2018-01-01

The total electron content (TEC) measured from the interferometric synthetic aperture radar (InSAR) and froma dense network of global navigation satellite system (GNSS) receivers are used to assess the capability of InSAR to retrieve ionospheric information, when the tropospheric contribution...

Characterising the potential of sheep wool for ancient DNA analyses

DEFF Research Database (Denmark)

Brandt, Luise Ørsted; Tranekjer, Lena D.; Mannering, Ulla

2011-01-01

can be PCR-amplified from wool derived from a variety of breeds, regardless of the body location or natural pigmentation. Furthermore, although DNA can be PCR-amplified from wool dyed with one of four common plant dyes (tansy, woad, madder, weld), the use of mordants such as alum or iron leads...... and content of DNA in hair shafts are known to vary, and it is possible that common treatments of wool such as dyeing may negatively impact the DNA. Using quantitative real-time polymerase chain reaction (PCR), we demonstrate that in general, short fragments of both mitochondrial and single-copy nuclear DNA...

Protein carbonyl content: a novel biomarker for aging in HIV/AIDS patients.

Science.gov (United States)

Kolgiri, Vaishali; Patil, Vinayak Wamanrao

The major complications of "treated" Human Immunodeficiency Virus (HIV) infection are cardiovascular disease, malignancy, renal disease, liver disease, bone disease, and perhaps neurological complications, which are phenomena of the normal aging process occurring at an earlier age in the HIV-infected population. The present study is aimed to explore protein carbonyl content as a biomarker for detecting oxidative DNA damage induced ART toxicity and/or accelerated aging in HIV/AIDS patients. To investigate the potential of carbonyl content as a biomarker for detecting oxidative Deoxyribonucleic acid (DNA) damage induced Antiretroviral Theraphy (ART) toxicity and/or accelerated aging in HIV/AIDS patients. In this case-control study a total 600 subjects were included. All subjects were randomly selected and grouped as HIV-negative (control group) (n=300), HIV-infected ART naive (n=100), HIV-infected on first line ART (n=100), and HIV-infected on second line ART (n=100). Seronegative control subjects were age- and sex-matched with the ART naive patients and the two other groups. Carbonyl protein was determined by the method described in Levine et al. DNA damage marker 8-OH-dG was determined using 8-hydroxy-2-deoxy Guanosine StressXpress ELA Kit by StressMarq Biosciences. Protein carbonyl content levels and oxidative DNA damage were significantly higher (paging in HIV/AIDS patients. Larger studies are warranted to elucidate the role of carbonyl content as a biomarker for premature aging in HIV/AIDS patients. Copyright © 2016 Sociedade Brasileira de Infectologia. Published by Elsevier Editora Ltda. All rights reserved.

Local chromatin structure of heterochromatin regulates repeated DNA stability, nucleolus structure, and genome integrity

Energy Technology Data Exchange (ETDEWEB)

Peng, Jamy C. [Univ. of California, Berkeley, CA (United States)

2007-01-01

Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in

Good quality Vitis RNA obtained from an adapted DNA isolation protocol

Directory of Open Access Journals (Sweden)

Isabel Baiges

2003-03-01

Full Text Available Grapevine is a woody plant, whose high carbohydrate and phenolic compound contents usually interferes with nucleic acid isolation. After we tried several protocols for isolating RNA from the Vitis rootstock Richter- 110 (R-110 with little or no success, we adapted a method reported to be satisfactory for grapevine DNA isolation, to extract RNA. With slight protocol modifications, we succeeded to obtain polysaccharide- and phenolic-free RNA preparations from all vegetative tissues, without excessive sample handling. RNA isolated by the reported method permitted to obtain highly pure mRNA (messenger RNA to construct a cDNA (complementary DNA library and allowed gene transcription analysis by reverse Northern, which guarantees RNA integrity. This method may also be suitable for other plant species with high polysaccharide or phenolic contents.

Template DNA-strand co-segregation and asymmetric cell division in skeletal muscle stem cells.

Science.gov (United States)

Shinin, Vasily; Gayraud-Morel, Barbara; Tajbakhsh, Shahragim

2009-01-01

Stem cells are present in all tissues and organs, and are crucial for normal regulated growth. How the pool size of stem cells and their progeny is regulated to establish the tissue prenatally, then maintain it throughout life, is a key question in biology and medicine. The ability to precisely locate stem and progenitors requires defining lineage progression from stem to differentiated cells, assessing the mode of cell expansion and self-renewal and identifying markers to assess the different cell states within the lineage. We have shown that during lineage progression from a quiescent adult muscle satellite cell to a differentiated myofibre, both symmetric and asymmetric divisions take place. Furthermore, we provide evidence that a sub-population of label retaining satellite cells co-segregate template DNA strands to one daughter cell. These findings provide a means of identifying presumed stem and progenitor cells within the lineage. In addition, asymmetric segregation of template DNA and the cytoplasmic protein Numb provides a landmark to define cell behaviour as self-renewal and differentiation decisions are being executed.

Near real-time estimation of ionosphere vertical total electron content from GNSS satellites using B-splines in a Kalman filter

Science.gov (United States)

Erdogan, Eren; Schmidt, Michael; Seitz, Florian; Durmaz, Murat

2017-02-01

Although the number of terrestrial global navigation satellite system (GNSS) receivers supported by the International GNSS Service (IGS) is rapidly growing, the worldwide rather inhomogeneously distributed observation sites do not allow the generation of high-resolution global ionosphere products. Conversely, with the regionally enormous increase in highly precise GNSS data, the demands on (near) real-time ionosphere products, necessary in many applications such as navigation, are growing very fast. Consequently, many analysis centers accepted the responsibility of generating such products. In this regard, the primary objective of our work is to develop a near real-time processing framework for the estimation of the vertical total electron content (VTEC) of the ionosphere using proper models that are capable of a global representation adapted to the real data distribution. The global VTEC representation developed in this work is based on a series expansion in terms of compactly supported B-spline functions, which allow for an appropriate handling of the heterogeneous data distribution, including data gaps. The corresponding series coefficients and additional parameters such as differential code biases of the GNSS satellites and receivers constitute the set of unknown parameters. The Kalman filter (KF), as a popular recursive estimator, allows processing of the data immediately after acquisition and paves the way of sequential (near) real-time estimation of the unknown parameters. To exploit the advantages of the chosen data representation and the estimation procedure, the B-spline model is incorporated into the KF under the consideration of necessary constraints. Based on a preprocessing strategy, the developed approach utilizes hourly batches of GPS and GLONASS observations provided by the IGS data centers with a latency of 1 h in its current realization. Two methods for validation of the results are performed, namely the self consistency analysis and a comparison

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

Spectroscopic quantification of 5-hydroxymethylcytosine in genomic DNA.

Science.gov (United States)

Shahal, Tamar; Gilat, Noa; Michaeli, Yael; Redy-Keisar, Orit; Shabat, Doron; Ebenstein, Yuval

2014-08-19

5-Hydroxymethylcytosine (5hmC), a modified form of the DNA base cytosine, is an important epigenetic mark linked to regulation of gene expression in development, and tumorigenesis. We have developed a spectroscopic method for a global quantification of 5hmC in genomic DNA. The assay is performed within a multiwell plate, which allows simultaneous recording of up to 350 samples. Our quantification procedure of 5hmC is direct, simple, and rapid. It relies on a two-step protocol that consists of enzymatic glucosylation of 5hmC with an azide-modified glucose, followed by a "click reaction" with an alkyne-fluorescent tag. The fluorescence intensity recorded from the DNA sample is proportional to its 5hmC content and can be quantified by a simple plate reader measurement. This labeling technique is specific and highly sensitive, allowing detection of 5hmC down to 0.002% of the total nucleotides. Our results reveal significant variations in the 5hmC content obtained from different mouse tissues, in agreement with previously reported data.

The American Satellite Company (ASC) satellite deployed from payload bay

Science.gov (United States)

1985-01-01

The American Satellite Company (ASC) communications satellite is deployed from the payload bay of the Shuttle Discovery. A portion of the cloudy surface of the earth can be seen to the left of the frame.

TOL plasmid carriage enhances biofilm formation and increases extracellular DNA content in Pseudomonas putida KT2440

DEFF Research Database (Denmark)

D'Alvise, Paul; Sjoholm, O.R.; Yankelevich, T.

2010-01-01

laser scanning microscopy. The TOL-carrying strains formed pellicles and thick biofilms, whereas the same strains without the plasmid displayed little adherent growth. Microscopy using fluorescent nucleic acid-specific stains revealed differences in the production of extracellular polymeric substances......: TOL carriage leads to more extracellular DNA (eDNA) in pellicles and biofilms. Pellicles were dissolved by DNase I treatment. Enhanced cell lysis due to plasmid carriage was ruled out as the mechanism for eDNA release. We report, for the first time, that carriage of a conjugative plasmid leads...

Mitochondrial DNA alteration in obstructive sleep apnea.

Science.gov (United States)

Lacedonia, Donato; Carpagnano, Giovanna E; Crisetti, Elisabetta; Cotugno, Grazia; Palladino, Grazia P; Patricelli, Giulia; Sabato, Roberto; Foschino Barbaro, Maria P

2015-04-07

Obstructive Sleep Apnea (OSAS) is a disease associated with the increase of cardiovascular risk and it is characterized by repeated episodes of Intermittent Hypoxia (IH) which inducing oxidative stress and systemic inflammation. Mitochondria are cell organelles involved in the respiratory that have their own DNA (MtDNA). The aim of this study was to investigate if the increase of oxidative stress in OSAS patients can induce also MtDNA alterations. 46 OSAS patients (age 59.27 ± 11.38; BMI 30.84 ± 3.64; AHI 36.63 ± 24.18) were compared with 36 control subjects (age 54.42 ± 6.63; BMI 29.06 ± 4.7; AHI 3.8 ± 1.10). In blood cells Content of MtDNA and nuclear DNA (nDNA) was measured in OSAS patients by Real Time PCR. The ratio between MtDNA/nDNA was then calculated. Presence of oxidative stress was evaluated by levels of Reactive Oxygen Metabolites (ROMs), measured by diacron reactive oxygen metabolite test (d-ROM test). MtDNA/nDNA was higher in patients with OSAS than in the control group (150.94 ± 49.14 vs 128.96 ± 45.8; p = 0.04), the levels of ROMs were also higher in OSAS subjects (329.71 ± 70.17 vs 226 ± 36.76; p = 0.04) and they were positively correlated with MtDNA/nDNA (R = 0.5, p DNA damage induced by the increase of oxidative stress. Intermittent hypoxia seems to be the main mechanism which leads to this process.

Video Streaming Transfer in a Smart Satellite Mobile Environment

OpenAIRE

Celandroni, Nedo; Davoli, Franco; Ferro, Erina; Gotta, Alberto

2009-01-01

In the near future, transportation media are likely to become "smart spaces", where sophisticated services are offered to the passengers. Among such services, we concentrate on video streaming provided on buses that move in urban, suburban, or highway environments. A contents' source utilizes a satellite DVB-S2 link for transmitting video streams to a bus, which, in its turn, relays it to its passengers' devices. A bus works in a smart mode taking advantage of the knowledge of the exact point...

Melanin photosensitizes ultraviolet light (UVC) DNA damage in pigmented cells

International Nuclear Information System (INIS)

Huselton, C.A.; Hill, H.Z.

1990-01-01

Melanins, pigments of photoprotection and camouflage, are very photoreactive and can both absorb and emit active oxygen species. Nevertheless, black skinned individuals rarely develop skin cancer and melanin is assumed to act as a solar screen. Since DNA is the target for solar carcinogenesis, the effect of melanin on Ultraviolet (UV)-induced thymine lesions was examined in mouse melanoma and carcinoma cells that varied in melanin content. Cells prelabeled with 14C-dThd were irradiated with UVC; DNA was isolated, purified, degraded to bases by acid hydrolysis and analyzed by HPLC. Thymine dimers were detected in all of the extracts of irradiated cells. Melanotic and hypomelanotic but not mammary carcinoma cell DNA from irradiated cells contained hydrophilic thymine derivatives. The quantity of these damaged bases was a function of both the UVC dose and the cellular melanin content. One such derivative was identified by gas chromatography-mass spectroscopy as thymine glycol. The other appears to be derived from thymine glycol by further oxidation during acid hydrolysis of the DNA. The finding of oxidative DNA damage in melanin-containing cells suggests that melanin may be implicated in the etiology of caucasian skin cancer, particularly melanoma. Furthermore, the projected decrease in stratospheric ozone could impact in an unanticipated deleterious manner on dark-skinned individuals

Trends in mobile satellite communication

Science.gov (United States)

Johannsen, Klaus G.; Bowles, Mike W.; Milliken, Samuel; Cherrette, Alan R.; Busche, Gregory C.

1993-01-01

Ever since the U.S. Federal Communication Commission opened the discussion on spectrum usage for personal handheld communication, the community of satellite manufacturers has been searching for an economically viable and technically feasible satellite mobile communication system. Hughes Aircraft Company and others have joined in providing proposals for such systems, ranging from low to medium to geosynchronous orbits. These proposals make it clear that the trend in mobile satellite communication is toward more sophisticated satellites with a large number of spot beams and onboard processing, providing worldwide interconnectivity. Recent Hughes studies indicate that from a cost standpoint the geosynchronous satellite (GEOS) is most economical, followed by the medium earth orbit satellite (MEOS) and then by the low earth orbit satellite (LEOS). From a system performance standpoint, this evaluation may be in reverse order, depending on how the public will react to speech delay and collision. This paper discusses the trends and various mobile satellite constellations in satellite communication under investigation. It considers the effect of orbital altitude and modulation/multiple access on the link and spacecraft design.

JPSS Preparations at the Satellite Proving Ground for Marine, Precipitation, and Satellite Analysis

Science.gov (United States)

Folmer, Michael J.; Berndt, E.; Clark, J.; Orrison, A.; Kibler, J.; Sienkiewicz, J.; Nelson, J.; Goldberg, M.; Sjoberg, W.

2016-01-01

The ocean prediction center at the national hurricane center's tropical analysis and forecast Branch, the Weather Prediction center and the Satellite analysis branch of NESDIS make up the Satellite Proving Ground for Marine, Precipitation and Satellite Analysis. These centers had early exposure to JPSS products using the S-NPP Satellite that was launched in 2011. Forecasters continue to evaluate new products in anticipation for the launch of JPSS-1 sometime in 2017.

The satellite situation center

International Nuclear Information System (INIS)

Teague, M.J.; Sawyer, D.M.; Vette, J.I.

1982-01-01

Considerations related to the early planning for the International Magnetospheric Study (IMS) took into account the desirability of an establishment of specific entities for generating and disseminating coordination information for both retrospective and predictive periods. The organizations established include the IMS/Satellite Situation Center (IMS/SSC) operated by NASA. The activities of the SSC are related to the preparation of reports on predicted and actually achieved satellite positions, the response to inquiries, the compilation of information on satellite experiments, and the issue of periodic status summaries. Attention is given to high-altitude satellite services, other correlative satellite services, non-IMS activities of the SSC, a summary of the SSC request activity, and post-IMS and future activities

Plan of Time Management of Satellite Positioning System using Quasi-zenith Satellite

Science.gov (United States)

Takahashi, Yasuhiro; Fujieda, Miho; Amagai, Jun; Yokota, Shoichiro; Kimura, Kazuhiro; Ito, Hiroyuki; Hama, Shin'ichi; Morikawa, Takao; Kawano, Isao; Kogure, Satoshi

The Quasi-Zenith satellites System (QZSS) is developed as an integrated satellite service system of communication, broadcasting and positioning for mobile users in specified regions of Japan from high elevation angle. Purposes of the satellite positioning system using Quasi-Zenith satellite (QZS) are to complement and augment the GPS. The national institutes concerned have been developing the positioning system using QZS since 2003 and will carry out experiments and researches in three years after the launch. In this system, National Institute of Information and Communications Technology (NICT) is mainly in charge of timing system for the satellite positioning system using QZS, such as onboard hydrogen maser atomic clock and precise time management system of the QZSS. We started to develop the engineering model of the time management system for the QZSS. The time management system for the QZSS will be used to compare time differences between QZS and earth station as well as to compare between three onboard atomic clocks. This paper introduces time management of satellite positioning system using the QZSS.

DNA of HeLa cells during caffeine-promoted recovery from X-ray induced G2 arrest

International Nuclear Information System (INIS)

Bases, R.; Mendez, F.; Liebeskind, D.; Elequin, F.; Neubort, S.

1980-01-01

Progression of X-irradiated HeLa cells from G2 arrest through mitosis was promoted by 1mM caffeine. Caffeine promoted the return from abnormally high levels of radiation-induced immunoreactivity to antinucleoside antibodies, which indicates persistent DNA strand separation, to the low levels normally found in G2. With caffeine, the irradiated cells progressed through mitosis, producing daughter cells with the normal G1 content of DNA. Without caffeine, the DNA content of individual radiation-arrested cells retained G2 values and the abnormally high levels of immunoreactivity to antinucleoside antibodies. (author)

Protein carbonyl content: a novel biomarker for aging in HIV/AIDS patients

Directory of Open Access Journals (Sweden)

Vaishali Kolgiri

2017-01-01

Conclusions: Carbonyl content may has a role as a biomarker for detecting oxidative DNA damage induced ART toxicity and/or accelerated aging in HIV/AIDS patients. Larger studies are warranted to elucidate the role of carbonyl content as a biomarker for premature aging in HIV/AIDS patients.

Appraising city-scale pollution monitoring capabilities of multi-satellite datasets using portable pollutant monitors

Science.gov (United States)

Aliyu, Yahaya A.; Botai, Joel O.

2018-04-01

The retrieval characteristics for a city-scale satellite experiment was explored over a Nigerian city. The study evaluated carbon monoxide and aerosol contents in the city atmosphere. We utilized the MSA Altair 5× gas detector and CW-HAT200 particulate counter to investigate the city-scale monitoring capabilities of satellite pollution observing instruments; atmospheric infrared sounder (AIRS), measurement of pollution in the troposphere (MOPITT), moderate resolution imaging spectroradiometer (MODIS), multi-angle imaging spectroradiometer (MISR) and ozone monitoring instrument (OMI). To achieve this, we employed the Kriging interpolation technique to collocate the satellite pollutant estimations over 19 ground sample sites for the period of 2015-2016. The portable pollutant devices were validated using the WHO air filter sampling model. To determine the city-scale performance of the satellite datasets, performance indicators: correlation coefficient, model efficiency, reliability index and root mean square error, were adopted as measures. The comparative analysis revealed that MOPITT carbon monoxide (CO) and MODIS aerosol optical depth (AOD) estimates are the appropriate satellite measurements for ground equivalents in Zaria, Nigeria. Our findings were within the acceptable limits of similar studies that utilized reference stations. In conclusion, this study offers direction to Nigeria's air quality policy organizers about available alternative air pollution measurements for mitigating air quality effects within its limited resource environment.

Determination of chromium combined with DNA, RNA and proteins in chromium-rich brewer's yeast by NAA

International Nuclear Information System (INIS)

Ding, W.J.; Qian, Q.F.; Hou, X.L.; Feng, W.Y.; Chai, Z.F.

2000-01-01

The content of chromium in the DNA, RNA and protein fractions separated from chromium-rich and normal brewer's yeast was determined by neutron activation analysis (NAA). Our results show that the extracted relative amounts and concentrations of DNA, RNA and proteins have no significant difference for two types of yeast, but the chromium content in DNA, RNA and proteins fractions extracted from the chromium-rich yeast are substantially higher than those from the normal. In addition, the concentration of chromium in DNA is much higher than that in RNA and proteins. It is evident that the inorganic chromium compounds can enter the yeast cell during the yeast cultivation in the chromium-containing culture medium and are converted into organic chromium species, which are combined with DNA, RNA and proteins. (author)

W-enriched satellite sequence in the Indian meal moth, Plodia interpunctella (Lepidoptera, Pyralidae)

Czech Academy of Sciences Publication Activity Database

Dalíková, Martina; Zrzavá, Magda; Kubíčková, S.; Marec, František

2017-01-01

Roč. 25, 3-4 (2017), s. 241-252 ISSN 0967-3849 R&D Projects: GA ČR(CZ) GA14-22765S; GA ČR(CZ) GA17-13713S Grant - others:GA ČR(CZ) GA17-17211S Institutional support: RVO:60077344 Keywords : satellite DNA * sex chromosomes * transcription Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 2.385, year: 2016 https://link.springer.com/article/10.1007%2Fs10577-017-9558-8

Mitochondrial DNA copy number, but not haplogroup, confers a genetic susceptibility to leprosy in Han Chinese from Southwest China.

Directory of Open Access Journals (Sweden)

Dong Wang

Full Text Available BACKGROUND: Leprosy is a chronic infectious disease caused by Mycobacterium leprae, an unculturable pathogen with an exceptionally eroded genome. The high level of inactivation of gene function in M. leprae, including many genes in its metabolic pathways, has led to a dependence on host energy production and nutritional products. We hypothesized that host cellular powerhouse--the mitochondria--may affect host susceptibility to M. leprae and the onset of clinical leprosy, and this may be reflected by mitochondrial DNA (mtDNA background and mtDNA copy number. METHODS: We analyzed the mtDNA sequence variation of 534 leprosy patients and 850 matched controls from Yunnan Province and classified each subject by haplogroup. mtDNA copy number, taken to be proportional to mtDNA content, was measured in a subset of these subjects (296 patients and 231 controls and 12 leprosy patients upon diagnosis. RESULTS: Comparison of matrilineal components of the case and control populations revealed no significant difference. However, measurement of mtDNA copy number showed that lepromatous leprosy patients had a significantly higher mtDNA content than controls (P = 0.008. Past medical treatments had no effect on the alteration of mtDNA copy number. CONCLUSIONS: Our results suggested that mtDNA content, but not haplogroup, affects leprosy and this influence is limited to the clinical subtype of lepromatous leprosy.

Hoechst 33258 dye generates DNA-protein cross-links during ultraviolet light-induced photolysis of bromodeoxyuridine in replicated and repaired DNA

Energy Technology Data Exchange (ETDEWEB)

Guo Xicang; Morgan, W.F.; Cleaver, J.E.

1986-08-01

Substitution of bromodeoxyuridine for thymidine in the DNA of mammalian cells sensitizes them to a range of wavelengths of ultraviolet light. Cells are also sensitized to photochemical reactions involving dyes such as Hoechst 33258, which is used to produce differential staining of chromatids according to their bromodeoxyuridine content. Irradiation with 313 nm light of human and hamster cells containing bromodeoxyuridine in their DNA produced single-strand breaks but no DNA-protein cross-links. Irradiation with 360 nm light in the presence of Hoechst 33258 produced extensive DNA-protein cross-linkage as well as single-strand breaks. These cross-links were observed in DNA containing bromodeoxyuridine incorporated by either semiconservative or repair replication. When the protein was removed with proteinase K, bromodeoxyuridine in repair patches after irradiation by doses of ultraviolet (254 nm) light as low as 0.26 J/m/sup 2/ could readily be detected. Hoechst 33258-mediated photolysis, therefore, provides a sensitive new technique for measuring repair replication after ultraviolet light irradiation.

Satellite Based Education and Training in Remote Sensing and Geo-Information AN E-Learning Approach to Meet the Growing Demands in India

Science.gov (United States)

Raju, P. L. N.; Gupta, P. K.

2012-07-01

One of the prime activities of Indian Space Research Organisation's (ISRO) Space Program is providing satellite communication services, viz., television broadcasting, mobile communication, cyclone disaster warning and rescue operations etc. so as to improve their economic conditions, disseminate technical / scientific knowledge to improve the agriculture production and education for rural people of India. ISRO, along with National Aeronautical and Space Administration (NASA) conducted experimental satellite communication project i.e. Satellite Instructional Television Experiment (SITE) using NASA's Advanced Telecommunication Satellite (i.e. ATS 6) with an objective to educate poor people of India via satellite broadcasting in 1975 and 1976, covering more than 2600 villages in six states of India and territories. Over the years India built communication satellites indigenously to meet the communication requirements of India. This has further lead to launch of an exclusive satellite from ISRO for educational purposes i.e. EDUSAT in 2004 through which rich audio-video content is transmitted / received, recreating virtual classes through interactivity. Indian Institute of Remote Sensing (IIRS) established in 1966, a premier institute in south East Asia in disseminating Remote Sensing (RS) and Geographical Information System (GIS), mainly focusing on contact based programs. But expanded the scope with satellite based Distance Learning Programs for Universities, utilizing the dedicated communication satellite i.e. EDUSAT in 2007. IIRS conducted successfully eight Distance Learning Programs in the last five years and training more than 6000 students mainly at postgraduate level from more than 60 universities /Institutions spread across India. IIRS obtained feedback and improved the programs on the continuous basis. Expanded the scope of IIRS outreach program to train user departments tailor made in any of the applications of Remote Sensing and Geoinformation, capacity

SATELLITE BASED EDUCATION AND TRAINING IN REMOTE SENSING AND GEO-INFORMATION: AN E-LEARNING APPROACH TO MEET THE GROWING DEMANDS IN INDIA

Directory of Open Access Journals (Sweden)

P. L. N. Raju

2012-07-01

Full Text Available One of the prime activities of Indian Space Research Organisation's (ISRO Space Program is providing satellite communication services, viz., television broadcasting, mobile communication, cyclone disaster warning and rescue operations etc. so as to improve their economic conditions, disseminate technical / scientific knowledge to improve the agriculture production and education for rural people of India. ISRO, along with National Aeronautical and Space Administration (NASA conducted experimental satellite communication project i.e. Satellite Instructional Television Experiment (SITE using NASA’s Advanced Telecommunication Satellite (i.e. ATS 6 with an objective to educate poor people of India via satellite broadcasting in 1975 and 1976, covering more than 2600 villages in six states of India and territories. Over the years India built communication satellites indigenously to meet the communication requirements of India. This has further lead to launch of an exclusive satellite from ISRO for educational purposes i.e. EDUSAT in 2004 through which rich audio-video content is transmitted / received, recreating virtual classes through interactivity. Indian Institute of Remote Sensing (IIRS established in 1966, a premier institute in south East Asia in disseminating Remote Sensing (RS and Geographical Information System (GIS, mainly focusing on contact based programs. But expanded the scope with satellite based Distance Learning Programs for Universities, utilizing the dedicated communication satellite i.e. EDUSAT in 2007. IIRS conducted successfully eight Distance Learning Programs in the last five years and training more than 6000 students mainly at postgraduate level from more than 60 universities /Institutions spread across India. IIRS obtained feedback and improved the programs on the continuous basis. Expanded the scope of IIRS outreach program to train user departments tailor made in any of the applications of Remote Sensing and

Metagenomic and satellite analyses of red snow in the Russian Arctic

Directory of Open Access Journals (Sweden)

Nao Hisakawa

2015-12-01

Full Text Available Cryophilic algae thrive in liquid water within snow and ice in alpine and polar regions worldwide. Blooms of these algae lower albedo (reflection of sunlight, thereby altering melting patterns (Kohshima, Seko & Yoshimura, 1993; Lutz et al., 2014; Thomas & Duval, 1995. Here metagenomic DNA analysis and satellite imaging were used to investigate red snow in Franz Josef Land in the Russian Arctic. Franz Josef Land red snow metagenomes confirmed that the communities are composed of the autotroph Chlamydomonas nivalis that is supporting a complex viral and heterotrophic bacterial community. Comparisons with white snow communities from other sites suggest that white snow and ice are initially colonized by fungal-dominated communities and then succeeded by the more complex C. nivalis-heterotroph red snow. Satellite image analysis showed that red snow covers up to 80% of the surface of snow and ice fields in Franz Josef Land and globally. Together these results show that C. nivalis supports a local food web that is on the rise as temperatures warm, with potential widespread impacts on alpine and polar environments worldwide.

The Future of Satellite Communications Technology.

Science.gov (United States)

Nowland, Wayne

1985-01-01

Discusses technical advances in satellite technology since the 1960s, and the International Telecommunications Satellite Organization's role in these developments; describes how AUSSAT, Australia's domestic satellite system, exemplifies the latest developments in satellite technology; and reviews satellite system features, possible future…

Detection of urea-induced internal denaturation of dsDNA using solid-state nanopores.

Science.gov (United States)

Singer, Alon; Kuhn, Heiko; Frank-Kamenetskii, Maxim; Meller, Amit

2010-11-17

The ability to detect and measure dsDNA thermal fluctuations is of immense importance in understanding the underlying mechanisms responsible for transcription and replication regulation. We describe here the ability of solid-state nanopores to detect sub-nanometer changes in DNA structure as a result of chemically enhanced thermal fluctuations. In this study, we investigate the subtle changes in the mean effective diameter of a dsDNA molecule with 3-5 nm solid-state nanopores as a function of urea concentration and the DNA's AT content. Our studies reveal an increase in the mean effective diameter of a DNA molecule of approximately 0.6 nm at 8.7 M urea. In agreement with the mechanism of DNA local denaturation, we observe a sigmoid dependence of these effects on urea concentration. We find that the translocation times in urea are markedly slower than would be expected if the dynamics were governed primarily by viscous effects. Furthermore, we find that the sensitivity of the nanopore is sufficient to statistically differentiate between DNA molecules of nearly identical lengths differing only in sequence and AT content when placed in 3.5 M urea. Our results demonstrate that nanopores can detect subtle structural changes and are thus a valuable tool for detecting differences in biomolecules' environment.

Detection of urea-induced internal denaturation of dsDNA using solid-state nanopores

International Nuclear Information System (INIS)

Singer, Alon; Kuhn, Heiko; Frank-Kamenetskii, Maxim; Meller, Amit

2010-01-01

The ability to detect and measure dsDNA thermal fluctuations is of immense importance in understanding the underlying mechanisms responsible for transcription and replication regulation. We describe here the ability of solid-state nanopores to detect sub-nanometer changes in DNA structure as a result of chemically enhanced thermal fluctuations. In this study, we investigate the subtle changes in the mean effective diameter of a dsDNA molecule with 3-5 nm solid-state nanopores as a function of urea concentration and the DNA's AT content. Our studies reveal an increase in the mean effective diameter of a DNA molecule of approximately 0.6 nm at 8.7 M urea. In agreement with the mechanism of DNA local denaturation, we observe a sigmoid dependence of these effects on urea concentration. We find that the translocation times in urea are markedly slower than would be expected if the dynamics were governed primarily by viscous effects. Furthermore, we find that the sensitivity of the nanopore is sufficient to statistically differentiate between DNA molecules of nearly identical lengths differing only in sequence and AT content when placed in 3.5 M urea. Our results demonstrate that nanopores can detect subtle structural changes and are thus a valuable tool for detecting differences in biomolecules' environment.

On the way to identify microorganisms in drinking water distribution networks via DNA analysis of the gut content of freshwater isopods.

Science.gov (United States)

Mayer, Michael; Keller, Adrian; Szewzyk, Ulrich; Warnecke, Hans-Joachim

2015-05-10

Pure drinking water is the basis for a healthy society. In Germany the drinking water regulations demand for analysis of water via detection of certain microbiological parameters by cultivation only. However, not all prokaryotes can be detected by these standard methods. How to gain more and better information about the bacteria present in drinking water and its distribution systems? The biofilms in drinking water distribution systems are built by bacteria and therefore represent a valuable source of information about the species present. Unfortunately, these biofilms are badly accessible. We thus exploited the circumstance that a lot of metazoans graze the biofilms, so that the content of their guts partly reflects the respective biofilm biocenosis. Therefore, we collected omnivorous isopods, prepared their guts and examined and characterized their contents based on 16S und 18S rDNA analysis. These molecularbiological investigations provide a profound basis for the characterization of the biocenosis and thereby biologically assess the drinking water ecosystems. Combined with a thorough identification of the species and the knowledge of their habitats, this approach can provide useful indications for the assessment of drinking-water quality and the early detection of problems in the distribution system. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Automatic analysis of flow cytometric DNA histograms from irradiated mouse male germ cells

International Nuclear Information System (INIS)

Lampariello, F.; Mauro, F.; Uccelli, R.; Spano, M.

1989-01-01

An automatic procedure for recovering the DNA content distribution of mouse irradiated testis cells from flow cytometric histograms is presented. First, a suitable mathematical model is developed, to represent the pattern of DNA content and fluorescence distribution in the sample. Then a parameter estimation procedure, based on the maximum likelihood approach, is constructed by means of an optimization technique. This procedure has been applied to a set of DNA histograms relative to different doses of 0.4-MeV neutrons and to different time intervals after irradiation. In each case, a good agreement between the measured histograms and the corresponding fits has been obtained. The results indicate that the proposed method for the quantitative analysis of germ cell DNA histograms can be usefully applied to the study of the cytotoxic and mutagenic action of agents of toxicological interest such as ionizing radiations.18 references

Bacterial DNA in water and dialysate: detection and significance for patient outcomes.

Science.gov (United States)

Handelman, Garry J; Megdal, Peter A; Handelman, Samuel K

2009-01-01

The fluid used for hemodialysis may contain DNA fragments from bacteria, which could be harmful for patient outcomes. DNA fragments from bacteria, containing the nonmethylated CpG motif, can trigger inflammation through the monocyte and lymphocyte Toll-like receptor 9, and these DNA fragments have been observed in dialysate. The fragments may transfer across the dialyzer into the patient's bloodstream during hemodialysis treatment. During hemodiafiltration, the fragments would be introduced directly into the bloodstream. The DNA fragments may arise from biofilm in the pipes of the water system, from growth of bacteria in the water, or as contaminants in the bicarbonate and salt mixture used for preparation of dialysate. Current filtration methods, such as Diasafe filters, are not able to remove these fragments. It would be prudent to seek to reduce or eliminate these contaminants. However, the cost and effort of decreasing bacterial DNA content may ultimately require substantial facility improvements; we therefore need to fund research studies to determine if modifications to reduce bacterial DNA content are clinically warranted. This research will require methods to accurately determine the species of bacteria that contribute the DNA, since this information will allow the source to be established as biofilm, bicarbonate mixtures, or other problems in the dialysis system such as bacterial growth or leakage during water preparation. In this review, the evidence for bacterial DNA fragments will be examined and suggestions for further studies will be described.

Satellite Communications for ATM

Science.gov (United States)

Shamma, Mohammed A.

2003-01-01

This presentation is an overview on Satellite Communication for the Aeronautical Telecommunication Management (ATM) research. Satellite Communications are being considered by the FAA and NASA as a possible alternative to the present and future ground systems supporting Air Traffic Communications. The international Civil Aviation Organization (ICAO) have in place Standards and Recommended Practices (SARPS) for the Aeronautical Mobile Satellite Services (AMSS) which is mainly derived from the pre-existing Inmarsat service that has been in service since the 1980s. The Working Group A of the Aeronautical Mobile Communication Panel of ICAO has also been investigating SARPS for what is called the Next Generation Satellite Service (NGSS) which conforms less to the Inmarsat based architecture and explores wider options in terms of satellite architectures. Several designs are being proposed by Firms such as Boeing, ESA, NASA that are geared toward full or secondary usage of satellite communications for ATM. Satellite communications for ATM can serve several purposes ranging from primary usage where ground services would play a minimal backup role, to an integrated solution where it will be used to cover services, or areas that are less likely to be supported by the proposed and existing ground infrastructure. Such Integrated roles can include usage of satellite communications for oceanic and remote land areas for example. It also can include relieving the capacity of the ground network by providing broadcast based services of Traffic Information Services messages (TIS-B), or Flight Information Services (FIS-B) which can take a significant portion of the ground system capacity. Additionally, satellite communication can play a backup role to support any needs for ground replacement, or additional needed capacity even after the new digital systems are in place. The additional bandwidth that can be provided via satellite communications can also open the door for many new

Genome-Wide Prediction of DNA Methylation Using DNA Composition and Sequence Complexity in Human.

Science.gov (United States)

Wu, Chengchao; Yao, Shixin; Li, Xinghao; Chen, Chujia; Hu, Xuehai

2017-02-16

DNA methylation plays a significant role in transcriptional regulation by repressing activity. Change of the DNA methylation level is an important factor affecting the expression of target genes and downstream phenotypes. Because current experimental technologies can only assay a small proportion of CpG sites in the human genome, it is urgent to develop reliable computational models for predicting genome-wide DNA methylation. Here, we proposed a novel algorithm that accurately extracted sequence complexity features (seven features) and developed a support-vector-machine-based prediction model with integration of the reported DNA composition features (trinucleotide frequency and GC content, 65 features) by utilizing the methylation profiles of embryonic stem cells in human. The prediction results from 22 human chromosomes with size-varied windows showed that the 600-bp window achieved the best average accuracy of 94.7%. Moreover, comparisons with two existing methods further showed the superiority of our model, and cross-species predictions on mouse data also demonstrated that our model has certain generalization ability. Finally, a statistical test of the experimental data and the predicted data on functional regions annotated by ChromHMM found that six out of 10 regions were consistent, which implies reliable prediction of unassayed CpG sites. Accordingly, we believe that our novel model will be useful and reliable in predicting DNA methylation.

The histone H3K9 methylation and RNAi pathways regulate normalnucleolar and repeated DNA organization by inhibiting formation ofextrachromosomal DNAs

Energy Technology Data Exchange (ETDEWEB)

Peng, Jamy C.; Karpen, Gary H.

2006-06-15

In order to identify regulators of nuclear organization, Drosophila mutants in the Su(var)3-9 histone H3K9 methyltransferase, RNAi pathway components, and other regulators of heterochromatin-mediated gene silencing were examined for altered nucleoli and positioning of repeated DNAs. Animals lacking components of the H3K9 methylation and RNAi pathways contained disorganized nucleoli, ribosomal DNA (rDNA) and satellite DNAs. The levels of H3K9 dimethylation (H3K9me2) in chromatin associated with repeated DNAs decreased dramatically in Su(var)3-9 and dcr-2 (dicer-2) mutant tissues compared to wild type. We also observed a substantial increase in extrachromosomal repeated DNAs in mutant tissues. The disorganized nucleolus phenotype depends on the presence of Ligase 4 (Lig4), and ecc DNA formation is not induced by removal of cohesin. We conclude that H3K9 methylation of rDNA and satellites, maintained by Su(var)3-9, HP1, and the RNAi pathway, is necessary for the structural stability of repeated DNAs, which is mediated through suppression of non-homologous end joining (NHEJ). These results suggest a mechanism for how local chromatin structure can regulate genome stability, and the organization of chromosomal elements and nuclear organelles.

Satellite-enabled educational services specification and requirements analysis based on user feedback

OpenAIRE

Tsekeridou, Sofia; Tiropanis, Thanassis; Rorris, Dimitris; Constantinos, Makropoulos; Serif, Tacha; Stergioulas, Lampros

2008-01-01

Advanced tele-education services provision in remote geographically dispersed user communities (such as agriculture and maritime), based on the specific needs and requirements of such communities, implies significant infrastructural and broadband connectivity requirements for rich media, timely and quality-assured content delivery and interactivity. The solution to broadband access anywhere is provided by satellite-enabled communication infrastructures. This paper aims to present such satelli...

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

Full Service ISDN Satellite (FSIS) network model for advanced ISDN satellite design and experiments

Science.gov (United States)

Pepin, Gerard R.

1992-01-01

The Full Service Integrated Services Digital Network (FSIS) network model for advanced satellite designs describes a model suitable for discrete event simulations. A top down model design uses the Advanced Communications Technology Satellite (ACTS) as its basis. The ACTS and the Interim Service ISDN Satellite (ISIS) perform ISDN protocol analyses and switching decisions in the terrestrial domain, whereas FSIS makes all its analyses and decisions on-board the ISDN satellite.

Flow-injection chemiluminescence assay for ultra-trace determination of DNA using rhodamine B-Ce(IV)-DNA ternary system in sulfuric acid media

International Nuclear Information System (INIS)

Ma Yongjun; Zhou Min; Jin Xiaoyong; Zhang Ziyu; Teng Xiulan; Chen Hui

2004-01-01

A novel flow-injection chemiluminescence method for the determination of DNA at ultra-trace level has been established. In 0.8 M sulfuric acid media, the chemiluminescence of the rhodamine B-cerium (IV) or Ce(IV) system is enhanced by DNA, activated previously by imidazole-HCl buffer solution (pH 7.0). The enhanced intensity of chemiluminescence is in proportion to log DNA concentration 1.0x10 -8 to 0.1 μg ml -1 for herring sperm DNA and 2.0x10 -6 to 0.2 μg ml -1 for calf thymus DNA with 3σ detection limits of 8.3x10 -9 μg ml -1 for herring sperm DNA and 3.5x10 -7 μg ml -1 for calf thymus DNA, respectively. The relative standard deviation for 1.0x10 -4 μg ml -1 herring sperm DNA was 0.99% and 2.0x10 -3 μg ml -1 for calf thymus DNA was 1.1% (n=11). Using the optimized system, DNA contents in six synthetic samples has been determined with recoveries of 99.5-109.0%. The possible mechanism has also been studied in this paper

Flow-injection chemiluminescence assay for ultra-trace determination of DNA using rhodamine B-Ce(IV)-DNA ternary system in sulfuric acid media

Energy Technology Data Exchange (ETDEWEB)

Ma Yongjun; Zhou Min; Jin Xiaoyong; Zhang Ziyu; Teng Xiulan; Chen Hui

2004-01-09

A novel flow-injection chemiluminescence method for the determination of DNA at ultra-trace level has been established. In 0.8 M sulfuric acid media, the chemiluminescence of the rhodamine B-cerium (IV) or Ce(IV) system is enhanced by DNA, activated previously by imidazole-HCl buffer solution (pH 7.0). The enhanced intensity of chemiluminescence is in proportion to log DNA concentration 1.0x10{sup -8} to 0.1 {mu}g ml{sup -1} for herring sperm DNA and 2.0x10{sup -6} to 0.2 {mu}g ml{sup -1} for calf thymus DNA with 3{sigma} detection limits of 8.3x10{sup -9} {mu}g ml{sup -1} for herring sperm DNA and 3.5x10{sup -7} {mu}g ml{sup -1} for calf thymus DNA, respectively. The relative standard deviation for 1.0x10{sup -4} {mu}g ml{sup -1} herring sperm DNA was 0.99% and 2.0x10{sup -3} {mu}g ml{sup -1} for calf thymus DNA was 1.1% (n=11). Using the optimized system, DNA contents in six synthetic samples has been determined with recoveries of 99.5-109.0%. The possible mechanism has also been studied in this paper.

Genome organization and DNA methylation patterns of B chromosomes in the red fox and Chinese raccoon dogs.

Science.gov (United States)

Bugno-Poniewierska, Monika; Solek, Przemysław; Wronski, Mariusz; Potocki, Leszek; Jezewska-Witkowska, Grażyna; Wnuk, Maciej

2014-12-01

The molecular structure of B chromosomes (Bs) is relatively well studied. Previous research demonstrates that Bs of various species usually contain two types of repetitive DNA sequences, satellite DNA and ribosomal DNA, but Bs also contain genes encoding histone proteins and many others. However, many questions remain regarding the origin and function of these chromosomes. Here, we focused on the comparative cytogenetic characteristics of the red fox and Chinese raccoon dog B chromosomes with particular attention to the distribution of repetitive DNA sequences and their methylation status. We confirmed that the small Bs of the red fox show a typical fluorescent telomeric distal signal, whereas medium-sized Bs of the Chinese raccoon dog were characterized by clusters of telomeric sequences along their length. We also found different DNA methylation patterns for the B chromosomes of both species. Therefore, we concluded that DNA methylation may maintain the transcriptional inactivation of DNA sequences localized to B chromosomes and may prevent genetic unbalancing and several negative phenotypic effects. © 2014 The Authors.