Genome-wide exploration of silicon (Si) transporter genes, <Emphasis Type="Italic">Lsi1</Emphasis> and <Emphasis Type="Italic">Lsi2</Emphasis> in plants; insights into Si-accumulation status/capacity of plants

Silicon (Si) is a nonessential, beneficial micronutrient for plants. It increases the plant stress tolerance in relation to its accumulation capacity. In this work, root Si transporter genes were characterized in 17 different plants and inferred for their Si-accumulation status. A total of 62 Si transporter genes (31 Lsi1 and 31 Lsi2) were identified in studied plants. Lsi1s were 261–324 residues protein with a MIP family domain whereas Lsi2s were 472–547 residues with a citrate transporter family domain. Lsi1s possessed characteristic sequence features that can be employed as benchmark in prediction of Si-accumulation status/capacity of the plants. Silicic acid selectivity in Lsi1s was associated with two highly conserved NPA (Asn-Pro-Ala) motifs and a Gly-Ser-Gly-Arg (GSGR) ar/R filter. Two NPA regions were present in all Lsi1 members but some Ala substituted with Ser or Val. GSGR filter was only available in the proposed high and moderate Si accumulators. In phylogeny, Lsi1s formed three clusters as low, moderate and high Si accumulators based on tree topology and availability of GSGR filter. Low-accumulators contained filters WIGR, AIGR, FAAR, WVAR and AVAR, high-accumulators only with GSGR filter, and moderate-accumulators mostly with GSGR but some with A/CSGR filters. A positive correlation was also available between sequence homology and Si-accumulation status of the tested plants. Thus, availability of GSGR selectivity filter and sequence homology degree could be used as signatures in prediction of Si-accumulation status in experimentally uncharacterized plants. Moreover, interaction partner and expression profile analyses implicated the involvement of Si transporters in plant stress tolerance.     

Genome-wide identification and expression analysis of sulphate transporter (<Emphasis Type="Italic">SULTR</Emphasis>) genes under sulfur deficiency in <Emphasis Type="Italic">Brachypodium distachyon</Emphasis>

Sulphur is an important mineral element for plant growth and development. It involves in a number of metabolic processes with crucial functions. This study has performed a genome-wide analysis of sulfate transporter (SULTR) genes in Brachypodium distachyon. Ten putative SULTR genes were identified in Brachypodium genome. BdSULTR genes included 6–17 exons encoding a protein of 647–693 residues with basic nature. BdSULTR proteins included both sulfate_transp (PF00916) and STAS (PF01740) domains. BdSULTRs were classified into 4 groups based on the phylogenetic distribution. Promoter regions of all BdSULTR genes, except for BdSULTR3;3 and 3;5 included the SURECOREATSULTR11 elements. A considerable structural overlap was identified between superimposed SULTR1;3 and 3;1 proteins, indicating that SULTR1 members may also involve in plant stress response/tolerance like SULTR3 members. Microarray and RNA-Seq analyses also revealed the differential expression of SULTR 1 and 3 genes under different biotic/abiotic stresses. Protein–protein interaction partners of BdSULTRs were mainly related with adenylyl-sulfate kinases, 5′-adenylylsulfate reductases, ATP sulfurylases, and acyl carrier proteins. Moreover, expression profiles of identified BdSULTR genes under S-deficiency were analyzed using RT-qPCR. It was revealed that BdSULTR1;1 and 3;1 are highly expressed in plant roots as ~tenfold and ~fivefold, respectively, while BdSULTR2 (~15-fold) and 3;1 (~twofold) are abundantly expressed in leaf tissues.     

Genetic differentiation between clone collections and natural populations of European black poplar (<Emphasis Type="Italic">Populus nigra</Emphasis> L.) in turkey

The European black poplar (Populus nigra L.) is an ecologically and economically important tree species for Turkey. The important and major genetic resources of species for future breeding and ex situ conservation purposes have been archived in a clone bank in Ankara by selecting clones from natural populations and old plantations throughout Turkey. There is no study to date assessing genetic composition these materials. Two-hundred-thirty-three P. nigra clones from six geographic region of Turkey (clone collection populations), and 32 trees from two natural populations (Tunceli and Melet) were genotyped by using 12 nuclear microsatellite DNA markers. There were nine clones which duplicated in various frequencies. The analysis carried out with removal of the duplicated clones revealed a moderately high genetic diversity in studied populations. The observed heterozygosities ranged from 0.59 in Tunceli natural to 0.69 in Central Anatolia clone collection populations. In general, there was excess of heterozygosity in the studied populations. Populations composed of clone collections were significantly differentiated from natural populations (F _ST = 0.17), while there was little differentiation among those populations in the clone collection (F _ST = 0.03). Two distantly located natural populations with small sizes also differed from each other (F _ST = 0.17). Genetic structure analysis revealed two distinct groups (clone collection vs natural populations) with very high membership values (>92%). Clone collection populations had high level of admixture while natural populations had homogenous genetic structure. The presence of large number of clonal duplication, reduced genetic differentiation, and high level of admixture in clone collection populations indicate that genetic resources of European black poplar were highly degraded through genetic erosion and pollution caused by intensive cultural practices and extensive dispersal of clonal materials. To understand genetic diversity and its structural pattern thoroughly in the six clone collection populations, a further study with extensive and systematic sampling of European black poplar populations in major river ecosystems in Turkey will be useful.     

The relationship between trace elements and cardiac markers in acute coronary syndromes

Previous studies have demonstrated increased serum copper and iron levels and decreased selenium and zinc levels in patients with myocardial infarction. Furthermore, the prognostic value of the levels of trace elements in myocardial infarction has been stressed. We examined serum levels of Cu, Fe, Zn and Se, as well as glutathione peroxidase (GPx), a selenoenzyme with antioxidant properties, and C-reactive protein (CRP), a marker of inflammation, in acute coronary syndromes (ACS) regarding their relationship to cardiac troponins and creatine kinase-MB mass (CK-MBm), important prognostic markers. Serum trace elements, GPx activity and CRP were determined in 70 patients with ACS who were admitted within 12 h after the onset. Differences in these parameters were evaluated in three groups of patients divided according to the levels of cardiac markers: group III consisted of patients with high increases in cTnT, cTnI and CK-MBm (> or =0.9 ng/mL, > or =1.0 ng/mL, > or =30 ng/mL, respectively), patients with milder increases in these markers were included in groups II and I consisted of patients with values just above the upper reference limits. Serum Fe levels increased significantly in group II and even more prominently in group III compared to group I (p = 0.04, 0.002, respectively). There was no significant difference between groups II and III. The increase in serum Cu was significant in group III compared to both groups II and I (p = 0.04, 0.001, respectively). There was no significant difference between groups I and II regarding Cu and Zn. The decrease in serum Se and GPx levels was significant only between groups III and I (p = 0.004 for Se and p = 0.0001 for GPx). CRP levels showed a significant increase in group III compared to groups II and I (p = 0.03 and 0.001). CRP showed a significant positive and GPx a significant negative correlation to the cardiac markers cTnT, cTnI and CK-MBm. Cu was positively correlated to all cardiac markers, while the positive correlation between Fe and cardiac markers was significant only for cTnI. Both Zn and Se were negatively correlated to cTnT, and Se was also to cTnI. In conclusion, the increase in serum levels of Cu and Fe and the decrease in serum levels of Zn and Se in patients with higher levels of troponins and CK-MBm imply that trace element levels are related to the degree of myocardial damage and thus may play a role in the pathogenesis of ischemic heart disease. The strong correlations between cardiac markers and both CRP and GPx suggest that these parameters are promising prognostic factors in acute coronary syndromes.     

Identification and Characterization of the Glucosinolate–Myrosinase System in Caper (<Emphasis Type="Italic">Capparis ovata</Emphasis> Desf.)

Myrosinase (EC 3.2.1.147) catalyzes cleavage of glucosinolates, which consist of a thioglucoside moiety linked to amino acid-derived side chains. Myrosinase activity and expression profiles were investigated together with glucosinolate contents in Capparis ovata (caper) in order to characterize the glucosinolate–myrosinase system. The desulfoglucosinolates—glucocapparin, glucoiberin, progoitrin, epiprogoitrin, sinigrin, gluconapin, glucosinalbin, and glucobrassicin—were extracted and quantified from leaves, seeds, flowers, flower buds, and young shoots. The major desulfoglucosinolate was glucocapparin, which accumulated to values of 39.35 ± 0.09 and 25.56 ± 0.11 μmol g⁻¹ dry weight in seed and leaf extracts, respectively. Myrosinase has high activity in caper seeds, leaves, flowers, and flower bud tissues having the highest total activities in seed extracts (79.23 ± 0.18 U). However, specific activities were the highest in flower bud extracts (200.44 ± 0.09 U mg⁻¹ protein). The myrosinase protein migrated as a single band with a molecular weight of 65 kDa on sodium dodecyl sulfate polyacrylamide gel electrophoresis and on Western blots probed with the myrosinase-specific 3D7 antibodies. Native gel electrophoresis revealed two putative myrosinase isoenzymes in seeds, leaves, and flower tissues. The caper homolog of the Arabidopsis thaliana TGG1 gene was differentially expressed in seeds, leaves, flowers, and flower buds with the highest expression levels in leaves and flower bud tissues.     

Neutral sphingomyelinase inhibition alleviates apoptosis,but not ER stress,in liver ischemia–reperfusion injury

Previous studies have revealed the activation of neutral sphingomyelinase (N-SMase)/ceramide pathway in hepatic tissue following warm liver ischemia reperfusion (IR) injury. Excessive ceramide accumulation is known to potentiate apoptotic stimuli and a link between apoptosis and endoplasmic reticulum (ER) stress has been established in hepatic IR injury. Thus, this study determined the role of selective N-SMase inhibition on ER stress and apoptotic markers in a rat model of liver IR injury. Selective N-SMase inhibitor was administered via intraperitoneal injections. Liver IR injury was created by clamping blood vessels supplying the median and left lateral hepatic lobes for 60?min, followed by 60?min reperfusion. Levels of sphingmyelin and ceramide in liver tissue were determined by an optimized multiple reactions monitoring (MRM) method using ultrafast-liquid chromatography (UFLC) coupled with tandem mass spectrometry (MS/MS). Spingomyelin levels were significantly increased in all IR groups compared with controls. Treatment with a specific N-SMase inhibitor significantly decreased all measured ceramides in IR injury. A significant increase was observed in ER stress markers C/EBP-homologous protein (CHOP) and 78?kDa glucose-regulated protein (GRP78) in IR injury, which was not significantly altered by N-SMase inhibition. Inhibition of N-SMase caused a significant reduction in phospho-NF-kB levels, hepatic TUNEL staining, cytosolic cytochrome c, and caspase-3, -8, and -9 activities which were significantly increased in IR injury. Data herein confirm the role of ceramide in increased apoptotic cell death and highlight the protective effect of N-SMase inhibition in down-regulation of apoptotic stimuli responses occurring in hepatic IR injury.     

Polymersomes Containing Iron Sulfide (FeS) as Primordial Cell Model

According to Wächtershäuser??s ??Iron-Sulfur-World?? one major requirement for the development of life on the prebiotic Earth is compartmentalization. Vesicles spontaneously formed from amphiphilic components containing a specific set of molecules including sulfide minerals may have lead to the first autotrophic prebiotic units. The iron sulfide minerals may have been formed by geological conversions in the environment of deep-sea volcanos (black smokers), which can be observed even today. Wächtershäuser postulated the evolution of chemical pathways as fundamentals of the origin of life on earth. In contrast to the classical Miller-Urey experiment, depending on external energy sources, the ??Iron-Sulfur-World?? is based on the catalytic and energy reproducing redox system $ FeS + {H_2}S \to FeS{}_2 + {H_2} $ . The energy release out of this redox reaction (?_RG°?=??38 kJ/mol, pH 0) could be the cause for the subsequent synthesis of complex organic molecules and the precondition for the development of more complex units similar to cells known today. Here we show the possibility for precipitating iron sulfide inside vesicles composed of amphiphilic block-copolymers as a model system for a first prebiotic unit. Our findings could be an indication for a chemoautotrophic FeS based origin of life.     

Determination of stress responses induced by aluminum in maize (Zea mays)

To assess the alternative responses to aluminum toxicity, maize (Zea mays L. cv Karadeniz y?ld?z?) roots were exposed to different concentrations of AlCl3 (150, 300 and 450 μM). Aluminum reduced the root elongation by 39.6% in 150 μM, 44.1% in 300 μM, 50.1% in 450 μM AlCl3 after 96 h period. To correlate the root elongation with the alternative stress responses including aluminum accumulation, lipid peroxidation, mitotic abnormalities, reduction of starch content, intracellular Ca2+ accumulation, callose formation, lignin deposition and peroxidase activity, cytochemical and biochemical tests were performed. The results indicated that aluminum accumulation and lipid peroxidation were observed more densely on the root cap and the outer cortex cells. In addition to morphological deformations, cytochemical analysis displayed cellular deformations. Furthermore, mitotic abnormalities were observed such as c-mitosis, micronuclei, bi- and trinucleated cells in aluminum treated root tips. Aluminum treatment induced starch reduction, callose formation, lignin accumulation and intracellular Ca2+ increase. Moreover, the peroxidase activity increased significantly by 3, 4.4 and 7.7 times higher than in that of control after 96 h, respectively. In conclusion, aluminum is significantly stressful in maize culminating in morphological and cellular alterations.