Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedaries

PLoS ONE

Volumn 5, Issue 5, 2010, Pages

  Al Swailem, Abdulaziz M ^a   Shehata, Maher M ^a   Abu Duhier, Faisel M ^a   Al Yamani, Essam J ^a   Al Busadah, Khalid A ^b   Al Arawi, Mohammed S ^a   Al Khider, Ali Y ^a   Al Muhaimeed, Abdullah N ^a   Al Qahtani, Fahad H ^a   Manee, Manee M ^a   Al Shomrani, Badr M ^a   Al Qhtani, Saad M ^a   Al Harthi, Amer S ^a   Akdemir, Kadir C ^c   Inan, Mehmet S ^a   Otu, Hasan H ^a,c  

^a KING ABDULAZIZ CITY FOR SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^b KING FAISAL UNIVERSITY   (Saudi Arabia)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

AGED; ANIMAL TISSUE; ARTICLE; CAMEL; CAMELUS DROMEDARIUS; CONTIG MAPPING; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; DNA LIBRARY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENETIC DATABASE; HUMAN VERSUS ANIMAL COMPARISON; NONHUMAN; ONLINE SYSTEM; OPEN READING FRAME; PROTEIN DATABASE; SEQUENCE HOMOLOGY; START CODON; WEB BROWSER; ANIMAL; CATTLE; CLUSTER ANALYSIS; GENE REGULATORY NETWORK; GENETICS; HUMAN; METHODOLOGY; MOUSE; NUCLEOTIDE SEQUENCE; RAT; SIGNAL TRANSDUCTION;

BOVINAE; CAMELUS DROMEDARIUS; RATTUS;

ANIMALS; BASE SEQUENCE; CATTLE; CLUSTER ANALYSIS; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE REGULATORY NETWORKS; HUMANS; MICE; OPEN READING FRAMES; RATS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SIGNAL TRANSDUCTION;

EID: 77956287507     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010720     Document Type: Article

References (50)

1. Al-Swailem AM, Al-Busadah KA, Shehata MM, Al-Anazi IO, Askari E (2007) Classification of Saudi Arabian camel (Camelus dromedarius) subtypes based on RAPD technique. Journal of Food, Agriculture & Environment 5: 143-148.
2. Emmanuel B, Nahapetian A (1980) Fatty acid composition of depot fats and rumen wall of the camel (Camelus dromedarius). Comparative Biochemistry Physiology Part B: Biochemistry and Molecular Biology 67: 701-704.
3. Duncan WRH, Garton GA (1967) The fatty acid composition and intermolecular structure of triglycerides derived from different sites in the body of the sheep. Journal of the Science of Food and Agriculture 18: 99-102.
4. Al-Ani FK (2004) Camel management and diseases. Amman, Jordan: Al-Shraq Printing Press & Dar Ammar Book Publishing.
5. Muyldermans S (2001) Single domain camel antibodies: current status. J Biotechnol 74: 277-302.
6. Holt LJ, Herring C, Jespers LS, Woolven BP, Tomlinson IM (2003) Domain antibodies: proteins for therapy. Trends Biotechnol 21: 484-490.
7. Tibary A, Anouassi A, Sghiri A, Khatir H (2007) Current knowledge and future challenges in camelid reproduction. Soc Reprod Fertil Suppl 64: 297-313.
8. Schmidt-Nielsen K (1979) Desert Animals, Physiological Problems of Heat and Water. New York: Dover Publications Inc.
9. Yagil R (1985) The Desert Camel: Comparative Physiological Adaptation (Comparative Animal Nutrition). Switzerland: S. Karger AG.
10. Elmahdi B, Sallmann HP, Fuhrmann H, von Engelhardt W, Kaske M (1997) Comparative aspects of glucose tolerance in camels, sheep, and ponies. Comp Biochem Physiol A Physiol 118: 147-151.
11. Abdel-Fattah M, Amer H, Ghoneim MA, Warda M, Megahed Y (1999) Response of one-humped camel (Camelus dromedarius) to intravenous glucagon injection and to infusion of glucose and volatile fatty acids, and the kinetics of glucagon disappearance from the blood. Zentralbl Veterinarmed A 46: 473-481.
12. Holler H, Breves G, Lechner-Doll M, Schulze E (1989) Concentrations of volatile fatty acids and acetate production rates in the forestomachs of grazing camels. Comp Biochem Physiol B 93: 413-416.
13. Shirazi-Beechy SP, Wood IS, Dyer J, Scott D, King TP () Ruminant Physiology: Digestion, Metabolism, Growth Physiology and Reproduction: Proceedings of the Eighth International Symposium on Ruminant Physiology; 1994.
14. Kaske M, Elmahdi B, von Engelhardt W, Sallmann HP (2001) Insulin responsiveness of sheep, ponies, miniature pigs and camels: results of hyperinsulinemic clamps using porcine insulin. J Comp Physiol B 171: 549-556.
15. Zierath JR, Krook A, Wallberg-Henriksson H (1998) Insulin action in skeletal muscle from patients with NIDDM. Mol Cell Biochem 182: 153-160.
16. Parkinson J, Blaxter M (2009) Expressed sequence tags: an overview. Methods Mol Biol 533: 1-12.
17. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
18. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.
19. Li S, Chou HH (2004) LUCY2: an interactive DNA sequence quality trimming and vector removal tool. Bioinformatics 20: 2865-2866.
20. Mao C, Cushman JC, May GD, Weller JW (2003) ESTAP-an automated system for the analysis of EST data. Bioinformatics 19: 1720-1722.
21. Edgar RC, Batzoglou S (2006) Multiple sequence alignment. Curr Opin Struct Biol 16: 368-373.
22. Smit AF (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 9: 657-663.
23. Malde K, Schneeberger K, Coward E, Jonassen I (2006) RBR: library-less repeat detection for ESTs. Bioinformatics 22: 2232-2236.
24. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, et al. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19: 651-652.
25. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
26. Strausberg RL, Feingold EA, Klausner RD, Collins FS (1999) The mammalian gene collection. Science 286: 455-457.
27. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
28. Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, et al. (2001) Functional annotation of a full-length mouse cDNA collection. Nature 409: 685-690.
29. Knight KL, Burnett RC, McNicholas JM (1985) Organization and polymorphism of rabbit immunoglobulin heavy chain genes. J Immunol 134: 1245-1250.
30. Knight KL, Suter M, Becker RS (1988) Genetic engineering of bovine Ig. Construction and characterization of hapten-binding bovine/murine chimeric IgE, IgA, IgG1, IgG2, and IgG3 molecules. J Immunol 140: 3654-3659.
31. Flanagan JG, Rabbitts TH (1982) Arrangement of human immunoglobulin heavy chain constant region genes implies evolutionary duplication of a segment containing gamma, epsilon and alpha genes. Nature 300: 709-713.
32. Shimizu A, Takahashi N, Yaoita Y, Honjo T (1982) Organization of the constant-region gene family of the mouse immunoglobulin heavy chain. Cell 28: 499-506.
33. Bruggemann M, Free J, Diamond A, Howard J, Cobbold S, et al. (1986) Immunoglobulin heavy chain locus of the rat: striking homology to mouse antibody genes. Proc Natl Acad Sci U S A 83: 6075-6079.
34. Butler JE, Brown WR (1994) The immunoglobulins and immunoglobulin genes of swine. Vet Immunol Immunopathol 43: 5-12.
35. Wagner B, Overesch G, Sheoran AS, Holmes MA, Richards C, et al. (1998) Organization of the equine immunoglobulin heavy chain constant region genes; III. Alignment of c mu, c gamma, c epsilon and c alpha genes. Immunobiology 199: 105-118.
36. Wagner B, Greiser-Wilke I, Wege AK, Radbruch A, Leibold W (2002) Evolution of the six horse IGHG genes and corresponding immunoglobulin gamma heavy chains. Immunogenetics 54: 353-364.
37. Rosati M, Marino M, Franze A, Tramontano A, Grimaldi G (1991) Members of the zinc finger protein gene family sharing a conserved N-terminal module. Nucleic Acids Res 19: 5661-5667.
38. Baghiani A, Harrison R, Benboubetra M (2003) Purification and partial characterisation of camel milk xanthine oxidoreductase. Arch Physiol Biochem 111: 407-414.
39. Bierhaus A, Wolf J, Andrassy M, Rohleder N, Humpert PM, et al. (2003) A mechanism converting psychosocial stress into mononuclear cell activation. Proc Natl Acad Sci U S A 100: 1920-1925.
40. Morita K, Saito T, Ohta M, Ohmori T, Kawai K, et al. (2005) Expression analysis of psychological stress-associated genes in peripheral blood leukocytes. Neurosci Lett 381: 57-62.
41. Dusek JA, Otu HH, Wohlhueter AL, Bhasin M, Zerbini LF, et al. (2008) Genomic counter-stress changes induced by the relaxation response. PLoS One 3: e2576.
42. Al-Hashem FH (2009) Camel's milk alleviates oxidative stress and lipid peroxidation induced by chronic aluminum chloride exposure in rat's testes. American Journal of Applied Sciences 6: 1868-1875.
43. Saleh MA, Al-Salahy MB, Sanousi SA (2009) Oxidative stress in blood of camels (Camelus dromedaries) naturally infected with Trypanosoma evansi. Vet Parasitol 162: 192-199.
44. Laity JH, Lee BM, Wright PE (2001) Zinc finger proteins: new insights into structural and functional diversity. Curr Opin Struct Biol 11: 39-46.
45. Morishita D, Katayama R, Sekimizu K, Tsuruo T, Fujita N (2008) Pim kinases promote cell cycle progression by phosphorylating and down-regulating p27Kip1 at the transcriptional and posttranscriptional levels. Cancer Res 68: 5076-5085.
46. Wen X, Duus KM, Friedrich TD, de Noronha CM (2007) The HIV1 protein Vpr acts to promote G2 cell cycle arrest by engaging a DDB1 and Cullin4Acontaining ubiquitin ligase complex using VprBP/DCAF1 as an adaptor. J Biol Chem 282: 27046-27057.
47. Terada Y, Inoshita S, Nakashima O, Tamamori M, Ito H, et al. (1999) Cell cycle inhibitors (p27Kip1 and p21CIP1) cause hypertrophy in LLC-PK1 cells. Kidney Int 56: 494-501.
48. Wolf G, Schroeder R, Zahner G, Stahl RA, Shankland SJ (2001) High glucoseinduced hypertrophy of mesangial cells requires p27(Kip1), an inhibitor of cyclin-dependent kinases. Am J Pathol 158: 1091-1100.
49. Nguyen T, Huang HC, Pickett CB (2000) Transcriptional regulation of the antioxidant response element. Activation by Nrf2 and repression by MafK. J Biol Chem 275: 15466-15473.
50. Kobayashi M, Yamamoto M (2005) Molecular mechanisms activating the Nrf2-Keap1 pathway of antioxidant gene regulation. Antioxid Redox Signal 7: 385-394.