A Genetic Algorithm on Multiple Sequences Alignment Problems in Biology

The study and comparison of sequences of characters from a finite alphabet is relevant to various areas of science, notably molecular biology. The measurement of sequence similarity involves the consideration of the possible sequence alignments in order to find an optimal one for which the “distance” between sequences is minimum. In biology informatics area, it is a more important and difficult problem due to the long length (100 at least) of sequence, this cause the compute complexity and large memory require. By associating a path in a lattice to each alignment, a geometric insight can be brought into the problem of finding an optimal alignment, this give an obvious encoding of each path. This problem can be solved by applying genetic algorithm, which is more efficient than dynamic programming and hidden Markov model using commomly now.

Genetic Evolution Analysis on Wild Isolates of Citrus Tristeza Virus Originated in China Based on Coat Protein Genes Sequences

The coat protein （CP） genes were cloned and sequenced from viral particles of 11 isolates of citrus tristeza virus （CTV） collected from wild citrus plants in China and 4 Chinese isolates from cultivated sweet orange and pummelo varieties, respectively. By analyzing and comparing the nucleotide and amino acid sequences of CP genes, the 11 wild CTV isolates were found over 92% identical with 4 Chinese CTV isolates and 21 exotic CTV isolates from cultivated citrus. From 91 to 100% of the CTV CP gene sequences in wild type citrus plants were generally well conserved. Genetic evolution analysis indicated that the GC% of the CP gene was less than AT%, and more transition were found in the CP genes than transversion with the transition/transversion ratio ranging from 6.3 to 7.0 among species. The substitution frequency was the highest at the third codon, followed by the first and second codon. The ratio of non-synonymous mutations （du） to synonymous mutations （ds） was far lower than 1, suggesting that the CP gene might have experienced purifying selection in the evolution. Phylogenetic analysis revealed that the 11 CTV isolates in Chinese wild type citrus belonged to different phylogenetic clusters, and shared higher homology and closer relationships with other cultivated citrus CTV isolates from different countries, which indicated complicated genetic relationships among the CTV isolates. In addition, CTV isolates with similar biological characteristics usually located into the same clusters. Therefore, the conclusion was drawn that pathogenicity was critical to evolution and origin of CTV.

Nucleotide Sequence Assessment of Four ORFs of Citrus Tristeza Virus: Evidence of Recombination

Citrus Tristeza Virus(CTV),usually occurs in nature as a mixture of genotypes.Six naturally infected citrus(Citrus sinensis)trees grafted on sour orange rootstock were collected from three citrus growing governorates in Egypt(Sharqia,Qalyubia and Garbia).In this study,RT-PCR,Single-Strand Conformation Polymorphism(SSCP)and nucleotide sequence analysis were used for four independent CTV genomic regions(p65,p18,p20,and p23)to detect and assess the sequence and genetic variabilities among CTV Egyptian isolates.RTPCR products(650 bp)for the CTV p23 gene obtained from the selected isolates were used for the SSCP analysis and DNA sequencing.SSCP patterns of p23 gene for individual isolates yielded different complex haplotype patterns.Nucleotide sequence analysis of p23 region amplified from six isolates under study revealed that p23 shared high nucleotide identity 98.7%with T36 isolate from USA,Florida.Phylogenetic analysis of p23 gene indicated a close evolutionary relationship between all examined isolates and Qaha isolate(T36 isolate group),suggesting that they may have originated from closely related ancestors.Nucleotide sequence analysis of the three genes located on CTV 3′-coterminal overhang,p18,p20 and p65,amplified from isolate A3,Sharqia governorate,revealed that the p18,p65,and p20 genes were related to the T3-KB isolate from South Africa with 99%–100%sequence homology.Phylogenetic relationship analysis for p65,p18 and p20 ORFs clustered the current A3 isolate with T3 genotype group.The recombination analysis identified three of six isolates from Sharqia,and Garbia as potential recombinant for p23 gene.The isolates T36 and T3 were identified as major donors for recombination events in isolate A3.Our results concluded that p23 ORF likely to be as a hotspot region for recombination and originated through recombination event.The current study indicated that recombination is an important factor for the origin of CTV strains in Egypt.

Molecular Cloning and Characteristics of Catalase cDNA from Chinese Soft-shelled Turtle(Pelodiscus sinensis)

A catalase cDNA was cloned from the liver of the Chinese soft-shelled turtle （Pelodiscus sinensis） using reverse transcription-polymerase chain reaction （RT-PCR） with degenerate primers. Both 3＇-and 5＇-untranslated regions were isolated by the rapid amplification of cDNA ends method （RACE）. Analysis of nucleotide sequence revealed that the catalase cDNA clone consisted of 2173 bp with an open reading frame of 1587 bp encoding a protein of 528 amino acids. The calculated molecular mass of the mature protein is 59.8 kDa with an estimated pI of 6.84. The peroxisomal targeting signal SNL at the C-terminal and two putative N-glycosylation sites NLSV and NVSQ were found in the catalase. Sequence comparison showed that this catalase, deduced by the amino acid sequence, had high similarity and identity with those of vertebrates recorded in GenBank. Four functional domains and conserved amino acids responsible for binding heme and NAPDH including four essential residues were observed. The 3-D homology model of the turtle catalase was predicted by SwissModel based on the relative domains of bovine catalase structure （PDB ID： 3rgp）. The mRNA expression and enzyme activities in liver, brain, spleen, kidney, heart, gut, lung and muscle were investigated, and the results showed that the mRNA and enzyme activities of catalase in these tissues were species-specific.

General space-efficient sampling algorithm for suboptimal alignment

Suboptimal alignments always reveal additional interesting biological features and have been successfully used to informally estimate the significance of an optimal alignment. Besides, traditional dynamic programming algorithms for sequence comparison require quadratic space, and hence are infeasible for long protein or DNA sequences. In this paper, a space-efficient sampling algorithm for computing suboptimal alignments is described. The algorithm uses a general gap model, where the cost associated with gaps is given by an affine score, and randomly selects an alignment according to the distribution of weights of all potential alignments. If x and y are two sequences with lengths n and m, respectively, then the space requirement of this algorithm is linear to the sum of n and m. Finally, an example illustrates the utility of the algorithm.

CLONING AND COMPARISON OF THE GENES ENCODING PREPROAPAMIN FROM THE VENOM OF 2 HONEYBEE AND 4 WASP SPECIES

Preproapamin genes were amplified by RT-PCR from total RNA from the venom glands of 2 honeybee species, Apis mellifera, A. cerana cerana, and 4 wasp species, Vespa magnifica, V. velutina nigrothorax and Polistes hebraeus, respectively. Their PCR products were ligated into pGEM -T easy vector and the nucleotide sequences analyzed. The six fragments were all 141?bp in length and contained a n ORF coding the precursor of apamin. The apamin precursors of V. magnifica, V. velutina nigrothorax and P. hebraeus had 95% and 93% similarity with that of A. melliera in nucleotide and amino acid sequences, respectively. That of Vespu la maculifrons was identical to that of A. mellifera in nucleotide and amino acid sequences. Apamin precursors of V. magnifica, P. hebraeus and V. velutina nigrothorax also had the same nucleotide sequences. The nucleotide sequences o f preproapamin genes from the Chinese honeybee, A. cerana cerana and 4 wasp sp ecies are described for the first time. A notable discovery was that the wasps species had exactly same apamins as the honeybees despite the fact they belong to different insect families.

Protein sequence analysis based on hydropathy profile of amino acids

Biology sequence comparison is a fundamental task in computational biology.According to the hydropathy profile of amino acids,a protein sequence is taken as a string with three letters.Three curves of the new protein sequence were defined to describe the protein sequence.A new method to analyze the similarity/dissimilarity of protein sequence was proposed based on the conditional probability of the protein sequence.Finally,the protein sequences of ND6(NADH dehydrogenase subunit 6)protein of eight species were taken as an example to illustrate the new approach.The results demonstrated that the method is convenient and efficient.

Primary structure of p-momorcharin, a ribosome-inactivating protein from the seeds of Momordica Charantia Linn (Cucurbitaceae)

The complete amino acid sequence of β-momorcharin, a ribosome-inactivating protein from the seeds of Momordica charantia Linn (Cucurbitaceae) has been determined. This has been done by the sequence analysis of peptides obtained by enzymatic digestion with trypsin, chymotrypsin and S. aureus V8 protease, as well as by chemical cleavage with BNPS-skatole. The protein consists of 249 amino acid residues containing one asparagine - linked sugar group attached to the site of Asn 5 1 and has a calculated relative molecular mass of 28,452 Da without addition of the carbohydrate. Comparison of this sequence with those of trichosanthin and other ribosome-inactivating proteins from different species of plants shows a significant homology with each other. Regarding the similarity of their biological properties, an active domain of these proteins has been predicted here.