Rational design of Bacillus stearothermophilus US100 l-arabinose isomerase: Potential applications for d-tagatose production

l-Arabinose isomerases catalyze the bioconversion of d-galactose into d-tagatose. With the aim of producing an enzyme optimized for d-tagatose production, three Bacillus stearothermophilus US100 l-arabinose isomerase mutants were constructed, purified and characterized. Our results indicate that mutant Q268K was significantly more acidotolerant and more stable at acidic pH than the wild-type enzyme. The N175H mutant has a broad optimal temperature range from 50 to 65 °C. With the aim of constructing an acidotolerant mutant working at relatively low temperatures we generated the Q268K/N175H construct. This double mutant displays an optimal pH in the range 6.0–7.0 and an optimal activity around 50–65 °C, temperatures at which the enzyme was stable without addition of metal ions.     

Gating-induced Conformational Rearrangement of the γ-Aminobutyric Acid Type A Receptor β-α Subunit Interface in the Membrane-spanning Domain

GABA(A) receptors mediate fast inhibitory synaptic transmission. The transmembrane ion channel is lined by a ring of five α helices, M2 segments, one from each subunit. An outer ring of helices comprising the alternating M1, M3, and M4 segments from each subunit surrounds the inner ring and forms the interface with the lipid bilayer. The structural rearrangements that follow agonist binding and culminate in opening of the ion pore remain incompletely characterized. Propofol and other intravenous general anesthetics bind at the βM3-αM1 subunit interface. We sought to determine whether this region undergoes conformational changes during GABA activation. We measured the reaction rate of p-chloromercuribenzenesulfonate (pCMBS) with cysteines substituted in the GABA(A) receptor α1M1 and β2M3 segments. In the presence of GABA, the pCMBS reaction rate increased significantly in a cluster of residues in the extracellular third of the α1M1 segment facing the β2M3 segment. Mutation of the β2M2 segment 19' position, R269Q, altered the pCMBS reaction rate with several α1M1 Cys, some only in the resting state and others only in the GABA-activated state. Thus, β2R269 is charged in both states. GABA activation induced disulfide bond formation between β2R269C and α1I228C. The experiments demonstrate that α1M1 moves in relationship to β2M2R269 during gating. Thus, channel gating does not involve rigid body movements of the entire transmembrane domain. Channel gating causes changes in the relative position of transmembrane segments both within a single subunit and relative to the neighboring subunits.     

Alternative oxidase 1 (Aox1) gene expression in roots of Medicago truncatula is a genotype-specific component of salt stress tolerance

Alternative oxidase (AOX) is the central component of the non-phosphorylating alternative respiratory pathway in plants and may be important for mitochondrial function during environmental stresses. Recently it has been proposed that Aox can be used as a functional marker for breeding stress tolerant plant varieties. This requires characterization of Aox alleles in plants with different degree of tolerance in a certain stress, affecting plant phenotype in a recognizable way. In this study we examined Aox1 gene expression levels in Medicago truncatula genotypes differing in salt stress tolerance, in order to uncover any correlation between Aox expression and tolerance to salt stress. Results demonstrated a specific induction of Aox1 gene expression in roots of the tolerant genotype that presented the lowest modulation in phenotypic and biochemical stress indices such as morphologic changes, protein level, lipid peroxidation and ROS generation. Similarly, in a previous study we reported that induction of antioxidant gene expression in the tolerant genotype contributed to the support of the antioxidant cellular machinery and stress tolerance. Correlation between expression patterns of the two groups of genes was revealed mainly in 48 h treated roots. Taken together, results from both experiments suggest that M. truncatula tolerance to salt stress may in part due to an efficient control of oxidative balance thanks to (i) induction of antioxidant systems and (ii) involvement of the AOX pathway. This reinforces the conclusion that differences in antioxidant mechanisms can be essential for salt stress tolerance in M. truncatula and possibly the corresponding genes, especially Aox, could be utilized as functional marker.     

Synergistic Effects of Efflux Pump Modulators on the Azole Antifungal Susceptibility of Microsporum canis

The microbiologic and clinical resistance of dermatophytes is seldom reported, and the mechanisms associated with resistance are not well known. This study investigated the effect of efflux pump modulators (EPMs) (i.e., haloperidol HAL and promethazine PTZ) and their inhibiting activity on the minimum inhibitory concentrations of itraconazole (ITZ) and fluconazole (FLZ) against selected M. canis strains. M. canis strains with low (≤?1 μg/ml itraconazole and?<?64 μg/ml fluconazole) and high (>?1 μg/ml itraconazole and?≥?64 μg/ml fluconazole) azole MIC values were tested using Checkerboard microdilution assay. The disk diffusion assay, the minimum fungicidal concentration and the time-kill assay were also performed in order to confirm the results of checkerboard microdilution assay. The MIC values of ITZ and FLZ of M. canis decreased in the presence of subinhibitory concentrations of HAL and PTZ, the latter being more effective with a greater increased susceptibility. Synergism was observed in all strains with high azole MICs (FICI?<?0.5) and no synergism in the strains with low azole MICs. A fungicidal activity was observed after 48 h of incubation when ITZ and FLZ were tested in combination with HAL or PTZ. These results suggest that the drug efflux pumps are involved in the defense mechanisms to azole drugs in M. canis strains. The synergism might be related to an increased expression of efflux pump genes, eventually resulting in azole resistance phenomena. Complementary studies on M. canis resistance are advocated in order to investigate the molecular mechanisms of this phenomenon.

     

Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging

Since its discovery nearly 30 years ago, more than 60 million people have been infected with the human immunodeficiency virus (HIV) (www.usaid.gov). The virus infects and destroys CD4+ T-cells thereby crippling the immune system, and causing an acquired immunodeficiency syndrome (AIDS) ². Infection begins when the HIV Envelope glycoprotein "spike" makes contact with the CD4 receptor on the surface of the CD4+ T-cell. This interaction induces a conformational change in the spike, which promotes interaction with a second cell surface co-receptor ^5,9. The significance of these protein interactions in the HIV infection pathway makes them of profound importance in fundamental HIV research, and in the pursuit of an HIV vaccine.The need to better understand the molecular-scale interactions of HIV cell contact and neutralization motivated the development of a technique to determine the structures of the HIV spike interacting with cell surface receptor proteins and molecules that block infection. Using cryo-electron tomography and 3D image processing, we recently demonstrated the ability to determine such structures on the surface of native virus, at ˜20 Å resolution ^9,14. This approach is not limited to resolving HIV Envelope structures, and can be extended to other viral membrane proteins and proteins reconstituted on a liposome. In this protocol, we describe how to obtain structures of HIV envelope glycoproteins starting from purified HIV virions and proceeding stepwise through preparing vitrified samples, collecting, cryo-electron microscopy data, reconstituting and processing 3D data volumes, averaging and classifying 3D protein subvolumes, and interpreting results to produce a protein model. The computational aspects of our approach were adapted into modules that can be accessed and executed remotely using the Biowulf GNU/Linux parallel processing cluster at the NIH (http://biowulf.nih.gov). This remote access, combined with low-cost computer hardware and high-speed network access, has made possible the involvement of researchers and students working from school or home.Download video file.^{(47M, mov)}     

Effects of CaCl2 pretreatment on antioxidant enzyme and leaf lipid content of faba bean (Vicia faba L.) seedlings under cadmium stress

Most polyploids can survive better under multiple stress conditions than their corresponding diploid; however, there is no established theory that can adequately explain this phenomenon at the molecular or physiological level. Here, we attempt to explain this interesting but puzzling problem from the perspectives of resource requirement and antioxidant response. In this experiment, we compared the antioxidative response and stomatal behavior of two ploidy levels of tobacco plants (tetraploid and its colchicine-induced octaploid) under drought, cold and nutrient deficit stress conditions. In comparison to tetraploid, less H₂O₂ accumulation and stronger reactive oxygen scavenging capacity (antioxidant enzyme activities and DPPH radical scavenging capacity) were observed in octaploid under stress free or stressful conditions. In accordant with these, less oxidative damage and higher redox values (ASC/DHA and GSH/GSSG) were also monitored in the octaploid than in the tetraploid under same conditions. In addition, a higher net rate of photosynthesis (Pn) and slower decline in the concentration of intercellular CO₂(Ci) were measured in the octaploid compared to the tetraploid following high concentration ABA treatment (20 mg L⁻¹), with more severe oxidative damage observed in the tetraploid than in the octaploid. On the basis of the resource acquisition theory, we consider that any environmental stress that can lower plant resource availability would favor survival in a slow-growing polyploid compared with that in a fast-growing diploid.     

Upper Albian planktic foraminifera and radiolarian biostratigraphy (Nebeur – northern Tunisia)

Preliminary lithostratigraphic and biostratigraphic data recovered from Upper Albian pelagic successions of the Jebel Srassif area (Tunisian trough) reveal the presence of a moderately well preserved radiolarian fauna. This fauna is fossilized in blackshale beds of Rotalipora subticinensis, R. ticinensis and the lower part of the R. appenninica foraminifer zones. Thirty-five radiolarian morphotypes were identified. A correlation established with foraminifer planktic biochronology allows us to distinguish three radiolarian assemblages. The close association between organic-rich deposits and the radiolarian bloom can be interpreted as productivity proxy triggered by semi-enclosed basin configuration and an intensified upwelling currents provided by a possibly halokinetic-induced hydrothermalism.     

Diversity of terrestrial isopods in the northern Tunisian wetlands

To evaluate the influence of wetland types on the distribution of terrestrial isopods, species richness, relative abundance and diversity indices were studied in the supralittoral zone of 95 wetlands in the north‐western of Tunisian dorsal, belonging to six types: lagoon, hill reservoir, river, dam, lake and sebkha. We tested the following hypothesis: (i) is isopod diversity influenced by wetland types? (ii) is isopod diversity influenced by bioclimatic zones? and (iii) what are the environmental factors influencing isopod distribution? A total of 3255 individuals belonging to twenty species of terrestrial isopods were captured. Species richness differs significantly between wetland types. A highly significant positive relationship between species richness and both humidity and altitudinal gradient was described. The dendrogram of similarities showed a divergence of the lagoons compared to the remaining wetland types.     

New three-dimensional model based on finite element method of bone nanostructure: single TC molecule scale level

At the macroscopic scale, the bone mechanical behavior (fracture, elastic) depends mainly on its components’ nature at the nanoscopic scale (collagen, mineral). Thus, an understanding of the mechanical behavior of the elementary components is demanded to understand the phenomena that can be observed at the macroscopic scale. In this article, a new numerical model based on finite element method is proposed in order to describe the mechanical behavior of a single Tropocollagen molecule. Furthermore, a parametric study with different geometric properties covering the molecular composition and the rate hydration influence is presented. The proposed model has been tested under tensile loading. While focusing on the entropic response, the geometric parameter variation effect on the mechanical behavior of Tropocollagen molecule has been revealed using the model. Using numerical and experimental testing, the obtained numerical simulation results seem to be acceptable, showing a good agreement with those found in literature.