Morphological and molecular identification of pennate diatoms isolated from Urla, İzmir, coast of the Aegean Sea

Kesici, Kutsal; Tüney, İnci; Zeren, Doğuş; Güden, Mustafa; Sukatar, Atakan

doi:10.3906/biy-1205-40

Cited by 12 publications

(11 citation statements)

References 19 publications

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“…Recently, bioinformatics and genomic tools have revolutionized the studies of organisms' metabolism by showing new results about proteins and their structure (Altay et al 2013;Darabi & Farhadi-Nejad 2013;Kesici et al 2013;Seddigh & Darabi 2014). The aim of the present study was to deliver structural, functional and phylogenetic analyses on a key gene in insects to determine the biochemical characterization in order to gain a better understanding of the digestive physiology of insects.…”

Section: Introductionmentioning

confidence: 99%

Structural and phylogenetic analysis of α-glucosidase protein in insects

Seddigh

Darabi

2015

Biologia

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α-Glucosidases (αglus) (EC 3.2.1.20) have been detected in a wide range of plants, animals and microorganisms and are described by their ability to catalyze the hydrolysis of 1,4-α-glucosidic linkages, releasing α-glucose. In this study, 96 αglu protein sequences from 33 organisms species including different insects species, plants (including thale cress and rice), mammals (including human and mouse) and Mycobacterium tuberculosis as a bacterium were aligned. Sequences were analyzed by computational tools to predict the protein properties, such as molecular mass, isoelectric point, signal peptide, conserved motifs, transmembrane domain and secondary structure. Drosophila melanogaster (GenBank Accession No.: NP 610382) was chosen as one of the representatives of insects for further analyses. The tertiary structure of representative samples were acquired using the tertiary structure of oligo-1,6-glucosidase from Bacillus cereus (Protein Data Bank code: 1UOK) as a template by Phyre2 server. Protein structure analysis revealed there is a high identity among insects and other organisms. There were some similar functional domains between D. melanogaster and M. tuberculosis. The modeled αglu has a typical spatial structure in insects and exhibits a high similarity with other organisms, especially Arabidopsis thaliana. Phylogenetic analysis indicated that D. melanogaster αglu has a close relationship with other αglus from different insect families. According to these results, αglu in insects should be evolved from a common ancestor.

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Section: Introductionmentioning

confidence: 99%

Structural and phylogenetic analysis of α-glucosidase protein in insects

Seddigh

Darabi

2015

Biologia

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“…Moreover, some abiotic (e.g., light intensity, nutrient concentrations, heavy metals and temperature), and biotic factors (e.g., herb ivores) significantly trigger the morphological plasticity in Scenedesmus, Desmodesmus and other related morphospecies (Jonson et al, 2007). In Turkey, there are a few phylogenetic studies on different microalgal g roups but none of them gave more interest to members of family Scenedesmaceae (e.g., Tüney & Sukatar, 2010;Soylu & Gönülo l, 2011;Kesici et al, 2013;Kızılkaya-Tüney, Demirel, Kesici, K., Kesici, E., & Su katar, 2016). Thus, the main aim o f the present study was to investigate the mo lecular and morphological relat ionships of some Scenedesmus-like species isolated fro m the River Basin of Ergene (Turkey ) using the light microscopy (LM) and PCR analysis.…”

Section: Introductionmentioning

confidence: 99%

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Akgül¹,

Kızılkaya²,

Akgül³

et al. 2017

Turk. J. Fish. Aquat. Sci.

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The genus Scenedesmus and other allied morphospecies can not only been identified morphologically due to their smaller sizes and phenotypic plasticity. In this study, six Scenedesmus-like species were isolated and investigated from the inland freshwater of Ergene River Basin (Thrace, Turkey). These strains were studied in-depth using the light microscopy (LM ) and the molecular ITS1-ITS4 gene sequencing. The combined morphological and phylogenetic analysis revealed that the strains studied belonged to the genera Desmodesmus (2 strains were characterized as D. communis and one strain identified as D. armatus var. subalternas), Acutodesmus (2 strains related to A. obliquus), and only one strain of the genus Pectinodesmus that identified as P. pectinatus.This study confirms that morphological identification of Scenedesmus-like species is considered not only enough for accurate species delineation but also the molecular approaching techniques should be applied. However, more deep molecular studies using other genes sequencing should be integrated for more easily species identification.

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“…Because of its effectiveness and low cost, bioinformatics has been widely used to predict antigenic epitopes on proteins (Bai et al, 2012). Thus, it seems that these tools have revolutionized the study of genetics (Darabi et al, 2012;Darabi and Farhadi-Nejad, 2013;Kesici et al, 2013;Seddigh and Darabi, 2014). In conclusion, our study employed bioinformatics methods to explain the structure, function, and molecular mechanism of AP protein in insects.…”

Section: Discussionmentioning

confidence: 99%

Proteomics comparison of aspartic protease enzyme in insects

Seddigh¹,

Darabi²

2016

Turk J Biol

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IntroductionProteases (peptidases or proteinases) are a large category of enzymes that catalyze the hydrolysis of peptide bonds. Proteases that cleave peptide bonds within the polypeptide chain are classified as endopeptidases, and those that cleave peptide bonds at the N or C termini of polypeptide chains are known as exopeptidases (López-Otín and Bond, 2008). Thus, the term "protease" includes both "endopeptidases" and "exopeptidases", while the term "proteinase" is used to describe only "endopeptidases" (Ryan, 1990). Proteases are present in all organisms and are involved in various physiological processes, including the production of nutrients for cell growth and proliferation (Lin et al., 2011), for protein degradation (Ciechanover, 2005), and as regulatory components for diverse physiological functions (Ehrmann and Clausen, 2004;Oikonomopoulou et al., 2006). Proteases include aspartic, cysteine, glutamic, serine, and threonine proteases, depending on the amino acids present in the active site, or the metalloproteases, if a metal ion is required for catalytic activity (Alagarsamy et al., 2006). Microbial-sourced proteases are invaluable commercial enzymes and account for approximately 60% of the total worldwide sales of industrial enzymes

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Morphological and molecular identification of pennate diatoms isolated from Urla, İzmir, coast of the Aegean Sea

Cited by 12 publications

References 19 publications

Structural and phylogenetic analysis of α-glucosidase protein in insects

Structural and phylogenetic analysis of α-glucosidase protein in insects

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Proteomics comparison of aspartic protease enzyme in insects

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