Determination of some heavy metals and mineral nutrients of bay tree (Laurus nobilis L.) in Bartin city, Turkey

Concentrations of Al, Cd, Cu, Ni, and Pb in Laurus nobilis L. were examined for assessment of the impact of heavy metal exposure during winter periods, since these metals have the highest toxic potential. In this study, leaf (washed and unwashed), bark and branch samples of L. nobilis and soil samples were collected from 13 different localities, belonged to three stations. In conjunction with analyzing impact of the heavy metal exposure on the city using L. nobilis as a biomonitoring tool, the uptake and composition of mineral nutrients of L. nobilis were also investigated for determining the effects of heavy metals on mineral nutrition metabolism of the plant. The heavy metal and mineral nutrient concentrations of the collected samples were measured by using ICP-OES. The obtained data was analyzed with SPSS statistics program. As a result of measurements, the lowest and highest heavy metal accumulations and the amount of mineral nutrients measured in plants were as follows; Al (14.69-122.44 mg/kg d. wt), Cd (0.23-0.89 mg/kg d. wt), Cu (1.64-14.25 mg/kg d. wt.), Ni (0.001-0.45 mg/kg d. wt.), Pb (2.06-5.28 mg/kg d. wt.) and B (1.04- 6.67 mg/kg d. wt.), Ca (1195.34-4919.03 mg/kg d. wt.), Fe (17.13-203.25 mg/kg d. wt.), K (538.99-3778.37 mg/kg d. wt.), Mg(48.1-268.5 mg/kg d. wt.), Na (24.91-77.43 mg/kg d. wt.) and Zn (4.75-15.74 mg/kg d. wt.). According to the experimental data, the volume of the air pollution was analyzed and found significant in the city. Also, it was noticed that the metabolism of mineral nutrients of L. nobilis was altered by heavy metals. Finally, it was proved that L. nobilis is a suitable organism to be used as a biomonitoring tool for conducting research on heavy metal pollution

Mineral element uptake status of endemic Isoetes anatolica Prada & Rolleri populations from Bolu-Turkey

Isoetes genus is commonly known as the "quillworts" and considered to be "fern allies". There are about 200-250 species, with a cosmopolitan distribution but often scarce to rare. Isoetes genus members often grow in extremely sensitive aquatic environments such as temporary ponds, streams and lakes. They are therefore good indicators of environmental quality. Isoetes anatolica Prada & Rolleri is an endemic plant grows on calcareous sediment/soil on the edges of seasonal ponds located in a mountainous area near the southern coast of the Black Sea at 1400 m above sea level at Bolu, Turkey. In this study, mineral element uptake statuses of I. anatolica populations were studied on the background of plant-sediment/soil-water interactions. The study materials were collected from the place where this narrow endemic species only lives in the world (Abant Region, Bolu/Turkey) by using standard methods and plant and sediment/soil mineral element measurements (Al, B, Ca, Cu, Fe, K, Mg, Mn, Na, Ni and Zn) were done. ICP-OES was employed for the measurements during the study. Interrelations between mineral element contents in the sediment/soil, water and plant were discussed. The data revealed that I. anatolica is capable of accumulating considerable amounts of certain mineral elements (B, Ca, Mn and Na).Marmara University, Commission of Scientific Research Project (FEN-D-040712-0291

Çocuklarda Aortik Balon Valvüloplasti Uygulaması

Advances in pediatric cardiology in the past 30 years, allowed transcatheter treatment of valvular aortic stenosis, as well as many other diseases. The aim of this study is to investigate the characteristics; procedure findings and long term follow up results of patients who had undergone aortic valvuloplasty between 2000 and 2012 in Hacettepe University Ihsan Dogramaci Children’s Hospital, Department of Pediatric Cardiology. The hospital records of patients were retrospectively evaluated. One-hundred and thirty balloon valvuloplasty procedures were performed to a total of 120 patients, with an age range between 1 day and 18 years; and body weight range of 1.-80 kilograms. The hemodynamic studies at the catheter laboratory revealed that the mean left ventricle pressure before the procedure declined from mean 162 ± 32 mmHg (72-276; median:160 mmHg) to a mean 126 ± 34 mmHg (64-254; median: 120 mmHg) after the procedure. The systolic gradient of the aortic valve decreased from mean 69.7 ± 23 mmHg (7-145; median: 69.5 mmHg) before the procedure to a mean 27.4 ± 21 mmHg (0-149; median: 25 mmHg) after. Third grade aortic insufficiency was found in 18 procedures (13%) during control injections after the procedure. Fast pacing method for valvuloplasty was performed in 56 patients. Balloon valvuloplasty failed in two patients (3.6%) who had the procedure with a fast pacing; only 2 patients developed third grade aortic insufficiency. Among the patients who valvüloplasty performed by standard method, balloon valvuloplasty failed in 6 patients (8.3%), whereas third grade aortic insufficiency was seen in 15 (20.2%). Fast pacing balloon valvuloplasty decreased the incidence of post-procedure severe aortic insufficiency significantly (p<0.01) but it had no effect on the success rate of the procedure. Fast pacing did not change the procedure duration, but decreased the flouroscopy duration significantly (p<0.01). Twenty six surgical procedures were performed after ballon valvuloplasty; the indications were v valvular aortic stenosis in 17 patients (15%); coarctation of the aorta in 3 patients and subaortic membrane resection and valvular aortic stenosis in 2 patients. Long term follow up results of the patients revelead that the peak gradient which was calculated as 28 ± 19.2 mmHg with echocardiographic continuous doppler measurements one day after the procedure, became 37.48 ± 20.5 mmHg, which was not statistically different. The degree of aortic insufficiency did not change significantly in time, but 6 patients required aortic valve replacement. Eight patients (6.6%) died; only one of these patients died due to cardiovascular arrest during the procedure. In conclusion, balloon valvuloplasty is a safe, palliative treatment of valvular aortic stenosis. It should be preferred in newborns with valvular aortic stenosis who are not hemodynamically stable. Fast pacing can be used safely in all age groups; it decreases failure rate, eases the procedure and prevents the development of aortic insufficiency with stabilization of the balloon.Son 30 yıldır girişimsel kardiyoloji alanındaki gelişmeler birçok hastalığın olduğu gibi valvüler aort darlığının da transkateter tedavisini sağlamaktadır. Bu çalışmada 2000-2012 yılları arasında Hacettepe Üniversitesi İhsan Doğramacı Çocuk Hastanesi Çocuk Kardiyoloji Bilim Dalında aortik valvüloplasti uygulanan hastaların özellikleri, işlem bulguları ve uzun dönem takip sonuçlarının değerlendirilmesi amaçlanmıştır. Balon valvüloplasti uygulanan hastaların hastane kayıtları retrospektif olarak incelendiğinde; yaşları 1 gün ile 18 yaş ve ağırlıkları 1.1-80 kg arasında değişen 120 hastaya, 130 balon valvüloplasti işlemi uygulanmıştır. Kateter laboratuvarında yapılan hemodinamik çalışmada işlem öncesi sol ventrikül basıncının ortalama 162 ± 32 mmHg (ortanca 160 mmHg; 72-276 mmHg)’dan 126 ± 34 mmHg (ortanca 120 mmHg; 64-254 mmHg)’ya, aort kapağı üzerindeki sistolik gradiyentin ortalama 69,7 ± 23 mmHg (ortanca 69.5 mmHg; 7-145 mmHg)’dan, ortalama 27.4 ± 21 mmHg (ortanca 25 mmHg; 0-149 mmHg)’ya gerilediği, işlem sonrasında yapılan kontrol enjeksiyonlarında 18 işlemde (%13) 3.derece aort yetmezliği geliştiği izlenmiştir. Elli altı hastada sistemik bazal değerinin %40-50 altına düşüren hızda ‘‘pace’’ edilirken valvüloplasti uygulanmıştır. Hızlı ‘‘pacing’’ ile balon valvüloplasti uygulanan hastaların 2’sinde (%3.6) başarısız olunduğu; sadece 2 hastada 3.derece aort yetmezliği geliştiği tespit edildi. Bu yöntemin uygulanmadığı hastalarda ise 6 hastada (%8.3) başarısız olunduğu; 15 hastada (%20.2) 3.derece aort yetmezliği geliştiği izlendi. Hızlı ‘‘pacing’’ ile balon valvüloplasti uygulamasının ağır aort yetmezliğini istatiksel olarak anlamlı şekilde azalttığı (p < 0.01), ancak işlem başarısı üzerine istatiksel olarak anlamlı olmadığı, bununla birlikte işlem süresini değiştirmese de skopi süresini istatiksel olarak anlamlı şekilde azalttığı (p < 0.01) saptanmıştır. Balon valvüloplasti uygulanan hastaların 17’sine (%15) valvüler aort darlığı, 3 hastaya aort koarktasyonu, 2 hastaya subaortik membran rezeksiyonu ve iii valvüler aort darlığı nedeniyle 26 cerrahi girişim uygulanmıştır. Hastaların uzun dönem izlemlerinde aort kapak üzerinde ekokardiyografi ile yapılan devamlı doppler ölçümlerinde işlemden bir gün sonra 28 ± 19.2 mmHg olan tepe gradientin, 37.48 ± 20.5 olduğu ve izlemlerinde istatiksel olarak anlamlı değişiklik saptanmadığı, aort yetmezlik derecelerinin ise istatiksel olarak anlamlı düzeyde yükselmediği ancak 6 hastada aort kapak replasmanı uygulanması gerektiği, 8 (%6.6) hastanın eksitus olduğu, bu hastalardan sadece bir tanesinin işlem sırasında arrest olup izleminde kaybedildiği saptanmıştır. Sonuç olarak balon valvüloplasti valvüler aort darlıklı hastalarda güvenle uygulanabilecek palyatif bir tedavi yöntemidir. Valvüler aort darlıklarının tedavisinde özellikle hemodinamik olarak stabil olmayan yenidoğanlarda öncelikli olarak tercih edilmelidir. Hızlı ‘’pacing’’ yöntemi her yaş grubunda güvenle uygulanabilir, işlem başarısızlığını azaltırken, işlemi kolaylaştırır, balon stabilizasyonunu sağlayarak aort yetmezliği gelişimini engeller

In silico analysis of simple sequence repeats (SSRs) in chloroplast genomes of Glycine species

Microsatellites, also known as simple sequence repeats, are short (1-6 bp long) repetitive DNA sequences present in chloroplast genomes (cpSSRs). In this work, chloroplast genomes (cpDNA) of eight different species (G. canescens, G. cyrtoloba, G. dolichocarpa, G. falcata, G. max, G. soja, G. stenophita, and G. tomentella) from Glycine genus were screened for cpSSRs by MISA perl script with a repeat size of ?10 for mono-, 5 for di-, 3 for tri-, tetra-, penta- and hexa-nucleotide, including frequency, distributions, and putative codon repeats of cpSSRs. According to our results, a total of 1273 cpSSRs were identified and among them, 413 (32.4%) were found to be in genic regions and the remaining (67.6%) were all located in intergenic regions, with an average of 1.04 cpSSRs per kb. Trinucleotide repeats (45%) were the most abundant motifs, followed by mononucleotides (36%) and dinucleotides (11.8%) in the plastomes of the Glycine species. In genic regions, trimeric repeats, the most frequent one reached the maximum of 70.7%. Among the other repeats, mono- and tetrameric repeats were represented in proportions of 25.7% and 3.6%, respectively. Interestingly, there were no di-, penta-, and hexameric repeats in coding sequences. The most common motifs found in all plastomes were A/T (97.8%) for mono-, AT/AT (98%) for di-, and AAT/ATT (41.5%) for trinucleotides. Among the chloroplast genes, ycf1 had the highest number of cpSSRs, and G. cyrtoloba and G. falcata species had the maximum number of genes containing cpSSRs. The most frequent putative codon repeats located in coding sequences were found to be glutamic acid (21.2%), followed by serine (15.5%), arginine (8.3%) and phenylalanine (7.8%) in all species. Also, tryptophan, proline, and aspartic acid were not detected in all plastomes

Insights into a key sulfite scavenger enzyme sulfite oxidase (SOX) gene in plants

Filiz, Ertugrul/0000-0001-9636-6389; Ozyigit, Ibrahim Ilker/0000-0002-0825-5951WOS: 000399687900012PubMed: 28461726Sulfite oxidase (SOX) is a crucial molybdenum cofactor-containing enzyme in plants that re-oxidizes the sulfite back to sulfate in sulfite assimilation pathway. However, studies of this crucial enzyme are quite limited hence this work was attempted to understand the SOXs in four plant species namely, Arabidopsis thaliana, Solanum lycopersicum, Populus trichocarpa and Brachypodium distachyon. Herein studied SOX enzyme was characterized with both oxidoreductase molybdopterin binding and Mo-co oxidoreductase dimerization domains. The alignment and motif analyses revealed the highly conserved primary structure of SOXs. The phylogeny constructed with additional species demonstrated a clear divergence of monocots, dicots and lower plants. In addition, to further understand the phylogenetic relationship and make a functional inference, a structure-based phylogeny was constructed using normalized RMSD values in five superposed models from four modelled plant SOXs herein and one previously characterized chicken SOX structure. The plant and animal SOXs showed a clear divergence and also implicated their functional divergences. Based on tree topology, monocot B. distachyon appeared to be diverged from other dicots, pointing out a possible monocot-dicot split. The expression patterns of sulfite scavengers including SOX were differentially modulated under cold, heat, salt and high light stresses. Particularly, they tend to be up-regulated under high light and heat while being down-regulated under cold and salt stresses. The presence of cis-regulatory motifs associated with different stresses in upstream regions of SOX genes was thus justified. The protein-protein interaction network of AtSOX and network enrichment with gene ontology (GO) terms showed that most predicted proteins, including sulfite reductase, ATP sulfurylases and APS reductases were among prime enzymes involved in sulfite pathway. Finally, SOX-sulfite docked structures indicated that arginine residues particularly Arg374 is crucial for SOX-sulfite binding and additional two other residues such as Arg51 and Arg103 may be important for SOX-sulfite bindings in plants

Comparative and phylogenetic analysis of zinc transporter genes/proteins in plants

Filiz, Ertugrul/0000-0001-9636-6389; Ozyigit, Ibrahim Ilker/0000-0002-0825-5951WOS: 000378689400009Zinc is an important catalytic element for more than 300 enzymes and plays a structural role in the stabilization of many proteins. Protein domain analysis showed that identified Zn transporter proteins belong to the ZIP protein family (PF02535). Zn transporter sequences were found to have similar molecular weights (33.1-51.4 kDa) and amino acid lengths (306-478 amino acids) with 5.31-8.92 pI values. Subcellular localization of Zn transporters was predicted as the plasma membrane. They had 6-9 putative transmembrane domains with a variable region between TM-3 and TM-4, which could contain a potential histidine-rich metal-binding domain. Moreover, alignment analysis showed that the TM-2, -4, and -5 domains could be potential metal-binding sites because they contain highly conserved His residues. Based on a homology search, the retrieved sequences were identified as corresponding homologs of either Arabidopsis thaliana or Oryza sativa. Phylogenetic analysis also supported that A. thaliana and O. sativa sequences could be used as a reference/benchmark to identify Zn transporter homologs in various plant species. The findings of this study will be valuable theoretical knowledge for feature studies in terms of understanding the gene and protein features of Zn transporters in various plants

Analysis of EST-SSRs in silver birch (Betula pendula Roth.)

Filiz, Ertugrul/0000-0001-9636-6389; Ozyigit, Ibrahim Ilker/0000-0002-0825-5951WOS: 000375452300017Simple sequence repeats (SSRs) defined as sequence repeat units between 1 and 6 bp occur abundantly in both coding and non-coding regions in eukaryotic genomes and these repeats can affect gene expression. In this study, ESTs (expressed sequence tags) of Betula pendula (silver birch) were analyzed for in silico mining of EST-SSRs, protein annotation, open reading frames (ORFs), designing primers, and identifying codon repetitions. In B. pendula, the frequency of ESTs containing SSRs was 7.8 % with an average of 1SSR/4. 78 kb of EST sequences. A total of 188 SSRs was identified by using MISA software and di-nucleotide SSR motifs (65.9 %) were found to be the most abundant type of repeat motif followed by tri- (27.1 %), tetra- (4.8 %), and penta- (2.2 %) motifs. Based on ORF analysis, 175 of 178 sequences were predicted as ORFs and the most frequent SSRs were detected in 5' UTR (58.43 %), followed by in ORF (31.46 %) and in 3' UTR (8.43 %). 102 of 178 ESTs were annotated as ribosomal protein, transport protein, membrane protein, carrier protein, binding protein, and transferase protein. For a total of 102 SSRs (57.3 %) with significant matches, a set of 102 primers (100 %) with forward and reverse strands was designed by using Primer3 software. Serine (Ser, 19.6 %) was predominant in putative encoded amino acids and most of amino acids showed nonpolar (35.3 %) nature. Our data provide resources for B. pendula and can be useful for in silico comparative analyses of Betulaceae species, including SSR mining

Bioinformatics database resources for plant transcription factors

[No abstract available

Genome-wide analysis of IQ67 domain (IQD) gene families in Brachypodium distachyon

Tombuloglu, Huseyin/0000-0001-8546-2658; Filiz, Ertugrul/0000-0001-9636-6389; Ozyigit, Ibrahim Ilker/0000-0002-0825-5951WOS: 000330275800007In plants, Ca2+ concentration is important for the regulation of developmental processes and responses against biotic and abiotic stress factors. The eukaryotic Ca2+ binding protein calmodulin (CaM: CALcium MODULating protelN) was found in Arabidopsis which contains a characteristic plant-specific IQ67 (Ile, Glu) domain (IQD). In this study, a genome wide analysis was performed in Bracyhpodium distachyon to identify IQD genes. Using several bioinformatics tools, we determined 23 BdIQD genes which were distributed on all chromosomes and the highest gene number was detected on chromosome 2 including 12 IQD genes. 22 of the predicted proteins were considered to be basic proteins. Gene duplication analysis revealed that 8 of 23 BdIQD genes were involved in duplication event, either segmental or tandem. Phylogenetic analysis showed that two main groups were observed in joined tree with rice and Arabidopsis. Especially, monocot species (Brachypodium and rice) were grouped together with the highest bootstrap value (100%), whereas monocot and dicot species (Arabidopsis) were clustered with lower bootstrap values. Digital expression profile analysis indicated that the most of the BdIQD genes were expressed in leaves (8 genes) and flowers (6 genes), respectively. In conclusion, this comparative genomics analysis contributes to understanding IQD genes in grass species

Comparative analyses of pathogenesis-related protein-10 (PR10) in plants

WOS: 000425580800024In the present study, we have comparatively analyzed PR10 genes and proteins from 28 plant species in order to understand the relationship (conservation or divergence) between different PR1Os in various plant species. In analyzed species, PR10 proteins were found to be small (157-166 as long and 14.3-18.2 kDa weight) and acidic (4.69-6.17) in nature. Besides, PR10 sequences had highly conserved GxGGxG motif (P-loop motif) structure at various positions. These positional variations in glycine (Gly) residues may become the result of substitution, deletions and insertions occurred during the course of PR10 evolution. In general, primary sequences of PR1Os in various plant species may have a well conserved structure. Digital expression data of tomato and maize showed that expression of PR10 genes may significantly increase in plant parts (root, lateral root and root tips) where it is more open to the mechanical perturbation and pathogenic attack, supporting the involvement of PR10 in plant defense. In phylogenetic tree, a clear monocot/polycot and dicot separation were observed. This separation could have been arising from the well conserved structure of PR10 genes of monocots and polycots than dicots. All modeled species contained the same number of beta-strands (seven) but alpha-helices varied between 2 and 4 depending on species. The results of this study will provide a theoretical reference regarding the primary, secondary and tertiary structure of PR1Os in various plant species and will support the future studies that aiming to characterize the pathogenesis-related (PR) proteins