Impedimetric aptasensor for tobramycin detection in human serum

An RNA aptamer is proposed as a recognition element for the detection of tobramycin in human serum. A displacement assay was developed using faradaic-electrochemical impedance spectroscopy (F-EIS) as a detection technique. Two modified aptamers, a partially (ATA) and a fully O-methylated aptamer (FATA) were evaluated and compared. The affinity constant, K(D), for both aptamers was estimated by F-EIS resulting virtually identical within the experimental error. The selectivity towards other aminoglycosides was also studied. The analytical characteristics were evaluated in aqueous solution using both aptamers and FATA was selected for human serum experiments. Using a 1:0.5 dilution of the serum, a linear range between 3 μM and 72.1 μM was obtained, which included the therapeutic range of the antibiotic.     

Chemical and biological characterisation of a sensor surface for bioprocess monitoring

This paper describes the step-wise fabrication and characterisation of a multi-layer dual polarization interferometry (DPI) based biosensor utilising Protein G (ProG) as the bio-recognition layer for the detection of a fragment antibody (Fab'). The biosensor is capable of monitoring the concentration of Fab' product within the extracellular medium of a fed-batch fermentation after leakage from Escherichia coli (E.coli). The activity, stability and functionality of each sensor layer were analysed in situ using DPI, whilst the chemical identity and homogeneity of the chemical layers were assessed ex situ using X-ray photoelectron spectroscopy (XPS) and secondary ion mass spectrometry (SIMS). Two different biotin linkers were found to produce hugely differing surfaces after the capture of NeutrAvidin? (NA) and biotinylated Protein G (b-ProG). The hydrophilic (PEG)(4)-biotin linker resulted in a surface where the b-ProG layer was deposited and organised above the NA layer producing an active and stable surface, whilst the hydrophobic LC-biotin linker generated a surface where the b-ProG layer was buried within the NA layer leading to variable surfaces and poor binding of the Fab' target. The biosensor has a detection limit of 1.7 μg/ml with a dynamic range covering two orders of magnitude. The sensor can detect the onset of Fab' leakage as early as 2h following product induction, with high signal-to-noise ratios and little interference from extracellular components. Leakage of Fab' followed a biphasic profile, switching to a more rapid rate 20 h after induction, indicating accelerated product loss and the need for cultivation harvest.     

Long-term consequences of mechanical fuel management for the conservation of Mediterranean forest herb communities

Mechanical clearing of understory vegetation is increasingly used in Euro-Mediterranean forests to reduce fire hazard, yet its long-term consequences for biodiversity remain poorly understood. This study analysed the influence of time since understory management and management frequency, on herbaceous species richness, cover and composition, functional richness and composition, and richness and cover within functional groups (life and growth forms, dispersal strategy, clonality, and plant height), using a chronosequence of cork oak (Quercus suber) stands spanning about 70 years. Overall species richness was virtually constant over time, but the richness of species with annual life form and plasticity in height was much higher in recently and recurrently treated stands; the opposite was found for perennial (mainly hemicryptophytes and chamaephytes), tussock-forming and clonal species richness, and functional richness. Overall herbaceous cover and that of annual, semi-basal, non-clonal and plastic species (in height) were favoured by recent and recurrent fuel treatments; cover by perennial (hemicryptophytes and chamaephytes), short basal, tussock-forming, and clonal species tended to increase for >10–20 years after management, and declined with management frequency. There was a marked shift in species and functional composition associated with time since understory management and management frequency. These findings suggest that widespread fuel management at <10 year intervals may shift understory herb communities to early-successional stages, impairing the persistence of species and functional groups recovering slowly after disturbance. Fuel management needs to balance the dual goals of fire hazard reduction and biodiversity conservation, retaining undisturbed patches in landscapes otherwise managed to reduce fuel accumulation.     

Effects of urban habitat fragmentation on common small mammals: species versus communities

There is an increasing interest in understanding how species respond to the modifications of habitat attributes in urban areas. Patterns in the occurrence and abundance of small mammal communities in 15 isolated patches of remnant natural and semi-natural habitat of Porto Metropolitan Area (Portugal) were assessed against environmental characteristics (from both the patch and the surrounding matrix) of each patch using multiple regressions and canonical correspondence analysis. Four species of common small mammals were found: wood mouse (Apodemus sylvaticus), greater white-toothed shrew (Crocidura russula), Algerian mouse (Mus spretus) and house mouse (Mus musculus). Our results showed that both relative abundance and species richness were negatively affected by urbanization. The species richness also displayed a negative association with the increase of forest around the patch but relative abundance showed the opposite trend. At the species level, the relative abundance of A. sylvaticus and C. russula showed a negative association with urbanization. Our results reveal that these two species also benefit from a mosaic of habitats and pervious areas in the surrounding matrix. The relative abundance of M. spretus and M. musculus showed a negative effect of forest area around the patch. Understanding how the increase of urbanization affects small mammals will be particularly useful for the managers of urban landscapes, as these animals occupy a pivotal position in the ecosystems.     

Thermodynamic and kinetic destabilization of triosephosphate isomerase resulting from the mutation of conserved and non-conserved cysteines

Several variants of Saccharomyces cerevisiae triosephosphate isomerase (yTIM) were studied to determine how mutations of conserved and non-conserved Cys residues affect the enzyme. Wild-type yTIM has two buried free cysteines: Cys 41 (non-conserved) and the invariant Cys 126. Single-site mutants, containing substitutions of these cysteines with Ala, Val, or Ser (the three most conservative changes for a buried Cys, according to substitution matrices), were examined for stability and enzymatic activity. Neither of the Cys residues was found to be essential for enzyme catalysis. Determination of the global stability of the mutants indicated that, regardless of which Cys was substituted, individual Cys→Ala and Cys→Val mutations, as well as the C41S substitution, all decrease the unfolding free energy of the dimeric protein by less than 23 kJ mol(-1) (at 37 °C, pH 7.4), as compared to the wild-type enzyme. In contrast, a substantially larger destabilization (37 kJ mol(-1)) was found in the C126S mutant. These results suggest that, with the exception of C126S, all of these mutations can be regarded as neutral (i.e., mutations that do not impair the reproductive success of the organism). Accordingly, Cys 126 has remained invariant across evolution because its neutral substitutions by Ala or Val would require a highly unlikely, concerted double mutation at any of the Cys codons. Furthermore, detrimental effects to a cell expressing the C126S TIM mutant more likely arise from the high unfolding rate of this enzyme.     

Purification of plasmid DNA from Escherichia coli ferments using anion-exchange membrane and hydrophobic chromatography

A novel downstream bioprocess was developed to obtain purified plasmid DNA (pDNA) from Escherichia coli ferments. The intermediate recovery and purification of the pDNA in cell lysate was conducted using hollow-fiber tangential filtration and frontal anion-exchange membrane and elution hydrophobic chromatographies. The purity of the solutions of pDNA obtained during each process stage was investigated. The results show that the pDNA solution purity increased 30-fold and more than 99% of RNA in the lysate was removed during the process operations. The combination of membrane operations and hydrophobic interaction chromatography resulted in an efficient way to recover pDNA from cell lysates. A better understanding of membrane-based technology for the purification of pDNA from clarified E. coli lysate was developed in this research.     

Scheduled food hastens re-entrainment more than melatonin does after a 6-h phase advance of the light-dark cycle in rats

Circadian desynchrony occurs when individuals are exposed to abrupt phase shifts of the light-dark cycle, as in jet lag. For reducing symptoms and for speeding up resynchronization, several strategies have been suggested, including scheduled exercise, exposure to bright light, drugs, and especially exogenous melatonin administration. Restricted feeding schedules have shown to be powerful entraining signals for metabolic and hormonal daily cycles, as well as for clock genes in tissues and organs of the periphery. This study explored in a rat model of jet lag the contribution of exogenous melatonin or scheduled feeding on the re-entrainment speed of spontaneous general activity and core temperature after a 6-h phase advance of the light-dark cycle. In a first phase, the treatment was scheduled for 5 days prior to the phase shift, while in a second stage, the treatment was simultaneous with the phase advance of the light-dark cycle. Melatonin administration and especially scheduled feeding simultaneous with the phase shift improved significantly the re-entrainment speed. The evaluation of the free-running activity and temperature following the 5-day treatment proved that both exogenous melatonin and specially scheduled feeding accelerated re-entrainment of the SCN-driven general activity and core temperature, respectively, with 7, 5 days (p < 0.01) and 3, 3 days (p < 0.001). The present results show the relevance of feeding schedules as entraining signals for the circadian system and highlight the importance of using them as a strategy for preventing internal desynchrony.     

Genetic divergence over small geographic scales and conservation implications for Commerson's dolphins (Cephalorhynchus commersonii) in southern Argentina

Cephalorhynchus commersonii is distributed in the nearshore coastal waters of South America, and thus is particularly vulnerable to bycatch in coastal nets and trawls. Our study documents genetic structure in presumed Commerson's dolphin subpopulations along the southern Argentina coastline, from the Ría Deseado in the north to Ría Gallegos in the south, and focuses on the potential for depletion in the apparently more heavily impacted Ría Gallegos area. Only two control region (423 bp) haplotypes were shared among all these locations (out of 11 identified), and striking differences in haplotype frequencies between areas are apparent. AMOVA analysis, using mitochondrial sequence data, indicates significant population subdivision (overall F_ST= 0.21, P < 0.001) between Ría Deseado (n= 8), Bahía San Julián (n= 11), Ría Gallegos (n= 31), and a small sample of dolphins from the captive colony at San Diego Seaworld (n= 7) derived from animals originally captured in the Strait of Magellan. Comparisons based on haplotypic distances indicated relatively strong differences between regions (Φ_ST= 0.30, P < 0.001). This research provides the first indication of reduced gene flow and genetic differentiation within local subpopulations of Commerson's dolphins, along a relatively small stretch of coastline.     

Evidence for increased exposure of the Notch1 metalloprotease cleavage site upon conversion to an activated conformation

Notch proteins are transmembrane receptors that normally adopt a resting state poised to undergo activating proteolysis upon ligand engagement. Receptor quiescence is maintained by three LIN12/Notch repeats (LNRs), which wrap around a heterodimerization domain (HD) divided by furin cleavage at site S1 during maturation. Ligand binding initiates signaling by inducing sensitivity of the HD to proteolysis at the regulated S2 cleavage site. Here, we used hydrogen exchange mass spectrometry to examine the solution dynamics of the Notch1 negative regulatory region in autoinhibited states before and after S1 cleavage, in a proteolytically sensitive "on" state, and in a complex with an inhibitory antibody. Conversion to the "on" state leads to accelerated deuteration in the S2 region and in nearby secondary structural elements within the HD. In contrast, complexation with the inhibitory antibody retards deuteration around the S2 site. Together, these studies reveal how S2 site exposure is promoted by receptor activation and suppressed by inhibitory antibodies.