Exploring the nature of the H-bonds between the human class II MHC protein,HLA-DR1 (DRB*0101) and the influenza virus hemagglutinin peptide,HA306-318, using the quantum theory of atoms in molecules

The nature of the H-bonds between the human protein HLA-DR1 (DRB*0101) and the hemagglutinin peptide HA306-318 has been studied using the Quantum Theory of Atoms in Molecules for the first time. We have found four H-bond groups: one conventional CO··HN bond group and three nonconventional CO··HC, π··HC involving aromatic rings and HN··HC_aliphatic groups. The calculated electron density at the determined H-bond critical points suggests the follow protein pocket binding trend: P1 (2,311) >> P9 (1.109) > P4 (0.950) > P6 (0.553) > P7 (0.213) which agrees and reveal the nature of experimental findings, showing that P1 produces by a long way the strongest binding of the HLA-DR1 human protein molecule with the peptide backbone as consequence of the vast number of H-bonds in the P1 area and at the same time the largest specific binding of the peptide Tyr308 residue with aromatic residues located at the binding groove floor. The present results suggest the topological analysis of the electronic density as a valuable tool that allows a non-arbitrary partition of the pockets binding energy via the calculated electron density at the determined critical points.     

Effect of the Nature of the 3β-Substitution in Manoyl Oxides on the Thermotropic Behavior of DPPC Lipid Bilayer and on DPPC Liposomes

Functionalized manoyl oxide derivatives have been proved over the years to evoke several biological responses. Among them, 3β-hydroxy-manoyl oxide (1) and 3β-acetoxy-manoyl oxide (2) have been shown to exhibit in vitro antimicrobial and cytotoxic activity, while N-imidazole-3 β-thiocarbonyl ester of manoyl oxide (3) was found to exhibit potent cytotoxic effect. Their partitioning into phospholipid bilayers may lead to membrane structure modifications that are crucial in liposome development as they may influence their maintenance and integrity. DSC was used to study the modifications induced in DPPC bilayers by incorporating increasing concentrations of the three manoyl oxide derivatives. All derivatives were found to strongly affect the bilayer structural organization in terms of a decrease of the cooperativity, the fluidization and partially destabilization of the gel phase and the induction of a lateral phase separation in clustering domains. Derivatives 1 and 3 were incorporated into DPPC liposomes and their physicochemical stability was monitored at 4°C. The stability of liposomes was strongly influenced by the presence of 1 and 3 at any molar ratio studied. DPPC/1 liposomes were found to retain its stability for 48 h at low concentration of 10% mol, while at higher concentrations up to 30% mol they collapsed into aggregated material. In all cases DPPC/3 liposomes were found unstable and sticky aggregated structures precipitated from the bulk suspension.     

The reaction force and the transition region of a reaction

The reaction force F(R) and the position-dependent reaction force constant κF(R) are defined by F(R)=-∂V(R)/∂R and κ(R)=∂²V(R)/∂R², where V(R) is the potential energy of a reacting system along a coordinate R. The minima and maxima of F(R) provide a natural division of the process into several regions. Those in which F(R) is increasing are where the most dramatic changes in electronic properties take place, and where the system goes from activated reactants (at the force minimum) to activated products (at the force maximum). κ(R) is negative throughout such a region. We summarize evidence supporting the idea that a reaction should be viewed as going through a transition region rather than through a single point transition state. A similar conclusion has come out of transition state spectroscopy. We describe this region as a chemically-active, or electronically-intensive, stage of the reaction, while the ones that precede and follow it are structurally-intensive. Finally, we briefly address the time dependence of the reaction force and the reaction force constant.     

Report of the Alpine Section

Background: Under climate-change scenarios, rock outcrops, by providing microclimatically diverse habitats, different from those of surrounding zonal vegetation matrix, may serve as climatic refugia and thereby facilitate the persistence of specialist species.

Aim: We tested whether rock outcrops of southern temperate latitudes could act as local refugia for a cold-adapted flora in the face of global warming.

Methods: We related species composition of 50 outcrops and that of their surrounding vegetation to climatic data at local and regional scales to establish whether species distributions reflected differences that could indicate the existence of climatic refugia.

Results: While at a regional scale, species composition of the outcrops across the study area was related to mean annual precipitation and mean annual maximum temperature, locally, southern faces of outcrops had different species and lower maximum temperatures than insolated north faces and surrounding vegetation plots.

Conclusions: South faces of outcrops by providing cool microhabitats, and currently harbouring species not found in the surrounding zonal vegetation matrix, could serve as local refugia for heat-intolerant plants and other microthermic organism. The degree of ‘stability’ of these refugia will depend on the degree of future change in climate. Therefore, it is important to plan protected area networks that maximise local environmental heterogeneity, including the protection of rock outcrops both as refugia for cold-adapted species and as potential stepping stones that would allow dispersal of these species between supportive environments through unfavourable ones.     

Production of N 2 O by Ammonia Oxidizing Bacteria at Subfreezing Temperatures as a Model for Assessing the N 2 O Anomalies in the Vostok Ice Core

It was suggested that the abnormally high N ₂ O values found in 130,000–160,000 year-old Vostok ice core samples, characterized by high δ ¹⁵ N and low δ ¹⁸ O values, resulted from in situ microbial N ₂ O production. To substantiate these observations we obtained new geochemical data from the last glacial period and showed the existence of additional small N ₂ O anomalies. To test the hypothesis that microbial metabolism could contribute to these anomalies, we developed protocols for examining the ability of Nitrosomonas cryotolerans cells to produce N ₂ O at subfreezing temperatures. Our results show that these model, frozen cultures produce N ₂ O at temperatures as low as ?32°C.     

Nucleosides and Nucleotides. 192. Toward the Total Synthesis of Cyclic ADP-Carbocyclic-Ribose. Formation of the Intramolecular Pyrophosphate Linkage by a Conformation-Restriction Strategy in a Syn-form Using a Halogen Substitution at the 8-Position of the Adenine Ring

Abstract

The synthesis of cyclic ADP-carbocyclic-ribose (2), as a stable mimic for cyclic ADP-ribose, was investigated. Construction of the 18-membered backbone structure was successfully achieved by condensation of the two phosphate groups of 19, possibly due to restriction of the conformation of the substrate in a syn-form using an 8-chloro substituent at the adenine moiety. SN2 reactions between an optically active carbocyclic unit 8, which was constructed by a previously developed method, and 8-bromo-N ⁶-trichloroacetyl-2′,3′-O-isopropylideneadenosine 9c gave N-1-carbocyclic derivative, which was deprotected to give 5′,5′-diol derivatives 18. When 18 was treated with POCl₃ in PO(OEt)₃, the bromo group at the 8-position was replaced to give N-1-carbocyclic-8-chloroadenosine 5′,5′-diphosphate derivative 19 in 43% yield. Treatment of 19 with 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride gave the desired intramolecular condensation product 20 in 10% yield. This is the first chemical construction of the 18-membered backbone structure containing an intramolecular pyrophosphate linkage of a cADPR-related compound with an adenine base.     

Kinetics and DFT studies on the reaction of copper(II) complexes and H2O2

Copper(II) complexes supported by bulky tridentate ligands L1^H (N,N-bis(2-quinolylmethyl)-2-phenylethylamine) and L1^Ph (N,N-bis(2-quinolylmethyl)-2,2-diphenylethylamine) have been prepared and their crystal structures as well as some physicochemical properties have been explored. Each complex exhibits a square pyramidal structure containing a coordinated solvent molecule at an equatorial position and a weakly coordinated counter anion (or water) at an axial position. The copper(II) complexes reacted readily with H₂O₂ at a low temperature to give mononuclear hydroperoxo copper(II) complexes. Kinetics and DFT studies have suggested that, in the initial stage of the reaction, deprotonated hydrogen peroxide attacks the cupric ion, presumably at the axial position, to give a hydroperoxo copper(II) complex retaining the coordinated solvent molecule (H ^R ·S). H ^R ·S then loses the solvent to give a tetragonal copper(II)-hydroperoxo complex (H ^R ), in which the –OOH group may occupy an equatorial position. The copper(II)–hydroperoxo complex H ^R exhibits a relatively high O–O bond stretching vibration at 900 cm⁻¹ compared to other previously reported examples.Electronic Supplementary Material Supplementary material is available for this article at     

Antioxidative Activities of Galloyl Glucopyranosides from the Stem-Bark of Juglans mandshurica

Two phenolics, 1,2,6-trigalloylglucose (1) and 1,2,3,6-tetragalloylglucose (2), isolated from the stem-bark of Juglans mandshurica were evaluated for their antioxidative activities. The results showed that compounds 1 and 2 exhibited strong scavenging activities against 1,1′-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis-(3-ethylbenzenthiazoline-6-sulphonic) acid (ABTS^?+), and superoxide radicals (O₂ ^??), and also had a significant inhibitory effect on lipid peroxidation and low-density lipoprotein (LDL) oxidation. The strong superoxide radical scavenging of 1 and 2 resulted from the potential competitive inhibition with xanthine at the active site of xanthine oxidase (OX). In addition, compounds 1 and 2 displayed significant lipoxygenase inhibitory activity, the mode of inhibition also being identified as competitive. In comparison, the antioxidative activities of compounds 1 and 2, together with gallic acid, indicated that the number of galloyl moieties could play an important role in the antioxidative activity.     

Morpho-histochemical characterization of salivary gland cells of males of the tick <Emphasis Type="Italic">Rhipicephalus</Emphasis><Emphasis Type="Italic">sanguineus</Emphasis> (Acari: Ixodidae) at different feeding stages: description of new cell types

This study describes the changes undergone by cells of the salivary glands of unfed and feeding (at day two and four post-attachment) Rhipicephalus sanguineus males, as well as new cell types. In unfed males, types I and II acini are observed with cells “undifferentiated”, undefined 1 and 2 (the latter, with atypical granules), a, c1 and c3; type III is composed of cells d and e; and type IV present cells g. In males at day two post-attachment, type I acini exhibit the same morphology of unfed individuals. An increase in size is observed in types II, III, and IV, as cells are filled with secretion granules. Some granules are still undergoing maturation. In type II acinus, cells a, b and c1–c8 are observed. Cells c7 and c8 are described for the first time. Cells c7 are termed as such due to the addition of polysaccharides in the composition of the secretion granules (in unfed individuals, they are termed undefined 1). Type III acini exhibit cells d and e completely filled with granules, and in type IV, cells g contain granules in several stages of maturation. In males at day four post-attachment, type I acini do not exhibit changes. Granular acini exhibit cells with fewer secretion granules, which are already mature. In type II acini, cells a, b, c1–c5 are present, type III exhibit cells d and e, and type IV contain cells g with little or no secretion. This study shows that in the salivary glands of R. sanguineus males, cells a, c1, and c3 of type II acinus, and cells d and e of type III do not exhibit changes in granular content, remaining continuously active during the entire feeding period. This indicates that during the intervals among feeding stages, gland cells reacquire the same characteristics found in unfed individuals, suggesting that they undergo reprogramming to be active in the next cycle.     

The movements of the Kittiwake

Capsule During winter songbirds were far more abundant in game cover crops than conventional agricultural habitats.

Aims To quantify game crop use during winter by farmland songbirds when compared with conventional farmland at a regional scale.

Methods Songbirds were counted on 20 farms in eastern Scotland. The number of songbirds using game crops was compared with a sample of nearby conventional crops – with particular emphasis on set-aside and cereal stubbles.

Results Game crops supported up to 100 times as many birds per hectare, of significantly more species, than the other two habitat categories. Many of these species were those currently causing concern because of their declining populations.

Conclusion Game crops could provide opportunities for increasing food resources to songbirds whose populations may be limited by food availability and possibly arrest population declines. At present, the only measures likely to facilitate this are the government's various agri-environment schemes.     

Tree recruitment at the treeline across the Continental Divide in the Northern Rocky Mountains,USA: the role of spring snow and autumn climate

ABSTRACT

Background: Topoclimate can influence tree establishment within treeline ecotones. Yet much less is known about how regional topography, such as the Continental Divide, Rocky Mountains, mediates the role of climate in governing treeline dynamics.

Aims: To utilise the Continental Divide to test whether contrasts in growing-season moisture regimes to the west (summer-dry) and east (summer-wet) impact the spatio-temporal patterns of tree establishment and rates of treeline advance in the Northern Rocky Mountains.

Methods: We sampled trees at sites on north- and south-facing slopes, west and east of the Continental Divide. We used dendroecological techniques to reconstruct patterns of tree establishment. Age-structure data were quantitatively compared with climate to evaluate possible mechanistic linkages.

Results: Across all sites, 96% of trees established after 1950. There was a treeline advance (range = 39–140 m) accompanied by increases in tree density. Significantly more trees established during wet springs on both sides of the Divide.

Conclusions: Overall, snow duration in spring and autumn temperatures appear to influence patterns of tree recruitment at the treeline. Continued warming will likely amplify the role of autumn climate in regulating tree establishment throughout treeline ecotones in the Northern Rocky Mountains, particularly west of the Divide where summer-dry conditions persist.     

Inhibitory effect of the compounds from the water extract of Curcuma longa on the production of PGE2 and NO in a macrophage cell line stimulated by LPS

ABSTRACT

We wished to search for the compounds contributing to the anti-inflammatory effects of the water extract of Curcuma longa (WEC). WEC was fractioned and the fractions were evaluated with regard to their inhibitory effect on the production of nitric oxide (NO) from the macrophage cell line stimulated by lipopolysaccharide. Compounds in the active fractions were isolated and identified. One isolated compound was identified as new: (6S)-2-methyl-5-hydroxy-6-(3-hydroxy-4-methylphenyl)-2-heptene-4-one (1). Four isolated compounds were identified as known: (6S)-2-methyl-6-(4-hydroxyphenyl)-2-heptene-4-one (4), bisabolone-4-one (5), curcumenone (6), and turmeronol A (8). Three isolated compounds were not identified their stereostructures but their planar structures: 2-methyl-6-(4-hydroxymethyl-phenyl)-2-heptene-4-one (2), 2-methyl-6-(2,3-epoxy-4-methyl-4-cyclohexene)-2-heptene (3), and 4-methylene-5-hydroxybisabola-2,10-diene-9-one (7). Compounds 1, 4, 7 and 8 inhibited production of prostaglandin E2 and NO. Others inhibited NO production only. These results (at least in part) show the active compounds contributing to the anti-inflammatory effects of WEC, and may be useful for elucidating its various beneficial physiologic effects.     

The effect of the formulation on the shelf-life of biopesticides based on two colombian isolates of Trichoderma koningiopsis Th003 and Trichoderma asperellum Th034

BackgroundFour biopesticide prototypes formulated as dispersible granules and dry powders based on 2 Colombian isolates of Trichoderma koningiopsis (Th003) and T. asperellum (Th034) were developed. These microorganisms have antagonist activity against Fusarium oxysporum f. sp. lycopersici and Rhizoctonia solani with a reduction in incidence of between 70 and 100% in tomato crops and potato crops, respectively.AimTo determine the effect of the formulation on the shelf-life of 4 biopesticides based on T. koningiopsis Th003 and Trichoderma asperellum Th034 at 3 different temperatures.MethodsThe formulation effect was determined by evaluating the germination of unformulated and formulated conidia (dispersible granules and dry powder) stored at 8, 18 and 28 °C for 18 months. Germination kinetics were used to estimate the shelf-life by using different mathematical models (zero order, first order, second order, Higuchi model, Korsmeyer-Peppas model and polynomial model).ResultsThe products showed high stability of the conidia germination when they were stored at 8 and 18° C, with shelf-lives of 14.4 and 13.9 months for dry powder based on Th003, and 12.0 and 10.8 months for dry powder based on Th034, respectively. Prototypes formulated as dispersible granules stored at the same temperatures (8 and 18 °C) showed lower shelf-lives, with values of 11.6 and 10.9 months for the Th003 product, and 10.7 and 7.2 months for the dispersible granules based on Th034. Significant reductions in germination were observed on unformulated conidia at all storage temperatures evaluated.ConclusionsThe formulation type affected the conidia stability of the 2 Trichoderma spp. Colombian isolates. Dry powder was the prototype with the highest stability and shelf-life at all temperatures evaluated.     

Host-Guest Interactions as a Model for the Solvent Influence on the Conformational Populations in [2.2.2.2]Paracyclophane

The interaction of a number of small organic molecules with the two lowest energy minimum conformations of [2.2.2.2]paracyclophane (4°-PCP), 1 and 2, are studied by MMP2(87) force field calculations. Formations of nesting as well as inclusion complexes were identified on the potential energy surface. With CH₂Cl₂ and CHCl₃ used as guests, the nesting complexes are lower in energy than the inclusion ones with both conformations 1 and 2. Furthermore, the nesting complexes with 2 are found to be more stable than the nesting ones with 1. Formation of the double nesting complexes of CH₂Cl₂ and CHCl₃ with 1 and 2 raise the difference in complexation energy in favour of 2. The preference of 4°-PCP for the form 2 in solution is explained based on the above analysis, although 2 is calculated to be 0.2 kcal·mol^–1 higher in steric energy than 1 in the gas phase.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s0089490050218     

生物医药科技前沿领域的识别研究

目的:采用定量分析与定性分析相结合的方法识别生物医药科技前沿领域。方法:本研究从典型国家医学科技战略规划的重点领域分析,生物医药科技前沿动态与专家评述,文献和专利计量学分析三个维度进行识别,综合三个维度的识别结果,将至少满足两个维度的定为生物医药科技前沿领域。结果:共识别出34个生物医药科技前沿领域,包括精准医学、肿瘤免疫、靶向治疗、医学人工智能、医疗机器人等。结论:采用多维度综合识别方法对生物医药科技前沿领域进行分析,可为我国医学科技前沿领域的发展布局提供决策支持,也可为生物医药领域的创新提供方向引导。     

Nitrogen status of conifer needles at the alpine treeline

Background and Aims: High elevation treelines occur worldwide at similar mean growing season temperatures. Does this result from direct impact of low temperature on growth or carbon metabolism, or does nutrient limitation, induced by low soil temperature, play a role? Similar treeline elevations at contrasting soil fertility argue against the latter, but the actual nutritional status of treeline trees (here addressed as foliage nitrogen concentration) has never been assessed systematically. Although needle nitrogen (N) concentration does not necessarily indicate growth limitation by N, the relative abundance of N would indicate obvious depletions at the treeline.

Methods: A central problem with any foliage nutrient assay is that the units for describing the element concentration are dependent on elevation themselves. Here we separate changes in N per unit tissue from changes in reference units.

Results: Needles of Pinus cembra and Picea abies in the Alps do not show elevational differences in N concentration per dry weight, water content, area or volume, thus, there is no N depletion near the elevational tree limit. Hence, nutrient supply is either unaltered, or growth is adjusted so that nutrient depletion in needle tissue does not occur.

Conclusions: Chronic N shortage at needle level is not an explanation for low tree vigour at the treeline.     

Phylogenetic diversity,structure and diversification patterns of endemic plants along the elevational gradient in the Eastern Himalaya

ABSTRACT

Background: Several studies have documented the variation in species diversity patterns along elevational gradients in the Himalaya, but few have reported the evolutionary and biogeographic processes behind these patterns.

Aims: To understand whether evolutionary history and phylogeny have any role in structuring plant species communities along an elevational gradient in the Sikkim Himalaya.

Methods: We used data on endemic plant species occurrence from primary and secondary sources to construct family-level phylogenetic supertrees for different growth forms with the help of Phylomatic tool of Phylocom. These phylogenetic supertrees were used as a base for testing phylogenetic diversity (PD), niche conservatism, diversification time patterns and phylogenetic structure of various plant growth forms along an elevational gradient.

Results: PD was the highest at mid-elevations for all growth forms and PD had a significant positive correlation with endemic species richness. Species at mid-elevations were dominated by the ancestral/primitive taxa. There was phylogenetic clustering at higher elevations and phylogenetic overdispersion at lower and mid-elevations for the majority of the growth forms.

Conclusions: Time-for-speciation effect and niche conservatism along elevation (retention of niche-related ancestral elevational distribution over evolutionary time scale by species) together determine plant species diversity patterns in the Himalaya.     

基于FMEA的C形臂X线机的使用风险分析与控制

??????? 目的 基于失效模式与效应分析（FMEA）方法分析控制C形臂X线机的使用风险。方法 成立FMEA 5人小组,运用现场观察和访谈的方法,识别C形臂X线机使用的潜在失效模式,并对其发生的严重度、发生概率及检测的难易度进行评价打分,计算失效原因的风险优先指数。结果 FMEA小组找出了必须优先解决的C臂机使用的失效模式,制定并实施了改进措施,在不增加管理成本的基础上,取得了良好的管理效果。结论 FMEA可以评估医疗设备使用过程的失效,并能排序优先解决的问题,不增加管理成本就能预防问题的发生,是有效的过程管理工具。     

Differences in the diurnal and nocturnal use of intertidal feeding grounds by Redshank Tringa totanus

Capsule Redshank used more sites and had larger ranges at night than during the day.

Aims To determine whether there were differences in how wintering Redshank used intertidal feeding grounds during the day and night.

Methods The movements of 38 Redshank caught and radiotagged at two neighbouring sites on the Severn Estuary were monitored during four different study periods between January 1997 and October 1999.

Results Individuals used a greater number of sites at night than in the day (on average, two as opposed to one). Kernel home range analyses also indicated that individuals used larger core areas and home ranges at night. In addition, there was a significant difference between the sizes of ranges of birds caught at two neighbouring sites. One foraging site was almost entirely avoided during the day, probably due to disturbance from an adjacent heliport, but was used by the majority of individuals at night when the heliport was unused. This site was rich in invertebrates as a result of the high organic and nutrient input from a sewage outfall pipe. Redshank also used riverine mudflats less during the night, preferring more open mudflats – perhaps to avoid nocturnal predators.

Conclusions Comparison with previous studies suggests that the importance of sites predominantly used at night and the total extent of the areas used by waders may be underestimated by studies that rely on daytime surveys alone. It is important, therefore, that information on nocturnal distributions should be available to inform decisions on site management and protection.     

Mechanism of the aromatic aminotransferase encoded by the Aro8 gene from Saccharomyces cerevisiae

The amino acid l-lysine is synthesized in Saccharomyces cerevisiae via the α-aminoadipate pathway. An as yet unidentified PLP-containing aminotransferase is thought to catalyze the formation of α-aminoadipate from α-ketoadipate in the l-lysine biosynthetic pathway that could be the yeast Aro8 gene product. A screen of several different amino acids and keto-acids showed that the enzyme uses l-tyrosine, l-phenylalanine, α-ketoadipate, and l-α-aminoadipate as substrates. The UV–visible spectrum of the aminotransferase exhibits maxima at 280 and 343 nm at pH 7.5. As the pH is decreased the peak at 343 nm (the unprotonated internal aldimine) disappears and two new peaks at 328 and 400 nm are observed representing the enolimine and ketoenamine tautomers of the protonated aldimine, respectively. Addition, at pH 7.1, of α-ketoadipate to free enzyme leads to disappearance of the absorbance at 343 nm and appearance of peaks at 328 and 424 nm. The V/E_t and V/K_{α-ketoadipate}E_t pH profiles are pH independent from pH 6.5 to 9.6, while the V/K_l-tyrosine pH-rate profile decreases below a single pK_a of 7.0 ± 0.1. Data suggest the active enzyme form is with the internal aldimine unprotonated. We conclude the enzyme should be categorized as a α-aminoadipate aminotransferase.