Genome

Development and characterization of novel SSR markers in Siniperca kneri Garman

M. Yang, Zheng, H. Z., Liang, X. - F., Tian, C. X., Dou, Y. Q., Zhu, K. C., and Yuan, Y. C., Development and characterization of novel SSR markers in Siniperca kneri Garman, vol. 13, pp. 7593-7606, 2014.

In this study, 37 transcriptome-derived simple sequence repeat (SSR) markers and 18 genomic SSR markers were developed and characterized in the Chinese perch, Siniperca kneri Garman. The average allele number per locus was 5.1 (range: 2-8) for transcriptome-derived SSRs and 3.8 (range: 2-5) for genomic SSRs. The average observed and expected heterozygosities were 0.666 (range: 0.000-1.000) and 0.692 (range: 0.230-0.857) for transcriptome-derived SSRs, respectively. These values were 0.380 (range: 0.000-1.000) and 0.527 (range: 0.201-0.799) for genomic SSRs, respectively.

Optimization of dengue virus genome assembling using GSFLX 454 pyrosequencing data: evaluation of assembling strategies

S. M. M. Casseb, Cardoso, J. F., Ramos, R., Carneiro, A., Nunes, M., Vasconcelos, P. F. C., and Silva, A., Optimization of dengue virus genome assembling using GSFLX 454 pyrosequencing data: evaluation of assembling strategies, vol. 11, pp. 3688-3695, 2012.

Currently assembling genomes without reference is one of the most important challenges for bioinformaticists all over the world in an attempt to characterize new organisms. The current study has used two dengue virus type 4 (DENV-4) strains recently isolated in Brazil, which have its genomes sequenced using the GSFLX 454 sequencer (Roche, Life Science) by the pyrosequencing method. The GSFLX 454 data were used for testing different genome assembling strategies.

Survey of simple sequence repeats in woodland strawberry (Fragaria vesca)

L. Guan, Huang, J. F., Feng, G. Q., Wang, X. W., Wang, Y., Chen, B. Y., and Qiao, Y. S., Survey of simple sequence repeats in woodland strawberry (Fragaria vesca), vol. 12, pp. 2637-2651, 2013.

The use of simple sequence repeats (SSRs), or microsatellites, as genetic markers has become popular due to their abundance and variation in length among individuals. In this study, we investigated linkage groups (LGs) in the woodland strawberry (Fragaria vesca) and demonstrated variation in the abundances, densities, and relative densities of mononucleotide, dinucleotide, and trinucleotide repeats. Mononucleotide, dinucleotide, and trinucleotide repeats were more common than longer repeats in all LGs examined.

Single nucleotide polymorphisms in CAPN and leptin genes associated with meat color and tenderness in Nellore cattle

L. F. B. Pinto, Ferraz, J. B. S., Pedrosa, V. B., Eler, J. P., Meirelles, F. V., Bonin, M. N., Rezende, F. M., Carvalho, M. E., Cucco, D. C., and Silva, R. C. G., Single nucleotide polymorphisms in CAPN and leptin genes associated with meat color and tenderness in Nellore cattle, vol. 10, pp. 2057-2064, 2011.

We analyzed single nucleotide polymorphisms in calpain, leptin, leptin receptor, and growth hormone receptor genes and their association with color, drip and cooking losses of longissimus muscle at 7, 14 and 21 days postmortem in 638 purebred Nellore bulls slaughtered between 22 and 26 months of age. Meat samples were vacuum-packed and aged at 4°C. The single nucleotide polymorphisms T945M, GHR2, E2FB, and CAPN4751 were evaluated. All genotypic classes were observed; however, the T/T genotype of T945M and E2FB was found at a low frequency.

Report of a chimeric origin of transposable elements in a bovine-coding gene

L. M. Almeida, Amaral, M. E. J., Silva, I. T., Silva, Jr., W. A., Riggs, P. K., and Carareto, C. M., Report of a chimeric origin of transposable elements in a bovine-coding gene, vol. 7, pp. 107-116, 2008.

Despite the wide distribution of transposable elements (TEs) in mammalian genomes, part of their evolutionary significance remains to be discovered. Today there is a substantial amount of evidence showing that TEs are involved in the generation of new exons in different species. In the present study, we searched 22,805 genes and reported the occurrence of TE-cassettes in coding sequences of 542 cow genes using the RepeatMasker program.

Molecular characterization of wheat germplasm using microsatellite markers

S. Ijaz and Khan, I. A., Molecular characterization of wheat germplasm using microsatellite markers, vol. 8, pp. 809-815, 2009.

We investigated the genetic diversity of 63 wheat genotypes, composed of 48 accessions and 15 varieties, using 56 polymorphic simple sequence repeat primers. One hundred and eighty-six loci were found, with a mean of 131.26 alleles per locus. Cluster analysis based on microsatellite allelic diversity discrimi­nated the accessions and varieties into different clusters; genetic di­versity was the highest between variety Kohistan-97 and accession number 011512, giving a genetic similarity value of 0.4198.

Coordinated, network-based research as a strategic component of science in Brazil

A. J. G. Simpson, Camargo, A. A., Ferro, J. Aparecido, Parra, J., and Vasconcelos, A. Tereza, Coordinated, network-based research as a strategic component of science in Brazil, vol. 3, pp. 18-25, 2004.

Scientific research plays a fundamental role in the health and development of any society, since all technological advances depend ultimately on scientific discovery and the generation of wealth is intricately dependent on technological advance. Due to their importance, science and technology generally occupy important places in the hierarchical structure of developed societies, and they receive considerable public and private investment.

DNA repair in Chromobacterium violaceum

F. Teixeira Duarte, de Carvalho, F. Marques, Silva, U. Bezerra e, Scortecci, K. Castanho, Blaha, C. Alfredo Ga, Agnez-Lima, L. Fassarella, and de Medeiros, S. Regina Bat, DNA repair in Chromobacterium violaceum, vol. 3, pp. 167-180, 2004.

Chromobacterium violaceum is a Gram-negative β-proteobacterium that inhabits a variety of ecosystems in tropical and subtropical regions, including the water and banks of the Negro River in the Brazilian Amazon. This bacterium has been the subject of extensive study over the last three decades, due to its biotechnological properties, including the characteristic violacein pigment, which has antimicrobial and anti-tumoral activities. C.

Transport genes of Chromobacterium violaceum: an overview

T. Barbosa Grangeiro, Jorge, D. Macedo de, Bezerra, W. Melgaço, Vasconcelos, A. Tereza Rib, and Simpson, A. John Georg, Transport genes of Chromobacterium violaceum: an overview, vol. 3, pp. 117-133, 2004.

The complete genome sequence of the free-living bacterium Chromobacterium violaceum has been determined by a consortium of laboratories in Brazil. Almost 500 open reading frames (ORFs) coding for transport-related membrane proteins were identified in C. violaceum, which represents 11% of all genes found. The main class of transporter proteins is the primary active transporters (212 ORFs), followed by electrochemical potential-driven transporters (154 ORFs) and channels/pores (62 ORFs).

Chromobacterium violaceum genome: molecular mechanisms associated with pathogenicity

C. F. Alves de Brito, Carvalho, C. M. B., Santos, F. R., Gazzinelli, R. T., Oliveira, S. C., Azevedo, V., and Teixeira, S. M. R., Chromobacterium violaceum genome: molecular mechanisms associated with pathogenicity, vol. 3, pp. 148-161, 2004.

Chromobacterium violaceum is a versatile, Gram-negative β-protebacterium that grows in a variety of ecosystems in tropical and subtropical areas, such as the water and borders of the Negro River, in the Amazon region of Brazil. Although it is a saprophyte and is generally considered non-pathogenic, sporadic cases of human infection have been described, mainly in young children and in immunodeficient individuals. Although rare, infections with C. violaceum are characterized by rapid dissemination and high mortality. With the complete genome sequence of C.

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