NMR for structural proteomics of Thermotoga maritima: Screening and structure determination

This paper describes the NMR screening of 141 small (<15 kDa) recombinant Thermotoga maritima proteins for globular folding. The experimental data shows that approximately 25% of the screened proteins are folded under our screening conditions, which makes this procedure an important step for selecting those proteins that are suitable for structure determination. A comparison of screening based either on 1D 1H NMR with unlabeled proteins or on 2D [1H,15N]-COSY with uniformly 15N-labeled proteins is presented, and a comprehensive analysis of the 1D 1H NMR screening data is described. As an illustration of the utility of these methods to structural proteomics, the NMR structure determination of TM1492 (ribosomal protein L29) is presented. This 66-residue protein consists of a N-terminal 3(10)-helix and two long alpha-helices connected by a tight turn centered about glycine 35, where conserved leucine and isoleucine residues in the two alpha-helices form a small hydrophobic core.     

Cholesterol-degrading bacteria: isolation,characterization and bioconversion

Agrobacterium sp. M4, a gram negative, motile, oxidase- and catalase-positive bacterium isolated from 410 colonies from soil was found to degrade cholesterol with high efficiency (within 9 days). The first and most probably the main metabolite of cholesterol degradation was detectable on TLC from the second day of incubation, and it was identified as 4-cholestene-3-one. No substances with cyclopentenoperhydrophenanthrene structure was found under U.V. radiation at 256 and 336nm, or by staining with sulphuric acid after 9 days of incubation. Morphological, cultural and biochemical characteristics of the isolate placed it in the genus Agrobacterium although its urease activity was negative. Further investigation on this newly isolated strain is under way.     

Hepatocellular carcinoma versus carcinoma metastatic to the liver. Value of stains for carcinoembryonic antigen and naphthylamidase in fine needle aspiration biopsy material

Staining for amino acid naphthylamidase and carcinoembryonic antigen (CEA) was examined as an ancillary technique to improve the accuracy of differentiating hepatocellular carcinoma from metastatic carcinoma to the liver in fine needle aspiration (FNA) biopsy specimens. Twenty-four cases of FNA specimens from the liver, in which air-dried smears and/or cell blocks were available, were examined. Naphthylamidase-positive bile canalicular structures were present in 2 cases of hepatocellular carcinoma and absent in 8 cases of metastatic carcinoma studied. Ninety percent of the hepatocellular carcinomas were immunoreactive with the antibody to CEA, showing a predominantly bile canalicular pattern. Ninety percent of the cases of metastatic carcinoma were positive with the antibody to CEA, showing a diffuse cytoplasmic pattern. These findings indicate that both staining techniques may be useful in differentiating hepatocellular carcinoma from metastatic carcinoma. Since the naphthylamidase stain requires air-dried smears, which may not be available, whereas immunocytochemistry can be done on fixed material, the latter technique is more practical.     

The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel

Voltage-gated potassium (K_V) channels are membrane proteins that respond to changes in membrane potential by enabling K⁺ ion flux across the membrane. Polyunsaturated fatty acids (PUFAs) induce channel opening by modulating the voltage-sensitivity, which can provide effective treatment against refractory epilepsy by means of a ketogenic diet. While PUFAs have been reported to influence the gating mechanism by electrostatic interactions to the voltage-sensor domain (VSD), the exact PUFA-protein interactions are still elusive. In this study, we report on the interactions between the Shaker K_V channel in open and closed states and a PUFA-enriched lipid bilayer using microsecond molecular dynamics simulations. We determined a putative PUFA binding site in the open state of the channel located at the protein-lipid interface in the vicinity of the extracellular halves of the S3 and S4 helices of the VSD. In particular, the lipophilic PUFA tail covered a wide range of non-specific hydrophobic interactions in the hydrophobic central core of the protein-lipid interface, while the carboxylic head group displayed more specific interactions to polar/charged residues at the extracellular regions of the S3 and S4 helices, encompassing the S3-S4 linker. Moreover, by studying the interactions between saturated fatty acids (SFA) and the Shaker K_V channel, our study confirmed an increased conformational flexibility in the polyunsaturated carbon tails compared to saturated carbon chains, which may explain the specificity of PUFA action on channel proteins.     

Using universal degenerate primers for restriction digestion mapping by PCR.

In this study, a polymerase chain reaction (PCR) is developed to determine the restriction map without using restriction endonucleases. A 937 bp fragment of pUC 19 which contained one cut site for EcoRI and two recognition sites for PvuII was used as a model. The PCR was carried out using designed degenerate primers and the products were analyzed on 1.5% agarose gel. The number of cut sites, length of fragments and the arrangement of the fragments from 3' or 5' end of desired sequence were determined.     

Novel material concepts of transducers for chemical and biosensors

The objectives of this work are to contribute to the knowledge about physical and chemical properties of WBG semiconductors, such as ZnO and GaN towards development of advanced bio- and chemical sensors. For the semiconductors, growth techniques typically yielding single crystal material are applied. Thin epitaxial quality films of ZnO and GaN are fabricated on SiC or sapphire substrates. An emphasis is given to ZnO due to the interesting combination of the semiconductor and oxide properties. Surface bio-functionalization of ZnO is performed by APTES, MPA or MP-TMS molecules. We have compared some of the results to (hydroxylated) GaN surfaces functionalized by MP-TMS. The covalent attachment of the self-assembled biomolecular layers has been proven by XPS analysis. For complementary electrical characterization impedance spectroscopy measurements were performed. The results are intended to serve the realization of bioelectronic transducer devices based on SiC or GaN transistors with a ZnO gate layer.

To take advantage of the catalytic properties of ZnO, initial prototypes of chemical sensors for gas sensing are processed on ZnO deposited either on SiC or on sapphire and they are further tested for the response to reducing or oxidizing gas ambient. The sensor devices show sensitivity to oxygen in the surface resistivity mode while a Pt Schottky contact ZnO/SiC device responds to reducing gases. These results are compared to published results on Pt/GaN Schottky diodes.     

Production of cholesterol oxidase by a newly isolated Rhodococcus sp.

Fifteen strains of microorganisms with ability to degrade cholesterol were isolated. Among them a Gram-positive, non-motile, non-sporing bacterium with meso-DAP in the cell wall and with a rod-coccus cycle showed the highest ability for cholesterol degradation. It was identified as Rhodococcus sp. strain 2C and was deposited by code 1633 in Persian type culture collection (PTCC). This strain was able to produce high levels of both extracellular and cell-bound cholesterol oxidases in media containing cholesterol as a sole carbon source. The effects of medium composition and physical parameters on cholesterol oxidase production were studied. The optimized medium was found to contain cholesterol 0.15% (w/v), yeast extract 0.3% (w/v), diammonium hydrogen phosphate 0.1% (w/v), Tween 80 (0.05%). The optimum pH and temperature for cholesterol oxidase production in optimized medium were found to be 8–30 °C respectively. Triton X-100 showed the greatest effect in releasing the cell-bound enzyme. The first and most probably the main metabolite of cholesterol degradation was purified and identified as 4-cholestene-3-one.     

Nicotine improves ethanol-induced memory impairment: The role of dorsal hippocampal NMDA receptors

AimsThe current study was undertaken to determine the role of dorsal hippocampal N-methyl-d-aspartate (NMDA) receptors in nicotine's effect on impairment of memory by ethanol.Main methodsAdult male mice were cannulated in the CA1 regions of dorsal hippocampi and trained on a passive avoidance learning task for memory assessment.Key findingsWe found that pre-training intraperitoneal (i.p.) administration of ethanol (0.5 and 1 g/kg) decreased memory retrieval when tested 24 h later. Pre-test administration of ethanol reversed the decrease in inhibitory avoidance response induced by pre-training ethanol. Similar to ethanol, pre-test administration of nicotine (0.125–0.75 mg/kg, s.c.) prevented impairment of memory by pre-training ethanol. In the animals that received ethanol (1 g/kg, i.p) before training and tested following intra-CA1 administration of different doses of NMDA (0.0005–0.005 µg/mouse), no significant change was observed in the retrieval latencies. Co-administration of the same doses of NMDA with an ineffective dose of nicotine (0.125 mg/kg, s.c.) significantly improved the memory retrieval and mimicked the effects of pre-test administration of a higher dose of nicotine. Pre-test intra-CA1 microinjection of MK-801 (0.25–1 µg/mouse), which had no effect alone, in combination with an effective dose of nicotine (0.75 mg/kg, s.c.) prevented the improving effect of nicotine on memory impaired by pre-training ethanol. Moreover, intra-CA1 microinjection of MK-801 reversed the NMDA-induced potentiation of the nicotine response.SignificanceThe results suggest the importance of NMDA glutamate system(s) in the CA1 regions of dorsal hippocampus for improving the effect of nicotine on the ethanol-induced amnesia.