Solution structure of the E.coli TolA C-terminal domain reveals conformational changes upon binding to the phage g3p N-terminal domain

The Tol-Pal system of Escherichia coli is a macromolecular complex located in the cell envelope. It is involved in maintaining the integrity of the outer membrane and is required for the uptake of two different types of macromolecules, which are bacteriotoxins (colicins) and DNA of filamentous bacteriophages. The TolA protein plays a central role in these import mechanisms. Its C-terminal domain (TolAIII) is involved in the translocation step via direct interaction with the N-terminal domain of colicins and the N-terminal domain of the phage minor coat gene 3 protein (g3pN1). Extreme behaviours of TolAIII have been previously observed, since the structure of TolAIII either remained unaffected or adopted disordered conformation upon binding to different pore-forming colicins. Here, we have solved the 3D structure of free TolAIII by heteronuclear NMR spectroscopy and compared it to the crystal structure of TolAIII bound to g3pN1 in order to study the effect of g3pN1 on the tertiary structure of TolAIII. Backbone 1H, 15N and 13C resonances of the g3pN1-bound TolAIII were also assigned and used to superimpose the solution structure of free TolAIII on the crystal structure of the g3pN1-TolAIII fusion protein. This allowed us to track conformational changes of TolAIII upon binding. While the global fold of free TolAIII is mainly identical to that of g3pN1-bound TolAIII, shift of secondary structures does occur. Thus, TolAIII, which interacts also in vivo with Pal and TolB, is able to adapt its conformation upon binding to various partners. Possible models for protein binding mechanisms are discussed to explain this so-far unobserved behaviour of TolAIII.     

Periodic Solutions of N-Species Competition System with Time Delays

1IntroductionWeconsiderherethefollowingpeiodicn-speCiescompetitionSyStemwithtimedelaystogetherwithinitialvalueconditionswherer,(i=1,..',n)arepeitivecontinuousdeperiedicfUnctionsandail,ry(i,j=1,...f,n)arenormeqativeconStants.Whenr.(i=1,..',n)arepeitiveconStants,(1.1)isknoWnasan"speCies~a-VolterracompetitionsystemintheliteratureonmathematicaleCOIOgyandhashostudiedextensivelybySevelal.thorstl-j.ShibataandAntot')haveshownthetimedelaysinatwcrspeCies~a-Volterra~itionsystemcanleadto"~ic~ior".O…     

Inhibition of random amplified polymorphic DNAs (RAPDs) by plant polysaccharides

A survey of the inhibition of the amplification of spinach DNA by various plant polysaccharides revealed that neutral polysaccharides (arabinogalactan, dextran, gum guar, gum locust bean, inulin, mannan, and starch) were not inhibitory. In contrast, the acidic polysaccharides (carrageenan, dextran sulfate, gum ghatti, gum karaya, pectin, and xylan)were inhibitory. In the process of preparing random amplified polymorphic DNAs (RAPDs), the loss of large DNA bands appears to be an indicator that the fingerprint pattern has been affected by polysaccharides. The addition of various concentrations of Tween 20, DMSO, or PEG 400 to the PCR reaction mixture resulted in partial restoration of amplification of RAPDs for the acidic polysaccharides. The most effective way to eliminate the effects of polysaccharide inhibition was by diluting the DNA extracts, and thereby diluting the polysaccharide inhibitors.     

Activity and HPLC measured action pattern of Bacillus amyloliquefaciens α -amylase in water soluble organic solvents

The influence of two water miscible solvents (ethanol and isopropanol) on the activity of Bacillus amyloliquefaciens -amylase was studied.In ethanol-aqueous buffer (1:4, v/v) retained about 60% of the activity shown in water alone, both after l h hydrolysis. Isopropanol - aqueous buffer (1: 4,v/v) reduced the activity at 40%. The amount and the quality of produced oligosaccharides were effected by ethanol and isopropanol presence. In the mixture of produced oligosaccharides formed in the presence of the solvents only DP2, DP3 and DP6 were found. The disappearance of DP4, DP5 and DP7 which were formed in aqueous buffer suggest that a change in substrate affinity at the active centre is induced in the ethanol or isopropanol presence in buffer.Abbreviations DP degree of polymerization     

Establishment of the Woody Grass Arundinaria gigantea for Riparian Restoration

Canebrakes are dense stands of Arundinaria gigantea (Walt.) Muhl. that covered large areas of the southeastern North America. With agricultural development, canebrakes were quickly converted to crop and pastureland and now occur only in small, isolated patches. There is growing interest in the use of A. gigantea and other temperate bamboo species in riparian and floodplain revegetation in North America, but lack of detailed information on propagation and management of woody perennial grasses hinders reestablishment activities. Our study assesses the influence of nutrient and woodchip mulch amendments on survival and growth of A. gigantea transplanted as part of a riparian restoration project in central Kentucky. After two growing seasons, culm number (aboveground stems) increased 4‐fold and extent of transplanted clumps expanded 26‐fold. The survival rate of transplanted cane clumps was 98%. Hardwood chip mulch significantly increased the emergence of new culms, culm height growth, and clump area. Composted manure, applied at a rate that contributed a similar mass of organic matter as the hardwood mulch, also significantly increased new culm number and clump area. Our findings demonstrate that addition of manure or hardwood mulch can significantly enhance aboveground production of A. gigantea transplants. However, survival and initial growth of untreated clumps were also adequate in this study. It appears that careful site selection, transplantation, and site maintenance may be sufficient to ensure A. gigantea establishment on many sites. Practitioners should assess soil drainage, water stress, and fertility along with herbaceous competition and incidence of overbank flooding before determining the necessity of organic amendments to supplement establishment of A. gigantea or other woody grasses for riparian restoration.     

The unusual internal motion of the villin headpiece subdomain

The thermostable 36‐residue subdomain of the villin headpiece (HP36) is the smallest known cooperatively folding protein. Although the folding and internal dynamics of HP36 and close variants have been extensively studied, there has not been a comprehensive investigation of side‐chain motion in this protein. Here, the fast motion of methyl‐bearing amino acid side chains is explored over a range of temperatures using site‐resolved solution nuclear magnetic resonance deuterium relaxation. The squared generalized order parameters of methyl groups extensively spatially segregate according to motional classes. This has not been observed before in any protein studied using this methodology. The class segregation is preserved from 275 to 305 K. Motions detected in Helix 3 suggest a fast timescale of conformational heterogeneity that has not been previously observed but is consistent with a range of folding and dynamics studies. Finally, a comparison between the order parameters in solution with previous results based on solid‐state nuclear magnetic resonance deuterium line shape analysis of HP36 in partially hydrated powders shows a clear disagreement for half of the sites. This result has significant implications for the interpretation of data derived from a variety of approaches that rely on partially hydrated protein samples.     

The Solution Structure of CCL28 Reveals Structural Lability that Does Not Constrain Antifungal Activity

The chemokine CCL28 is constitutively expressed in mucosal tissues and is abundant in low-salt mucosal secretions. Beyond its traditional role as a chemoattractant, CCL28 has been shown to act as a potent and broad-spectrum antimicrobial agent with particular efficacy against the commensal fungus and opportunistic pathogen Candida albicans. However, the structural features that allow CCL28 to perform its chemotactic and antimicrobial functions remain unknown. Here, we report the structure of CCL28, solved using nuclear magnetic resonance spectroscopy. CCL28 adopts the canonical chemokine tertiary fold, but also has a disordered C-terminal domain that is partially tethered to the core by a non-conserved disulfide bond. Structure–function analysis reveals that removal of the C-terminal tail reduces the antifungal activity of CCL28 without disrupting its structural integrity. Conversely, removal of the non-conserved disulfide bond destabilizes the tertiary fold of CCL28 without altering its antifungal effects. Moreover, we report that CCL28 unfolds in response to low pH but is stabilized by the presence of salt. To explore the physiologic relevance of the observed structural lability of CCL28, we investigated the effects of pH and salt on the antifungal activity of CCL28 in vitro. We found that low pH enhances the antifungal potency of CCL28, but also that this pH effect is independent of CCL28's tertiary fold. Given its dual role as a chemoattractant and antimicrobial agent, our results suggest that changes in the salt concentration or pH at mucosal sites may fine-tune CCL28's functional repertoire by adjusting the thermostability of its structure.     

Effects of temperature on parameters of root growth relevant to nutrient uptake: Measurements on oilseed rape and barley grown in flowing nutrient solution

Summary Effects of root temperature on the growth and morphology of roots were measured in oilseed rape (Brassica napus L.) and barley (Hordeum vulgare L.). Plants were grown in flowing solution culture and acclimatized over several weeks to a root temperature of 5°C prior to treatment at a range of root temperatures between 3 and 25°C, with common shoot temperature. Root temperature affected root extension, mean radius, root surface area, numbers and lengths of root hairs. Total root length of rape plants increased with temperature over the range 3–9°C, but was constant at higher temperatures. Root length of barley increased with temperature in the range 3–25°C, by a factor of 27 after 20 days. Root radii had a lognormal distribution and their means decreased with increasing temperature from 0.14 mm at 3°C to 0.08 mm at 25°C. The density of root hairs on the root surface increased by a factor of 4 in rape between 3 and 25°C, but in barley the highest density was at 9°C. The contribution of root hairs to total root surface area was relatively greater in rape than in barley. The changes in root system morphology may be interpreted as adaptive responses to temperature stress on nutrient uptake, providing greater surface area for absorption per unit root weight or length.     

Global behaviour of age-dependent logistic population models

We study the large time behaviour of a nonlinear population model with a general logistic term. It is proved that every solution must have a limit when time becomes infinite. We present conditions that guarantee the boundedness of the solution. Furthermore, we prove that in general no oscillation is possible for the total number of population. This is in sharp contrast to the linear case.This work was carried out with the aid of a grant from the International Development Centre, Ottawa, Canada