Analysis of the conformational profile of trishomocubane amino acid dipeptide

4-Amino-(D3)-trishomocubane-4-carboxylic acid is a constrained alpha-amino acid residue that exhibits promising conformational characteristics, i.e., helical and beta-turns. As part of the development of conformational guidelines for the design of peptides and protein surrogates, the conformational energy calculations on trishomocubane using molecular mechanics and ab initio methods are presented. The C(alpha) carbon of trishomocubane forms part of the cyclic structure, and consequently a peptidic environment was simulated with an acetyl group on its N-terminus and a methylamide group on its C-terminus. Ramachandran maps computed at the molecular mechanics level using the standard AMBER (parm94) force field libraries compared reasonably well with the corresponding maps computed at the Hartree Fock level, using the 6-31G* basis set. Trishomocubane peptide (Ac-Tris-NHMe) is characterized by four low energy conformers corresponding to the C7ax, C7eq, 3(10), and alpha(L) helical structures.     

The mechanism of proton transfer between adjacent sites on the molecular surface

The surface of a protein, or a membrane, is spotted with a multitude of proton binding sites, some of which are only few Å apart. When a proton is released from one site, it propagates through the water by a random walk under the bias of the local electrostatic potential determined by the distribution of the charges on the protein. Eventually, the released protons are dispersed in the bulk, but during the first few nanoseconds after the dissociation, the protons can be trapped by encounter with nearby acceptor sites. While the study of this reaction on the surface of a protein suffers from experimental and theoretical difficulties, it can be investigated with simple model compounds like derivatives of fluorescein. In the present study, we evaluate the mechanism of proton transfer reactions that proceed, preferentially, inside the Coulomb cage of the dye molecules. Kinetic analysis of the measured dynamics reveals the role of the dimension of the Coulomb cage on the efficiency of the reaction and how the ordering of the water molecules by the dye affects the kinetic isotope effect.     

Spatial aggregation and association in different resource-patch distributions: experimental analysis with Drosophila

1. Laboratory experiments using homogeneous resources were conducted to examine intra- and interspecific spatial egg distribution of D. simulans, D. auraria and D. immigrans in three different resource-patch distribution patterns: patchy, even and clustered. 2. Individuals of each species were introduced separately or simultaneously into the cage, into which artificial substrates were placed and allowed to oviposit for 24 h. Spatial analyses were performed with indices of intraspecific aggregation (J), interspecific association (C) and L-function based on Ripley's K-function. 3. Eggs were always spatially aggregated irrespective of species and the resource-patch distribution patterns. Spatial egg aggregation was influenced significantly by the resource-patch distribution pattern and tended to be weaker in the clustered resource-patch distribution than in the patchy or even resource-patch distribution. 4. Spatial extent of egg aggregation was always beyond the single resource patch scale, indicating aggregation of ovipositing females. 5. Interspecific association of egg distribution was absent or very weak. Thus, these results present experimental evidence of independent egg aggregation among drosophilids.     

Temperature and urea induced denaturation of the TRP‐cage mini protein TC5b: A simulation study consistent with experimental observations

The effects of temperature and urea denaturation (6M urea) on the dominant structures of the 20‐residue Trp‐cage mini‐protein TC5b are investigated by molecular dynamics simulations of the protein at different temperatures in aqueous and in 6M urea solution using explicit solvent degrees of freedom and the GROMOS force‐field parameter set 45A3. In aqueous solution at 278 K, TC5b is stable throughout the 20 ns of MD simulation and the trajectory structures largely agree with the NMR‐NOE atom–atom distance data available. Raising the temperature to 360 K and to 400 K, the protein denatures within 22 ns and 3 ns, showing that the denaturation temperature is well below 360 K using the GROMOS force field. This is 40–90 K lower than the denaturation temperatures observed in simulations using other much used protein force fields. As the experimental denaturation temperature is about 315 K, the GROMOS force field appears not to overstabilize TC5b, as other force fields and the use of continuum solvation models seem to do. This feature may directly stem from the GROMOS force‐field parameter calibration protocol, which primarily involves reproduction of condensed phase thermodynamic quantities such as energies, densities, and solvation free energies of small compounds representative for protein fragments. By adding 6M urea to the solution, the onset of denaturation is observed in the simulation, but is too slow to observe a particular side‐chain side‐chain contact (Trp6‐Ile4) that was experimentally observed to be characteristic for the denatured state. Interestingly, using temperature denaturation, the process is accelerated and the experimental data are reproduced.     

Effects of radio frequency magnetic fields on iron release from cage proteins

Ferritin, the iron cage protein, contains a superparamagnetic ferrihydrite nanoparticle formed from the oxidation and absorption of Fe²⁺ ions. This nanoparticle increases its internal energy when exposed to alternating magnetic fields due to magnetization lag. The energy is then dissipated to the surrounding proteic cage, affecting its functioning. In this article we show that the rates of iron chelation with ferrozine, an optical marker, are reduced by up to a factor of 3 in proteins previously exposed to radio frequency magnetic fields of 1 MHz and 30 µT for several hours. The effect is non‐thermal and depends on the frequency‐amplitude product of the magnetic field. Bioelectromagnetics 30:336–342, 2009. © 2009 Wiley‐Liss, Inc.     

Changes in amino acids in Cucumis melo in relation to life-history traits and flight propensity of Bemisia tabaci

Phloem amino acids in Cucumis melo L. were measured to determine whether changes in nitrogen availability might affect life-history traits and flight activity of Bemisia tabaci Gennadius (Homoptera: Aleyrodidae). During plant development, nineteen of the twenty common amino acids, plus hydroxyproline, citrulline, ornithine and -aminobutyric acid (GABA) were identified. For most essential amino acids, there were two peaks observed: an initial large peak associated with young plants, and a later small peak associated with senescing plants. For histidine, ornithine and citrulline, medium to large peaks in relative abundance were observed in mature plants. Arginine peaked during the first few weeks of development and was no longer detectable after wk 7. Serine and glutamine/glutamic acid were the only amino acids that peaked during plant senescence. Factor analysis was used to create a reduced number of orthogonal factors, which corresponded well with the trends that were observed for the various groups of amino acids. No single or combination of factors explained a significant amount of the variability in oviposition. For both males and females, factor 1 (predominantly essential amino acids) was the single most important predictor of adult weight. As the relative concentrations of essential amino acids decreased, whitefly weights decreased. Factors 1 and 3 (predominantly histidine and ornithine) were the most important predictors of developmental time. As these amino acids decreased in relative concentration, developmental time increased. Percent emergence was positively associated with factor 1 and negatively associated with factor 6 (predominantly aspartic acid). The distributions of flight duration for whiteflies emerging from young, mature and senescing melon plants were compared and they were always skewed towards short flights; however, the frequency of long-duration flights increased when melon plants began to senesce. Whiteflies from all plant-age categories were capable of flying for more than 2 h with fully developed eggs, but the presence of more than four mature eggs was associated with flights of reduced duration.     

Overwintering in Drosophila melanogaster: outdoor field cage experiments on clinal and laboratory selected populations help to elucidate traits under selection

Insects can adapt to temperate environments by increasing levels of resistance to cold conditions over winter and/or altering reproductive patterns to focus reproduction in favourable conditions. In temperate areas, Drosophila melanogaster persists over winter at the adult stage. A previous experiment, conducted with flies kept in outdoor population cages in the temperate winter, indicated that temperate populations produced more eggs than did tropical populations following an abrupt increase in reproduction in late winter. In contrast, the tropical populations produced more eggs prior to the increase. Both patterns resulted in a higher net number of surviving offspring for temperate populations. Here we again examine the clinal pattern in reproduction using outdoor cages, this time held under tropical winter conditions. In this environment, surprisingly, egg production was higher and on average earlier in populations originating from temperate areas. However, mortality rates also increased with latitude of origin, and the relationship of lifetime egg production to latitude should therefore be measured. To test the role of altered pattern of egg production per se in the reproductive advantage of temperate populations in the temperate winter, we tested the performance of laboratory lines selected for altered reproductive patterns, under temperate winter conditions. Lines selected for high early fecundity exhibited this characteristic in the field cages and lines selected for late reproduction exhibited a relatively high fecundity in spring. The timing of the abrupt increase in egg production was identical in these sets of lines and occurred at the same time in recently collected populations, suggesting evolutionary conservation of the switch. These findings suggest that changes in early and late reproduction per se determine adaptation to temperate winter conditions, and illustrate how laboratory selection lines can be used to understand traits underlying adaptive shifts in field performance.     

胸腔镜辅助小切口对多发肋骨骨折患者手术及康复的影响

摘要 目的：探讨胸腔镜辅助小切口术式在严重多发肋骨骨折患者手术及术后康复中的应用前景。方法：选取我科收治的严重多发肋骨骨折患者作为研究对象,随机分为对照组和实验组,分别采取传统开胸手术方式和胸腔镜辅助小切口术式。术中记录手术时间、失血量等信息,术后记录引流管引流时间、术后住院时间以及发热、肺不张、肺炎、伤口感染、下肢静脉血栓、房颤等并发症发生率;分别于术前、术后1天、术后3天、术后5天、术后7天进行疼痛评分;在术后1、3、6个月评估患者的生活质量。通过统计学分析,对比两组间有无统计学差异。结果：（1）实验组在手术时间、术中出血量、术后胸腔引流时间、术后住院天数等方面均显著优于对照组;（2）在术后并发症方面,实验组肺炎发生率显著低于对照组,其他并发症组间无明显差异;（3）实验组术后第三天,疼痛评分已降至轻度疼痛,不影响正常生活,对照组在术后第五天降为轻度疼痛,显著低于实验组;（4）实验组在术后3个月生活质量基本恢复正常,对照组至术后6个月才基本正常,显著低于实验组。结论：胸腔镜辅助小切口术式在严重胸部外伤患者手术的应用中显著优于传统开胸术式,值得临床推广借鉴。