Variation in sensitivity of the cardiac glycoside receptor characteristics of (Na+ + K+)-ATPase to lipolysis and temperature.

1. The rate of binding of [3H]ouabain to untreated membrane preparations of [Na+ +K+]-ATPase is a timperature--dependent process displaying a thermal transition close to 25degreesC. The apparent energies of activation which can be calculated above and below this transition are similar to, but not identical with, those previously reported for activation of the enzyme by cations. 2. Treatment of the enzyme preparation with detergents or lipolysis with phospholipase A eliminates the thermal transition resulting in linear Arrhenius plots. 3. The number of sites available for [3H]ouabain binding is not temperature dependent as the amount of [3H]ouabain bound at equillbrium is not changed between 10 and 37 degrees C. 4. Treatment of the enzyme with phospholipase A results in time-dependent changes in the number of binding sites for [3H]ouabain at equilibrium. 5. Treatment of the membrane enzyme preparations with detergents reveals additional [3H]ouabain binding sites which are extremely sensitive to lipolysis with phospholipase A. 6. There are a number of [3H]ouabain binding sites which remain resistant to lipolysis by phospholipase A in either untreated or detergent-treated membrane preparations. 7. It is suggested that [3H]ouabain binding sites exist in the membrane in at least two different environments, one of which is resistant the other sensitive to attack by phopholipase A.     

Direct measurements of cell number using computer-aided video microscopy

Quantitative studies in cell culture require accurate measurements of cell density and kinetics. We have developed a direct, rapid, and noninvasive method for measuring cell number in monolayer culture. Using computer-aided video microscopy, cell number was measured without detaching or chemically destroying the cells, thereby allowing sequential measurements in the same cell population. Cell number measured by computer-aided microscopy closely correlated with hemocytometer counts and determinations of total cell protein. For high-density monolayers of mesenchymal cells, however, staining was required for accurate counts. Unlike other techniques for measuring cell density, computer-aided microscopy was especially accurate in medium- to low-density cultures (less than 6000 cells/cm2). In addition, we applied this technique to the construction of separate proliferation curves for glomerular mesangial and vascular endothelial cells in coculture. These measurements by cell type in coculture are impossible using conventional methods for determining cell number.     

Laboratory studies of the effects of reduced prey choice caused by Bt plants on a predatory insect

Crops transformed to express Bacillus thuringiensis (Bt) toxins can cause close to 100% mortality of certain target pest species. This study assessed the effect of target pest reduction on the predatory insect Chrysoperla carnea (Stephens) in the presence of alternative prey. Numbers of lacewings recovered from Bt oilseed rape (cultivar Oscar, event O52) did not differ significantly from numbers of lacewings recovered from conventional oilseed rape in cage experiments with the target pest Plutella xylostella (Linnaeus) and the non-target pest Myzus persicae (Sulzer) when aphid densities were high. However, significantly fewer lacewings were recovered from Bt plants as aphid densities were lowered. Lacewing weights were not affected by plant type.     

Cell-based therapy for epithelial wounds

Background aimsBone marrow-derived cells (BMDC) form a significant portion of regenerating epithelial tissue. The purpose of this study was to determine whether exogenous BMDC (containing stroma, stem and progenitor cells), introduced systemically or within the injury site, could enhance the injury repair response.MethodsExcisional wounds (10-mm diameter) were treated by systemic (intravenous; i.v.) and local (subcutaneous; s.c.) administration of BMDC (10–20 × 10⁶/100 μL phosphate-buffered saline). Young and aged BMDC and recipients were studied.ResultsYoung BMDC (2 months old) increased the healing rate compared with older BMDC (1 year old), as measured by the rate of healing and the percentage of healed tissue. Young recipients had statistically better healing efficiency than older recipients. When old BMDC were used, young recipients had a better healing ability than older recipients. In addition, when the size of the healed tissue, the area of repigmentation and hair growth at the injury site were compared, young BMDC and young recipients had superior effects compared with old BMDC and old recipients.ConclusionsThese results demonstrate that cellular therapy is important for wound healing in older recipients that do not heal significantly without intervention. BMDC injections result in normal healing, indistinguishable from young recipients. Significantly, a single injection into the wound margin is sufficient to reverse the wounding process and promote normal wound healing. Although younger recipients eventually healed without therapy, BMDC injections accelerated the process, reduced scarring and increased hair regrowth. These findings provide insight into the treatment of non-healing epithelial tissue with BMDC.     

Redesigning the stereospecificity of tyrosyl‐tRNA synthetase

d ‐Amino acids are largely excluded from protein synthesis, yet they are of great interest in biotechnology. Unnatural amino acids have been introduced into proteins using engineered aminoacyl‐tRNA synthetases (aaRSs), and this strategy might be applicable to d ‐amino acids. Several aaRSs can aminoacylate their tRNA with a d ‐amino acid; of these, tyrosyl‐tRNA synthetase (TyrRS) has the weakest stereospecificity. We use computational protein design to suggest active site mutations in Escherichia coli TyrRS that could increase its d ‐Tyr binding further, relative to l ‐Tyr. The mutations selected all modify one or more sidechain charges in the Tyr binding pocket. We test their effect by probing the aminoacyl‐adenylation reaction through pyrophosphate exchange experiments. We also perform extensive alchemical free energy simulations to obtain l ‐Tyr/d ‐Tyr binding free energy differences. Agreement with experiment is good, validating the structural models and detailed thermodynamic predictions the simulations provide. The TyrRS stereospecificity proves hard to engineer through charge‐altering mutations in the first and second coordination shells of the Tyr ammonium group. Of six mutants tested, two are active towards d ‐Tyr; one of these has an inverted stereospecificity, with a large preference for d ‐Tyr. However, its activity is low. Evidently, the TyrRS stereospecificity is robust towards charge rearrangements near the ligand. Future design may have to consider more distant and/or electrically neutral target mutations, and possibly design for binding of the transition state, whose structure however can only be modeled. Proteins 2016; 84:240–253. © 2015 Wiley Periodicals, Inc.     

Protein side chain conformation predictions with an MMGBSA energy function

The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an “MMGBSA” energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803–819. © 2016 Wiley Periodicals, Inc.     

Oviposition behaviour and host colony size discrimination in Episyrphus balteatus (Diptera: Syrphidae)

Three bioassays were used to examine the oviposition behaviour of the hoverfly, Episyrphus balteatus (Degeer) in which various stimuli purported to influence host assessment and choice were tested. Episyrphus balteatus failed to exhibit enhanced behavioural responses, in terms of approaches and landings, to artificial leaves with the highest numbers of aphids, suggesting that females are merely responding to the colour of the artificial leaves. A density-dependent oviposition response was reported in a second bioassay using whole bean plants, although there was an asymptotic relationship. Syrphid responses, which were measured by oviposition over a five-day period, were greatest towards those plants with the highest number of aphids. In a final series of trials, gravid female E. balteatus showed a behavioural preference for filter papers treated with the greatest honeydew concentrations (0.26 mg microl(-1) honeydew). More time was spent in the treated areas and syrphids demonstrated more proboscis and ovipositor extensions in these treatments. These bioassays provided an opportunity to isolate some of the individual components of decision-making by female E. balteatus during egg-laying behaviour. A greater understanding of natural enemy behaviour is essential before enhanced control of pest populations in the field can be established.     

Protein-protein recognition: an experimental and computational study of the R89K mutation in Raf and its effect on Ras binding

Binding of the protein Raf to the active form of Ras promotes activation of the MAP kinase signaling pathway, triggering cell growth and differentiation. Raf/Arg89 in the center of the binding interface plays an important role determining Ras-Raf binding affinity. We have investigated experimentally and computationally the Raf-R89K mutation, which abolishes signaling in vivo. The binding to [gamma-35S]GTP-Ras of a fusion protein between the Raf-binding domain (RBD) of Raf and GST was reduced at least 175-fold by the mutation, corresponding to a standard binding free energy decrease of at least 3.0 kcal/mol. To compute this free energy and obtain insights into the microscopic interactions favoring binding, we performed alchemical simulations of the RBD, both complexed to Ras and free in solution, in which residue 89 is gradually mutated from Arg into Lys. The simulations give a standard binding free energy decrease of 2.9+/-1.9 kcal/mol, in agreement with experiment. The use of numerous runs with three different force fields allows insights into the sources of uncertainty in the free energy and its components. The binding decreases partly because of a 7 kcal/mol higher cost to desolvate Lys upon binding, compared to Arg, due to better solvent interactions with the more concentrated Lys charge in the unbound state. This effect is expected to be general, contributing to the lower propensity of Lys to participate in protein-protein interfaces. Large contributions to the free energy change also arise from electrostatic interactions with groups up to 8 A away, namely residues 37-41 in the conserved effector domain of Ras (including 4 kcal/mol from Ser39 which loses a bifurcated hydrogen bond to Arg89), the conserved Lys84 and Lys87 of Raf, and 2-3 specific water molecules. This analysis will provide insights into the large experimental database of Ras-Raf mutations.     

Geneflow from GM plants--towards a more quantitative risk assessment

Assessing the risks associated with geneflow from GM crops to wild relatives is a significant scientific challenge. Most researchers have focused on assessing the frequency of gene flow, too often on a localized scale, and ignoring the hazards caused by geneflow. To quantify risk, multi-disciplinary research teams need to unite and scale up their studies.     

Leukocytosis occurs in response to resistance exercise in men

The purpose of this study was to determine the effects of a single bout of resistance exercise on immune cell numbers of moderately active men. Subjects were 16 male volunteers (mean +/- standard deviation [SD] age 30 +/- 7 years, height 180.1 +/- 7.0 cm, mass 83.97 +/- 10.33 kg); 8 were randomly assigned to treatment and 8 to control groups. Treatment was a common resistance training routine (3 sets of 8-10 repetitions at 75% of 1 repetition maximum) of 8 large muscle mass exercises using resistance machines. Blood samples were drawn before exercise and at 0 minutes (P0), 15 minutes (P15), and 30 minutes (P30) postexercise. Control subjects sat quietly in the training facility; blood was drawn at the same intervals as treatment. Leukocyte and lymphocyte (LY) subpopulation numbers were determined. Statistical analysis was analysis of variance (ANOVA) (repeated measures, p < or = 0.050) and multiple comparisons (Dunn method) to isolate variability. All leukocyte subpopulations, except basophils (BA) and eosinophils (EO), increased and counts declined by P15 and P30. Only neutrophils (NE) did not return to preexercise levels by P30. The majority of resistance exercise induced leukocytosis was due to an increase in circulating LY (natural killer cells increased most, CD4+/CD8+ ratio unchanged) and monocytes (MO). The transient, inconsequential immune cell population responses to resistance exercise are similar to those during aerobic activity. The lack of large alterations in and rapid recovery from cell number changes suggests that resistance exercise is not immunosuppressive.