Effect of filaments within the synaptic cleft on the response of excitatory synapses simulated by computer experiments

Mathematical models of the excitatory synapse are furnishing valuable information about the synaptic response. Based on Brownian-diffusion of glutamate molecules, a synapse model was utilized to investigate the synaptic response on a femto-second time scale by the use of a parallel computer. In particular, the presence of fibrils crossing the synaptic cleft was simulated, which could have a role in shaping the brain activity. To this aim the model of synapse was modified by considering trans-synaptic filaments with diameters ranging from 7 nm to 3 nm, disposed on a grid with spacing of 14 nm or 8 nm. The simulation demonstrated that the presence of filaments induced an increase in the synaptic response, most likely linked to an increment in the probability of encounter between glutamate molecules and receptors. The increase was small - from 5 to 20%, but metabolic and functional considerations provide substantive hints about the importance of these small changes for brain activity. Moreover, it was shown that the presence of filaments made more stable the response of the synapse to random variations of pre-synaptic elements. Originated by these computational results, some inferences about the biological bases of mind diseases such as autism, mental retardation and schizophrenia, are reported in the Discussion.     

Prediction of whole-genome DNA G + C content within the genus Aeromonas based on housekeeping gene sequences

Different methods are available to determine the G + C content (e.g. thermal denaturation temperature or high performance liquid chromatography, HPLC), but obtained values may differ significantly between strains, as well as between laboratories. Recently, several authors have demonstrated that the genomic DNA G + C content of prokaryotes can be reliably estimated from one or several protein coding gene nucleotide sequences. Few G + C content values have been published for the Aeromonas species described and the data, when available, are often incomplete or provide only a range of values. Our aim in this current work was twofold. First, the genomic G + C content of the type or reference strains of all species and subspecies of the genus Aeromonas was determined with a traditional experimental method in the same laboratory. Second, we wanted to see if the sequence-based method to estimate the G + C content described by Fournier et al. [7] could be applied to determine the G + C content of the different species of Aeromonas from the sequences of the genes used in taxonomy or phylogeny for this genus.     

Preparation of (1 → 3)-β-d-glucan oligosaccharides by hydrolysis of curdlan with commercial α-amylase

Water soluble (1 → 3)-β-d-glucan oligosaccharides were prepared by hydrolyzing curdlan with α-amylase. The hydrolysis process was monitored by the DE values of the hydrolysates. Under the optimized conditions (pH, 5.98; temperature, 55.92 °C; α-amylase amount, 31.94 mg α-amylase/500 mL of reaction mixture containing 5 g curdlan; reaction time, 30 min), maximum DE value (15.62%) was obtained. The resulting products were composed of (1 → 3)-β-d-glucan oligosaccharides of DP 2-9. The hydrolysates were filtered, concentrated to ∼20% (w/v), and precipitated with 5 volumes of ethanol, which were then freeze dried to yield a water soluble powder. The (1 → 3)-β-d-glucan oligosaccharides content of the product and the yield were 97.7% and 97.6% (w/w), respectively.     

Coordination polymers of manganese(II) and cobalt(II) of a flexible tetradentate pyridine amide ligand: 1D zigzag network and non-covalent interactions

Synthesis and crystal structure of two coordination polymers of composition [Mn^II(H₂bpbn)_1.5][ClO₄]₂ · 2MeOH · 2H₂O (1) and [Co^II(H₂bpbn)(H₂O)₂]Cl₂ · H₂O (2) [H₂bpbn = N,N′-bis(2-pyridinecarboxamido)-1,4-butane], formed from the reaction between [Mn(H₂O)₆][ClO₄]₂/CoCl₂ · 4H₂O with H₂bpbn in MeCN, are described. In 1 each Mn^II ion is surrounded by three pyridine amide units, providing three pyridine nitrogen and three amide oxygen donors. Each Mn^II center in 1 has distorted MnN₃O₃ coordination. In 2 each Co^II ion is coordinated by two pyridine amide moieties in the equatorial plane and two water molecules provide coordination in the axial positions. Thus, the metal center in 2 has trans-octahedral geometry. In both 1 and 2, the existence of 1D zigzag network structure has been revealed. Owing to π-π stacking of pyridine rings from adjacent layers 1 forms 2D network; 2 forms 2D and 3D network assemblies via N-H?Cl and O-H?Cl secondary interactions. Both the metal centers are high-spin.     

Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology

Next generation pyrosequencing of high G + C content genomes still poses problems to automated sequencing and assembly processes which necessitates cost and time intensive manual work in order to finish such genomes completely. The sequencing of the high G + C actinomycete Actinoplanes sp. SE50/110 was performed with standard pyrosequencing technology (454 Life Sciences) and revealed a high number of gaps. The reasons for the introduction of gaps were analyzed on a previously known 41 kb long DNA reference sequence from Actinoplanes sp. SE50/110, hosting the acarbose biosynthesis gene cluster. Mapping of the sequencing results on the reference gene cluster sequence revealed a fragmentation into 30 contiguous sequences of different lengths. The gaps between these sequences were characterized by extremely low read coverage which strongly correlated with the G + C content in the gap regions in a negative manner. Furthermore, the gap-sequences contained strong stem-loop structures which hindered the amplification of these sequences during the emulsion PCR. Being significantly underrepresented or absent in the subsequent sequencing process, these sequences lead to weakly or uncovered genomic regions which forces the assembly algorithm to output multiple contiguous sequences instead of one finished genome. However, by applying a different pyrosequencing protocol, it was possible to sequence the complete acarbose biosynthesis gene cluster. The changes to the protocol include longer read length and addition of chemicals to the amplification chemistry, which reduces the self-annealing of DNA fragments during the amplification process and enables the complete reconstruction of high G + C content genomes without manual intervention.     

DNA aptamers bind specifically and selectively to (1 → 3)-β-d-glucans

(1 → 3)-β-d-Glucans are structural cell wall components of fungi, plants, and some bacteria and have been linked with human respiratory symptoms following aerosol exposure. A clear interpretation of the health impact of (1 → 3)-β-d-glucans is limited by the high cost and uncertainties associated with current glucan quantitation methods. The objective of this research is to develop DNA aptamers for the measurement of (1 → 3)-β-d-glucans. Aptamers are synthetic DNA functional binding molecules that fold into unique conformations, allowing them to bind specifically to their target. Through the in vitro selection process SELEX, we have produced aptamers that are able to bind with sub-micromolar affinity to curdlan, a linear unbranched form of (1 → 3)-β-d-glucans. These aptamers display high selectivity to curdlan and do not bind to non-(1 → 3)-β-d-polysaccharides, suggesting specificity for the β-(1 → 3)-glycosidic linkage. The aptamers produced here will enable the production of more cost-effective, less ambiguous assays for the environmental measurement of (1 → 3)-β-d-glucans.     

Use of an adenosine triphosphate assay, and simultaneous staining with fluorescein diacetate and propidium iodide, to evaluate the effects of cryoprotectants on hard coral (Echinopora spp.) oocytes

The objective was to examine the effects of cryoprotectants on oocytes of hard corals (Echinopora spp.) to obtain basic knowledge for cryopreservation procedures. Oocytes were exposed to various concentrations of cryoprotectants (0.25 to 5.0 M) for 20 min at room temperature (25 °C). Two tests were used to assess ovarian follicle viability: fluorescein diacetate (FDA) + propidium iodide (PI) staining, and adenosine triphosphate (ATP) assay. Both FDA + PI staining and ATP assay indicated that cryoprotectant toxicity to oocytes increased in the order methanol, dimethyl sulfoxide (DMSO), propylene glycol (PG), and ethylene glycol (EG). The no observed effect concentrations for Echinopora spp. oocytes were 1.0, 0.5, 0.25, and 0.25 M for methanol, DMSO, PG, and EG, respectively, when assessed with FDA + PI. The ATP assay was more sensitive than FDA + PI staining (P < 0.05). Oocyte viability after 1.0 M methanol, DMSO, EG, or PG treatment for 20 min at room temperature assessed with FDA + PI tests and ATP assay were 88.9 ± 3.1% and 72.2 ± 4.4%, 66.2 ± 5.0% and 23.2 ± 4.9%, 58.9 ± 5.4% and 1.1 ± 0.7%, and 49.1 ± 5.1% and 0.9 ± 0.5%, respectively. We inferred that the ATP assay was a valuable measure of cellular injury after cryoprotectant incubation. The results of this study provided a basis for development of protocols to cryopreserve coral oocytes.     

Human beta-2 microglobulin W60V mutant structure: Implications for stability and amyloid aggregation

Beta-2 microglobulin (β2m) is the light chain of class I major histocompatibility complex (MHC-I). β2m is an intrinsically amyloidogenic protein that can assemble into amyloid fibrils in a concentration dependent manner. β2m is accumulated in serum of haemodialysed patients, and deposited in the skeletal joints, causing dialysis related amyloidosis. Recent reports suggested that the loop comprised between β2m strands D and E is crucial for protein stability and for β2m propensity to aggregate as cross-β structured fibrils. In particular, the role of Trp60 for β2m stability has been highlighted by showing that the Trp60 → Gly β2m mutant is more thermo-stable and less prone to aggregation than the wild type protein. On the contrary the Asp59 → Pro β2m mutant shows lower Tm and stronger tendency to fibril aggregation. To further analyse such properties, the Trp60 → Val β2m mutant has been expressed and purified; the propensity to fibrillar aggregation and the folding stability have been assessed, and the X-ray crystal structure determined to 1.8 Å resolution. The W60V mutant structural features are discussed, focusing on the roles of the DE loop and of residue 60 in relation to β2m structure and its amyloid aggregation trends.     

Nile Tilapia Neu3 sialidases: Molecular cloning,functional characterization and expression in Oreochromis niloticus

Mammalian Neu3 is a ganglioside specific sialidase. Gangliosides are involved in various physiological events such as cell growth, differentiation and diseases. Significance of Neu3 and gangliosides is still unclear in aquaculture fish species. To gain more insights of fish Neu3 sialidases, molecular cloning and characterization were carried out in tilapia (Oreochromis niloticus). A tilapia genome-wide search for orthologues of human NEU1, NEU2, NEU3 and NEU4 yielded eight putative tilapia sialidases, five of which were neu3-like and designated as neu3a, neu3b, neu3c, neu3d and neu3e. Among five neu3 genes, neu3a, neu3d and neu3e were amplified by PCR from adult fish brain cDNA with consensus sequences of 1227 bp, 1194 bp and 1155 bp, respectively. Multiple alignments showed conserved three Asp-boxes (SXDXGXTW), YRIP and VGPG motifs. The molecular weights for Neu3a, Neu3d and Neu3e were confirmed using immunoblotting analysis as 45.9 kDa, 44.4 kDa and 43.6 kDa, respectively. Lysate from neu3 genes transfected HEK293 cells showed sialidase activity in Neu3a towards ganglioside mix optimally at pH 4.6. Using pure gangliosides as substrates, highest sialidase activity for Neu3a was observed towards GD3 followed by GD1a and GM3, but not GM1. On the other hand, sialidase activities were not observed in Neu3d and Neu3e towards various sialoglycoconjugates. Indirect immunofluorescence showed that tilapia Neu3a and Neu3d are localized at the plasma membrane, while most Neu3e showed a cytosolic localization. RT-PCR analyses for neu3a showed significant expression in the brain, liver, and spleen tissues, while neu3d and neu3e showed different expression patterns. Based on these results, tilapia Neu3 exploration is an important step towards full understanding of a more comprehensive picture of Neu3 sub-family of proteins in fish.     

Hydrogen atom abstraction from HOOOCl by chlorine atom and OH radical

Gas-phase reactions of HOOOCl with both Cl atom and OH radical are investigated using ab initio methods. The structures of all reactants, products, intermediates, and transition states have been optimized and characterized with the quadratic configuration interaction (QCISD) method. The overall mechanism for the Cl + HOOOCl and OH + HOOOCl reaction is the formation of HCl + O₂ + ClO and H₂O + O₂ + ClO, respectively. The rate-limiting step in each reaction is the abstraction of hydrogen from HOOOCl by either Cl or OH radicals and the barrier height is predicted to be 1.9 kcal mol⁻¹ and 8.1 kcal mol⁻¹ for abstraction by Cl atom and OH radical, respectively. Since both barriers for hydrogen abstraction are high, the reaction is suggested to be slow. These results also suggest that an atmospheric removal mechanism for HOOOCl may result from reaction with Cl atoms rather than with OH radicals, and that photolysis of HOOOCl may be the major removal mechanism for the intermediate.     

Ground,dry-rolled and steam-processed barley grain for midlactation Holstein cows

Fine grinding of barley grain has traditionally been considered to be a potential risk to rumen function, feed intake and milk yield. These concerns are thought to be reduced by steam-rolling or coarse dry rolling. We hypothesized that finely ground barley grain is as effective in stimulating feed intake and milk production as are dry- and steam-rolled barley grain, and so the objective was to determine effects of feeding either (1) finely ground, (2) steam-rolled, (3) finely dry-rolled, or (4) coarsely dry-rolled barley grain on rumen fermentation, digestibility and milk yield and composition. Eight multiparous midlactation Holstein cows were used in a replicated 4×4 Latin square design experiment with four periods of 21 d. Diets contained 256 g barley grain/kg on a dry matter (DM) basis. Processing method did not affect milk yield and composition, DM intake, rumen pH and volatile fatty acids, fecal and urine pH, and apparent total tract nutrient digestibility. Results suggest that finely ground barley grain is no different than dry-rolled and steam-rolled barley grains in stimulating feed intake and productivity of midlactation cows, when 256 g of dietary DM/kg is barley grain.     

Development of cryopreservation protocols for early stage zebrafish (Danio rerio) ovarian follicles using controlled slow cooling

Cryopreservation of germplasm of aquatic species offers many benefits to the fields of aquaculture, conservation and biomedicine. Although successful fish sperm cryopreservation has been achieved with many species, there has been no report of successful cryopreservation of fish embryos and late stage oocytes which are large, chilling sensitive and have low membrane permeability. In the present study, cryopreservation of early stage zebrafish ovarian follicles was studied for the first time using controlled slow freezing. The effect of cryoprotectant, freezing medium, cooling rate, method for cryoprotectant removal, post-thaw incubation time and ovarian follicle developmental stage were investigated. Stages I and II ovarian follicles were frozen in 4 M methanol and 3 M DMSO in either L-15 medium or KCl buffer. Ovarian follicle viability was assessed using trypan blue, FDA + PI staining and ADP/ATP assay. The results showed that KCl buffer was more beneficial than L-15 medium, methanol was more effective than DMSO, optimum cooling rates were 2-4 °C/min, stepwise removal of cryoprotectant improved ovarian follicle viability significantly and stage I ovarian follicles were more sensitive to freezing. The results also showed that FDA + PI staining and ADP/ATP assay were more sensitive than TB staining. The highest follicle viabilities after post-thaw incubation for 2 h obtained with FDA + PI staining were 50.7 ± 4.0% although ADP/ATP ratios of the cryopreserved follicles were significantly increased indicating increased cell damage. Studies are currently being carried out on in vitro maturation of these cryopreserved ovarian follicles.     

Synthesis, characterization and deepening in the comprehension of the biological action mechanisms of a new nickel complex with antiproliferative activity

Thiosemicarbazones are versatile organic compounds that present considerable pharmaceutical interest because of a wide range of properties. In our laboratory we synthesised some new metal-complexes with thiosemicarbazones derived from natural aldehydes which showed peculiar biological activities. In particular, a nickel complex [Ni(S-tcitr)₂] (S-tcitr = S-citronellalthiosemicarbazonate) was observed to induce an antiproliferative effect on U937, a human histiocytic lymphoma cell line, at low concentrations (IC₅₀ = 14.4 μM). Therefore, we decided to study the interactions of this molecule with various cellular components and to characterise the induced apoptotic pathway. Results showed that [Ni(S-tcitr)₂] causes programmed cell death via down-regulation of Bcl-2, alteration of mitochondrial membrane potential and caspase-3 activity, regardless of p53 function. The metal complex is not active on G₀ cells (i.e. fresh leukocytes) but is able to induce perturbation of the cell cycle on stimulated lymphocytes and U937 cells, in which a G₂/M block was detected. It reaches the nucleus where it induces, at low concentrations (2.5-5.0 μM), DNA damage, which could be partially ascribed to oxidative stress. [Ni(S-tcitr)₂] is moreover able to strongly reduce the telomerase activity. Although the biological target of this metal complex is still unknown, the reported data suggest that [Ni(S-tcitr)₂] could be a good model for the synthesis of new metal thiosemicarbazones with specific biological activity.     

Structural and stoichiometric determinants of Ca release-activated Ca (CRAC) channel Ca-dependent inactivation

Depletion of intracellular Ca^2 + stores in mammalian cells results in Ca^2 + entry across the plasma membrane mediated primarily by Ca^2 + release-activated Ca^2 + (CRAC) channels. Ca^2 + influx through these channels is required for the maintenance of homeostasis and Ca^2 + signaling in most cell types. One of the main features of native CRAC channels is fast Ca^2 +-dependent inactivation (FCDI), where Ca^2 + entering through the channel binds to a site near its intracellular mouth and causes a conformational change, closing the channel and limiting further Ca^2 + entry. Early studies suggested that FCDI of CRAC channels was mediated by calmodulin. However, since the discovery of STIM1 and Orai1 proteins as the basic molecular components of the CRAC channel, it has become apparent that FCDI is a more complex phenomenon. Data obtained using heterologous overexpression of STIM1 and Orai1 suggest that, in addition to calmodulin, several cytoplasmic domains of STIM1 and Orai1 and the selectivity filter within the channel pore are required for FCDI. The stoichiometry of STIM1 binding to Orai1 also has emerged as an important determinant of FCDI. Consequently, STIM1 protein expression levels have the potential to be an endogenous regulator of CRAC channel Ca^2 + influx. This review discusses the current understanding of the molecular mechanisms governing the FCDI of CRAC channels, including an evaluation of further experiments that may delineate whether STIM1 and/or Orai1 protein expression is endogenously regulated to modulate CRAC channel function, or may be dysregulated in some pathophysiological states.     

Simplified process for ethanol production from sugarcane bagasse using hydrolysate-resistant Escherichia coli strain MM160

Hexose and pentose sugars from phosphoric acid pretreated sugarcane bagasse were co-fermented to ethanol in a single vessel (SScF), eliminating process steps for solid-liquid separation and sugar cleanup. An initial liquefaction step (L) with cellulase was included to improve mixing and saccharification (L + SScF), analogous to a corn ethanol process. Fermentation was enabled by the development of a hydrolysate-resistant mutant of Escherichia coli LY180, designated MM160. Strain MM160 was more resistant than the parent to inhibitors (furfural, 5-hydroxymethylfurfural, and acetate) formed during pretreatment. Bagasse slurries containing 10% and 14% dry weight (fiber plus solubles) were tested using pretreatment temperatures of 160-190 °C (1% phosphoric acid, 10 min). Enzymatic saccharification and inhibitor production both increased with pretreatment temperature. The highest titer (30 g/L ethanol) and yield (0.21 g ethanol/g bagasse dry weight) were obtained after incubation for 122 h using 14% dry weight slurries of pretreated bagasse (180 °C).     

Thermodynamics and laser luminescence spectroscopy of binary and ternary complexation of Am, Cm and Eu with citric acid, and citric acid + EDTA at high ionic strength

The binary complexation of Am³⁺, Cm³⁺and Eu³⁺ with citrate has been studied at I = 6.60 m (NaClO₄), pcH 3.60 and in the temperatures range of 0-60 °C employing a solvent extraction technique with di-(2-ethylhexyl)phosphoric acid/heptane. Two complexes, MCit and , were formed at all temperatures. For the three metal ions, the log β₁₀₁ was between 5.9 and 6.2 and log β₁₀₂ between 10.2 and 10.6 at 25 °C. The thermodynamic parameters for the Am-Cit system have been calculated from the temperature dependence of the β₁₀₁ and β₁₀₂ values. Positive enthalpy and entropy values for the formation of both complexes are interpreted as due to the contributions from the dehydration of the metal ions exceeding the exothermic cation-anion pairing. The formation of the ternary complex M(EDTA)(Cit)⁴⁻ (M = Cm and Eu) was measured to have large stability constants (log β₁₁₁ between 20.9 and 24.4) at 25 and 60 °C. Time resolved laser luminescence spectroscopy and lifetime measurement data validated the nature of the complexes of Eu(III) formed in the presence of Cit and EDTA + Cit in 6.60 m (NaClO₄) solution.     

NGF blocks polyunsaturated fatty acids biosynthesis in n − 3 fatty acid-supplemented PC12 cells

Regulation of polyunsaturated fatty acid (PUFA) biosynthesis in proliferating and NGF-differentiated PC12 pheochromocytoma cells deficient in n − 3 docosahexaenoic acid (DHA 22:6n − 3) was studied. A dose- and time-dependent increase in eicosapentaenoic acid (EPA, 20:5n − 3), docosapentaenoic acid (DPA, 22:5n − 3) and DHA in phosphatidylethanolamine (PtdEtn) and phosphatidylserine (PtdSer) glycerophospholipids (GPL) via the elongation/desaturation pathway following alpha-linolenic acid (ALA, 18:3n − 3) supplements was observed. That was accompanied by a marked reduction of eicosatrienoic acid (Mead acid 20:3n − 9), an index of PUFA deficiency. EPA supplements were equally effective converted to 22:5n − 3 and 22:6n − 3. On the other hand, supplements of linoleic acid (LNA, 18:2n − 6) were not effectively converted into higher n − 6 PUFA intermediates nor did they impair elongation/desaturation of ALA. Co-supplements of DHA along with ALA did not interfere with 20:5n − 3 biosynthesis but reduced further elongation to 22-hydrocarbon PUFA intermediates. A marked decrease in the newly synthesized 22:5n − 3 and 22:6n − 3 following ALA or EPA supplements was observed after nerve growth factor (NGF)-induced differentiation. NGF also inhibited the last step in 22:5n − 6 formation from LNA. These results emphasize the importance of overcoming n − 3 PUFA deficiency and raise the possibility that growth factor regulation of the last step in PUFA biosynthesis may constitute an important feature of neuronal phenotype acquisition.