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      Expression Analysis of Cathepsin F during Embryogenesis and Early Developmental Stage in Olive Flounder ( Paralichthys olivaceus)

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          Abstract

          Cathepsins are members of the multigene family of lysosomal cysteine proteinases and have regulated function in several life processes. The potential role of cathepsin F cysteine gene was expected as protease in the yolk processing mechanism during early developmental stage, but expression analysis was unknown after fertilization. The alignment analysis showed that amino acid sequence of cathepsin F from olive flounder liver expressed sequence tag (EST) homologous to cathepsin F of other known cathepsin F sequences with 87-98% identity. In this study, we examined the gene expression analysis of cathepsin F in various tissues at variety age flounder. Tissue distribution of the cathepsin F mRNA has been shown to be ubiquitous and constitutive pattern regardless of age in each group, although derived from cDNA library using liver sample. The mRNA level of cathepsin F more increased as developmental proceed during embryogenesis and early developmental stage, especially increased in the blastula, hatching stage and 3 days post hatching (dph). As a result, it may suggest that the proteolysis of yolk proteins (YPs) has been implicated as a mechanism for nutrient supply during early larval stages in olive flounder.

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          Most cited references27

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          MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.

          S. KUMAR (2004)
          With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
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            A comprehensive comparison of multiple sequence alignment programs.

            In recent years improvements to existing programs and the introduction of new iterative algorithms have changed the state-of-the-art in protein sequence alignment. This paper presents the first systematic study of the most commonly used alignment programs using BAliBASE benchmark alignments as test cases. Even below the 'twilight zone' at 10-20% residue identity, the best programs were capable of correctly aligning on average 47% of the residues. We show that iterative algorithms often offer improved alignment accuracy though at the expense of computation time. A notable exception was the effect of introducing a single divergent sequence into a set of closely related sequences, causing the iteration to diverge away from the best alignment. Global alignment programs generally performed better than local methods, except in the presence of large N/C-terminal extensions and internal insertions. In these cases, a local algorithm was more successful in identifying the most conserved motifs. This study enables us to propose appropriate alignment strategies, depending on the nature of a particular set of sequences. The employment of more than one program based on different alignment techniques should significantly improve the quality of automatic protein sequence alignment methods. The results also indicate guidelines for improvement of alignment algorithms.
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              Composition, accumulation and utilization of yolk lipids in teleost fish

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                Author and article information

                Journal
                Balsaenggwa Saengsig
                Balsaenggwa Saengsig
                DR
                Development & Reproduction
                Korean Society of Developmental Biology
                1226-6752
                2287-7967
                September 2013
                : 17
                : 3
                : 221-229
                Affiliations
                Genetics and Breeding Research Center, NFRDI, Geoje 656-842, Republic of Korea
                Author notes
                [] Corresponding author: Jeong-Ho Lee, Genetics and Breeding Research Center, NFRDI, Geoje 656-842, Republic of Korea. Tel. : +82-55-639-5811, Fax : +82-55-639-5809, E-mail : jhlee7124@ 123456korea.kr
                Article
                DR-17-221
                10.12717/DR.2013.17.3.221
                4282294
                a86bddeb-95bc-4b40-afa9-55961d77e205
                © Copyright A Official Journal of the Korean Society of Developmental Biology. All Rights Reserved.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 23 August 2013
                : 28 August 2013
                : 5 September 2013
                Categories
                Article

                olive flounder,paralichthys olivaceus,cysteine proteinase,cathepsin f,developmental stage,gene expression,yolk protein,yolk syncytial layer (ysl).

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