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Dna genoma sequencer

Justin A Fincher, Daniel L Vera, Diana D Hughes, Karen M McGinnis, Jonathan H Dennis, Hank W Bass
The nucleosome is a fundamental structural and functional chromatin unit that affects nearly all DNA-templated events in eukaryotic genomes. It is also a biochemical substrate for higher order, cis-acting gene expression codes and the monomeric structural unit for chromatin packaging at multiple scales. To predict the nucleosome landscape of a model plant genome, we used a support vector machine computational algorithm trained on human chromatin to predict the nucleosome occupancy likelihood (NOL) across the maize (Zea mays) genome...
June 2013: Plant Physiology
Enrico Marchese, A Vignati, A Albanese, C G Nucci, G Sabatino, B Tirpakova, G Lofrese, G Zelano, G Maira
Few studies have evaluated the over or the underexpression of genes directly in samples of aneurysmal wall and extracranial pericranial vascular tissue to investigate the genetic influence in formation and rupture of intracranial aneurysms. We present the results obtained using the DNA microarray technique analysis on sample tissues collected during surgery. We collected and analyzed 12 aneurismal and 9 peripheral arteries (superficial temporal (STA) and middle meningeal artery (MMA) specimens from ruptured aneurysm group patients (13 cases), 10 aneurismal and 12 STA and MMA samples from unruptured aneurysm group patients (14 cases) and 5 STA and MMA artery specimens from control group patients (4 cases)...
April 2010: Journal of Biological Regulators and Homeostatic Agents
Mariano Latorre, Herman Silva, Juan Saba, Carito Guziolowski, Paula Vizoso, Veronica Martinez, Jonathan Maldonado, Andrea Morales, Rodrigo Caroca, Veronica Cambiazo, Reinaldo Campos-Vargas, Mauricio Gonzalez, Ariel Orellana, Julio Retamales, Lee A Meisel
BACKGROUND: Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. RESULTS: In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline...
2006: BMC Bioinformatics
Fernanda Sarquis Jehee, Luis G Alonso, Denise P Cavalcanti, Chong Kim, Steven A Wall, John B Mulliken, Miao Sun, Ethylin Wang Jabs, Simeon A Boyadjiev, Andrew O M Wilkie, Maria Rita Passos-Bueno
OBJECTIVE: Screen the known craniosynostotic related gene, FGFR1 (exon 7), and two new identified potential candidates, CER1 and CDON, in patients with syndromic and nonsyndromic metopic craniosynostosis to determine if they might be causative genes. DESIGN: Using single-strand conformational polymorphisms (SSCPs), denaturing high-performance liquid chromatography, and/or direct sequencing, we analyzed a total of 81 patients for FGFR1 (exon 7), 70 for CER1, and 44 for CDON...
March 2006: Cleft Palate-craniofacial Journal
Aurora Sánchez Sousa, Fernando Baquero, César Nombela
Both genetic and musical sequences are ordered structures composed of combinations of a small number of elements, of nucleotides and musical notes. In the case of the genome, the emergence of cellular functions makes the order meaningful; in the case of musical sequences, the consequence of order is the production of mysterious esthetical effects in the human mind. Can any musical significance be found in DNA sequence? In this work, we present the technique used to convert DNA sequences into musical sequences...
December 2005: Revista Iberoamericana de Micología
Fernán Agüero, Karim Ben Abdellah, Valeria Tekiel, Daniel O Sánchez, Antonio González
We have generated 2771 expressed sequence tags (ESTs) from two cDNA libraries of Trypanosoma cruzi CL-Brener. The libraries were constructed from trypomastigote and amastigotes, using a spliced leader primer to synthesize the cDNA second strand, thus selecting for full-length cDNAs. Since the libraries were not normalized nor pre-screened, we compared the representation of transcripts between the two using a statistical test and identify a subset of transcripts that show apparent differential representation...
August 2004: Molecular and Biochemical Parasitology
Andrés Moreira, Alejandro Maass
UNLABELLED: Several applications require the backtranslation of a protein sequence into a nucleic acid sequence. The degeneracy of the genetic code makes this process ambiguous; moreover, not every translation is equally viable. The usual answer is to mimic the codon usage of the target species; however, this does not capture all the relevant features of the 'genomic styles' from different taxa. The program TIP ' Traducción Inversa de Proteínas') applies genetic algorithms to improve the backtranslation, by minimizing the difference of some coding statistics with respect to their average value in the target...
September 1, 2004: Bioinformatics
Fernán Agüero, Vanina Campo, Laura Cremona, Adriana Jäger, Javier M Di Noia, Peter Overath, Daniel O Sánchez, Alberto Carlos Frasch
A total of 1,921 expressed sequence tags (ESTs) were obtained from bloodstream trypomastigotes of Trypanosoma carassii, a parasite of economic importance due to its high prevalence in fish farms. Analysis of the data set allowed us to identify a trans-sialidase (TS)-like gene and three ESTs coding for putative mucin-like genes. TS activity was detected in cell extracts of bloodstream trypomastigotes. We have also used the sequence information obtained to identify genes that have not been previously described in trypanosomatids...
December 2002: Infection and Immunity
R Boldorini, R Caldarelli-Stefano, G Monga, M Zocchi, M Mediati, A Tosoni, P Ferrante
Pleomorphic xanthoastrocytoma (PXA) is a rare cerebral tumor of young adults with a slow growth and a good prognosis. Due to its peculiar histopathological findings, the tumor resemble to the lytic phase of progressive multifocal leukoencephalopathy (PML), a JC Virus (JCV) induced disease. For these reasons, the presence of JCV genoma and viral particles were searched for by means of nested polymerase chain reaction (nPCR) and electron microscopy (EM) in a 9-year-old child with PXA. Although EM did not reveal any viral particles, nPCR did reveal genomic sequences of the LT, R, and VP1 regions of JCV...
April 1998: Journal of Neurovirology
M Jablonská
The etiological association between primary hepatocellular carcinoma (PHCC) and chronic viral hepatitis has been proved by now beyond doubt in the hepatitis B virus (HBV) and C virus (HCV). PHCC develops most frequently in cirrhotic livers, sometimes also in the absence of cirrhosis. Extensive epidemiological studies provided convincing evidence of this etiological relationship which is also supported by observations and animal experiments. An important factor in hepatocarcinogenesis due to the influence of HBV is integration of the viral genoma into the liver cell genoma...
October 22, 1997: Casopís Lékar̆ů C̆eských
T Castrignanò, A Colosimo, S Morante, V Parisi, G C Rossi
In this paper we present a general strategy designed to study the occurrence frequency distributions of oligonucleotides in DNA coding segments and to deal with the problem of detecting possible patterns of genomic compositional inhomogeneities and disuniformities. Identifying specific tendencies or peculiar deviations in the distributions of the effective occurrence frequencies of oligonucleotides, with respect to what can be a priori expected, is of the greatest importance in biology. Differences between expected and actual distributions may in fact suggest or confirm the existence of specific biological mechanisms related to them...
February 21, 1997: Journal of Theoretical Biology
A M Coelho
The new EEC Biomedical and Health Research Programme (BIOMED 1) is presented. After a brief introduction on the background of the Programme--in which an overview of the ongoing Medical and Health Research Programme (MHR 4) is given--the main features of the new Programme are pointed out. On what concerns its aims and objectives, concertation and coordination of national research programmes at community level are stressed as well as the need to apply to the maximum possible extent the principles of subsidiary and community added value, in order to ensure an European dimension to the actions which are going to be supported and to achieve the harmonization of research methodologies, procedures and data...
February 1992: Acta Médica Portuguesa
C Magistrelli, E Colombo, A Tognoni, G Grandi
In the ambit of the B. subtilis genoma sequencing and mapping project, we have set up an electroporation method to transfect E. coli cells with lambda DNA. This methodology presents features that make it preferable to traditional in vitro packaging for some purposes. Here we will illustrate the experimental procedure and the possible applications.
October 1992: Microbiologica
R J Owen, R M Legors, S P Lapage
The mean base compositions of DNA from 27 strains of Pseudomonas putrefaciens, P. rubescens and P. piscicida ranged from 43-4 to 53-2 mol% GC with genome sizes from 3.04 X 10(9) to 4.23 X 10(9) daltons. On the basis of in vitro DNA-DNA binding, estimated spectrophotometrically from initial renaturation rates, P. putrefaciens strains were heterogenous in the extent to which they shared similar nucleotide sequences, and were divided into four DNA homology groups. The DNA characteristics of strains in these groups correlated with several biochemical characteristics that facilitated identification of clinical isolates of P...
January 1978: Journal of General Microbiology
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