Effect of mutations involving charged residues on the stability of staphylococcal nuclease: a continuum electrostatics study

A continuum electrostatics model is used to calculate the relative stabilities of 117 mutants of staphylococcal nuclease (SNase) involving the mutation of a charged residue to an uncharged residue. The calculations are based on the crystallographic structure of the wild‐type protein and attempt to take implicitly into account the effect of the mutations in the denatured state by assuming a linear relationship between the free energy changes caused by the mutation in the native and denatured states. A good correlation (linear correlation coefficient of ∼0.8) is found with published experimental relative stabilities of these mutants. The results suggest that in the case of SNase (i) charged residues contribute to the stability of the native state mainly through electrostatic interactions, and (ii) native‐like electrostatic interactions may persist in the denatured state. The continuum electrostatics method is only moderately sensitive to model parameters and leads to quasi‐predictive results for the relative mutant stabilities (error of 2-3 kJ mol-1 or of the order of kBT), except for mutants in which a charged residue is mutated to glycin

Long-term effects of no-take zones in Swedish waters

Marine protected areas (MPAs) are increasingly established worldwide to protect and restore degraded ecosystems. However, the level of protection varies among MPAs and has been found to affect the outcome of the closure. In no-take zones (NTZs), no fishing or extraction of marine organisms is allowed. The EU Commission recently committed to protect 30% of European waters by 2030 through the updated Biodiversity Strategy. Importantly, one third of these 30% should be of strict protection. Exactly what is meant by strict protection is not entirely clear, but fishing would likely have to be fully or largely prohibited in these areas. This new target for strictly protected areas highlights the need to evaluate the ecological effects of NTZs, particularly in regions like northern Europe where such evaluations are scarce. The Swedish NTZs made up approximately two thirds of the total areal extent of NTZs in Europe a decade ago. Given that these areas have been closed for at least 10 years and can provide insights into long-term effects of NTZs on fish and ecosystems, they are of broad interest in light of the new 10% strict protection by 2030 commitment by EU member states.In total, eight NTZs in Swedish coastal and offshore waters were evaluated in the current report, with respect to primarily the responses of focal species for the conservation measure, but in some of the areas also ecosystem responses. Five of the NTZs were established in 2009-2011, as part of a government commission, while the other three had been established earlier. The results of the evaluations are presented in a synthesis and also in separate, more detailed chapters for each of the eight NTZs. Overall, the results suggest that NTZs can increase abundances and biomasses of fish and decapod crustaceans, given that the closed areas are strategically placed and of an appropriate size in relation to the life cycle of the focal species. A meta-regression of the effects on focal species of the NTZs showed that CPUE was on average 2.6 times higher after three years of protection, and 3.8 times higher than in the fished reference areas after six years of protection. The proportion of old and large individuals increased in most NTZs, and thereby also the reproductive potential of populations. The increase in abundance of large predatory fish also likely contributed to restoring ecosystem functions, such as top-down control. These effects appeared after a 5-year period and in many cases remained and continued to increase in the longer term (>10 years). In the two areas where cod was the focal species of the NTZs, positive responses were weak, likely as an effect of long-term past, and in the Kattegat still present, recruitment overfishing. In the Baltic Sea, predation by grey seal and cormorant was in some cases so high that it likely counteracted the positive effects of removing fisheries and led to stock declines in the NTZs. In most cases, the introduction of the NTZs has likely decreased the total fishing effort rather than displacing it to adjacent areas. In the Kattegat NTZ, however, the purpose was explicitly to displace an unselective coastal mixed bottom-trawl fishery targeting Norway lobster and flatfish to areas where the bycatches of mature cod were smaller. In two areas that were reopened to fishing after 5 years, the positive effects of the NTZs on fish stocks eroded quickly to pre-closure levels despite that the areas remained closed during the spawning period, highlighting that permanent closures may be necessary to maintain positive effects.We conclude from the Swedish case studies that NTZs may well function as a complement to other fisheries management measures, such as catch, effort and gear regulations. The experiences from the current evaluation show that NTZs can be an important tool for fisheries management especially for local coastal fish populations and areas with mixed fisheries, as well as in cases where there is a need to counteract adverse ecosystem effects of fishing. NTZs are also needed as reference for marine environmental management, and for understanding the effects of fishing on fish populations and other ecosystem components in relation to other pressures. MPAs where the protection of both fish and their habitats is combined may be an important instrument for ecosystembased management, where the recovery of large predatory fish may lead to a restoration of important ecosystem functions and contribute to improving decayed habitats.With the new Biodiversity Strategy, EUs level of ambition for marine conservation increases significantly, with the goal of 30% of coastal and marine waters protected by 2030, and, importantly, one third of these areas being strictly protected. From a conservation perspective, rare, sensitive and/or charismatic species or habitats are often in focus when designating MPAs, and displacement of fisheries is then considered an unwanted side effect. However, if the establishment of strictly protected areas also aims to rebuild fish stocks, these MPAs should be placed in heavily fished areas and designed to protect depleted populations by accounting for their home ranges to generate positive outcomes. Thus, extensive displacement of fisheries is required to reach benefits for depleted populations, and need to be accounted for e.g. by specific regulations outside the strictly protected areas. These new extensive EU goals for MPA establishment pose a challenge for management, but at the same time offer an opportunity to bridge the current gap between conservation and fisheries management

Industrial scale high-throughput screening delivers multiple fast acting macrofilaricides.

Nematodes causing lymphatic filariasis and onchocerciasis rely on their bacterial endosymbiont, Wolbachia, for survival and fecundity, making Wolbachia a promising therapeutic target. Here we perform a high-throughput screen of AstraZeneca's 1.3 million in-house compound library and identify 5 novel chemotypes with faster in vitro kill rates (<2 days) than existing anti-Wolbachia drugs that cure onchocerciasis and lymphatic filariasis. This industrial scale anthelmintic neglected tropical disease (NTD) screening campaign is the result of a partnership between the Anti-Wolbachia consortium (A∙WOL) and AstraZeneca. The campaign was informed throughout by rational prioritisation and triage of compounds using cheminformatics to balance chemical diversity and drug like properties reducing the chance of attrition from the outset. Ongoing development of these multiple chemotypes, all with superior time-kill kinetics than registered antibiotics with anti-Wolbachia activity, has the potential to improve upon the current therapeutic options and deliver improved, safer and more selective macrofilaricidal drugs

Effect of mutations involving charged residues on the stability of staphylococcal nuclease: A continuum electrostatics study

ISSN:0269-2139ISSN:1460-213

Electrostatic Interactions in Biomolecular Systems

Electrostatic interactions are of fundamental importance in determining the structure, dynamics, and function of biomolecules. In particular, they play a key role in protein folding and stability, pH-induced conformational changes, recognition of substrates by receptors, enzymatic catalysis, and in the formation of polysaccharide-based gels. However, due to their magnitude and long-range nature, the accurate representation of electrostatic interactions in classical computer simulations is a difficult task. There is thus considerable effort in the scientific community towards the goals of (i) improving the representation of electrostatic interactions in biomolecular simulations, and (ii) understanding their specific role in biomolecular processes. The present article reviews some of the work carried out in our group along these two lines

Phosphate-solubilising rhizobacteria associated with Coffea arabica L. in natural coffee forests of southwestern Ethiopia

Phosphate-solubilising rhizobacteria associated with Coffea arabica L. in natural coffee forests of southwestern Ethiopia were investigated. The main purpose was to screen for potential microbial biofertilisers by assessing isolated strains for phosphate solubilisation efficiency and organic acid production in different media. Initial screening was performed on Pikovskaya’s agar (PA). Quantitative colorimetric estimations of mobilised phosphate were made in different broth media in the presence of two phosphate sources. HPLC was employed for the detection of organic acids. From a total of 395 rhizobacterial isolates tested for P solubilisation, over 72% (mostly Pseudomonas spp.) formed visible dissolution haloes on PA. Two Erwinia species and a P. chlororaphis strain produced the largest solubilisation indices and also solubilised hydroxyapatite strongly in broth medium. Solubilisation of hydroxyapatite (HAP)/tricalcium phosphate (TCP) by all isolates coincided with a decrease in medium pH. HPLC analyses of culture supernatants confirmed the presence of several organic acids, with 2-ketogluconic acid dominating. The production of organic acids by these coffee-associated phosphobacteria could be considered the major mechanism involved in the solubilisation of insoluble HAP/TCP. Certain isolates deserve particular attention for bioinoculant development due to their remarkable efficiency of insoluble phosphate solubilisation. The present study could therefore be important with respect to screening of Coffea arabica-associated rhizobacteria that possess direct plant growth-promoting traits for extending the use of indigenous microbes as microbial biofertilisers

Internationaliseringsprocessen - en fallstudie av små innovativa företag

Uppsatsens huvudsakliga tema är internationaliseringsprocessen för små innovativa företag. Vårt syfte har varit att undersöka huruvida de evolutionistiska modellerna kan förklara internationaliseringsmönstret hos små innovativa företag eller om det är andra faktorer som styr. Några av de teorier vi behandlar är uppsalamodellen och nätverksmodellen samt den så kallade born global teorin. Vi vill med vår studie komma fram till om den stegvisa internationaliseringen, som uppsalamodellen förespråkar, även kan förklara de innovativa företagens internationaliseringsprocess. Den huvudsakliga empirin har vi hämtat från fallstudier med tre små innovativa företag där vi närmare granskat dess olika internationaliseringsprocesser. Våra fallföretag utgörs av tjänsteföretaget Q-labs och de utvecklingsinriktade företagen Anoto AB och Biogaia AB. Resultatet vi har kommit fram till är att de innovativa företag skiljer sig från det traditionella tillvägagångssättet. Här kännetecknas det mer av en tidig samt snabb internationalisering där de innovativa företagen snarare söker sig direkt ut på internationella marknader än att de väntar på att hemmamarknaden först ska mättas. Det vill säga företagen ser den globala marknaden som sin hemmamarknad

Slow dynamics of wormlike micelles

We present an extensive rheology study of the wormlike micelle system lecithin-water-cyclohexane. In this system the micelles are really wormlike, meaning that there are no signs of micellar branching, as it has previously been demonstrated by NMR self-diffusion experiments (R. Angelico, U. Olsson, G. Palazzo and A. Ceglie, Phys. Rev. Lett., 1998, 81, 2823). Wormlike micelles break and recombine, processes that are important for the stress relaxation. When branching is highly unfavorable, micelle recombination reactions only involve micelle ends, the concentration of which are very low when the micelles are very long. Hence, the break and recombination kinetics is very slow for true wormlike micelles. In the present system, the stress relaxation times are of the order of an hour. This is about three to four orders of magnitude longer than what commonly is observed in systems claimed to contain wormlike micelles. We conclude that systems with true wormlike micelles are very rare. An exponential stress relaxation is observed except at lower concentrations, where the micellar breaking time appears to exceed the reptation time. Because of the slow dynamics, the linear elastic modulus can be obtained from small rapid shear deformations, for which the system obeys Hooke's law. Larger deformations result in a fracture of the micellar network at a critical strain gamma* similar to phi(-1), where phi is the micelle volume fraction. For gamma < gamma* we may still obtain fracture, although with a lag time, tau*, that decreases with increasing gamma, and vanishes when gamma = gamma*. Extrapolating tau* to zero deformation we obtain the estimate approximate to 250 s at the highest concentration phi = 0.29. We interpret this time as the equilibrium micellar breaking time at rest, a quantity not previously measured