UV-A Irradiation Guards the Photosynthetic Apparatus Against UV-B-Induced Damage

In clusterbean leaves UV-B radiation caused a reduction in contents of chlorophylls and carotenoids and in the efficiency of photosystem 2 photochemistry. The degree of damage was reduced when UV-A accompanied the UV-B radiation. This indicates the counteracting effect of UV-A radiation against UV-B-induced impairment.     

Structural consequences of D481N/K483Q mutation at glycine binding site of NMDA ionotropic glutamate receptors: a molecular dynamics study

N-Methyl-D-Aspartate (NMDA) receptors are the ligand gated as well as voltage sensitive ionotropic glutamate receptors, widely distributed in the vertebrate central nervous system and they play critical role in the pathogenesis of schizophrenia. Molecular dynamics simulations have been carried out on high resolution crystal structure of NR1 subunit of NMDA receptor ligand binding core (S1S2) in four different conformations. We have investigated consequence of D481N/K483Q double mutation of NR1 subunit from simulation results of (a) glycine bound form (WG), (b) unbound (closed-apo) form (WOG), (c) a double mutated form (DM), and (d) the antagonist (5,7-dichlorokynuric acid) bound form (DCKA). The MD simulations and simulated annealing for 4ns show a distinct conformation for the double mutated conformation that neither follows the antagonist nor apo conformation. There are two distinct sites, loop1 and loop2 where the double mutated structure in its glycine bound form shows significant RMSD deviations as compared to the wild-type. The interactions of glycine with the receptor remain theoretically unchanged in the double mutated structure and there is no detachment of S1S2 domains. The results suggest that separation of S1 and S2 domains may not be essential for channel inactivation. Therefore, it is hypothesized that hypoactivation of NMDA receptor channels may arise out of the conformational changes at non-conserved Loop1 and Loop2 regions observed in the mutated structure. The Loop1 and Loop2 regions responsible for inter-subunit interactions in a functional NMDA receptor, may therefore, render the ligand bound form defunct. This may account for behavioral anomalies due to receptor inactivation seen in grin1 mutated mice.     

Evolutionary trace analysis of ionotropic glutamate receptor sequences and modeling the interactions of agonists with different NMDA receptor subunits

The ionotropic N-methyl-d-aspartate (NMDA) receptor is of importance in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 or NR3 subunits. We have carried out evolutionary trace (ET) analysis of forty ionotropic glutamate receptor (IGRs) sequences to identify and characterize the residues forming the binding socket. We have also modeled the ligand binding core (S1S2) of NMDA receptor subunits using the recently available crystal structure of NR1 subunit ligand binding core which shares ~40% homology with other NMDA receptor subunits. A short molecular dynamics simulation of the glycine-bound form of wild-type and double-mutated (D481N; K483Q) NR1 subunit structure shows considerable RMSD at the hinge region of S1S2 segment, where pore forming transmembrane helices are located in the native receptor. It is suggested that the disruption of domain closure could affect ion-channel activation and thereby lead to perturbations in normal animal behavior. In conclusion, we identified the amino acids that form the ligand-binding pocket in many ionotropic glutamate receptors and studied their hydrogen bonded and nonbonded interaction patterns. Finally, the disruption in the S1S2 domain conformation (of NR1 subunit- crystal structure) has been studied with a short molecular dynamics simulation and correlated with some experimental observations.Figure The figure shows the binding mechanism of glutamate with NR2B subunit of the NMDA receptor. Glutamate is shown in cpk, hydrogen bonds in dotted lines and amino acids in blue. The amino acids shown here are within a 4-Å radius of the ligand (glutamate)     

Herbicide resistance from a divided EPSPS protein: the split Synechocystis DnaE intein as an in vivo affinity domain

We report that the N- and C-terminal splicing domains of the intein found in the dnaE gene of Synechocystis sp. PCC6803 (Ssp DnaE intein) are capable of association in vivo and in vitro, even with key splicing residues changed to alanine (Cys(1), Asn(159), and Cys(+1) to Ala). These studies utilized the herbicide resistant form of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Salmonella typhimurium and an Escherichia coli strain with the EPSPS gene deleted from its genome (E. coli strain ER2799). EPSPS was mapped to identify potential split sites using a facile Tn7 linker scanning procedure. Forty positions were found to tolerate a five amino acid insertion while 21 sites did not, as assayed by the rescue of growth of E. coli strain ER2799. Further characterization of these sites by inserting a full length Ssp DnaE intein identified residue 235 of EPSPS as the optimal position. The EPSPS gene was then divided into amino acids 1-235 and 236-427 which were fused to residues 1-123 and 124-159 of a splicing defective Ssp DnaE intein, respectively. Expression of the EPSPS-intein fusions from separate DNA molecules conferred resistance to the herbicide glyphosate, indicating that the intein splicing domains were bringing the EPSPS fragments together to generate activity. As a control the split EPSPS without the intein-affinity domain did not allow cell growth. The use of an intein as an in vivo affinity domain was termed intein-mediated protein complementation (IPC). Intein fragment assembly was verified in vitro by immobilizing the C-terminal splicing domain of the Ssp DnaE intein on a resin and demonstrating that the N-terminal 235 amino acids of EPSPS only bound to the resin when fused to the N-terminal splicing domain of the Ssp DnaE intein. As chloroplast DNA is not transmitted by pollen in plants such as corn and soybean, transgene spread via pollen may be controlled in the future by expressing inactive gene fragments from separate DNA locations, such as the nuclear and chloroplast genome, and using the split intein to generate protein activity.     

Optimization of flow rate,initial metal ion concentration and biomass density for maximum removal of Cu2+ by immobilized Microcystis

The potential of alginate-immobilized Microcystis packed in a column for maximum removal of Cu²⁺ at different flow rates, biomass, and initial metal ion concentration was assessed in a continuous flow system. Although Cu²⁺ removal did occur at all the flow rates tested, it was maximum (54%) at 0.75-ml min⁻¹ flow rate, 30 μg ml⁻¹ initial metal ion concentration and 0.016 g biomass. Cu²⁺ removal was influenced by inlet metal ion concentration and biomass density. An increase in the biomass concentration from 0.016 to 0.128 g resulted in an apparent increase in percentage removal but the Cu²⁺ adsorbed per unit dry wt. declined. When the flow rate (0.75 ml min⁻¹) and biomass density (0.064 g) were kept constant and the inlet metal ion concentration was varied from 10 to 150 μg ml⁻¹, a 68% removal of Cu²⁺ was obtained at 50 μg ml⁻¹ initial concentration in a time duration of 15 min. The metal-laden columns were efficiently desorbed and regenerated following elution with double distilled water (DDW) (pH 2) (89%). This was followed by 1 mm EDTA > 1 mm NTA > 0.1 mm EDTA > 1 mm HCl > 1 mm HNO₃ > 5 mm CaCl₂ > DDW (pH 7.0) > 1 mm NaHCO₃ > 1 mm CaCl₂. Of the total (2.83 mg) adsorbed Cu²⁺, 1.89 mg (67%) was desorbed by DDW (pH 2) within the first 20 min of elution time. Thereafter the desorption rate slowed down and only 22% (0.632 mg) desorption was obtained in the last 20 min. In contrast to water pH 2, the desorption of Cu²⁺ by 1 mm EDTA was very slow, the maximum being 8% after 40 min of elution. This revised version was published online in July 2006 with corrections to the Cover Date.     

Evaluation of Wheat Chromosome Translocation Lines for High Temperature Stress Tolerance at Grain Filling Stage

High temperature (HT, heat) stress is detrimental to wheat (Triticum aestivum L.) production. Wild relatives of bread wheat may offer sources of HT stress tolerance genes because they grow in stressed habitats. Wheat chromosome translocation lines, produced by introgressing small segments of chromosome from wild relatives to bread wheat, were evaluated for tolerance to HT stress during the grain filling stage. Sixteen translocation lines and four wheat cultivars were grown at optimum temperature (OT) of 22/14°C (day/night). Ten days after anthesis, half of the plants were exposed to HT stress of 34/26°C for 16 d, and other half remained at OT. Results showed that HT stress decreased grain yield by 43% compared with OT. Decrease in individual grain weight (by 44%) was the main reason for yield decline at HT. High temperature stress had adverse effects on leaf chlorophyll content and Fv/Fm; and a significant decrease in Fv/Fm was associated with a decline in individual grain weight. Based on the heat response (heat susceptibility indices, HSIs) of physiological and yield traits to each other and to yield HSI, TA5594, TA5617, and TA5088 were highly tolerant and TA5637 and TA5640 were highly susceptible to HT stress. Our results suggest that change in Fv/Fm is a highly useful trait in screening genotypes for HT stress tolerance. This study showed that there is genetic variability among wheat chromosome translocation lines for HT stress tolerance at the grain filling stage and we suggest further screening of a larger set of translocation lines.     

Cross-talk between Serine/Threonine Protein Phosphatase 2A and Protein Tyrosine Phosphatase 1B Regulates Src Activation and Adhesion of Integrin αIIbβ3 to Fibrinogen

Integrin α_IIbβ₃ signaling mediated by kinases and phosphatases participate in hemostasis and thrombosis, in part, by supporting stable platelet adhesion. Our previous studies indicate that the genetic manipulation of PP2Acα (α isoform of the catalytic subunit of protein phosphatase 2A) negatively regulate the adhesion of human embryonal kidney 293 cells expressing α_IIbβ₃ to fibrinogen. Here, we demonstrated that small interference RNA (siRNA) mediated knockdown of PP2Acα in 293 α_IIbβ₃ cells led to the dephosphorylation of Src Tyr-529, phosphorylation of Src Tyr-418 and an increased Src kinase activity. Conversely, overexpression of PP2Acα decreased the basal Src activity. Pharmacological inhibition of PP2Ac in human platelets or PP2Acα knockdown in primary murine megakaryocytes resulted in Src activation. PP2Acα-depleted 293 α_IIbβ₃ cells did not alter the serine (Ser) phosphorylation of Src but enhanced the Ser-50 phosphorylation of protein tyrosine phosphatase 1B (PTP-1B) with a concomitant increase in the PTP-1B activity. Src activation in the PP2Acα-depleted 293 α_IIbβ₃ cells was abolished by siRNA mediated knockdown of PTP-1B. Pharmacological inhibition of Src or knockdown of Src, PTP-1B blocked the enhanced activation of extracellular signal-regulated kinase (ERK1/2) and the increased adhesiveness of PP2Acα-depleted 293 α_IIbβ₃ cells to fibrinogen, respectively. Thus, inactivation of PP2Acα promotes hyperphosphorylation of PTP-1B Ser-50, elevates PTP-1B activity, which dephosphorylates Src Tyr-529 to activate Src and its downstream ERK1/2 signaling pathways that regulate α_IIbβ₃ adhesion. Moreover, these studies extend the notion that a cross-talk between Ser/Thr and Tyr phosphatases can fine-tune α_IIbβ₃ outside-in signaling.     

Nature of hydrocortisone-elicited amplification of template activity of liver chromatin.

The template efficiency of euchromatin region and number of RNA polymerase binding sites on this region of rat liver chromatin were significantly elevated at 3.5 h after administration of hydrocortisone to adrenalectomised rats. The euchromatin from the liver chromatin of horomone-treated rats was also found to have significantly increased levels of nonhistone proteins as compared to those in euchromatin fraction derived from adrenalectomised rats.     

Closing Yield Gaps: How Sustainable Can We Be?

Global food production needs to be increased by 60–110% between 2005 and 2050 to meet growing food and feed demand. Intensification and/or expansion of agriculture are the two main options available to meet the growing crop demands. Land conversion to expand cultivated land increases GHG emissions and impacts biodiversity and ecosystem services. Closing yield gaps to attain potential yields may be a viable option to increase the global crop production. Traditional methods of agricultural intensification often have negative externalities. Therefore, there is a need to explore location-specific methods of sustainable agricultural intensification. We identified regions where the achievement of potential crop calorie production on currently cultivated land will meet the present and future food demand based on scenario analyses considering population growth and changes in dietary habits. By closing yield gaps in the current irrigated and rain-fed cultivated land, about 24% and 80% more crop calories can respectively be produced compared to 2000. Most countries will reach food self-sufficiency or improve their current food self-sufficiency levels if potential crop production levels are achieved. As a novel approach, we defined specific input and agricultural management strategies required to achieve the potential production by overcoming biophysical and socioeconomic constraints causing yield gaps. The management strategies include: fertilizers, pesticides, advanced soil management, land improvement, management strategies coping with weather induced yield variability, and improving market accessibility. Finally, we estimated the required fertilizers (N, P₂O₅, and K₂O) to attain the potential yields. Globally, N-fertilizer application needs to increase by 45–73%, P₂O₅-fertilizer by 22–46%, and K₂O-fertilizer by 2–3 times compared to the year 2010 to attain potential crop production. The sustainability of such agricultural intensification largely depends on the way management strategies for closing yield gaps are chosen and implemented.