Graphene/Graphene Oxide-Based Ultrasensitive Surface Plasmon Resonance Biosensor

Plasmonics - Surface plasmon resonance (SPR)-based biosensing is an accurate and sensitive technique used to evaluate the biomolecular interactions in real time in a label-free environment. Several...     

Assessment of the horizontal transfer of functional genes as a suitable approach for evaluation of the bioremediation potential of petroleum-contaminated sites: a mini-review

Petroleum sludge contains recalcitrant residuals. These compounds because of being toxic to humans and other organism are of the major concerns. Therefore, petroleum sludge should be safely disposed. Physicochemical methods which are used by this sector are mostly expensive and need complex devices. Bioremediation methods because of being eco-friendly and cost-effective overcome most of the limitations of physicochemical treatments. Microbial strains capable to degrade petroleum hydrocarbons are practically present in all soils and sediments and their population density increases in contact with contaminants. Bacterial strains cannot degrade alone all kinds of petroleum hydrocarbons, rather microbial consortium should collaborate with each other for degradation of petroleum hydrocarbon mixtures. Horizontal transfer of functional genes between bacteria plays an important role in increasing the metabolic potential of the microbial community. Therefore, selecting a suitable degrading gene and tracking its horizontal transfer would be a useful approach to evaluate the bioremediation process and to assess the bioremediation potential of contaminated sites.     

Affective pictures processing is reflected by an increased long-distance EEG connectivity

Analysis of affective picture processing by means of EEG has invaded the literature. The methodology of event-related EEG coherence is one of the essential methods used to analyze functional connectivity. The aims of the present study are to find out the long range EEG connectivity changes in perception of different affective pictures and analyze gender differences in these long range connected networks. EEGs of 28 healthy subjects (14 female) were recorded at 32 locations. The participants passively viewed emotional pictures (IAPS, unpleasant, pleasant, neutral). The long-distance intra-hemispheric event-related coherence was analyzed for delta (1–3.5 Hz), theta (4–7.5 Hz), and alpha (8–13 Hz) frequency ranges for F₃–T₇, F₄–T₈, F₃–TP₇, F₄–TP₈, F₃–P₃, F₄–P₄, F₃–O₁, F₄–O₂, C₃–O₁, C₄–O₂ electrode pairs. Unpleasant pictures elicited significantly higher delta coherence values than neutral pictures (p < 0.05), over fronto-parietal, fronto-occipital, and centro-occipital electrode pairs. Furthermore, unpleasant pictures elicited higher theta coherence values than pleasant (p < 0.05) and neutral pictures (p < 0.05). The present study showed that female subjects had higher delta (p < 0.05) and theta (p < 0.05) coherence values than male subjects. This difference was observed more for emotional pictures than for neutral pictures. This study showed that the brain connectivity was higher during emotional pictures than neutral pictures. Females had higher connectivity between different parts of the brain than males during emotional processes. According to these results, we may comment that increased valence and arousal caused increased brain activity. It seems that not just single sources but functional networks were also activated during perception of emotional pictures.     

A comparative study of oculomotor,trochlear and abducens nerves in Arabian foals

We investigated the microscopic structure of transverse sections of the oculomotor, trochlear and abducens nerves of Arabian foals using stereological methods. Bilateral nerve pairs from 2-month-old female Arabian foals were analyzed. The tissues were embedded in plastic blocks, then 1 µm thick sections were cut and stained with osmium tetroxide and methylene blue-azure II. Stereology was performed using light microscopy. Morphometry showed that the right and left pairs of nerves were similar. The transverse sectional areas of the oculomotor, trochlear and abducens nerves were 1.93 ± 0.19 mm², 0.32 ± 0.06 mm² and 0.70 ± 0.08 mm², respectively. The oculomotor nerve exhibited a significantly greater number of myelinated axons (16755 ± 1279) and trochlear (2656 ± 494) and the abducens nerves (4468 ± 447). The ratio of the axon diameter to myelinated nerve fiber diameter was 0.58, 0.55 and 0.55 for the oculomotor, trochlear and abducens nerves, respectively. Of the three nerves studied, the abducens nerve exhibited the greatest nerve fiber area, myelin area, nerve and axon diameters, and myelin thickness. The ratio of small myelinated nerve fibers was greatest in the oculomotor nerve.     

Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow

The high-level organization of the cell is embedded in indirect relationships that connect distinct cellular processes. Existing computational approaches for detecting indirect relationships between genes typically consist of propagating abstract information through network representations of the cell. However, the selection of genes to serve as the source of propagation is inherently biased by prior knowledge. Here, we sought to derive an unbiased view of the high-level organization of the cell by identifying the genes that propagate and receive information most effectively in the cell, and the indirect relationships between these genes. To this aim, we adapted a perturbation-response scanning strategy initially developed for identifying allosteric interactions within proteins. We deployed this strategy onto an elastic network model of the yeast genetic interaction profile similarity network. This network revealed a superior propensity for information propagation relative to simulated networks with similar topology. Perturbation-response scanning identified the major distributors and receivers of information in the network, named effector and sensor genes, respectively. Effectors formed dense clusters centrally integrated into the network, whereas sensors formed loosely connected antenna-shaped clusters and contained genes with previously characterized involvement in signal transduction. We propose that indirect relationships between effector and sensor clusters represent major paths of information flow between distinct cellular processes. Genetic similarity networks for fission yeast and human displayed similarly strong propensities for information propagation and clusters of effector and sensor genes, suggesting that the global architecture enabling indirect relationships is evolutionarily conserved across species. Our results demonstrate that elastic network modeling of cellular networks constitutes a promising strategy to probe the high-level organization and cooperativity in the cell.     

Molecular Characterization of a Phytoplasma Associated with Potato Witches’‐broom Disease in Iran

Potato plants showing symptoms suggestive of potato witches’‐broom disease including witches’‐broom, little leaf, stunting, yellowing and swollen shoots formation in tubers were observed in the central Iran. For phytoplasma detection, Polymerase Chain Reaction (PCR) and nested PCR assays were performed using phytoplasma universal primer pair P1/P7, followed by primer pair R16F2n/R16R2. Random fragment length polymorphism analysis of potato phytoplasma isolates collected from different production areas using the CfoI restriction enzyme indicated that potato witches’‐broom phytoplasma isolate (PoWB) is genetically different from phytoplasmas associated with potato purple top disease in Iran. Sequence analysis of the partial 16S rRNA gene amplified by nested PCR indicated that ‘Candidatus Phytoplasma trifolii’ is associated with potato witches’‐broom disease in Iran. This is the first report of potato witches’‐broom disease in Iran.     

Anaerobic treatment of a chemical synthesis-based pharmaceutical wastewater in a hybrid upflow anaerobic sludge blanket reactor

In this study, performance of a lab-scale hybrid up-flow anaerobic sludge blanket (UASB) reactor, treating a chemical synthesis-based pharmaceutical wastewater, was evaluated under different operating conditions. This study consisted of two experimental stages: first, acclimation to the pharmaceutical wastewater and second, determination of maximum loading capacity of the hybrid UASB reactor. Initially, the carbon source in the reactor feed came entirely from glucose, applied at an organic loading rate (OLR) 1 kg COD/m(3) d. The OLR was gradually step increased to 3 kg COD/m(3) d at which point the feed to the hybrid UASB reactor was progressively modified by introducing the pharmaceutical wastewater in blends with glucose, so that the wastewater contributed approximately 10%, 30%, 70%, and ultimately, 100% of the carbon (COD) to be treated. At the acclimation OLR of 3 kg COD/m(3) d the hydraulic retention time (HRT) was 2 days. During this period of feed modification, the COD removal efficiencies of the anaerobic reactor were 99%, 96%, 91% and 85%, and specific methanogenic activities (SMA) were measured as 240, 230, 205 and 231 ml CH(4)/g TVS d, respectively. Following the acclimation period, the hybrid UASB reactor was fed with 100% (w/v) pharmaceutical wastewater up to an OLR of 9 kg COD/m(3) d in order to determine the maximum loading capacity achievable before reactor failure. At this OLR, the COD removal efficiency was 28%, and the SMA was measured as 170 ml CH(4)/g TVS d. The hybrid UASB reactor was found to be far more effective at an OLR of 8 kg COD/m(3) d with a COD removal efficiency of 72%. At this point, SMA value was 200 ml CH(4)/g TVS d. It was concluded that the hybrid UASB reactor could be a suitable alternative for the treatment of chemical synthesis-based pharmaceutical wastewater.     

Improvement of olive oil phenolics content by means of enzyme formulations: Effect of different enzyme activities and levels

The present work deals with the development of an enzymatic treatment aiming at producing high-quality olive oil with increased phenolics content and antioxidant activity. Three different enzyme formulations, specifically pectinase, hemicellulase and cellulase (A), pectinase and hemicellulase (B), and only pectinase (C), were used either at three different level of each or in ternary and binary mixtures at a constant level. All of them were added to the olive paste (Italian cultivar Coratina) at the beginning of the malaxation step. Results demonstrated that an increased enzyme level led to higher phenolics content in the oils, and such an effect was found to be enzyme dependent, being greater when using formulation A, followed by formulations B and C. Two significant correlations were obtained between total polyphenols and o-diphenols contents versus antiradical power (R² = 0.8743 and R² = 0.8635, respectively), which pointed out the effectiveness of the proposed enzymatic treatment to produce olive oils characterized by low susceptibility to oxidation. A synergistic effect between the different enzymatic activities contained in the single formulations was observed by combining enzymes A and B. The ternary mixture was selected as the most efficient enzymatic system ensuring the highest phenolics content increase (40 and 37% for total polyphenols and o-diphenols contents, respectively) compared to the other enzymes when used at the same level.     

Secretome of Peripheral Blood Mononuclear Cells Enhances Wound Healing

Non-healing skin ulcers are often resistant to most common therapies. Treatment with growth factors has been demonstrated to improve closure of chronic wounds. Here we investigate whether lyophilized culture supernatant of freshly isolated peripheral blood mononuclear cells (PBMC) is able to enhance wound healing. PBMC from healthy human individuals were prepared and cultured for 24 hours. Supernatants were collected, dialyzed and lyophilized (SEC^PBMC). Six mm punch biopsy wounds were set on the backs of C57BL/6J-mice and SEC^PBMC containing emulsion or controls were applied daily for three days. Morphology and neo-angiogenesis were analyzed by H&E-staining and CD31 immuno-staining, respectively. In vitro effects on diverse skin cells were investigated by migration assays, cell cycle analysis, and tube formation assay. Signaling pathways were analyzed by Western blot analysis. Application of SEC^PBMC on 6 mm punch biopsy wounds significantly enhanced wound closure. H&E staining of the wounds after 6 days revealed that wound healing was more advanced after application of SEC^PBMC containing emulsion. Furthermore, there was a massive increase in CD31 positive cells, indicating enhanced neo-angiogenesis. In primary human fibroblasts (FB) and keratinocytes (KC) migration but not proliferation was induced. In endothelial cells (EC) SEC^PBMC induced proliferation and tube-formation in a matrigel-assay. In addition, SEC^PBMC treatment of skin cells led to the induction of multiple signaling pathways involved in cell migration, proliferation and survival. In summary, we could show that emulsions containing the secretome of PBMC derived from healthy individuals accelerates wound healing in a mouse model and induce wound healing associated mechanisms in human primary skin cells. The formulation and use of such emulsions might therefore represent a possible novel option for the treatment of non-healing skin ulcers.     

Coarse-grained normal mode analysis in structural biology

The realization that experimentally observed functional motions of proteins can be predicted by coarse-grained normal mode analysis has renewed interest in applications to structural biology. Notable applications include the prediction of biologically relevant motions of proteins and supramolecular structures driven by their structure-encoded collective dynamics; the refinement of low-resolution structures, including those determined by cryo-electron microscopy; and the identification of conserved dynamic patterns and mechanically key regions within protein families. Additionally, hybrid methods that couple atomic simulations with deformations derived from coarse-grained normal mode analysis are able to sample collective motions beyond the range of conventional molecular dynamics simulations. Such applications have provided great insight into the underlying principles linking protein structures to their dynamics and their dynamics to their functions.