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Recent X-ray structural work on the Drosophila epidermal growth factor receptor (EFGR) has suggested an asymmetric dimer that rationalizes binding affinity measurements that go back decades (Alvarado et al., Cell 2010;142:568–579; Dawson et al., Structure 2007;15:942–954; Lemmon et al., Embo J 1997;16:281–294; Mattoon et al., Proc Natl Acad Sci USA 2004;101:923–928; Mayawala et al., Febs Lett 2005;579:3043–3047; Ozcan et al., Proc Natl Acad Sci USA 2006;103:5735–5740). This type of asymmetric structure has not been seen for the human EGF receptor family and it may or may not be important for function in that realm. We hypothesize that conformational changes in the Drosophila system have been optimized for the transition, whereas the barrier for the same transition is much higher in the human forms. To address our hypothesis we perform dynamic importance sampling (DIMS) (Perilla et al., J Comput Chem 2010;32:196–209) for barrier crossing transitions in both Drosophila and human EFGRs. For each set of transitions, we work from the hypothesis, based on results from the AdK system, that salt-bridge pairs making and breaking connections are central to the conformational change. To evaluate the effectiveness of the salt-bridges as drivers for the conformational change, we use the effective transfer entropy based on stable state MD calculations (Kamberaj and Der Vaart, Biophys J 2009;97:1747–1755) to define a reduced subset of degrees of freedom that seem to be important for driving the transition (Perilla and Woolf, J Chem Phys 2012;136:164101). Our results suggest that salt-bridge making and breaking is not the dominant factor in driving the symmetric to asymmetric transition, but that instead it is a result of more concerted and correlated functional motions within a subset of the dimer structures. Furthermore, the analysis suggests that the set of residues involved in the transitions from the Drosophila relative to the human forms differs and that this difference in substate distributions relates to why the asymmetric form may be more common to Drosophila than to the human forms. We close with a discussion about the residues that may be changed in the human and the Drosophila forms to potentially shift the kinetics of the symmetric to asymmetric transition.

While the commercial benefits of high pressure processing (HPP) on pulp products (e.g. guacamole) are known, little information is available on HPP of whole avocado tissue. We examined HPP effects on the quality, physiology, biochemistry and microstructure of avocado slices. Flesh colour was affected, with L (lightness) and C (chroma) values decreasing after some treatments, although these changes were not obvious visually. HPP (> 300 MPa) dramatically reduced respiration rates and ethylene production 1 h after treatment, and particularly after 17 h at 20 °C. Treatment resulted in some peroxidase (POD) activity reduction, particularly at higher pressures, while polyphenoloxidase (PPO) activity was generally increased. HPP (600 MPa) induced changes in the cell wall structure, disruption of the cellular network and coalescence of oil vesicles. HPP treatment of avocado slices provides potentially beneficial reduced respiratory activity, without obvious colour changes — a solid foundation for examining shelf life quality implications. Industrial relevance • This work outlines underpinning science that may have commercial relevance in the future. • It is not directly relevant to HPP industries in the immediate future. • The effect of HPP on respiration rate and ethylene production is useful to industry in their understanding of the physiology of horticultural products after HPP.

New Zealand lower thrips (NZFT, Thrips obscuratus (Crawford)) were exposed to a range of ethyl formate (EF) and pyrethrum-based postharvest treatments on apricots. Research showed that EF+CO 2 or EF+N 2 were effective treatments against NZFT and caused negligible damage to apricot fruit quality. However, pyrethrum dipping did not effectively control NZFT and caused signiicant internal damage to apricot fruit. Lethal concentration (LC 99 ) estimates were developed for adult and larval NZFT using a range of EF concentrations (0-1.27% EF+CO 2 ) and temperatures (5, 15 and 25°C). It is estimated that treatments of 1% (30.7 g/m 3 ) EF at 5 or 25°C or a higher concentration of 1.5% (46.3 g/m 3 ) at 15°C will achieve 99% mortality of NZFT adults and larvae on apricot fruit with 95% conidence.

Metabolic stress disinfection and disinfestation (MSDD) has been demonstrated to effectively control longtailed mealybug, Pseudococcus longispinus (Targioni Tozzetti). Standard components previously used for testing MSDD system included a 30-min physical phase of short cycles pressure changes followed by a 60-min chemical phase using ethanol vapor at 10 kPa. This study investigated the effect of varying the following MSDD components on mealybug mortality: duration of the physical and chemical phases, ethanol concentration, and extent of vacuum during the chemical phase. Mealybug mortality responses were analyzed, and the components were optimized using binary logistical regression to achieve 99% mortality of three life stages of the longtailed mealybug (adults, second- and third-instar nymphs and crawlers). Data indicated that the optimal components to achieve 99% mortality of all life stages were a 30-min physical phase and a 45-min chemical phase with 275 mg/liter ethanol at 30 kPa. Optimized components were obtained using binary logistical regression models. These optimized components yielded a 15-min reduction in total treatment time and a 20-kPa decrease in pressure during the chemical phase. Achievement of optimal insecticidal efficacy required all four MSDD components. Nevertheless, optimization and validation achieved 17 and 22% reductions in duration of treatment time and extent of vacuum, respectively.

Several different mechanical models of double-helical nucleic-acid structures that have been presented in the literature are reviewed here together with a new analysis method that provides a reconciliation between these disparate models. In all cases, terminology and basic results from the theory of Lie groups are used to describe rigid-body motions in a coordinate-free way, and when necessary, coordinates are introduced in a way in which simple equations result. We consider double-helical DNAs and RNAs which, in their unstressed referential state, have backbones that are either straight, slightly precurved, or bent by the action of a protein or other bound molecule. At the coarsest level, we consider worm-like chains with anisotropic bending stiffness. Then, we show how bi-rod models converge to this for sufficiently long filament lengths. At a finer level, we examine elastic networks of rigid bases and show how these relate to the coarser models. Finally, we show how results from molecular dynamics simulation at full atomic resolution (which is the finest scale considered here) and AFM experimental measurements (which is at the coarsest scale) relate to these models.

SERCA is an important model system for understanding the molecular details of conformational change in membrane transport systems. This reflects the large number of solved X-ray structures and the equally large database of mutations that have been assayed. In this computational study, we provide a molecular dynamics description of the conformational changes during the E1P → E2P transitions. This set of states further changes with insertion mutants in the A-M3 linker region. These mutants were experimentally shown to lead to significant shifts in rates between the E1P → E2P states. Using the population shift framework and dynamic importance sampling method along with coarse-grained representations of the protein, lipid, and water, we suggest why these changes are found. The calculations sample on intermediates and suggest that changes in interactions, individual helix interactions, and water behavior are key elements in the molecular compositions that underlie shifts in kinetics. In particular, as the insertion length grows, it attracts more water and disrupts domain interactions, creating changes as well at the sites of key helix interactions between the A-Domain and the P-Domain. This provides a conceptual picture that aids understanding of the experimental results.

Metabolic stress disinfection and disinfestation (MSDD) is a potential quarantine treatment in which a combination of cycles of rapid decompression and compression are followed by exposure to ethanol vapour under decompression. The response of ‘Hass’ avocado ( Persea americana Mill., cv. Hass) to MSDD treatment for control of longtailed mealybug ( Pseudococcus longispinus ) was investigated. The best treatment for the most resistant life stage (2nd/3rd instars) was 90-min MSDD treatment with 371 mg L −1 ethanol. Early and late season ‘Hass’ avocados were subjected to MSDD treatments (with 371 mg L −1 ethanol), or in air (control). Following the treatments, early season fruit were ripened at 20 °C and 25 °C. Half of the late season fruit were ripened at either 20 °C or 25 °C, and the remainder were stored at 5.5 °C for 6 weeks, then ripened at 20 °C. There were no significant difference in quality and rot incidence between non-treated controls and MSDD-treated fruit. The main disorders found were stem-end and body rots, vascular browning and flesh greying for the stored fruit. There were also no significant differences in fruit respiration rate or ethylene production. Thus, MSDD was shown to be a potentially ‘soft’ disinfestation treatment for surface pests of avocado.

The vase life of Asiatic lilies can be limited by leaf yellowing, which can be caused by exposure to low light or temperature during winter growth or in storage. We examined the use of postharvest hot water treatments (HWTs) as a means of reducing leaf senescence in stored (4 °C for 2 weeks) and non-stored Asiatic hybrid lily ‘Elite’ ( Lilium sp.). A range of HWTs (45–55 °C for 2.5 or 5 min) was applied to leaves on cut lily stems (but not flowers). Higher temperatures and the longer duration resulted in heat damage, but treatments of 50 °C for 5 min and 52.5 °C for 2.5 min were found to be optimal for minimising leaf yellowing with trace levels of heat damage for both non-stored and stored stems. The onset of yellowing was delayed by 3–4 d, and the occurrence of an unacceptable level of yellowing eliminated for up to 12 d (compared with F v / F o ) over time, which was more marked in lower than upper leaves (thus correlating with yellowing, which was more severe in the lower leaves). Although both optimal HWTs resulted in an initial reduction in yield, there was a recovery over time resulting in a yield that, by 12 d, was as high or significantly higher than control leaves (particularly for the lower leaves). All treatments showed a reduction in chlorophyll content (total, chlorophyll a and chlorophyll b ), but control leaves had significantly lower levels after 7 d. HWTs show potential as a non-chemical, simple means of delaying leaf yellowing of Asiatic lilies and thus increasing vase life.

Global use of phosphine as a fumigant has increased in response to the need to replace methyl bromide, and with the improved formulations, ECO2FUME® and VAPORPH3OS®. Phosphine is registered as a postharvest fumigant on kiwifruit in New Zealand and has been used commercially to reduce the risk of detecting live pests. Scale insects, mealybugs and diapausing twospotted spider mites were exposed to a range of phosphine treatments. A 48-h low temperature (1.7-4.6°C) fumigation (6408-3311 ppm) achieved 100% mortality of all life stages of oleander scale insects, while a 12-h exposure killed all longtailed mealybug life stages. A 36-h low temperature (2.5-3.3°C) fumigation (4332-2712 ppm) treatment achieved 100% mortality of all greedy scale insect life stages. A 48- to 96-h treatment (3600-1200 ppm) at 1-15°C caused 91.3-100% mortality of diapausing twospotted spider mite adults. Use of phosphine as a commercial treatment for kiwifruit is discussed.

Metabolic stress disinfection and disinfestation (MSDD) is a relatively new quarantine treatment in which fruit are exposed to rapid decompression and compression cycles and high CO 2 atmosphere, followed by exposure to ethanol vapour under decompression. This study evaluated the ripening response of ‘Hayward’ kiwifruit ( Actinidia deliciosa ) and ‘Pink Lady’ apple ( Malus x domestica ) to MSDD treatment, which can control longtailed mealybug ( Pseudococcus longispinus ). Following the treatments, fruit were held at 20 °C for 7 d for shelf-life assessment, while the remainder were refrigerated at 0.5 °C for 16 weeks. Respiration rate, volatile (ethylene, ethanol and acetaldehyde) production rates, firmness and disorders were measured at regular time intervals. MSDD treatments did not affect the metabolic activities and quality of ‘Pink Lady’ apples. However, firmness was reduced by 4.9 N in non-refrigerated MSDD treated fruit. MSDD treatments did not control superficial scald disorder in refrigerated ‘Pink Lady’ apples. For ‘Hayward’ kiwifruit, treatments increased the respiration rate and ethylene production of short-term refrigerated fruit, promoted endogenous production of ethanol and acetaldehyde in both short-term and long-term refrigerated fruit. MSDD treatments also increased the incidence of rots in refrigerated ‘Hayward’ kiwifruit. MSDD treatments accelerated the softening of short-term refrigerated kiwifruit, but retarded the softening of ‘Hayward’ kiwifruit during the 16 weeks of refrigerated storage. MSDD could potentially be used as a quarantine treatment of apples. Further studies are required on the sensory effect of MSDD treatment.

The effect of the proportion of ‘Hass’ avocado skin tissue present during aqueous cold pressed avocado oil extraction on the pigment concentration and oil quality was determined. Increasing amounts of skin (i.e., from 0 to 100% of available skin) were included with the flesh before grinding and malaxing in a laboratory-scale cold pressed extraction process. The recovered oils were analyzed for oil quality and color. The pigment concentrations in the oil were determined by high performance liquid chromatography (HPLC). With increasing amounts of skin addition, there was an increase in the green color, as indicated by hue angle, of the avocado oils. There were also increased concentrations of carotenoids and chlorophylls in the oil as the proportion of skin during malaxing was increased. The lutein concentration in the oils increased from 1.13 to 3.21 μg g−1 as the amount of skin added to the malaxer increased from 0 to 100% skin, and the total chlorophyll concentration in the same oils increased from 7.3 to 27.5 μg g−1. The green color of cold pressed avocado oil and the pigment concentrations can be increased by adding more skin to the malaxer during oil extraction.

Kumara (sweet potato) roots are prone to soft rots after washing and prior to retail sale. Rots are caused mainly by the fungal pathogen Rhizopus stolonifer. For many years kumara packhouses in New Zealand have relied on Botran ® fungicide (a.i. dicloran) to minimise rots in washed kumara. Finding a non-chemical alternative to dicloran is vital if the fledgling kumara export industry is to reduce its reliance on fungicides and expand in the future. Laboratory studies over 2 years using inoculated kumara roots demonstrated the potential of hot water drenching (HWD) to control soft rots after washing. HWD was as effective as dicloran. A temperature of 55°C was the most effective HWD treatment and a 45 s drench was slightly more effective than 20 s. In 2008, Delta Produce Ltd of Dargaville (the largest kumara packhouse in New Zealand and a kumara exporter) tested HWD in a scale-up evaluation. Five runs were carried out comparing HWD, fungicide and a tap water wash control. The incidence of soft rots in stored kumara roots following HWD (55°C for 45 s) or dicloran fungicide was very similar. Mean rot levels were 1.7% for HWD, 2.3% for dicloran and 4.9% for the control treatment. No loss in quality of kumara skin or flesh was detected as a result of HWD treatment. HWD shows promise as an alternative treatment to fungicide for reducing or even eliminating soft rots in washed kumara (sweet potato). The process needs further testing to give industry confidence that it will work in practice, especially engineering input to design the most cost-effective HWD system.

A workshop was held during the Postharvest Pacifica conference, the scope of which was to summarise past, present and future research activities in postharvest disinfestation treatments of imported or exported agricultural crops and to encourage discussion of the systems risk analysis approach. The workshop was well received from over 28 researchers and industry representatives from New Zealand, Australia and around the world. It summarised key areas of market access research including: 1) emerging technologies, 2) technologies/treatments that have been recently rolled out to industry, and 3) the future of fumigation.

'Hort16A' kiwifruit (Actinidia chinensis Planch. var. chinensis) is sensitive to ethylene. Trace amounts of ethylene produced by small numbers of fruit could trigger softening and reduce storage life of all fruit in the same storage space (tray, bin or even cool store). Characterising ethylene-producing fruit before disorders become visible would allow early detection of at-risk fruit enabling differential inventory management. Commercially packed 'Hort16A' kiwifruit from three orchards were sampled and stored at 1.5°C. Ethylene production rate, flesh colour, penetrometer firmness, dry matter content, soluble solids content and firmness profiles of the outer pericarp, inner pericarp and core were measured at 1 to 2-week intervals using a sub-sample of 30 fruits per orchard each time. Fruits were equilibrated overnight at 20°C before measurement. Canonical discriminant analysis indicated that fruit producing detectable ethylene were characterized by a low percentage of solubilised dry matter, relatively low firmness profile toward the centre of the fruit (i.e. soft inner pericarp and core), low flesh hue, high flesh chroma, low flesh lightness and low flesh firmness. Potential use of such knowledge for inventory management is discussed.

This study investigated the effect of storage temperature (0, 3, and 6°C) and duration (2, 4 and 6 weeks) on fruit quality of 'Clutha Gold', 'Moorpark', 'Genevieve' and 'Southern Cross' apricot cultivars grown in New Zealand. After harvest, fruit were sorted based on size, colour and absence of physical injuries. Fruit samples were destructively assessed (penetrometer firmness, °Brix and pH) pre-storage and post-storage (at 20°C) after shelf life of three days for 2- and 6-week storage regimes and after shelf life of 0, 3 and 6 days following a 4-week storage regime. Each fruit was also tasted and scored for juiciness, mealiness and texture acceptability. The storage temperature at which apricot fruit were held significantly affected fruit quality within the first two weeks of storage. Fruit stored at 0°C showed the best overall quality in terms of fruit firmness, juiciness, lack of mealiness, and texture acceptability. There was significant variation in the effect of temperature on the different cultivars studied. Higher storage temperatures (3 and 6°C) were also more detrimental to fruit eating quality. Juiciness decreased and mealiness increased with longer storage duration, except for 'Southern Cross' held at 0°C. Texture acceptability also decreased with longer storage regardless of storage temperature.

How a biological system responds to a charge shift is a challenging question directly relevant to biological function. Time-resolved fluorescence of a tryptophan residue reflects protein and solvent response to the difference in pi-electron density between the excited and the ground state. In this study we use molecular dynamics to calculate the time-dependent spectral shift (TDSS) in the fluorescence of Trp-43 in GB1 protein. A new computational method for separating solvent, protein, and fluorophore contributions to TDSS is applied to 100 nonequilibrium trajectories for GB1 in TIP3P water. The results support several nontrivial conclusions. Both longitudinal and transverse relaxation modes of bulk solvent contribute to the TDSS in proteins. All relaxation components slower than the transverse relaxation of bulk solvent have significant contributions from both protein and solvent, with a negative correlation between them. Five exponential terms in the TDSS of GB1 are well separated by their relaxation times. A 0.036 ps term is due to both solvent (60%) and protein (40%). Two exponential terms represent longitudinal (tau(L) approximately = 0.4 ps) and transverse (tau(D) approximately = 5.6 ps) relaxation modes of TIP3P water. A 131 ps term is attributable to a small change in the tertiary structure, with the alpha-helix moving 0.2 A away from the beta-strand containing Trp-43. A 2580 ps term is due to the change in the conformation of the Glu-42 side chain that brings its carboxyl group close to the positively charged end of the excited fluorophore. Interestingly, water cancels 60% of the TDSS resulting from this conformational change.

The fusion between two lipid bilayers involves crossing a complicated energy landscape. The limiting barrier in the process appears to be between two closely opposed bilayers, and the intermediate state where the outer leaflets are fused. We have performed molecular dynamics simulations to characterize the free energy barrier for the fusion of two liposomes and to examine the molecular details of barrier crossing. In order to capture the slow dynamics of fusion, a model using coarse-grained representations of lipids was used. The fusion between pairs of liposomes was simulated for four systems: DPPC, DOPC, a 3:1 mixture of DPPC/DPPE and an asymmetric lipid tail system in which one tail of DPPC was reduced to half the length (ASTail). The weighted histogram method was used to compute the free energy as a function of separation distance. The relative barrier heights for these systems was found to be ASTail≫DPPC>DPPC/DPPE>DOPC, in agreement with experimental observations. Further, the free energy curves for all four can be overlayed on a single curve by plotting the free energy versus the surface separation (differing only in the point of fusion). These simulations also confirm that the two main contributions to the free energy barrier are the removal of water between the vesicles and the deformation of the vesicle. The most prominent molecular detail of barrier crossing in all cases examined was the splaying of lipid tails, where a single splayed lipid formed a bridge between the two outer leaflets that promotes additional lipid mixing between the vesicles and eventually leads to fusion. The tail splay appears to be closely connected to the energetics of the process. For example, the high barrier for the ASTail is the result of a smaller distance between terminal methyl groups in the splayed molecule. The shortening of this distance requires the liposomes to be closer together, which significantly increases the cost of water removal and bilayer deformation. Before tail splay can initiate fusion, contact must occur between a tail end and the external water. In isolated vesicles, the contact fraction is correlated to the fusogenicity difference between DPPC and DOPC. Moreover, for planar bilayers the contact fraction is much lower for DPPC, which is consistent with its lack of fusion in giant vesicles. The simulation results show the key roles of lipid tail dynamics in governing the fusion energy landscape.

In the export of ‘Fuyu’ persimmon, fruit are airfreighted at ambient temperatures, or seafreighted at low temperatures using modified atmosphere (MA) packaging. Since persimmons are climacteric and ethylene sensitive, exposure to exogenous ethylene may accelerate natural softening at ambient temperature (e.g. airfreight) as well as aggravate chilling injury during coolstorage (e.g. seafreight). In the present work, the response of this cultivar to exogenous ethylene exposure was studied in four critical handling scenarios that might occur in a commercial chain. Non-packed fruit exposed to ethylene and then held at 20 °C (simulated airfreight) showed the greatest sensitivity to ethylene; fruit firmness and colour during shelf life were affected by even 1 d of exposure to 0.2 μL L−1 ethylene. Lower sensitivity was observed when fruit were stored at 0 °C under MA conditions after ethylene exposure at 20 °C (simulated pre-packing exposure-seafreight), where fruit quality was not affected by exposures of 1 d at ≤1 μL L−1, and only slightly by 2 d at

Insights into the relative importance of various aspects of product quality can be provided through quantitative analysis of consumer preference and choice of fruit. In this study, methods previously used to establish taste preferences for kiwifruit (Harker et al., 2008) and conjoint approaches were used to determine the influence of three key aspects of avocado quality on consumer liking and willingness to purchase fruit: dry matter percentage (DM), level of ripeness (firmness) and internal defects (bruising). One hundred and seven consumers tasted avocados with a range of DM levels from ~20% (minimally mature) to nearly 40% (very mature), and at a range of fruit firmness (ripeness) stages (firm-ripe to soft-ripe). Responses to bruising, a common quality defect in fruit obtained from the retail shelf, were examined using a conjoint approach in which consumers were presented with photographs showing fruit affected by damage of varying severity. In terms of DM, consumers showed a progressive increase in liking and intent to buy avocados as the DM increased. In terms of ripeness, liking and purchase intent was higher in avocados that had softened to a firmness of 6.5 N or below (hand-rating 5). For internal defects, conjoint analysis revealed that price, level of bruising and incidence of bruising all significantly lowered consumers' future purchase decision, but the latter two factors had a greater impact than price. These results indicate the usefulness of the methodology, and also provide realistic targets for Hass avocado quality on the retail shelf.

Fresh-cut ‘Braeburn’ apple slices were dipped in calcium ascorbate (CaAsc; 0, 2, 6, 12 and 20%, w/w) and stored in air or under modified atmosphere (MA) conditions for up to 28 d at 4 °C. Changes in antioxidant levels were measured using free radical scavenging activity (DPPH), reducing activity (FRAP), ascorbic acid content (AA) and polyphenolic content (by HPLC). Changes in browning, sensory quality and microbial counts were measured to indicate eating quality. CaAsc dips increased the initial levels of AA from 0.19 g kg−1 in the untreated control to 3.8 g kg−1 for the 20% CaAsc treatment. Ascorbic acid content of treated slices during storage decreased by more than 50% in CaAsc concentrations of 6, 12 and 20%. Similar patterns were observed for FRAP and DPPH activities. Untreated or 2% CaAsc treated slices stored in air or MA showed browning, microbial deterioration and poor sensory quality, thus resulting in a short shelf life (

Using 237 all-atom double bilayer simulations, we examined the thermodynamic and structural changes that occur as a phosphatidylcholine lipid bilayer stack is dehydrated. The simulated system represents a micropatch of lipid multilayer systems that are studied experimentally using surface force apparatus, atomic force microscopy and osmotic pressure studies. In these experiments, the hydration level of the system is varied, changing the separation between the bilayers, in order to understand the forces that the bilayers feel as they are brought together. These studies have found a curious, strongly repulsive force when the bilayers are very close to each other, which has been termed the "hydration force," though the origins of this force are not clearly understood. We computationally reproduce this repulsive, relatively free energy change as bilayers come together and make qualitative conclusions as to the enthalpic and entropic origins of the free energy change. This analysis is supported by data showing structural changes in the waters, lipids and salts that have also been seen in experimental work. Increases in solvent ordering as the bilayers are dehydrated are found to be essential in causing the repulsion as the bilayers come together.

Recent structures of the potassium channel provide an essential beginning point for explaining how the pore is gated between open and closed conformations by changes in membrane voltage. Yet, the molecular details of this process and the connections to transmembrane gradients are not understood. To begin addressing how changes within a membrane environment lead to the channel’s ability to sense shifts in membrane voltage and to gate, we performed double-bilayer simulations of the Kv1.2 channel. These double-bilayer simulations enable us to simulate realistic voltage drops from resting potential conditions to depolarized conditions by changes in the bath conditions on each side of the bilayer. Our results show how the voltage sensor domain movement responds to differences in transmembrane potential. The initial voltage sensor domain movement, S4 in particular, is modulated by the gating charge response to changes in voltage and is initially stabilized by the lipid headgroups. We show this response is directly coupled to the initial stages of pore domain motion. Results presented here provide a molecular model for how the pre-gating process occurs in sequential steps: Gating charge response, movement and stabilization of the S4 voltage sensor domain, and movement near the base of the S5 region to close the pore domain.

The growing dataset of K(+) channel x-ray structures provides an excellent opportunity to begin a detailed molecular understanding of voltage-dependent gating. These structures, while differing in sequence, represent either a stable open or closed state. However, an understanding of the molecular details of gating will require models for the transitions and experimentally testable predictions for the gating transition. To explore these ideas, we apply dynamic importance sampling to a set of homology models for the molecular conformations of K(+) channels for four different sets of sequences and eight different states. In our results, we highlight the importance of particular residues upstream from the Pro-Val-Pro (PVP) region to the gating transition. This supports growing evidence that the PVP region is important for influencing the flexibility of the S6 helix and thus the opening of the gating domain. The results further suggest how gating on the molecular level depends on intra-subunit motions to influence the cooperative behavior of all four subunits of the K(+) channel. We hypothesize that the gating process occurs in steps: first sidechain movement, then inter-S5-S6 subunit motions, and lastly the large-scale domain rearrangements.

Experiments and simulations have been carried out for several polar protected peptides in reversed phase chromatography in order to demonstrate how simulation can describe the effects of varying temperature and cosolvent fraction. Comparisons of adsorption chemical potentials from mesoscopic simulations and experimental chromatographic retention data show very good agreement with only one temperature-independent solvent parameter from a single peptide. Such simulations should help guide the design of chromatography experiments with biomolecules and predict retention, including conditions for which empirical correlations such as hydrophobicity scales and molecular descriptors have not been developed.

Applied behavior analysis (ABA) experts were surveyed to examine their perceptions of treatment acceptability of commonly used decelerative consequence-based behavioral procedures and the factors that have influenced shifts in these perceptions over time. These results were then compared with the perceptions of positive behavior supports (PBS) experts from an earlier study. Both similarities and disparities in perceptions across groups of experts are reported. Differences were noted in the overall acceptability and frequency of use of various consequence-based decelerative procedures, with ABA experts expressing greater willingness to consider their use than PBS experts. However, there were many similarities across both groups, including the decade in which shifts occurred in perceptions of treatment acceptability, the reasons these changes occurred, and the rationales used to justify the use or nonuse of certain consequence-based strategies. These data support earlier work that found that perceptions of treatment acceptability were not static but, rather, changed across time.

Susceptibility of ‘satsuma’ mandarin fruit (Citrus unshiu Marc) to chilling injury limits the marketability of stored fruit. In this study, the effect of hot water dip (HWD) treatments on chilling injury tolerance, fruit quality, activity of antioxidant enzymes, and gene expression of proton transporters in the vacuole were investigated in New Zealand. Some treatments suppressed chilling injury development, but none of them could prevent it completely. The major reduction in chilling injury incidence (proportion of unacceptable fruit) and severity (level of damage) was observed in HWD at 50 °C, for 2 min. Temperatures higher than 50 °C increased fruit peel damage. Chilling injury was paralleled by higher ethylene production and respiration rate in affected fruit, and an increase in the amount of ethanol and acetaldehyde emitted in juice headspace. Afterwards, values decreased gradually with increasing chilling damage. Treatments that reduced chilling injury suppressed anaerobic products, ethylene evolution and respiration. During storage at 2 °C for 8 weeks, a decline in catalase (CAT) activity was observed, while peroxidase (POX) activity increased. This rapid increase in POX activity was associated with increased peel damage due to both chilling injury and heat damage. Decreasing chilling injury in HWD was correlated with decreased POX activity and maintenance of CAT activity during storage. Amounts of vacuolar pyrophosphatase (V-PPase) and vacuolar ATPase (V-ATPase) gene transcript in fruit peel were reduced by heat treatment. Storage periods reduced V-PPase and induced V-ATPase gene transcript level in fruit treated at 50 °C, but this was not associated with changes in the acid content in the juice. A significant induction (5–6-fold) of ATPase and V-PPase occurred in juice sacs and this may be associated with compensation for a loss of tonoplast integrity in fruit treated at 55 °C compared to those at 50 °C. We also found that V-ATPase and V-PPase transcript levels in juice sacs responded rapidly to heat treatments but were largely recovered after 8 weeks cold storage for successful (non-damaging) heat treatments. The optimal HWD treatments were 47.5–50 °C for 2 min.

We have simulated two conformations of the fusion domain of influenza hemagglutinin (HA) within explicit water, salt, and heterogeneous lipid bilayers composed of POPC:POPG (4:1). Each conformation has seven different starting points in which the initial peptide structure is the same for each conformation, but the location across the membrane normal and lipid arrangement around the peptide are varied, giving a combined total simulation time of 140 ns. For the HA5 conformation (primary structure from recent NMR spectroscopy at pH = 5), the peptide exhibits a stable and less kinked structure in the lipid bilayer compared to that from the NMR studies. The relative fusogenic behavior of the different conformations has been investigated by calculation of the relative free energy of insertion into the hydrophobic region of lipid bilayer as a function of the depth of immersion. For the HA7 conformations (primary structure from recent NMR spectroscopy at pH = 7.4), while the N-terminal helix preserves its initial structure, the flexible C-terminal chain produces a transient helical motif inside the lipid bilayer. This conformational change is pH-independent, and is closely related to the peptide insertion into the lipid bilayer. Proteins 2008. © 2008 Wiley-Liss, Inc.

To study ripening-related chilling injury (CI) of bell pepper (Capsicum annuum L.), fruit at mature green, breaker, and red-ripe stages were stored at 1, 5, 7, and 10 degrees C for 4 weeks. Surface pitting was evaluated after storage at 1 degrees C for 2 weeks followed by a 2-day exposure to room temperature (20 degrees C). Exposing fruit to 1 degrees C enhanced water loss, respiration, ethylene production, and electrolyte leakage, but slowed color change. Weight loss, respiration, ethylene production, electrolyte leakage, and color change increased more in breaker than in mature green and red-ripe fruit. No pitting symptom was observed at temperatures of 5 to 10 degrees C. After storing peppers at 1 degrees C for 2 weeks, breaker stage fruit exhibited chilling symptoms of severe surface pitting with more sheet pitting and deeper peel depression. Mature green fruit showed only moderate pitting. However, red-ripe peppers showed no injury and cells showed a normal appearance after low-temperature storage (1 degrees C). These results show that bell peppers tended to be more susceptible to chilling temperature while at the breaker stage and that the increase in visible CI is correlated with increased water loss, respiration, ethylene production, electrolyte leakage, and color change during storage.

The dry matter (DM) content in the flesh of harvested avocado is quite variable, ranging from low DM ( 35%) fruit that are potentially suitable for processing. Currently, no suitable method exists for segregating these categories in harvested lines. Compositional analysis of the skin, seed and flesh of 1000 mature ‘Hass’ avocado ( Persea americana Mill.) fruit was undertaken to determine the feasibility of employing a density technique to identify such fruit on the basis of their flesh DM. Measurements included whole-fruit density, and the mass, density and DM of both core plugs of individual tissues from unripe fruit, and the separated tissues of each fruit upon ripening. The proposition was evaluated by extending basic density theory to develop a generic multi-term expression for a whole-fruit system where the density of each component (the skin, seed and flesh) was characterized with regard to its water, DM and air content. At harvest whole-fruit densities ranged between 970 and 1018 kg m −3 , and flesh DMs between 23 and 43%, with a correlation of r = −0.29; P

SummarySpatial and temporal variation in mineral and dry matter (DM: % dry weight) concentrations were examined in ‘Hass’ avocado (Persea americana Mill.) fruit to identify sampling strategies for examining fruit mineral, DM and fruit quality relationships. Calcium (Ca), magnesium (Mg), potassium (K), and DM concentrations were compared from different parts of the same fruit, from fruit harvested from different shoot types and locations within the same tree, and at different stages during the growing season, from fruit set to commercial harvest. The main source of variation within fruit was longitudinal, with K and DM concentrations being higher at the distal end of the fruit. Sampling methods based on equatorial plugs of tissue provided the best estimates of whole fruit values for DM and mineral nutrients. While there was much variability in the internal distribution of minerals within the fruit, the distribution was the same for fruit from both the northern and southern aspects of the tree. During the f...

Pigments are important contributors to the appearance and healthful properties of both avocado fruits and the oils extracted from these fruits. This study determined carotenoid and chlorophyll pigment concentrations in the skin and three sections of the flesh (outer dark green, middle pale green, and inner yellow flesh-nearest the seed) and anthocyanin concentrations in the skin of Hass avocado during ripening at 20 degrees C. Pigments were extracted from frozen tissue with acetone and measured using high-performance liquid chromatography. Pigments were also measured in the oil extracted from freeze-dried tissue sections by an accelerated solvent extraction system using hexane. Carotenoids and chlorophylls identified in the skin, flesh, and oil were lutein, alpha-carotene, beta-carotene, neoxanthin, violaxanthin, zeaxanthin, antheraxanthin, chlorophylls a and b, and pheophytins a and b with the highest concentrations of all pigments in the skin. Chlorophyllides a and b were identified in the skin and flesh tissues only. As the fruit ripened and softened, the skin changed from green to purple/black, corresponding to changes in skin hue angle, and a concomitant increase in cyanidin 3-O-glucoside and the loss of chlorophyllide a. In flesh tissue, chroma and lightness values decreased with ripening, with no changes in hue angle. The levels of carotenoids and chlorophylls did not change significantly during ripening. As fruit ripened, the total chlorophyll level in the oil from the flesh sections remained constant but declined in the oil extracted from the skin.

Rhodopsin is the prototypical G-protein coupled receptor, coupling light activation with high efficiency to signaling molecules. The dark-state X-ray structures of the protein provide a starting point for consideration of the relaxation from initial light activation to conformational changes that may lead to signaling. In this study we create an energetically unstable retinal in the light activated state and then use molecular dynamics simulations to examine the types of compensation, relaxation, and conformational changes that occur following the cis–trans light activation. The results suggest that changes occur throughout the protein, with changes in the orientation of Helices 5 and 6, a closer interaction between Ala 169 on Helix 4 and retinal, and a shift in the Schiff base counterion that also reflects changes in sidechain interactions with the retinal. Taken together, the simulation is suggestive of the types of changes that lead from local conformational change to light-activated signaling in this prototypical system.

Dragon fruit ( Hylocereus undatus ) are a host of fruit fly ( Bactrocera spp.), and thus export to many markets will require a disinfestation treatment. This work investigated the potential for disinfestation by heat treatment (HT) of cv. Binh Thuan in order to meet the biosecurity requirements of importing countries. Main-season fruit from Viet Nam were subjected to hot air treatments and stored for 2–4 weeks storage at 5 °C in sealed polypropylene bags, and fruit quality examined during subsequent shelf-life at 20 °C. HTs applied were fruit core temperatures (FCT) of 46.5 °C for durations of 20 and 40 min, and 48.5 °C for 50, 70 and 90 min. Assessments included turgor of the bracts and stem, the appearance of the body of the fruit and presence of rots, skin colour, flesh firmness, soluble solids concentration, fruit acidity, taste, and flesh translucence. ‘Binh Thuan’ Dragon fruit proved to be tolerant of hot air treatment and at the lower HT temperature (FCT 46.5 °C for 20 min) fruit quality was not significantly different from non-heated control fruit, either after treatment at harvest, or after storage for up to 4 weeks. However, metrics quantifying the appearance of both control- and HT-fruit generally deteriorated with storage time at 5 °C, although the internal appearance of the flesh, and taste, remained acceptable throughout. Shelf-life effects were restricted to comparison of the lower HT temperature (FCT 46.5 °C for 20 min) and non-heated control fruit. Shelf-life after any of the storage periods was terminated after only 4 d, as fruit available for study had not been sprayed with fungicides during the season, and developed anthracnose rots readily at 20 °C. No differences in shelf-life characteristics were established between HT fruit and control fruit. Our results provide strong evidence that ‘Binh Thuan’ Dragon fruit are a suitable candidate for fruit fly disinfestation by hot air HTs, and that fruit quality during or after storage does not suffer as a consequence.

The ALLD simulation software implements a mesoscopic lattice method to model hydrophobic chromatographic systems and biomembranes. The basis and some initial results of these applications emphasizing reversed phase chromatography of peptides are reviewed. The program structure and coding are described along with concepts for parallelization to simulate massive systems and large biomolecules. Extensions of the method for simulations with variable temperature, solute and solvent polarization, effects of ionized solutes and added salts and heterogeneous media are presented.

Harvested fruit of feijoa (Feijoa sellowiana) are of mixed stages of maturity. To ascertain whether a non-destructive technique such as density grading could discriminate between fruit with different internal attributes, the density of 400 fruit (cv. 'Apollo') was recorded using fruit samples categorised as unripe, ripe and over-ripe. Density was subsequently correlated with physicochemical measurements and ripeness indices from dissected fruit. Fruit densities ranged between 920 and 990 kg m -3 . No convincing relationships with density were observed with dry matter (DM) (r = 0.20; P

The human erythrocyte sialoglycoprotein glycophorin A (GpA) has been used extensively in experiment and simulations as a model of transmembrane helix-dimer formation, emphasizing the critical role of specific residue-residue interactions between helices in dimer stability. While the tertiary dimer structure is modulated by the hydrophobic lipid bilayer environment, we show that interactions of GpA with ordered interfacial water are commensurate to intrahelical forces. The role of lipid-water interface in stabilizing transmembrane proteins is not yet understood; however, dramatic water reordering in the presence of the transmembrane domains is observed from simulations and is possibly measurable by experiment. Interfacial interactions including anisotropic interactions with the polar headgroups might favor parallel association of transmembrane helices. To quantify forces capable of disrupting the GpA dimer, we generate folding/unfolding intermediates by replacement of the lipid bilayer with water, eliminating not only the native hydrophobic environment but also the native interfacial water region. Dramatic changes in the secondary, helical structures occur, with a transition from i,i+4 α-helix to i,i+5 π-helix and concomitant perturbation of the tertiary structure. Enforcing the native α-helix secondary structure by soft dihedral restraints restores the native tertiary structure, in essence substituting for the lack of the lipid-water interface. We suggest that differentiation between interactions within the lipid bilayer, including interactions with lipid headgroups and interfacial water can enrich our understanding of the thermodynamic stability of transmembrane domains.

Physiological disorders occur when ‘Hass’ avocados are stored for more than approximately 4–6 weeks. The major disorder is diffuse flesh discolouration (“flesh greying”, or “internal chilling injury”), but others include vascular browning, vascular leaching (browning of flesh around the vascular bundles), stringy vascular tissue (thickening and separation of the vascular strands), and outer flesh blackening (blackening of the outmost layer of the mesocarp). We have examined 1-MCP effects on ‘Hass’ avocados stored for 4 or 7 weeks at 5.5 ◦ C following treatment with 50–1000 nl l −1 1-MCP for 6–24 h, at 6 or 15 ◦ C. The effect of harvest date (fruit maturity) on responsiveness to 100 and 500 nl l −1 1-MCP was examined. 1-MCP treated fruit were firmer following storage, had reduced skin colouration (purpling) at removal from storage (4 or 7 weeks), increased time to softening, and reduced physiological disorders associated with long-term storage. Relatively little difference was observed between fruit treated at 15 and 6 ◦ C, and thus a treatment temperature of 6 ◦ C was used in the remaining experiments. For lower 1-MCP concentrations, short treatment durations influenced time to ripen, but not fruit quality. Treatment times of 12 and 24 h produced similar results. Harvest date (fruit maturity) influenced the levels of disorders in non-1-MCP treated fruit, but had little overall effect on 1-MCP efficacy. 1-MCP treatment was of little benefit for fruit stored for 4 weeks but, particularly if the 1-MCP concentration was high (250 nl l −1 ), excessively delayed the time to ripen. After 7 weeks storage 100 nl l −1 1-MCP almost completely eliminated some long-term storage disorders. A small trial showed that 500 nl l −1 1-MCP did not reduce external chilling injury (skin blackening) of ‘Hass’ avocados induced by 0 ◦ C storage. Overall, 1-MCP shows promise as a tool

Pretreatments at moderate temperatures applied immediately prior to the high or low temperature treatments can reduce skin damage to avocados. These temperature tolerance-inducing pretreatments have generally been applied immediately prior to the high or low temperature. We examined whether a delay between the pretreatment and potentially damaging high and low temperatures may cause a loss in the induced tolerance. A hot air pretreatment (38 °C for 6 h) applied prior to storage at 0 °C for 3 weeks with intervening delays of 1–4 days at 20 °C, showed a large reduction in chilling injury as a result of the pretreatment but that this was progressively lost with increasing delay to storage. Hot water pretreatments (38 °C for 0, 5, 20 and 60 min) increasingly reduced chilling damage at 0 °C, and heat damage from a hot water treatment (HWT) at 50 °C/10 min. With delays of up to 3–24 h prior to the HWT, heat damage was reduced for the 5 and 20 min pretreatments. However, delays up to 5 days between pretreatment and HWT, loss of heat tolerance was observed. For delays of between 1 and 5 days there was a clear loss of chilling tolerance which was more rapid than the increase in chilling injury in control treatments for the same delays. However, the effect of delays

The association between monovalent salts and neutral lipid bilayers is known to influence global bilayer structural properties such as headgroup conformational fluctuations and the dipole potential. The local influence of the ions, however, has been unknown due to limited structural resolution of experimental methods. Molecular dynamics simulations are used here to elucidate local structural rearrangements upon association of a series of monovalent Na+ salts to a palmitoyl-oleoyl-phosphatidylcholine bilayer. We observe association of all ion types in the interfacial region. Larger anions, which are meant to rationalize data regarding a Hofmeister series of anions, bind more deeply within the bilayer than either Cl− or Na+. Although the simulations are able to reproduce experimentally measured quantities, the analysis is focused on local properties currently invisible to experiments, which may be critical to biological systems. As such, for all ion types, including Cl−, we show local ion-induced perturbations to headgroup tilt, the extent and direction of which is sensitive to ion charge and size. Additionally, we report salt-induced ordering of the water well beyond the interfacial region, which may be significant in terms of hydration repulsion between stacked bilayers.

Systematic inaccuracy is inherent in any computational estimate of a non-linear average, such as the free energy difference (Delta-F) between two states or systems, because of the availability of only a finite number of data values, N. In previous work, we outlined the fundamental statistical description of this ``finite-sampling error.'' We now give a more complete presentation of (i) rigorous general bounds on the free energy and other nonlinear averages, which underscore the universality of the phenomenon; (ii) asymptotic N->infinity expansions of the average behavior of the finite-sampling error in Delta-F estimates; (iii) illustrative examples of large-N behavior, both in free-energy and other calculations; and (iv) the universal, large-N relation between the average finite-sampling error and the fluctuation in the error. An explicit role is played by Levy and Gaussian limiting distributions., Version to appear in J. Stat. Phys. -- only minor corrections

Skin of 'Hass' avocados (Persea americana Mill.) changes colour from green to purple/black as fruit ripen. This colour change is important as an indicator of ripeness for both industry and consumers. We sought to characterise pigment changes during ripening of 'Hass' avocados. Skin colour and changes in chlorophyll and anthocyanin concentrations in relation to fruit firmness at three ripening temperatures (15, 20 and 25 °C) were studied. As fruit ripened, skin colour changed from green, to purple, to black, which was observed as a decrease in L, chroma and hue. Total anthocyanins in skin tissue increased during ripening, but this increase was due almost entirely to a single anthocyanin; cyanidin 3-O-glucoside. Cyanidin 3-O-glucoside concentration increased after 3-6 days postharvest (depending on ripening temperature), and levels increased earlier, and were higher, with higher ripening temperature. Chlorophyll a and b levels decreased until 4-5 days after harvest, but did not change significantly thereafter. No significant differences in chlorophyll concentration were observed among the three ripening temperatures. Fruit harvested directly from the tree (unripe) with skin darkening showed similar pigments changes to that during ripening (reduced chlorophyll and increased cyanidin 3-O-glucoside). Colour change in 'Hass' avocados from green to purple, then black, results from an initial decrease in chlorophyll content, followed by an increase in the levels of the anthocyanin, cyanidin 3-O-glucoside.

To identify binding partners of the A1AR (A1 adenosine receptor), yeast two-hybrid screening of a rat embryonic cDNA library was performed. This procedure led to the identification of erythrocyte membrane cytoskeletal protein (represented as 4.1G) as an A1AR-binding partner. Truncation studies revealed that the C-terminal domain of 4.1G was essential for binding to A1ARs and that the C-terminal domain of 4.1G and the third intracellular loop of A1ARs interacted. A1AR–4.1G interaction was also confirmed in studies using brain tissue. Studies in HEK-293 (human embryonic kidney 293) cells and Chinese-hamster ovary cells showed that 4.1G interfered with A1AR signal transduction, as 4.1G reduced A1AR-mediated inhibition of cAMP accumulation and intracellular calcium release. 4.1G also altered cell-surface A1AR expression. These observations identify 4.1G as a novel A1AR-binding partner that can regulate adenosine action.

The light-driven photocycle of rhodopsin begins the photoreceptor cascade that underlies visual response. In a sequence of events, the retinal covalently attached to the rhodopsin protein undergoes a conformational change that communicates local changes to a global conformational change throughout the whole protein. In turn, the large-scale protein change then activates G-proteins and signal amplification throughout the cell. The nature of this change, involving a coupling between a local process and larger changes throughout the protein, may be important for many membrane proteins. In addition, functional work has shown that this coupling occurs with different efficiency in different lipid settings. To begin to understand the nature of the efficiency of this coupling in different lipid settings, we present a molecular dynamics study of rhodopsin in an explicit dioleoyl-phosphatidylcholine bilayer. Our system was simulated for 40 ns and provides insights into the very early events of the visual cascade, before the full transition and activation have occurred. In particular, we see an event near 10 ns that begins with a change in hydrogen bonding near the retinal and that leads through a series of coupled changes to a shift in helical tilt. This type of event, though rare on the molecular dynamics time-scale, could be an important clue to the types of coupling that occur between local and large-scale conformational change in many membrane proteins.

‘Hass’ avocado harvested at four different times during a growing season, was analysed by both reflectance and interactance NIR spectroscopy to establish its reliability for the non-destructive determination of fruit dry matter (DM). Mean DM increased from 27.7 to 36.8% during the course of the study. Relationships between spectral wavelengths and DM were evaluated by application of chemometric techniques to partial least squares (PLS) and multiple linear regression (MLR) models, using calibration and validation statistics of predictions to compare their efficacy. The interactance mode was a superior predictor of fruit DM compared with reflectance. A PLS model applied to interactance data from fruit from all harvests combined (n=239) gave a goodness-of-fit (Rp2) between predicted and actual DM measurements of 0.88, and an error of prediction (RMSEP) of 1.8% DM. MLR models incorporating four wavelengths returned equivalent validation statistics. Three of these wavelengths, in the vicinity of 900–920 nm, are consistent with the CH absorbance band, leaving only a minor role for water-related absorbances. These observations suggest on-line commercial NIR systems capable of operating in an interactance mode have the potential to usefully grade avocado on the basis of their DM content, to improve taste and oil content.

The recent determination of crystal structures for several important membrane proteins opens the way for comparative modeling of their membrane-spanning regions. However, the ability to predict correctly the structures of loop regions, which may be critical, for example, in ligand binding, remains a considerable challenge. To meet this challenge, accurate scoring methods have to discriminate between candidate conformations of an unknown loop structure. Some success in loop prediction has been reported for globular proteins; however, the proximity of membrane protein loops to the lipid bilayer casts doubt on the applicability of the same scoring methods to this problem. In this work, we develop “decoy libraries” of non-native folds generated, using the structures of two membrane proteins, with molecular dynamics and Monte Carlo techniques over a range of temperatures. We introduce a new approach for decoy library generation by constructing a flat distribution of conformations covering a wide range of Cα–root-mean-square deviation (RMSD) from the native structure; this removes possible bias in subsequent scoring stages. We then score these decoy conformations with effective energy functions, using increasingly more cpu-intensive implicit solvent models, including (1) simple Coulombic electrostatics with constant or distance-dependent dielectrics; (2) atomic solvation parameters; (3) the effective energy function (EEF1) of Lazaridis and Karplus; (4) generalized Born/Analytical Continuum Solvent; and (5) finite-difference Poisson–Boltzmann energy functions. We show that distinction of native-like membrane protein loops may be achieved using effective energies with the assumption of a homogenous environment; thus, the absence of the adjacent lipid bilayer does not affect the scoring ability. In particular, the Analytical Continuum Solvent and finite-difference Poisson–Boltzmann energy functions are seen to be the most powerful scoring functions. Interestingly, the use of the uncharged states of ionizable sidechains is shown to aid prediction, particularly for the simplest energy functions. Proteins 2003;52:492–509. © 2003 Wiley-Liss, Inc.

Entropy and enthalpy compensation are frequently observed in thermodynamic measurements. To understand the molecular details of these compensating changes, molecular dynamics or Monte Carlo methods may, in principle, be used. Yet, in practice, computational methods to evaluate changes in entropy and enthalpy usually have much greater (e.g. order of magnitude worse) error than relative free energy calculations. In this paper, we examine ways to improve the computational ability to determine changes in both enthalpy and entropy. Toward that end we consider five different perturbation schemes for enthalpy determination and also consider the relative importance of staging the computation (i.e., dividing the entire perturbation calculation into a series of consecutive smaller ones) along the reaction coordinate. Two model systems are used for evaluation: a system of Lennard-Jones spheres, where the computation is directed to the addition/deletion of a sphere, and the alchemical transformation of an anion in e...

Storage of avocado fruit is limited by the development of skin damage (external chilling injury) when fruit are stored at temperatures of less than about 3 °C. The potential for low temperature conditioning to reduce external damage of ‘Hass’ avocados was examined. Avocados harvested in early summer were conditioned at temperatures of 4, 6, 8, 10, 12 and 15 °C for a period of 0, 1, 2, 3, 4 or 5 days before 3 weeks storage at 0 °C. Three days after removal from coolstore, external damage was rated, and internal quality assessed after ripening at 15 °C. The experiment was repeated in late summer, but fruit were stored for 4 weeks at 0 °C, and only external damage was measured. Control fruit stored at 0 °C for either 3 or 4 weeks exhibited severe external damage, manifested as blackening and pitting over almost the whole fruit surface. Conditioning temperatures of 4–10 °C reduced skin damage. The optimum temperature/time combinations were 6 or 8 °C for 3–5 days prior to 0 °C storage. Ripe-fruit quality was also highest in these treatments. Weight loss, ethylene and CO2 production were not associated with the reduction in external damage, and the response observed is therefore likely to be due to a low temperature, rather than a ripening response.

To model a concentration gradient across a biomembrane, we have performed all-atom molecular dynamics simulations of NaCl solutions separated by two oppositely charged plates. We have employed the recently formulated three-dimensional Ewald summation with correction (EW3DC) technique for calculations of long-range electrostatics in two-dimensionally periodic systems, allowing for different salt concentrations on the two sides of the plates. Six simulations were run, varying the salt concentrations and plate surface charge density in a biologically relevant range. The simulations reveal well-defined, atomic-level asymmetries between the two sides: distinct translational and rotational orderings of water molecules; differing ion residency times; a clear wetting layer adjacent only to the negative plate; and marked differences in charge density/potential profiles which reflect the microscopic behavior. These phenomena, which may play important roles in membrane and ion channel physiology, result primarily fr...

Research highlights that many students experience negative emotions during learning activities, and these can have a detrimental impact on behaviors and outcomes. Here, we investigate the impact of a particular kind of affective intervention, namely a learning dashboard, on two deactivating emotions: boredom and lack of excitement. The data comes from a study we conducted with over 200 middle school students interacting with an intelligent tutor that provided varying levels of support to encourage dashboard use. We analyze the data using a range of techniques to show that the learning dashboard is associated with reduced deactivating emotions, but that its utility also depends on the way its use is promoted and on students’ gender.