Fold prediction problem: the application of new physical and physicochemical-based features

One of the most important goals in bioinformatics is the ability to predict tertiary structure of a protein from its amino acid sequence. In this paper, new feature groups based on the physical and physicochemical properties of amino acids (size of the amino acids' side chains, predicted secondary structure based on normalized frequency of β-Strands, Turns, and Reverse Turns) are proposed to tackle this task. The proposed features are extracted using a modified feature extraction method adapted from Dubchak et al. To study the effectiveness of the proposed features and the modified feature extraction method, AdaBoost.M1, Multi Layer Perceptron (MLP), and Support Vector Machine (SVM) that have been commonly and successfully applied to the protein folding problem are employed. Our experimental results show that the new feature groups altogether with the modified feature extraction method are capable of enhancing the protein fold prediction accuracy better than the previous works found in the literature.     

Glucose biosensor prepared by glucose oxidase encapsulated sol-gel and carbon-nanotube-modified basal plane pyrolytic graphite electrode

A new glucose biosensor has been fabricated by immobilizing glucose oxidase into a sol-gel composite at the surface of a basal plane pyrolytic graphite (bppg) electrode modified with multiwall carbon nanotube. First, the bppg electrode is subjected to abrasive immobilization of carbon nanotubes by gently rubbing the electrode surface on a filter paper supporting the carbon nanotubes. Second, the electrode surface is covered with a thin film of a sol-gel composite containing encapsulated glucose oxidase. The carbon nanotubes offer excellent electrocatalytic activity toward reduction and oxidation of hydrogen peroxide liberated in the enzymatic reaction between glucose oxidase and glucose, enabling sensitive determination of glucose. The amperometric detection of glucose is carried out at 0.3 V (vs saturated calomel electrode) in 0.05 M phosphate buffer solution (pH 7.4) with linear response range of 0.2-20 mM glucose, sensitivity of 196 nA/mM, and detection limit of 50 microM (S/N=3). The response time of the electrode is < 5s when it is stored dried at 4 degrees C, the sensor showed almost no change in the analytical performance after operation for 3 weeks. The present carbon nanotube sol-gel biocomposite glucose oxidase sensor showed excellent properties for the sensitive determination of glucose with good reproducibility, remarkable stability, and rapid response and in comparison to bulk modified composite biosensors the amounts of enzyme and carbon nanotube needed for electrode fabrication are dramatically decreased.     

Involvement of PPAR-γ and p53 in DHA-induced apoptosis in Reh cells

Dendritic cells (DCs) are professional antigen-presenting cells and have come to be appreciated as critical controllers of the immune response, especially T cell responses. Apart from presenting antigens to T cells, DCs carry out many other functions in regulating immunity. DC-specific intercellular adhesion molecule (ICAM)-3 grabbing non-integrin (DC-SIGN) is a novel receptor that plays an important role in DC migration and adhesion, the inflammatory response, T cell activation, initiating the immune response, and immune escape of pathogens and tumors. DC-SIGN mediates DC binding to ICAM-3 on the T cell surface and ICAM-2 on the endothelial cell (EC) surface, and takes part in the initial interaction between DC and T cells or vascular ECs. The procedure of systematic evolution of ligands by exponential enrichment (SELEX) is a method in which single-stranded oligonucleotides are selected from a wide variety of sequences, based on their interaction with a target molecule. In this study, we selected DNA aptamers against DC-SIGN protein by SELEX, and measured their binding affinity for DC-SIGN. Finally, an appropriate aptamer with high affinity for DC-SIGN was obtained, and it blocked DC adhesion to ECs as effectively as anti-DC-SIGN monoclonal antibody.     

Effectiveness of nitrogen fixation in rhizobia

Biological nitrogen fixation in rhizobia occurs primarily in root or stem nodules and is induced by the bacteria present in legume plants. This symbiotic process has fascinated researchers for over a century, and the positive effects of legumes on soils and their food and feed value have been recognized for thousands of years. Symbiotic nitrogen fixation uses solar energy to reduce the inert N₂ gas to ammonia at normal temperature and pressure, and is thus today, especially, important for sustainable food production. Increased productivity through improved effectiveness of the process is seen as a major research and development goal. The interaction between rhizobia and their legume hosts has thus been dissected at agronomic, plant physiological, microbiological and molecular levels to produce ample information about processes involved, but identification of major bottlenecks regarding efficiency of nitrogen fixation has proven to be complex. We review processes and results that contributed to the current understanding of this fascinating system, with focus on effectiveness of nitrogen fixation in rhizobia.     

Examination of the protective roles of helmet/faceshield and directionality for human head under blast waves

A parametric study was conducted to delineate the efficacy of personal protective equipment (PPE), such as ballistic faceshields and advanced combat helmets, in the case of a blast. The propagations of blast waves and their interactions with an unprotected head, a helmeted one, and a fully protected finite element head model (FEHM) were modeled. The biomechanical parameters of the brain were recorded when the FEHM was exposed to shockwaves from the front, back, top, and bottom. The directional dependent tissue response of the brain and the variable efficiency of PPE with respect to the blast orientation were two major results of this study.     

The Effects of a Prophylactic Knee Brace and Two Neoprene Knee Sleeves on the Performance of Healthy Athletes: A Crossover Randomized Controlled Trial

Knee injury is one of the major problems in sports medicine, and the use of prophylactic knee braces is an attempt to reduce the occurrence and/or severity of injuries to the knee joint ligament(s) without inhibiting knee mobility. The aim of the present study was to examine the effect of one recently designed prophylactic knee brace and two neoprene knee sleeves upon performance of healthy athletes. Thirty-one healthy male athletes (age = 21.2±1.5) volunteered as participants to examine the effect of prophylactic knee brace/sleeves on performance using isokinetic and functional tests. All subjects were tested in four conditions in a random order: 1. nonbraced (control) 2. using a neoprene knee sleeve 3. using a knee sleeve with four bilateral metal supports and 4. using a prophylactic knee brace. The study design was a crossover, randomized, controlled trial. Subjects completed single leg vertical jump, cross-over hop, and the isokinetic knee flexion and extension (at 60, 180, 300°/sec). Data were collected from the above tests and analyzed for jump height, cross-over hop distance, peak torque to body weight ratio and average power, respectively. Comparisons of these variables in the four testing conditions revealed no statistically significant difference (p>0.05). The selected prophylactic brace/sleeves did not significantly inhibit athletic performance which might verify that their structure and design have caused no complication in the normal function of the knee joint. Moreover, it could be speculated that, if the brace or the sleeves had any limiting effect, our young healthy athletic subjects were well able to generate a mean peak torque large enough to overcome this possible restriction. Further studies are suggested to investigate the long term effect of these prophylactic knee brace and sleeves as well as their possible effect on the adjacent joints to the knee.     

High-level expression of functional recombinant human coagulation factor VII in insect cells

Recombinant coagulation factor VII (FVII) is used as a potential therapeutic intervention in hemophilia patients who produce antibodies against the coagulation factors. Mammalian cell lines provide low levels of expression, however, the Spodoptera frugiperda Sf9 cell line and baculovirus expression system are powerful systems for high-level expression of recombinant proteins, but due to the lack of endogenous vitamin K-dependent carboxylase, expression of functional FVII using this system is impossible. In the present study, we report a simple but versatile method to overcome the defect for high-level expression of the functional recombinant coagulation FVII in Sf9 cells. This method involves simultaneous expression of both human γ-carboxylase (hGC) and human FVII genes in the host. It may be possible to express other vitamin K-dependent coagulation factors using this method in the future.     

Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing

An alternative consolidated bioprocessing approach is the use of a co-culture containing cellulolytic and solventogenic clostridia. It has been demonstrated that the rate of cellulose utilization in the co-culture of Clostridium acetobutylicum and Clostridium cellulolyticum is improved compared to the mono-culture of C. cellulolyticum, suggesting the presence of syntrophy between these two species. However, the metabolic interactions in the co-culture are not well understood. To understand the metabolic interactions in the co-culture, we developed a genome-scale metabolic model of C. cellulolyticum comprising of 431 genes, 621 reactions, and 603 metabolites. The C. cellulolyticum model can successfully predict the chemostat growth and byproduct secretion with cellulose as the substrate. However, a growth arrest phenomenon, which occurs in batch cultures of C. cellulolyticum at cellulose concentrations higher than 6.7 g/L, cannot be predicted by dynamic flux balance analysis due to the lack of understanding of the underlying mechanism. These genome-scale metabolic models of the pure cultures have also been integrated using a community modeling framework to develop a dynamic model of metabolic interactions in the co-culture. Co-culture simulations suggest that cellobiose inhibition cannot be the main factor that is responsible for improved cellulose utilization relative to mono-culture of C. cellulolyticum.