**6. References**


<sup>\*</sup> Corresponding Author

[13] Letunic I, Doerks T and Bork P (2009). SMART 6: recent updates and new developments. Nucleic Acid Research. vol. 37, pp. 229-232.

Investigation on Nuclear Transport of *Trypanosoma brucei*: An *in silico* Approach 53

[27] Damelin M, S. P. (2000). Mapping interactions between nuclear transport factors in living cells reveals pathways through the nuclear pore complex. Mol Cell., 5(1), 133-

[28] Télles S, Abate T and Slezynger T C (1999). *Trypanosoma cruz*i and human ubiquitin are immunologically distinct proteins despite only three amino acid difference in their

[29] Bischoff F R, Krebber H, Smirnova E, Dong W H, and Ponstingl H. (1995). Coactivation of RanGTPase and inhibition of GTP dissociation by Ran GTP binding protein RanBP1.

[30] Bischoff F R and Görlich D. (1997). RanBP1 is crucial for the release of RanGTP from importin β -related nuclear transport factors. FEBS Lett, vol. 419, pp. 249–254. [31] Floer M, Blobel G and M. Rexach M (1997). Disassembly of RanGTP–karyopherin β complex, an intermediate in nuclear protein import. J Biol Chem, vol. 272, pp. 19538–

[32] Lounsbury K M and Macara I G (1997). Ran-binding protein 1 (RanBP1) forms a ternary complex with Ran and karyopherin β and reduces Ran GTPase-activating protein (RanGAP) inhibition by karyopherin β. J Biol Chem, vol. 272, pp. 551–

[33] Yokoyama N (1995). A giant nucleopore protein that binds Ran/TC4. Nature, vol. 376,

[34] Mahajan R, Delphin C, Guan T, Gerace L and Melchior F (1997). A small ubiquitinrelated polypeptide involved in targeting RanGAP1 to nuclear pore complex protein

[35] Matunis M J, Coutavas E, and Blobel G (1996). A novel ubiquitin-like modification modulates the partitioning of the Ran-GTPase-activating protein RanGAP1 between the

[36] Englmeier L, Olivo J C and Mattaj I W (1999). Receptor-mediated substrate translocation through the nuclear pore complex without nucleotide triphosphate hydrolysis. Curr

[37] Kose S, Imamoto N, Tachibana T, Shimamoto T, and Yoneda Y (1997). Ran-unassisted nuclear migration of a 97 kD component of nuclear pore- targeting complex. J Cell Biol,

[38] Ribbeck K, Kutay U, Paraskeva E and Görlich D (1999). The translocation of transportin–cargo complexes through nuclear pores is independent of both Ran and

[39] Weis K, Dingwall C, and Lamond A I (1996). Characterization of the nuclear protein import mechanism using Ran mutants with altered nucleotide binding specificities.

[40] Kodiha M, Banski P and Stochaj U (2009). Interplay between MEK and PI3 kinase signaling regulates the subcellular localization of protein kinases ERK1/2 and Akt upon

cytosol and the nuclear pore complex. J Cell Biol, vol. 135, pp. 1457–1470.

primary sequence. FEMS Immunol Med Microbio, 24(2), 123-30.

40.

19546.

555.

pp. 184–188.

EMBO J, vol. 14, pp. 705–715.

RanBP2. Cell, vol. 88, pp. 97–107.

energy. Curr Biol, vol. 9, pp. 47–50.

EMBO J, vol. 15, pp. 7120–7128.

oxidative stress. FEBS Lett, 583:1987-93.

Biol, vol. 9, pp. 30–41.

vol. 139, pp. 841–849.


[27] Damelin M, S. P. (2000). Mapping interactions between nuclear transport factors in living cells reveals pathways through the nuclear pore complex. Mol Cell., 5(1), 133- 40.

52 Bioinformatics

37, pp. 211-215.

227-230.

7 pp 412-416.

284.

570–594.

1538.

Biophysics, 367(1), 51-60.

Opin. Chem. Biol. vol. 2, pp. 529-534.

[13] Letunic I, Doerks T and Bork P (2009). SMART 6: recent updates and new

[14] Hunter S, Apweiler R, Attwood T K, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn R D, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, J. McDowall, Mistry J, Mitchell J A, Mulder N, Natale D, Orengo C, Quinn A F, Selengut J D, Sigrist C J, Thimma M, Thomas P D, Valentin F, Wilson D, Wu C H, and Yeats C (2009). InterPro: the integrative protein signature database. Nucleic Acids Research, vol.

[15] Hulo N, Bairoch A, Bulliard V, Cerutti L, De Castro E, Langendijk-Genevaux D S, Pagni M, and Sigrist C J A (2006). The PROSITE database. Nucleic Acid Research, vol. 34, pp.

[16] Jensen L J, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, and Von Mering C (2009). STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acid Research. Vol.

[17] Schmid M (1998). Novel approaches to the discovery of antimicrobial agents. Curr.

[18] Frankel M B and Knoll L J (2009). The Ins and Outs of Nuclear Trafficking: Unusual Aspects in Apicomplexan Parasites. DNA and Cell Biology vol. 28, pp. 277-

[19] Macara, I G (2001). Transport into and out of the nucleus. Microbiol Mol Biol Rev 65,

[21] Nett I R E, D. Martin D M A, Miranda-Saavedra D, Lamont D, Barber J D, and Mahlert A (2009). The phosphoproteome of bloodstream form *Trypanosoma brucei*, causative agent of African sleeping sickness. Molecular & Cellular Proteomics, vol. 8 pp. 1527-

[22] Miller, M. W., Caracciolo, M. R., Berlin, W. K., and Hanover, J. A. (1999). Phosphorylation and Glycosylation of Nucleoporins. Archives of Biochemistry and

[23] Gasiorowski, J. Z. and Dean, D. A. (2003). Mechanisms of nuclear transport and

[24] Schuldt, A. (2012). Post-translational modification: A monoubiquitylation pore anchor.

[25] Radu A, Blobel G and Moore M S (1995). Identification of a protein complex that is required for nuclear protein import and mediates docking of import substrate to

[26] Gasiorowski, J. Z. and Dean, D. A. (2003). Mechanisms of nuclear transport and

[20] Babior B M (1999). NADPH oxidase: an update. Blood 93 (5): 1464–76.

interventions. Advanced Drug Delivery Reviews, 55, 703-716.

distinct nucleoporins, Proc. Natl. Acad. Sci. USA 92: 1769– 1773.

interventions. Advanced Drug Delivery Reviews, 55, 703-716.

Nature Reviews Molecular Cell Biology, 13, 66.

developments. Nucleic Acid Research. vol. 37, pp. 229-232.


[41] Kodiha, M., Crampton, N., Shrivastava, S., Umar, R., and Stochaj, U. (2010). Traffic control at the nuclear pore. Aging, 237-244.

**Chapter 3** 

© 2012 García-Vallejo and Domínguez, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is

© 2012 García-Vallejo and Domínguez, licensee InTech. This is a paper distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use,

**Systemic Approach to the Genome Integration** 

The human genome is one of the most complex molecular structures ever seen in nature. Its extraordinary information content has revealed a surprising mosaicims between coding and non-coding sequences [1-4]. This highly regionalized structure introduces complex patterns for understanding the gene structure and repetitive DNA sequence composition providing a new scenario to study biological process such as Lentivirus cDNA integration into host genome. In the field of genome analysis, bioinformatics provides the key connection between all different forms of data gathered by new high-throughput techniques such as systematic sequencing, expression arrays, and high throughput screenings among others. Although the success of bioinformatics in the genome analysis is undeniable, in some cases has complicated the relationship of computation with experimental biology. There is a need to attend to our pressing needs of bioinformatics applications without forgetting other,

perhaps less evident but equally important, aspects of computation in biology.

biological complexity, including the simulation of molecular interaction networks.

The study of particular systems is the source of inspiration that guides the formation of general ideas from specific cases to general principles. Therefore the systemic approach extends towards the study of fundamental biological questions, such as gene assembly, protein folding and the nature of functional specificity. Such issues extend beyond the current perception of bioinformatics as a support discipline and address aspects of

The genome coding regions are defined, in part, by an alternative series of motifs responsible for a variety of functions that take place on the DNA and RNA sequences, such as, gene regulation, RNA transcription, RNA splicing, and DNA methylation. For example,

distribution, and reproduction in any medium, provided the original work is properly cited.

**Process of Human Lentivirus** 

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/52885

**1. Introduction** 

Felipe García-Vallejo and Martha Cecilia Domínguez

properly cited.

**2. An overview to human genome** 

[42] Czubryt M P, Austria J A and Pierce G N (2000). Hydrogen peroxide inhibition of nuclear protein import is mediated by the mitogen-activated protein kinase, ERK2. J Cell Biol, 148:7-16.
