Crystallization of membrane proteins from media composed of connected-bilayer gels

The use of hydrated-lipid gels in which the bilayer is an infinitely periodic (or at least continuous), three-dimensional structure offers a relatively new approach for the crystallization of membrane proteins. While excellent crystals of the Halobacterial rhodopsins have been obtained with such media, success remains poor in extending their use to other membrane proteins. Experience with crystallization of bacteriorhodopsin has led us to recognize a number of improvements that can be made in the use of such hydrated-gel media, which may now prove to be of general value for the crystallization of other membrane proteins.     

Clustering with neural networks

Partitioning a set ofN patterns in ad-dimensional metric space intoK clusters — in a way that those in a given cluster are more similar to each other than the rest — is a problem of interest in many fields, such as, image analysis, taxonomy, astrophysics, etc. As there are approximatelyK ^N/K! possible ways of partitioning the patterns amongK clusters, finding the best solution is beyond exhaustive search whenN is large. We show that this problem, in spite of its exponential complexity, can be formulated as an optimization problem for which very good, but not necessarily optimal, solutions can be found by using a Hopfield model of neural networks. To obtain a very good solution, the network must start from many randomly selected initial states. The network is simulated on the MPP, a 128 × 128 SIMD array machine, where we use the massive parallelism not only in solving the differential equations that govern the evolution of the network, but also in starting the network from many initial states at once thus obtaining many solutions in one run. We achieve speedups of two to three orders of magnitude over serial implementations and the promise through Analog VLSI implementations of further speedups of three to six orders of magnitude.Supported by a National Research Council-NASA Research Associatship     

Evaluating the roles of the heme a side chains in cytochrome c oxidase using designed heme proteins

Heme a is a redox cofactor unique to cytochrome c oxidases and vital to aerobic respiration. Heme a differs from the more common heme b by two chemical modifications, the C-8 formyl group and the C-2 hydroxyethylfarnesyl group. The effects of these porphyrin substituents on ferric and ferrous heme binding and electrochemistry were evaluated in a designed heme protein maquette. The maquette scaffold chosen, [Delta7-H3m](2), is a four-alpha-helix bundle that contains two bis(3-methyl-l-histidine) heme binding sites with known absolute ferric and ferrous heme b affinities. Hemes b, o, o+16, and heme a, those involved in the biosynthesis of heme a, were incorporated into the bis(3-methyl-l-histidine) heme binding sites in [Delta7-H3m](2). Spectroscopic analyses indicate that 2 equiv of each heme binds to [Delta7-H3m](2), as designed. Equilibrium binding studies of the hemes with the maquette demonstrate the tight affinity for hemes containing the C-2 hydroxyethylfarnesyl group in both the ferric and ferrous forms. Coupled with the measured equilibrium midpoint potentials, the data indicate that the hydroxyethylfarnesyl group stabilizes the binding of both ferrous and ferric heme by at least 6.3 kcal/mol via hydrophobic interactions. The data also demonstrate that the incorporation of the C-8 formyl substituent in heme a results in a 179 mV, or 4.1 kcal/mol, positive shift in the heme reduction potential relative to heme o due to the destabilization of ferric heme binding relative to ferrous heme binding. The two substituents appear to counterbalance each other to provide for tighter heme a affinity relative to heme b in both the ferrous and ferric forms by at least 6.3 and 2.1 kcal/mol, respectively. These results also provide a rationale for the reaction sequence observed in the biosynthesis of heme a.     

Amperometric detection of insulin at renewable sol-gel derived carbon ceramic electrode modified with nickel powder and potassium octacyanomolybdate(IV)

A renewable three-dimensional chemically modified carbon ceramic electrode (CCE) containing nickel powder and K4[Mo(CN)8] was constructed by sol-gel technique. The electrochemical properties and stability of modified electrode was evaluated by cyclic voltammetry in pH range 4-10. The redox couple of [Mo(CN)8] (4-/3-) was shown both as a solute in electrolyte solution and as a component of a carbon based conducting composite electrode. The apparent electron transfer rate constant (ks) and transfer coefficient (alpha) were determined by cyclic voltammetry and they were about 17.1 and 0.57 s(-1), respectively. The catalytic activity of the modified CCE toward insulin oxidation was investigated at pH range of 3-8 by cyclic votammetry. The modified electrode showed excellent electrocatalytic activity toward insulin electroxidation at physiological pH value. The modified electrode was used for insulin detection chronoamperometrically at pH 7. Under optimized condition in amperometry method, the concentration calibration range, detection limit and sensitivity were 0.5-500 nM, 0.45 nM and 6140 nA/microM, respectively. Flow injection amperometric determination of insulin at pH 7.4, at this modified electrode yielded a calibration curve with the following characteristics, linear dynamic range 100-500 pM; sensitivity 8.1 nA/nM and detection limit 40 pM (based on S/N = 3). The inherent stability at wide pH range, high sensitivity, low detection limit, low cost and ease of preparation are of advantageous of this insulin sensor. This sensor indicates great promise for monitory insulin in chromatographic effluents.     

Proteomic analysis of rice leaves during drought stress and recovery

Three-week old plants of rice (Oryza sativa L. cv CT9993 and cv IR62266) developed gradual water stress over 23 days of transpiration without watering, during which period the mid-day leaf water potential declined to approximately -2.4 MPa, compared with approximately -1.0 MPa in well-watered controls. More than 1000 protein spots that were detected in leaf extracts by proteomic analysis showed reproducible abundance within replications. Of these proteins, 42 spots showed a significant change in abundance under stress, with 27 of them exhibiting a different response pattern in the two cultivars. However, only one protein (chloroplast Cu-Zn superoxide dismutase) changed significantly in opposite directions in the two cultivars in response to drought. The most common difference was for proteins to be up-regulated by drought in CT9993 and unaffected in IR62266; or down-regulated by drought in IR62266 and unaffected in CT9993. By 10 days after rewatering, all proteins had returned completely or largely to the abundance of the well-watered control. Mass spectrometry helped to identify 16 of the drought-responsive proteins, including an actin depolymerizing factor, which was one of three proteins detectable under stress in both cultivars but undetectable in well-watered plants or in plants 10 days after rewatering. The most abundant protein up-regulated by drought in CT9993 and IR62266 was identified only after cloning of the corresponding cDNA. It was found to be an S-like RNase homologue but it lacked the two active site histidines required for RNase activity. Four novel drought-responsive mechanisms were revealed by this work: up-regulation of S-like RNase homologue, actin depolymerizing factor and rubisco activase, and down-regulation of isoflavone reductase-like protein.     

INFLUENCE OF UV-B RADIATION ON NITROGEN UTILIZATION BY A NATURAL ASSEMBLAGE OF PHYTOPLANKTON

A 7‐day mesocosm experiment was conducted in July 1996 to investigate the effects of ambient UV‐B radiation (UVBR) exclusion and two UVBR enhancements above ambient levels on NO₃^?, NH₄⁺ and urea utilization in a natural plankton community (<240 μm) from the Lower St. Lawrence Estuary. The phytoplankton community was dominated by diatoms during the first 3 days and, afterward, by flagellates and dinoflagellates. The results of 4‐h incubations just below the water surface show that, compared with ambient UVBR conditions, UVBR exclusion generally increased NO₃^?, NH₄⁺, and urea uptakes. During the last 4 days of the experiment, the percent increase in the specific uptake rate of urea under excluded UVBR conditions varied between 17% and 130% and was a linear function of the ambient UVBR dose removed. During the first 3 days, the phytoplankton community dominated by diatoms was able to withstand UVBR enhancements without any perceptible effect on nitrogen uptake. However, during the post‐diatom bloom period, UVBR enhancements resulted in decreases in NO₃^?, NH₄⁺, and urea uptake compared with ambient UVBR conditions. The reduction of urea uptake under UVBR enhancements during the last 3 days varied between 23% and 64% and was linearly related to the enhanced UVBR dose. However, the different UVBR treatments did not affect the internal organic nitrogen composition (internal urea, free amino acids, and proteins) of the phytoplankton community experiencing vertical mixing in the mesocosms. The discrepancy between short‐term uptake measurements at the surface and long‐term effects in the mesocosms emphasizes the importance of vertical mixing on UVBR effects in natural ecosystems. This suggests that an increase in ambient UVBR would have a minimal effect on nitrogen utilization by natural phytoplankton assemblages if these are vertically mixed.     

Enhanced resistance to two stem borers in an aromatic rice containing a synthetic cryIA(b) gene

Rice cultivars of isozyme group V include high-quality, aromatic rices that are difficult to improve by traditional methods because of the loss of quality characters upon sexual hybridization. Their low-tillering plant type predisposes them to economic loss from attack by stem borers, a group of insects to which they are susceptible. We report here the enhancement of stem borer resistance in cv. Tarom Molaii through transformation by microprojectile bombardment. Embryogenic calli derived from mature seeds were bombarded with gold particles coated with plasmid pCIB4421, carrying a synthetic truncated toxin gene based on the cryIA(b) gene from Bacillus thuringiensis, and plasmid pHygII, carrying the hygromycin phosphotransferase (hpt) selectable marker gene. Inclusion of 50 mg/l hygromycin B in culture media from bombardment through to rooting of plantlets eliminated escapes. The procedure generated three independent hpt transformants of which two also contained the cryIA(b) gene. One such line (No. 827) produced truncated (67 kDa) CryIA(b) protein equivalent to about 0.1% of total soluble protein. The cryIA(b) gene was controlled by the promoter of the maize C₄ PEP carboxylase gene and was expressed in leaf blades but was not expressed to a detectable level in dehulled mature grain. Line 827 contained about 3 copies of the cryIA(b) gene which segregated as a single dominant Mendelian locus in the second (T₁) and third (T₂) generations and co-segregated with enhanced resistance to first-instar larvae of striped stem borer (Chilo suppressalis) and yellow stem borer (Scirpophaga incertulas). T₂ line 827-6 homozygous for the cryIA(b) gene showed no dead hearts or whiteheads after infestation with stem borers, whereas T₂ line 827-25 lacking the gene averaged 7 dead hearts per plant and 2.25 whiteheads per plant. These results establish that transformation of high-quality rices of group V is a feasible alternative to sexual hybridization.     

Calreticulin regulates insulin receptor expression and its downstream PI3 Kinase/Akt signalling pathway

Defects in insulin signalling and glucose metabolism are associated with the development of diabetes. Insulin signalling is initiated by the binding of insulin to its receptor and triggering cascades of events including activation of PI3kinase/Akt signalling pathway. Calreticulin (CRT) is a calcium binding chaperone molecule located in the endoplasmic reticulum. Targeted deletion of CRT in mice is embryonic lethal as a result of developmental and metabolic abnormalities. Rescued CRT null mice develop severe hypoglycemia the reason for which is not known. In addition, ventricular cardiomyocytes isolated from CRT null (crt-/-) mice have increased glycogen deposits. Therefore, the aim of this study was to investigate the changes in the glucose uptake and insulin signalling pathway (mainly PI3 kinase/Akt) in the absence of CRT. Here we show a significant increase in the glucose uptake by the crt-/- cells. This increase was accompanied by a significant increase in both insulin receptor beta expression, Insulin receptor substrate-1 phosphorylation, GLUT-1 expression and in insulin stimulated Akt phosphorylation and kinase activity in the crt-/- cells. Intriguingly, the increased expression of insulin receptor beta in the crt-/- was due to decreased levels of p53 protein. The current study is the first evidence for the up-regulation of insulin receptor density and activity in the absence of CRT function.     

Dynamics of microbial planktonic food web components during a river flash flood in a Mediterranean coastal lagoon

Episodic river flash floods, characteristic of Mediterranean climates, are suspected to greatly affect the functioning of microbial food webs. For the first time, the abundance, biomass and diversities of microbial food web components were studied before and during 4 consecutive days after a flash flood that occurred in November 2008, in the surface waters of five stations along a salinity gradient from 20 to 36 in the Thau lagoon. Eukaryotic pico- and nanophytoplankton were discharged from the river into the lagoon and increased by 30- and 70-fold, respectively. Bacteria increased by only 2-fold in the lagoon, from around 4–8 × 10⁶ cells ml⁻¹, probably benefiting from river nutrient input. Chlorophyll a increased 4-fold, and pigment biomarkers showed that the dinophyceae, prasinophyceae and prymnesiophyceae were sensitive to the flood perturbation, whereas the bacillariophyceae, cryptophyceae and chlorophyceae were resistant and/or transported to the lagoon from the river. Predator responses were more complex as total heterotrophic flagellate abundance decreased slightly, whereas those of specific naked ciliates increased, particularly for Uronema sp. The flood also induced a specific change in diversity, from a community dominated by Strobilidium spiralis to a community dominated by Uronema sp. The tintinnid community was particularly sensitive to the flood event as the abundance of all species decreased greatly. The high increases in biomass, mainly brought by the river during the flood, could have eventually sedimented to the benthic layer and/or been transported further into the lagoon, supporting the pelagic food web, or have even been exported to the Mediterranean Sea.