Overcoming ammonium toxicity.

Ammonia (ammonium ion under physiological conditions) is one of the key nitrogen sources in cellular amino acid biosynthesis. It is continuously produced in living organisms by a number of biochemical processes, but its accumulation in cells leads to tissue damage. Current knowledge suggests that a few enzymes and transporters are responsible for maintaining the delicate balance of ammonium fluxes in plant tissues. In this study we analyze the data in the scientific literature and the publicly available information on the dozens of biochemical reactions in which endogenous ammonium is produced or consumed, the enzymes that catalyze them, and the enzyme and transporter mutants listed in plant metabolic and genetic databases (Plant Metabolic Network, TAIR, and Genevestigator). Our compiled data show a surprisingly high number of little-studied reactions that might influence cellular ammonium concentrations. The role of ammonium in apoptosis, its relation to oxidative stress, and alterations in ammonium metabolism induced by environmental stress need to be explored in order to develop methods to manage ammonium toxicity.

The changing epitome of species identification - DNA barcoding.

The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The 'DNA barcodes' show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more.

Transposable elements domesticated and neofunctionalized by eukaryotic genomes.

Whole genome sequencing has provided a massive amount of information about the origin, diversity and genomic impact of repetitive DNA sequences (repDNA). Among the many classes of repDNA, prokaryotic transposable elements (TEs) replicate, move, amplify and accumulate in invaded genomes and thus represent the major force in restructuring host genes and genomes during evolution. Similar to retroviruses, autonomous TEs became part of the host genomes, and after their molecular domestication, they became functional genes (genomic fossils) in eukaryotic genomes. In this review, examples of the domestication events are discussed, some of which are known to be induced by biotic and abiotic stressors.

[Direct comparison of working length determination by ProPex electronic apex locator and radiographic method--an in vitro study]. / ProPex apexlokátorral és radiológiai módszerrel végzett munkahossz-meghatározás összehasonlítása in vitro direkt eljárással.

The purpose of this study was to compare the accuracy of electronic and radiographical working length determination in extracted molars. Palatal root canals of twenty maxillary molars were used. Teeth were randomly divided into two groups. In case of the first group the working length was measured by apex locator (Propex, Dentsply-Maillefer), and in the second group it was measured with radiographic method (RVG, Trophy). The files, used for measuring the working length, were cemented into the teeth. The apical half of the root was ground, and the tips of the files visualised as well as the apical region of the root canal with the apical constriction. Standard digital photographs were taken from the prepared samples, and the distance between the tip of the file and the physiological foramen was measured. Two sample t test was used for statistical analysis. The physiological foramen was approached on average to 0.11 mm by the electronic method and to 0.58 mm by the radiological method. There was no significant difference in the measuring accuracy between the two methods (p=0.10). The electronic and radiological working length determination may prove to show an equivalent consistency.

Comparison of radiographic and electronical working length determination on palatal and mesio-buccal root canals of extracted upper molars.

OBJECTIVE: The objective of this work was to compare the accuracy of working length determination of ProPex (Dentsply-Maillefer) electronic apex locator (EAL) to the radiographic method on extracted molars. STUDY DESIGN: Root canal length was determined using the electronic apex locator and conventional radiographic method. Digital radiographs were taken and the distance between the tip of the file and the radiographic apex was measured. Mann-Whitney and chi(2) tests were used for the statistical analysis. RESULTS: The average distance between the tip of the file and the radiographic apex in the mesio-buccal canals was 0.46 mm with the radiologic method, and 0.23 mm with EAL, and 0.43 mm and 0.31 mm in the palatal canals, respectively. The difference at the mesio-buccal canals was significant (Mann-Whitney test P = .048). The number of overextensions was higher in the EAL group. CONCLUSION: The desired position of the file achieved by the EAL proved to be more accurate in the mesio-buccal canals than with the radiologic method alone.

RT-PCR analysis and stress response capacity of transgenic gshI-poplar clones (Populus x canescens) in response to paraquat exposure.

Stress response capacity (Fv/Fm at 690 nm and F690/F735 at Fmax) of untransformed hybrid poplar, Populus x canescens (P tremula x P alba), and two transgenic lines overexpressing gamma-ECS (gamma-glutamylcysteine synthetase) either in the cytosol (cyt-ECS) or in the chloroplast (chl-ECS) was studied in response to the herbicide paraquat (4.0 x 10(-9) to 4.0 x 10(-6) M) for 21 days. Significant differences at sublethal (4.0 x 10(-7) M) and bleaching (4.0 x 10(-6) M) concentrations of paraquat were observed with about a two-fold and eight-fold decrease in the photosynthetic activity (Fv/Fm at 690 nm and F690/F735 at Fmax), respectively. None of the gshI transgenic lines (cyt-ECS, chl-ECS) with elevated GSH content exhibited significant tolerance to paraquat. Semiquantitative RT-PCR of the cyt-ECS clone was used for gene expression analysis of the nuclear encoded rbcS gene and the stress responsive gst gene. Expression of the constitutively expressed 26SrRNA ribosomal gene was probed as a control for all RT-PCR reactions. The relative intensities of gene expressions normalized to the level of 26SrRNA intensity showed a 50% decrease in the nuclear encoded rbcS expression and a 120% increase in the stress responsive gst gene expression of the paraquat treated (4.0 x 10(-7) M) samples of the transgenic poplar line (cyt-ECS).

AFLP analysis and improved phytoextraction capacity of transgenic gshI-poplar clones (Populus x canescens L.) for copper in vitro.

Clone stability and in vitro phytoextraction capacity of vegetative clones of P. x canescens (2n = 4x = 38) including two transgenic clones (ggs11 and lgl6) were studied as in vitro leaf disc cultures. Presence of the gshI-transgene in the transformed clones was detected in PCR reactions using gshI-specific primers. Clone stability was determined by fAFLP (fluorescent amplified DNA fragment length polymorphism) analysis. In total, 682 AFLP fragments were identified generated by twelve selective primer pairs after EcoRI-MseI digestion. Four fragments generated by EcoAGT-MseCCC were different (99.4% genetic similarity) which proves an unexpectedly low bud mutation frequency in P. x canescens. For the study of phytoextraction capacity leaf discs (8 mm) were exposed to a concentration series of ZnSO4 (10(-1) to 10(-5) M) incubated for 21 days on aseptic tissue culture media WPM containing 1 microM Cu. Zn2+ caused phytotoxicity only at high concentrations (10(-1) to 10(-2) M). The transgenic poplar cyt-ECS (ggs11) clone, as stimulated by the presence of Zn, showed elevated heavy metal (Cu) uptake as compared to the non-transformed clone. These results suggest that gshI-transgenic poplars may be suitable for phytoremediation of soils contaminated with zinc and copper.

Ability of transgenic poplars with elevated glutathione content to tolerate zinc(2+) stress.

Phytoremediation potentials of four poplar lines, Populus nigra (N-SL clone), Populus canescens, and two transgenic P. canescens clones were investigated using in vitro leaf discs cultures. The transgenic poplars overexpressed a bacterial gene encoding gamma-glutamylcysteine synthetase in the cytosol (11ggs) or in the chlopoplasts (6LgI), and therefore, they contained an elevated level of glutathione. Leaf discs of poplar clones were exposed to different concentrations of ZnSO(4) for 21 days. Zinc(2+) was phytotoxic only at high concentrations (10(-2) to 10(-1) M) at all P. canescens lines, but P. nigra was more sensitive. Transgenic poplars showed elevated heavy metal uptake as compared to the nontransformed clones. Treatments with zinc(2+) strongly induced the activity of glutathione S-transferase enzyme in untransformed poplar lines but to a lesser extent in the transgenic clones. These results suggest that transgenic poplars are more suitable for phytoremediation of soils contaminated with zinc(2+) than wild-type plants.