- Email: [email protected]
The influence of temperature on the accessible surface area of the human alpha-defensin 2 (HNP2)
Abstracts / Journal of Biotechnology 185S (2014) S37–S125
including fully complementary mRNA of one gene. miR162* was bonded with mRNA of 13 MYB genes ((G/(Gm equal to 85-89%). miR164a* had a binding sites in 17 MYB genes mRNA ((G/(Gm - 8591%). miR166b-i and miR166?*,s*,g*,n* had several of target genes. Each of miR167d*,f-j* had two or more MYB target genes. All of the binding sites of miRNA with MYB gene mRNA was in CDS.
The influence of temperature on the accessible surface area of the human alpha-defensin 2 (HNP2)
http://dx.doi.org/10.1016/j.jbiotec.2014.07.184
1 National Institute of Research and Development for Biological Sciences, Bucharest, Romania 2 Faculty of Biotechnology, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Romania 3 Banat’s University of Agricultural Sciences and Veterinary Medicine “Regele Mihai I al României” from Timis¸oara, Romania 4 Faculty of Management, Economic Engineering in Agriculture and Rural Development, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Romania
Application of the bioinformatics tool of endemicity in Turkey biogeography: An example with aquatic beetles (Coleoptera: Hydraenidae) Mustafa Cemal Darilmaz Department of Biology, Faculty of Science and Letters, University of Aksaray, Aksaray, Turkey E-mail address: [email protected]. Bioinformatics is an interdisciplinary field that has made important advances in the development of systems and techniques to organize latest biological data. Bioinformatics is being used to analyze endemicity in biogeography. Several methods have been proposed to be used in identifying and classifying the areas of endemism. Being among the most widely used bioinformatics tools with the aim of understanding endemicity and biogeography to identify the areas of endemism and to determine tools is that of Parsimony analysis of endemicity (PAE), playing a relevant role in evolutionary biogeography. The areal distribution of the aquatic beetle family Hydraenidae in Turkey was analyzed quantitatively with the aims of determining the zoogeographic regions, areas of endemism and priority areas for conservation. Turkey was initially divided into 30 quadrats. Presence/absence data matrixes of 103 endemic species are used for PAE to determine the relationships among 30 quadrats. The analysis with options Heuristic and Wagner of Past (V. 2.17c) produced the most parsimonious trees. Subsequently, these quadrats were pooled into 23 areas based on topographical characteristics and to a lesser extent on the distributions of beetles. Five endemic areas were identified by PAE: Middle and Eastern Black Sea Region, Erzurum-Kars Plateau, Eastern Mediterranean, Antalya.
S55
Marian Butu 1 , Steliana Rodino 1,2,∗ , Constanta Negoescu 3 , Ioana Nicolae 4 , Reta Condei 4 , Alina Butu 1
E-mail address: [email protected] (S. Rodino). The human alpha-defensin 2 (HNP2) contains six cysteine residues and is an important peptide for the innate immune defense system against microbial and viral infection. This study investigated the influence of temperature on the accessible surface area (ASA) of HNP2 in molecular dynamics simulation. The simulation experiments were performed with GROMACS software package. The start structure was 1ZMI from the Protein Data Bank. The production dynamics had 10 ns with a step of 2 fs for 11 different values of temperature, between 0 and 225 ◦ C. The energy values and the coordinates were saved on every 2 ps. For each obtained trajectory it was calculated the ASA variation and the density variation of the simulated system. The results obtained for the two parameters were compared for the 11 temperatures experienced. Thus, it was found that there is an increase of the ASA with increasing temperature of the system. Acknowledgments This work has been financed by UEFISCDI, research contract no PN-II-PT-PCCA 106/2012. http://dx.doi.org/10.1016/j.jbiotec.2014.07.186
http://dx.doi.org/10.1016/j.jbiotec.2014.07.185 Comparative analysis of three-dimensional structure of protein classes Rafiga Ch Masmaliyeva 1,∗ , Vagif G. Amikishiyev 2 , Garib N. Murshudov 3 1
Institute of Botany, ANAS, Baku, Azerbaijan Institute of Genetics Resources, ANAS, Baku, Azerbaijan 3 Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK 2
E-mail address: [email protected] (R.C. Masmaliyeva). Classification of three dimensional protein structures and comparative analyses of those classes can facilitate understanding of relationship between protein classes and give insight into evolutionary and functional relationship between proteins. Although currently there are more than 99,000 protein structures in the Protein Data Bank, not all structures are independent. Classification according sequence alignment shows that the number of independent protein structure classes is not more than 15,000. Redundancy of protein structure allows analysis of conformational variances within the classes and comparison of these variances between classes. Conformational variations can be quantified using three
including fully complementary mRNA of one gene. miR162* was bonded with mRNA of 13 MYB genes ((G/(Gm equal to 85-89%). miR164a* had a binding sites in 17 MYB genes mRNA ((G/(Gm - 8591%). miR166b-i and miR166?*,s*,g*,n* had several of target genes. Each of miR167d*,f-j* had two or more MYB target genes. All of the binding sites of miRNA with MYB gene mRNA was in CDS.
The influence of temperature on the accessible surface area of the human alpha-defensin 2 (HNP2)
http://dx.doi.org/10.1016/j.jbiotec.2014.07.184
1 National Institute of Research and Development for Biological Sciences, Bucharest, Romania 2 Faculty of Biotechnology, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Romania 3 Banat’s University of Agricultural Sciences and Veterinary Medicine “Regele Mihai I al României” from Timis¸oara, Romania 4 Faculty of Management, Economic Engineering in Agriculture and Rural Development, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Romania
Application of the bioinformatics tool of endemicity in Turkey biogeography: An example with aquatic beetles (Coleoptera: Hydraenidae) Mustafa Cemal Darilmaz Department of Biology, Faculty of Science and Letters, University of Aksaray, Aksaray, Turkey E-mail address: [email protected]. Bioinformatics is an interdisciplinary field that has made important advances in the development of systems and techniques to organize latest biological data. Bioinformatics is being used to analyze endemicity in biogeography. Several methods have been proposed to be used in identifying and classifying the areas of endemism. Being among the most widely used bioinformatics tools with the aim of understanding endemicity and biogeography to identify the areas of endemism and to determine tools is that of Parsimony analysis of endemicity (PAE), playing a relevant role in evolutionary biogeography. The areal distribution of the aquatic beetle family Hydraenidae in Turkey was analyzed quantitatively with the aims of determining the zoogeographic regions, areas of endemism and priority areas for conservation. Turkey was initially divided into 30 quadrats. Presence/absence data matrixes of 103 endemic species are used for PAE to determine the relationships among 30 quadrats. The analysis with options Heuristic and Wagner of Past (V. 2.17c) produced the most parsimonious trees. Subsequently, these quadrats were pooled into 23 areas based on topographical characteristics and to a lesser extent on the distributions of beetles. Five endemic areas were identified by PAE: Middle and Eastern Black Sea Region, Erzurum-Kars Plateau, Eastern Mediterranean, Antalya.
S55
Marian Butu 1 , Steliana Rodino 1,2,∗ , Constanta Negoescu 3 , Ioana Nicolae 4 , Reta Condei 4 , Alina Butu 1
E-mail address: [email protected] (S. Rodino). The human alpha-defensin 2 (HNP2) contains six cysteine residues and is an important peptide for the innate immune defense system against microbial and viral infection. This study investigated the influence of temperature on the accessible surface area (ASA) of HNP2 in molecular dynamics simulation. The simulation experiments were performed with GROMACS software package. The start structure was 1ZMI from the Protein Data Bank. The production dynamics had 10 ns with a step of 2 fs for 11 different values of temperature, between 0 and 225 ◦ C. The energy values and the coordinates were saved on every 2 ps. For each obtained trajectory it was calculated the ASA variation and the density variation of the simulated system. The results obtained for the two parameters were compared for the 11 temperatures experienced. Thus, it was found that there is an increase of the ASA with increasing temperature of the system. Acknowledgments This work has been financed by UEFISCDI, research contract no PN-II-PT-PCCA 106/2012. http://dx.doi.org/10.1016/j.jbiotec.2014.07.186
http://dx.doi.org/10.1016/j.jbiotec.2014.07.185 Comparative analysis of three-dimensional structure of protein classes Rafiga Ch Masmaliyeva 1,∗ , Vagif G. Amikishiyev 2 , Garib N. Murshudov 3 1
Institute of Botany, ANAS, Baku, Azerbaijan Institute of Genetics Resources, ANAS, Baku, Azerbaijan 3 Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK 2
E-mail address: [email protected] (R.C. Masmaliyeva). Classification of three dimensional protein structures and comparative analyses of those classes can facilitate understanding of relationship between protein classes and give insight into evolutionary and functional relationship between proteins. Although currently there are more than 99,000 protein structures in the Protein Data Bank, not all structures are independent. Classification according sequence alignment shows that the number of independent protein structure classes is not more than 15,000. Redundancy of protein structure allows analysis of conformational variances within the classes and comparison of these variances between classes. Conformational variations can be quantified using three