Three-dimensional interdigitated electrode array as a transducer for label-free biosensors

A new transducer for biosensor applications has been developed based on a three-dimensional interdigitated electrode array (IDEA) with electrode digits separated by an insulating barrier. Binding of molecules to a chemically modified surface of the transducer induces important changes in conductivity between the electrodes. Three-dimensional sensor shows considerable improvement compared with a standard planar IDEA design. The potential of the developed device as a sensor transducer to detect immunochemical and enzymatic reactions, as well as DNA hybridization events is demonstrated. The immunosensor allows direct detection of the antibiotic sulfapyridine and shows the IC(50) parameter value of 5.6 microgL(-1) in a buffer. Immunochemical determination occurs under competitive configurations and without the use of any label. Each modified sensor is of a single use. Nevertheless, biochemical reagents can be easily cleaned off the sensor surface for its reuse. Layer-by-layer method of used to deposit polyethyleneimine and glucose oxidase showed that the sensor is also highly effective for detecting single and multilayered molecular assemblies.     

Phylogenetic characterization of bacterial consortia obtained of corroding gas pipelines in Mexico

Characterization of the microbial populations formed in gas pipelines is essential to understand the metallic surface-microbe interaction, their role in metal corrosion, and to implement efficient monitoring and control strategies. Microbial community analysis in a corroded gas pipeline in a petroleum-producing facility in the Southeast region in Mexico was performed by traditional cultivation techniques and identification based on 16S rRNA gene sequence. In all samples, thin bacterial biofilms were observed and pitting corrosion was reveled after removing the biofilms. Six pure or mixed cultures of anaerobic bacteria were obtained and their 16S rRNA libraries were constructed, respectively. At least two members of each RFLP profile were sequenced and the phylogenetic affiliations of cloned bacterial 16S rRNA genes indicated that native biofilms were mainly colonized by Desulfovibrio vulgaris and Desulfovibrio desulfuricans, sulfate-reducing bacteria members; Citrobacter freundii, an Enterobacteriaceae member; Clostridium celerecrescens and Clostridium sporogenes, spore-forming anaerobic species and Cetobacterium somerae, a microaerotolerant, non-spore-forming fusobacteria. Some of these species have been observed consistently in other steel pipelines previously, but Cetobacterium members and C. celerecrescens are described for the fist time in this corroded gas pipeline. The potential role of each species in biofilm formation and steel corrosion is discussed.     

Store-operated calcium entry in human oocytes and sensitivity to oxidative stress

Calcium signaling is a cellular event that plays a key role at many steps of fertilization and early development. However, little is known regarding the contribution of extracellular Ca(2+) influx into the cell to this signaling in gametes and early embryos. To better know the significance of calcium entry on oocyte physiology, we have evaluated the mechanism of store-operated calcium entry (SOCE) in human metaphase II (MII) oocytes and its sensitivity to oxidative stress, one of the major factors implicated in the outcome of in vitro fertilization (IVF) techniques. We show that depletion of intracellular Ca(2+) stores through inhibition of sarco(endo)plasmic Ca(2+)-ATPase with thapsigargin triggers Ca(2+) entry in resting human oocytes. Ba(2+) and Mn(2+) influx was also stimulated following inhibition, and Ca(2+) entry was sensitive to pharmacological inhibition because the SOCE blocker 2-aminoethoxydiphenylborate (2-APB) reduced calcium and barium entry. These results support the conclusion that there is a plasma membrane mechanism responsible for the capacitative divalent cation entry in human oocytes. Moreover, the Ca(2+) entry mechanism described in MII oocytes was found to be highly sensitive to oxidative stress. Hydrogen peroxide, at micromolar concentrations that could mimic culture conditions in IVF, elicited an increase of [Ca(2+)](i) that was dependent on the presence of extracellular Ca(2+). This rise was preventable by 2-APB, indicating that it was mainly due to the enhanced influx through store-operated calcium channels. In sum, our results demonstrate the occurrence of SOCE in human MII oocytes and the modification of this pathway due to oxidative stress, with possible consequences in IVF.     

Rectification properties and pH-dependent selectivity of meningococcal class 1 porin

We studied the current rectification properties and selectivity of class 1 porin (PorA) from Neisseria meningitidis (strain H44/76 Δ3Δ4) reconstituted in planar lipid membranes varying salt concentrations and pH. PorA channel shows voltage gating with a characteristic time remarkably longer than other porins. Its current-voltage asymmetry, evaluated as the current rectification ratio, changes nonmonotonically with salt concentration. Interestingly, it reaches its maximum value at physiological concentration. Porin selectivity, quantified by reversal potential measurements, is also significantly asymmetric. Depending on the direction of the salt gradient, the channel becomes more or less selective (10:1 vs. 5:1 Na⁺/Cl⁻). Besides, the reversal potential measurements suggest that porin inserts directionally following the concentration gradient. Measurements over a wide range of pH show that although PorA is strongly cation selective at pH >6, its selectivity gradually changes to anionic in an acidic medium (pH < 4). We show that a continuum electrodiffusion model quantitatively accounts for conductance and reversal potential measurements at positive and negative applied voltages.     

Exploring the control circuit of cell migration by mathematical modeling

We have developed a top-down, rule-based mathematical model to explore the basic principles that coordinate mechanochemical events during animal cell migration, particularly the local-stimulation-global-inhibition model suggested originally for chemotaxis. Cells were modeled as a shape machine that protrudes or retracts in response to a combination of local protrusion and global retraction signals. Using an optimization algorithm to identify parameters that generate specific shapes and migration patterns, we show that the mechanism of local stimulation global inhibition can readily account for the behavior of Dictyostelium under a large collection of conditions. Within this collection, some parameters showed strong correlation, indicating that a normal phenotype may be maintained by complementation among functional modules. In addition, comparison of parameters for control and nocodazole-treated Dictyostelium identified the most prominent effect of microtubules as regulating the rates of retraction and protrusion signal decay, and the extent of global inhibition. Other changes in parameters can lead to profound transformations from amoeboid cells into cells mimicking keratocytes, neurons, or fibroblasts. Thus, a simple circuit of local stimulation-global inhibition can account for a wide range of cell behaviors. A similar top-down approach may be applied to other complex problems and combined with molecular manipulations to define specific protein functions.     

The family 52 beta-xylosidase from Geobacillus stearothermophilus is a dimer: structural and biophysical characterization of a glycoside hydrolase

Xylans are the most abundant polysaccharides forming the plant cell wall hemicelluloses, and they are degraded, among other proteins, by beta-xylosidase enzymes. In this work, the structural and biophysical properties of the family 52 beta-xylosidase from Geobacillus stearothermophilus, XynB2, are described. Size exclusion chromatography, analytical centrifugation, ITC, CD, fluorescence (steady state and ANS-binding) and FTIR were used to obtain the structure, the oligomerization state and the conformational changes of XynB2, as pH, chemical denaturants or temperature were modified. This report describes the first extensive conformational characterization of a family 52 beta-xylosidase. The active protein was a highly hydrated dimer, whose active site was formed by the two protomers, and it probably involved aromatic residues. At low pH, the protein was not active and it populated a monomeric molten-globule-like species, which had a conformational transition with a pK(a) of approximately 4.0. Thermal and chemical-denaturations of the native protein showed hysteresis behaviour. The protein at physiological pH was formed by alpha-helix (30%) and beta-sheet (30%), as shown by CD and FTIR. Comparison with other xylosidases of the same family indicates that the percentages of secondary structure seem to be conserved among the members of the family.     

Plant Conservation in the Caribbean Island Biodiversity Hotspot

While the Caribbean is a recognized “biodiversity hotspot”, plant conservation has not received adequate attention; particularly, given the high levels of endemism in many plant groups. Besides establishing protected areas, there needs to be a sustained effort to study the taxonomy, systematics and ecology of the flora. Recent phylogenetic studies have shown high levels of endemism and conservation studies indicate a large propotion of the flora is threatened with extinction. Eight recommendations are given for plant conservation in the region.     

Physical activity related to forced vital capacity and strength performance in a sample of young males and females

To identify the extent of physical performance differences between active and sedentary subjects taking into account sexual dimorphism physical activity level was recorded by interview from a sample of 319 young university students of both sexes. Anthropometric variables and physical performance values were obtained. The sex factor was the main variable explaining the differences in physical performance between active and sedentary young. Also contributors to those differences were forced vital capacity (FVC), heart rate after exercise and rest heart rate, together with the explosive component of strength (vertical jump). The effect of physical activity was shown in the increment of FVC and the decrease of resting heart rate. In the overall sample, heart rate after exercise, either in active males or active females, was lowered with respect to the sedentary subjects, showing that active females experienced a greater cardiovascular benefit following adaptation to training than sedentary.     

Towards a molecular dynamics consensus view of B-DNA flexibility

We present a systematic study of B-DNA flexibility in aqueous solution using long-scale molecular dynamics simulations with the two more recent versions of nucleic acids force fields (CHARMM27 and parmbsc0) using four long duplexes designed to contain several copies of each individual base pair step. Our study highlights some differences between pambsc0 and CHARMM27 families of simulations, but also extensive agreement in the representation of DNA flexibility. We also performed additional simulations with the older AMBER force fields parm94 and parm99, corrected for non-canonical backbone flips. Taken together, the results allow us to draw for the first time a consensus molecular dynamics picture of B-DNA flexibility.