Damaged-self recognition as a general strategy for injury detection

Plants perceive endogenous molecules or their fragments as signals of danger when these appear at increased concentrations in the extracellular space, and they respond with increased endogenous levels of jasmonic acid. The wound hormone jasmonic acid represents a central player in the induced resistance of plants to herbivore feeding and infection by necrotrophic pathogens. This ‘damaged self recognition’ mechanism of plants exhibits astonishing similarities to the perception of ‘damage-associated molecular patterns’ (DAMPs) by the human immune system: endogenous cell constituents, or their fragments, that can be released into the extracellular milieu during states of cellular stress or damage function as ‘stress signals’ and trigger inflammatory and other immunity-related responses. Multicellular organisms use endogenous molecules as danger signals to mount adequate healing and resistance-related responses without depending on exogenous signals and to place exogenous, enemy-derived molecular signals into the adequate functional context.     

Microcolony and biofilm formation as a survival strategy for bacteria

Bacterial communities such as biofilms are widely recognized as being important for survival and persistence of bacteria in harsh environments. Mechanistic models of biofilm growth indicate that the way in which the surface is seeded can effect the morphology of simulated biofilms. Experimental studies indicate that genes which are important for chemotaxis also influence biofilm formation, perhaps by influencing aggregation on a surface. Understanding aggregation and microcolony formation could therefore help clarify factors influencing biofilm formation and illuminate how groups influence the fitness of bacteria. In this paper I develop an individual based model to examine how different behaviors involved in microcolony formation on a surface determine patterns of group sizes and link patterns to bacterial fitness.     

Albumin binding as a general strategy for improving the pharmacokinetics of proteins

Plasma protein binding can be an effective means of improving the pharmacokinetic properties of otherwise short lived molecules. Using peptide phage display, we identified a series of peptides having the core sequence DICLPRWGCLW that specifically bind serum albumin from multiple species with high affinity. These peptides bind to albumin with 1:1 stoichiometry at a site distinct from known small molecule binding sites. Using surface plasmon resonance, the dissociation equilibrium constant of peptide SA21 (Ac-RLIEDICLPRWGCLWEDD-NH(2)) was determined to be 266 +/- 8, 320 +/- 22, and 467 +/- 47 nm for rat, rabbit, and human albumin, respectively. SA21 has an unusually long half-life of 2.3 h when injected by intravenous bolus into rabbits. A related sequence, fused to the anti-tissue factor Fab of D3H44 (Presta, L., Sims, P., Meng, Y. G., Moran, P., Bullens, S., Bunting, S., Schoenfeld, J., Lowe, D., Lai, J., Rancatore, P., Iverson, M., Lim, A., Chisholm, V., Kelley, R. F., Riederer, M., and Kirchhofer, D. (2001) Thromb. Haemost. 85, 379-389), enabled the Fab to bind albumin with similar affinity to that of SA21 while retaining the ability of the Fab to bind tissue factor. This interaction with albumin resulted in reduced in vivo clearance of 25- and 58-fold in mice and rabbits, respectively, when compared with the wild-type D3H44 Fab. The half-life was extended 37-fold to 32.4 h in rabbits and 26-fold to 10.4 h in mice, achieving 25-43% of the albumin half-life in these animals. These half-lives exceed those of a Fab'(2) and are comparable with those seen for polyethylene glycol-conjugated Fab molecules, immunoadhesins, and albumin fusions, suggesting a novel and generic method for improving the pharmacokinetic properties of rapidly cleared proteins.     

Engineering whole-cell biosensors to evaluate the effect of osmotic conditions on bacteria

Enhanced green fluorescent protein (eGFP) is a variant of wild-type GFP humanized for optimal expression in mammalian cell lines. A computational approach comparing wtGFP and eGFP showed the occurrence of rare proline codons within the eGFP gene that could interfere with and hamper protein production in prokaryotic expression systems. The eGFP gene excised from mammalian plasmid pEGFP N3 was used for construction of two inducible promoter-reporter fusions, T7-eGFP and P_proU-eGFP, through directional cloning. The T7-eGFP fusion confirmed expression of eGFP protein within the bacterial strain, showing a fluorescent green cell pellet and overexpression of the ~29 kDa eGFP protein upon induction with IPTG. The proU operon aids in osmoadaptation by encoding a transport system for uptake of various compatible solutes, including glycine-betaine and proline. Expression of the proU operon is induced upon growth of bacteria in media of elevated osmolarity. When coupled to an eGFP reporter, a time course study using fluorometry demonstrated that induction of P_proU in Escherichia coli occurred rapidly. The P_proU induction and recombinant eGFP production depends on time and concentration of solute (NaCl) in the medium. Cells containing the P_proU-eGFP fusion showed maximum promoter activity at 500 mM concentration of NaCl with a sensitivity of the P_proU promoter being 50 mM. The relative fluorescence reflected the amount of protein synthesized proportional to the activity of induced promoter and effect of NaCl on growth was also taken into consideration. Thus, such environmentally regulated highly sensitive promoters with enhanced reporters could possibly be used as whole-cell biosensors.     

Sporulation as an effective strategy for the survival of bacteria in a biofilter with discontinuous operation

The microbial population of the biofilter developed for the treatment of air contaminated by solvent vapours was evaluated using plate count techniques. The number of total heterotrophic bacteria and bacteria utilizing contaminant as the only source of carbon and energy was estimated during the exchange of the filter-bed material and start-up of its operation. Spore-forming bacteria (Bacillus spp.) occupied a significant part of the filter-bed niche. It is proposed that sporulation helps bacteria to survive during the breaks in operation of the biofilter.     

Re-evaluation of the action potential upstroke velocity as a measure of the Na+ current in cardiac myocytes at physiological conditions

Background

The SCN5A encoded sodium current (I_Na) generates the action potential (AP) upstroke and is a major determinant of AP characteristics and AP propagation in cardiac myocytes. Unfortunately, in cardiac myocytes, investigation of kinetic properties of I_Na with near-physiological ion concentrations and temperature is technically challenging due to the large amplitude and rapidly activating nature of I_Na, which may seriously hamper the quality of voltage control over the membrane. We hypothesized that the alternating voltage clamp-current clamp (VC/CC) technique might provide an alternative to traditional voltage clamp (VC) technique for the determination of I_Na properties under physiological conditions.

Principal Findings

We studied I_Na under close-to-physiological conditions by VC technique in SCN5A cDNA-transfected HEK cells or by alternating VC/CC technique in both SCN5A cDNA-transfected HEK cells and rabbit left ventricular myocytes. In these experiments, peak I_Na during a depolarizing VC step or maximal upstroke velocity, dV/dt_max, during VC/CC served as an indicator of available I_Na. In HEK cells, biophysical properties of I_Na, including current density, voltage dependent (in)activation, development of inactivation, and recovery from inactivation, were highly similar in VC and VC/CC experiments. As an application of the VC/CC technique we studied I_Na in left ventricular myocytes isolated from control or failing rabbit hearts.

Conclusions

Our results demonstrate that the alternating VC/CC technique is a valuable experimental tool for I_Na measurements under close-to-physiological conditions in cardiac myocytes.     

A strategy for obtaining active mammalian enzyme from a fusion protein expressed in bacteria using phospholipase A2 as a model

An active preparation of human phospholipase A2 (PLA2) was made after expression as an insoluble fusion protein in Escherichia coli. The new key elements required for PLA2 isolation were the maintenance of the fusion protein in solution after the initial solubilization and the use of a tryptophan cleavage procedure for regeneration of native PLA2 from the fusion protein. The fusion protein was composed of a beta-galactosidase leader peptide incorporating six consecutive threonine residues to aid in insoluble inclusion body formation, followed by a tryptophan adjacent to the N-terminus of PLA2. The fusion protein was purified from cell lysates, and the leader peptide was cleaved on the C-terminal side of the tryptophan residue with N-chlorosuccinimide. The released PLA2 was refolded and renatured to produce an enzyme with activity comparable to that of other phospholipases A2.     

Reduced osmotic potential effects on photosynthesis : identification of stromal acidification as a mediating factor

Addition of sorbitol, which facilitated reductions in reaction medium osmotic potential from standard (0.33 molar sorbitol, −10 bars) isotonic conditions to a stress level of 0.67 molar sorbitol (−20 bars), inhibited the photosynthetic capacity of isolated spinach (Spinacia oleracea) chloroplasts. This inhibition, which ranged from 64 to 74% under otherwise standard reaction conditions, was dependent on reaction medium inorganic phosphate concentration, with the phosphate optimum for photosynthesis reduced to 0.05 millimolar at the low osmotic potential stress treatment from a value of 0.25 millimolar under control conditions.

Stromal alkalating agents such as NH₄Cl (0.75 millimolar) and KCl (35 millimolar) were also found to affect the degree of low osmotic potential inhibition of photosynthesis. Both agents doubled the rate of NaHCO₃-supported O₂ evolution under the stress treatment, while hardly affecting the control rate at optimal concentrations. These agents also reduced the length of the lag phase of photosynthetic O₂ evolution under the stress treatment to a much greater degree. The rate-enhancement effect of these agents under the stress treatment was reversed by sodium acetate, which is known to facilitate stromal acidification.

The reaction medium pH optimum for photosynthesis under the stress treatment was higher than under control conditions. In the presence of optimal NH₄Cl, this shift was no longer evident.

Internal pH measurements indicated that the stress treatment caused a 0.43 and 0.24 unit reduction in the stromal and intrathylakoid pH, respectively, under illumination. This osmotically induced acidification was not evident in the dark. The presence of 0.75 millimolar NH₄Cl partially reversed the osmotically induced reduction in the illuminated stromal pH. It was concluded that stromal acidification is a mediating mechanism of the most severe site of low osmotic potential inhibition of the photosynthetic process.

     

Schooling as a strategy for taxis in a noisy environment

Many aquatic animals face a fundamental problem during foraging and migratory movements: while their resources commonly vary at large spatial scales, they can only sample and assess their environment at relatively small, local spatial scales. Thus, they are unable to choose movement directions by directly sampling distant parts of their environment. A common strategy to overcome this problem is taxis, a behaviour in which an animal performs a biased random walk by changing direction more rapidly when local conditions are getting worse. Such an animal spends more time moving in right directions than wrong ones, and eventually gets to a favourable area. Taxis is inefficient, however, when environmental gradients are weak or overlain by noisy small-scale fluctuations. In this paper, I show that schooling behaviour can improve the ability of animals performing taxis to climb gradients, even under conditions when asocial taxis would be ineffective. Schooling is a social behaviour incorporating tendencies to remain close to and align with fellow members of a group. It enhances taxis because the alignment tendency produces tight angular distributions within groups, and dampens the stochastic effects of individual sampling errors. As a result, more school members orient up-gradient than in the comparable asocial case. However, overly strong schooling behaviour makes the school slow in responding to changing gradient directions. This trade-off suggests an optimal level of schooling behaviour for given spatio-temporal scales of environmental variations. Social taxis may enhance the selective value of schooling in pelagic grazers such as herrings, anchovies and Antarctic krill. Furthermore, the degree of aggregation in a population of schooling animals may affect directly the rate and direction of migration and foraging movements.     

Creatine as a therapeutic strategy for myopathies

Myopathies are genetic or acquired disorders of skeletal muscle that lead to varying degrees of weakness, atrophy, and exercise intolerance. In theory, creatine supplementation could have a number of beneficial effects that could enhance function in myopathy patients, including muscle mass, strength and endurance enhancement, lower calcium levels, anti-oxidant effects, and reduced apoptosis. Patients with muscular dystrophy respond to several months of creatine monohydrate supplementation (~0.075–0.1 g/kg/day) with greater strength (~9%) and fat-free mass (~0.63 kg). Patients with myotonic dystrophy do not show as consistent an effect, possibly due to creatine transport issues. Creatine monohydrate supplementation shows modest benefits only at lower doses and possibly negative effects (cramping) at higher doses in McArdle’s disease patients. Patients with MELAS syndrome show some evidence of benefit from creatine supplementation in exercise capacity, with the effects in patients with CPEO being less robust, again, possibly due to limited muscle creatine uptake. The evidence for side effects or negative impact upon serological metrics from creatine supplementation in all groups of myopathy patients is almost non-existent and pale in comparison to the very substantial and well-known side effects from our current chemotherapeutic interventions for some myopathies (i.e., corticosteroids).     

Nutritional and osmotic roles of nitrate in a euhalophyte and a xerophyte in saline conditions

The effects of salinity and nitrogen (N) on growth and the role of NO3- in osmotic adjustment in the leaf-succulent euhalophyte Suaeda physophora and the stem-succulent xerophyte Haloxylon persicum were evaluated. Seedlings were exposed to 1 or 300 mm NaCl in 0.05, 1 or 10 mm NO3- -N treatments for 24 d. At 10 mm NO3-, 300 mm NaCl had no adverse effect on the concentration of NO3-, the content of organic N, and the estimated contribution of NO3- to osmotic potential in leaves of S. physophora, but markedly reduced these in stems of H. persicum. At 300 mm NaCl, more NO3- but less Cl- and Na+ were involved in osmotic adjustment in leaves of S. physophora compared with that in stems of H. persicum. The contribution of NO3- to osmotic potential was much higher in S. physophora, but lower in H. persicum, than that of amino acids at 300 mm NaCl. The nutritional and osmotic roles of NO3- -N seem to be more important in the euhalophyte S. physophora than in the xerophyte H. persicum under saline conditions. These characteristics may determine the natural distributions of the two species in saline or arid environments.     

Pupylation as a signal for proteasomal degradation in bacteria

Posttranslational modifications in the form of covalently attached proteins like ubiquitin (Ub), were long considered an exclusive feature of eukaryotic organisms. The discovery of pupylation, the modification of lysine residues with a prokaryotic, ubiquitin-like protein (Pup), demonstrated that certain bacteria use a tagging pathway functionally related to ubiquitination in order to target proteins for proteasomal degradation. However, functional analogies do not translate into structural or mechanistic relatedness. Bacterial Pup, unlike eukaryotic Ub, does not adopt a β-grasp fold, but is intrinsically disordered. Furthermore, isopeptide bond formation in the pupylation process is carried out by enzymes evolutionary descendent from glutamine synthetases. While in eukaryotes, the proteasome is the main energy-dependent protein degradation machine, bacterial proteasomes exist in addition to other architecturally related degradation complexes, and their specific role along with the role of pupylation is still poorly understood. In Mycobacterium tuberculosis (Mtb), the Pup–proteasome system contributes to pathogenicity by supporting the bacterium's persistence within host macrophages. Here, we describe the mechanism and structural framework of pupylation and the targeting of pupylated proteins to the proteasome complex. Particular attention is given to the comparison of the bacterial Pup–proteasome system and the eukaryotic ubiquitin–proteasome system. Furthermore, the involvement of pupylation and proteasomal degradation in Mtb pathogenesis is discussed together with efforts to establish the Pup–proteasome system as a drug target. This article is part of a Special Issue entitled: Ubiquitin–Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.     

Polysulfide as a possible substrate for sulfur-reducing bacteria

Because of its low solubility it is unlikely that elemental sulfur serves as the direct substrate for sulfur-reducing bacteria. To test the hypothesis that polysulfide may represent a soluble intermediate of sulfur reduction, the maximal polysulfide concentrations formed from elemental sulfur in aqueous sulfide solutions were measured at near neutral pH and at temperatures up to 90°C. The saturation concentrations decreased by two orders of magnitude when the pH was lowered from 7 to 6 at a given temperature, and increased about tenfold when the temperature was raised from 37°C to 90°C at a given pH. The dissolution of 0.1 mM zerovalent sulfur in 1 mM sulfide (H₂S+HS^–) required a pH of 7.5 at 20°C and of only 6.1 at 100°C. A comparison with the growth optima of sulfur-reducers suggests that polysulfide is present at sufficient concentration at the growth conditions of the Bacteria and the moderately acidophilic Archaea. Polysulfide is apparently not available at the growth conditions of the extremely acidophilic Archaea. Alternative mechanisms for the sulfur utilization under these conditions are discussed.Abbreviations MOPS Morpholinopropanesulfonate - PIPES 1,4 piperazine-N,N-bis(2-ethanesulfonate) - HEPES N-2-hydroxy-ethylpiperazine-N-ethanesulfonate     

Newspaper as a substrate for cellulolytic landfill bacteria

Five cellulolytic bacterial isolates ( Clostridium and Eubacterium spp.) from a methane-producing landfill were examined to determine their ability to utilize newspaper as a substrate for growth. Solubilization was poor with even the most actively cellulolytic bacteria. The major factor causing the low activity seemed to be that as much as 24% of the newspaper was composed of the high molecular weight polymer lignin, which exerts a protective effect on the attack of otherwise susceptible polymers. The presence of ink on heavily printed paper also reduced the rate of cellulose solubilization. Although the ink did not appear directly toxic to the bacteria it masked the surface of the paper, covering the cellulose fibres and preventing bacterial adhesion to the substrate. The action of the cellulolytic isolates was also strongly inhibited below the optimum growth temperature of 37°C.     

Mutations as possible replication errors in bacteria growing under conditions of thymine deficiency

When Escherichia coli or Bacillus subtilis cells having inhibited thymidylate synthetase activity were incubated for a long time on solid medium supplemented with a limiting concentration of thymine or thymidine (0.1–0.3 μg/ml) most of them became mutants for one or more genetic markers. This “overall mutagenesis” was detected both in Thy^? bacteria and in prototrophs for thymine (Thy⁺) with thymidylate synthetase inhibited by the addition of 5-fluorodeoxyuridine (FUdR) to the growth medium. When thymine (or thymidine) was present in very low amounts (10^?3 μg/ml) or was totally absent, the efficiency of mutagenesis decreased some 100-fold. The solid growth medium is essential because it supports the filamentous cells grown under conditions of limiting thymine.For some of the mutants with identified deficiency their ability to revert under the action of different mutagens was studied. Most efficient was 5-bromouracil (BU). This reversion is the characteristic response of mutations due to AT → GC transitions. In addition to single mutants, many multiple mutants were induced. The repair-defective strain of E. coli pol A1^? and strains Rec A^? and Exr A^?, which are also defective in UV-induced mutagenesis, showed a high level of mutation induction under the conditions described. All these results are in accord with the hypothesis that overall low-thymine mutagenesis reflects the accumulation of replication errors in DNA under the conditions of a precursor deficiency.     

Preparation of erythrocyte ghosts by a glycol-induced osmotic lysis under isoionic conditions

A procedure has been developed for obtaining haemoglobin-free, erythrocyte ghosts under ionic conditions approximating that of the cell cytoplasm. Haemolysis was effected by incorporating glycol into cells suspended in the isoionic medium and then diluting with a large volume of glycol-free medium.The ghosts were of uniform spherical shape throughout the preparative procedure and were impermeable to macromolecules.Analysis of polypeptides by sodium dodecyl sulphate-gel elecrophoresis at each stage of preparation and comparison with ghosts prepared under hypo-ionic conditions served to distinguish membrane components from those of cytoplasm.     

Aggregation as a cost-reducing strategy for lycaenid larvae

If a mutualistic relationship entails providing services ata cost, selection will favor individuals that maximize the netbenefits of the interaction and minimize the costs. Larvae ofmany species of lycaenid butterflies secrete nutritious foodrewards to attending ants and, in return, receive protectionagainst predators and parasitoids. Because ants typically recruitmore workers to larger resources, by forming groups the larvaemay ensure more reliable access to ants and thereby gain betterprotection. A further consequence of aggregating should be achange of the cost-benefit relationship for individual larvae.The larger the group, the smaller a single larva's influencewill be on total ant density, which could lead to a smallerinvestment in secretion, thus reducing the per capita cost ofcooperation. In this study, die influence of ant attendance,group size, and companion quality on larval investment was investigated.The interaction between the obligately ant-dependent lycaenid,Jalmanus evagoras, and its attendant Iridomyrmax ants was manipulatedand the effect on larval secretion measured. As the level ofant attendance increased, the delivery of food rewards increased,bodi for solitary and for aggregated larvae. When aggregated,larvae provided less food rewards to ants dun when solitary,and secretion rate decreased with increasing group size. Furthermore,larvae had lower secretion rates when paired with a bigger,more attractive larva than when paired with a smaller one. Theconsiderable reduction in secretion rates for larvae in groupssuggests that gaining protection at a lower secretion cost couldbe one factor that promotes aggregation in myrmecophilous lycaenids.     

Professionalization as a governance strategy for synthetic biology

This article considers professionalization as a governance strategy for synthetic biology, reporting on social science interviews done with scientists, science journal editors, members of science advisory boards and authors of nongovernmental policy reports on synthetic biology. After summarizing their observations about the potential advantages and disadvantages of the professionalization of synthetic biology, we analyze professionalization as a strategy that overcomes dichotomies found in the current debates about synthetic biology governance, specifically “top down” versus “bottom up” governance and scientific fact versus public values. Professionalization combines community and state, fact and value. Like all governance options, professionalization has limitations, particularly regarding war and peace. It is best conceptualized as potentially part of a wider range of governance mechanisms working in concert: a “web of prevention”.