Determination of molecular associations of some hydrophobic and hydrophilic bile acids by infrared and Raman spectroscopy

The aim of this study was to analyse the Raman and infrared spectra of eight common mammalian bile acids in order to identify intermolecular interactions between hydroxyl and carbonyl groups. The results are considered in the light of the new hydrophilic/hydrophobic classification of bile acids. The alcohol OH group of the hydrophobic bile acids forms different intermolecular bonds. The most hydrophobic bile acid, lithocholic acid forms polymers, and this may explain its very low water solubility. The hydrophilic bile acids have some of their alcohol OH groups free of any intermolecular interaction. The strongly hydrophilic murideoxycholic acid also forms dimers, again consistent with a very low water solubility. The proposed structural arrangements are in agreement with published crystallographic studies. Received: 7 November 1996 / Accepted: 8 December 1996     

Effect of the support matrix on biotransformation of benzaldehyde to benzyl alcohol by yeast cells in aqueous and aqueous-organic two phase systems

Summary Biotransformation of benzaldehyde to benzyl alcohol bySaccharomyces cerevisiae immobilized in different support matrices was investigated. Polymers with intrinsic hydrophobic and/or hydrophilic nature as well as mixed hydrophobic and hydrophilic supports were examined both in aqueous and bisphasic aqueous-organic systems. The hydrophobic support material ENTP-2000 or mixed silicone:alginate (50-2550-75) proved to be most suitable not only for nonconventional media but also for conventional aqueous media for production of benzyl alcohol. With ENTP-2000, catalytic activity and maximum yield were 159 mol h^–1 g^–1 dry weight catalyst and 0.89 mM, respectively, in hexane containing 2% moisture. Corresponding values in aqueous media were 246 mol h^–1 g^–1 dry weight catalyst and 1.53 mM. With 5050 silicone:alginate, catalytic activity and maximum yield were 177 mol h^–1 g^–1 dry weight catalyst and 1.18 mM, respectively, in hexane containing 2% moisture. Corresponding values in aqueous media were 192 mol h^–1 g^–1 dry weight catalyst and 0.8 mM.     

Amino acid network and its scoring application in protein-protein docking

Protein-protein complex, composed of hydrophobic and hydrophilic residues, can be divided into hydrophobic and hydrophilic amino acid network structures respectively. In this paper, we are interested in analyzing these two different types of networks and find that these networks are of small-world properties. Due to the characteristic complementarity of the complex interfaces, protein-protein docking can be viewed as a particular network rewiring. These networks of correct docked complex conformations have much more increase of the degree values and decay of the clustering coefficients than those of the incorrect ones. Therefore, two scoring terms based on the network parameters are proposed, in which the geometric complementarity, hydrophobic-hydrophobic and polar-polar interactions are taken into account. Compared with a two-term energy function, a simple scoring function HPNet which includes the two network-based scoring terms shows advantages in two aspects, not relying on energy considerations and better discrimination. Furthermore, combing the network-based scoring terms with some other energy terms, a new multi-term scoring function HPNet-combine can also make some improvements to the scoring function of RosettaDock.     

Nucleotide-amino acid interactions and their relation to the genetic code

Summary The apparent dissociation constants of the complexes of AMP with the methyl esters of amino acids in aqueous solution exhibit good correlations with features of the genetic code and with the frequencies of occurrence of amino acid residues in proteins. Thus it is likely that chemically selective nucleotide-amino acid interactions were involved in the processes of chemical evolution that have led to the emergence of the genetic code. Based on these correlations a storage device for the information regarding nucleotide-amino acid interactions is proposed. It involves processes of simultaneous polymerization to polynucleotides and polypeptides.     

Freezing tolerance of ectomycorrhizal fungi in pure culture

The ability to survive freezing and thawing is a key factor for the existence of life forms in large parts of the world. However, little is known about the freezing tolerance of mycorrhizal fungi and their role in the freezing tolerance of mycorrhizas. Threshold temperatures for the survival of these fungi have not been assessed experimentally. We grew isolates of Suillus luteus, Suillus variegatus, Laccaria laccata, and Hebeloma sp. in liquid culture at room temperature. Subsequently, we exposed samples to a series of temperatures between +5°C and −48°C. Relative electrolyte leakage (REL) and re-growth measurements were used to assess the damage. The REL test indicated that the lethal temperature for 50% of samples (LT₅₀) was between −8.3°C and −13.5°C. However, in the re-growth experiment, all isolates resumed growth after exposure to −8°C and higher temperatures. As many as 64% of L. laccata samples but only 11% in S. variegatus survived −48°C. There was no growth of Hebeloma and S. luteus after exposure to −48°C, but part of their samples survived −30°C. The fungi tolerated lower temperatures than was expected on the basis of earlier studies on fine roots of ectomycorrhizal trees. The most likely freezing tolerance mechanism here is tolerance to apoplastic freezing and the concomitant intracellular dehydration with consequent concentrating of cryoprotectant substances in cells. Studying the properties of fungi in isolation promotes the understanding of the role of the different partners of the mycorrhizal symbiosis in the freezing tolerance.     

Reversible electrical breakdown of lipid bilayers: formation and evolution of pores

The mechanism of reversible electric breakdown of lipid membranes is studied. The following stages of the process of pore development are substantiated. Hydrophobic pores are formed in the lipid bilayer by spontaneous fluctuations. If these water-filled defects extend to a radius of 0.3 to 0.5 nm, a hydrophilic pore is formed by reorientation of the lipid molecules. This process is favoured by a potential difference across the membrane. The conductivity of the pores depends on membrane voltage, and the type of this dependence changes with the radius of the pore. Hydrophilic pores of an effective radius of 0.6 up to more than 1 nm are formed, which account for the membrane conductivity increase observed. The characteristic times of changes in average radius and number of pores during the voltage pulse and after it are investigated.     

Improving the antibacterial activity and selectivity of an ultra short peptide by hydrophobic and hydrophilic amino acid stretches

The principle of amino acid stretches tagged at the C terminal of Luecrocin I, which is an ultra-short antibacterial peptide, by tryptophan and arginine or lysine has been reported. The choice of amino acid type at each stretch position depends on the hydrophobic and hydrophilic regions visualized in the helical wheel pattern of Luecrocin I. Oligopeptide tagging should also consider the properties such as positive charge, hydrophobicity, the content of hydrophobic amino acids, polar angle, the properly hydrophilic and hydrophobic facets. Amidation at C terminal and lysine substitute for arginine can increase selectivity between mammalian cells (hemolytic and MTT assay) and bacterial cells tested. KT2 and RT2 which have 53% hydrophobic residues, 7 positive charges, 160° polar angle, ?0.02 (KT2) and ?0.04 (RT2) hydrophobicity were effective against S. typhi DMST 22842, S. epidermidis ATCC 12228, E. coli ATCC 25922 and V. cholerae non-O1, non-O139. The SEM images implied that the antibacterial mechanism of RT2 and KT2 may depend on concentration rather than time. Finally, RT2 and KT2 can be new antibacterial agents or may be further developed for alternative antibiotics.     

Production, isolation and characterization of [Leu4]- and [Ile4]surfactins from Bacillus subtilis

Summary Bacillus subtilis coproduces several surfactin variants that are powerful biosurfactants and have potential applications in biology and industry. A single amino acid substitution in the heptapeptide moiety of surfactins strongly modifies their properties. To better establish structure-activity relationships and to search new variants with enhanced properties, Bacillus subtilis was grown into two modified culture media. Two new variants were isolated by chromatographic methods and studied by NMR spectroscopy. As planned, modifications consisted in the substitution of the l-valine residue at the fourth position by a more hydrophobic residue, i.e., leucine or isoleucine. These [Leu⁴]- and [Ile⁴]surfactins have a higher affinity for hydrophobic solvents and a twice improved surfactant power. Structure-property correlations were confirmed by analysis of the hydrophobic residue distribution in the three-dimensional model of the structure of surfactin in solution.Abbreviations DMSO dimethylsulfoxide - 1D, 2D, 3D one-, two-, three-dimensional - TLC thin layer chromatography - CMC critical micellar concentration - NMR nuclear magnetic resonance     

Tilt angle of a trans-membrane helix is determined by hydrophobic mismatch

In order to investigate the compensation mechanism of a trans-membrane helix in response to hydrophobic mismatch, the tilt and rotation angles of the trans-membrane helix of Vpu aligned in lipid bilayers of various thickness were determined using orientation-dependent frequencies obtained from solid-state NMR experiments of aligned samples. A tilt angle of 18 degrees was observed in 18:1-O-PC/DOPG (9:1) lipid bilayers, which have a hydrophobic thickness that approximately matches the hydrophobic length of the trans-membrane helix of Vpu. Upon decreasing the hydrophobic thickness of lipid bilayers, no significant change in rotation angle was observed. However, the tilt angle increased systematically with increasing positive mismatch to 27 degrees in 14:0-O-PC/DMPG (9:1), 35 degrees in 12:0-O-PC/DLPG (9:1), and 51 degrees in 10:0 PC/10:0 PG (9:1) lipid bilayers, indicating that the change in tilt angle of the trans-membrane helix is a principal compensation mechanism for hydrophobic mismatch. In addition, the distinctive kink in the middle of the helix observed in 18:1 bilayers disappears in thinner bilayers. Although the opposite of what might be expected, this finding suggests that a helix kink may also be a part of the hydrophobic matching mechanism for trans-membrane helices.     

Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields

Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.     

How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation

Nuclear magnetic resonance (NMR) spin relaxation experiments currently probe molecular motions on timescales from picoseconds to nanoseconds. The detailed interpretation of these motions in atomic detail benefits from complementarity with the results from molecular dynamics (MD) simulations. In this mini-review, we describe the recent developments in experimental techniques to study the backbone dynamics from ¹⁵N relaxation and side-chain dynamics from ¹³C relaxation, discuss the different analysis approaches from model-free to dynamics detectors, and highlight the many ways that NMR relaxation experiments and MD simulations can be used together to improve the interpretation and gain insights into protein dynamics.     

Is there nascent structure in the intrinsically disordered region of troponin I?

In striated muscle, the binding of calcium to troponin C (TnC) results in the removal of the C‐terminal region of the inhibitory protein troponin I (TnI) from actin. While structural studies of the muscle system have been successful in determining the overall organization of most of the components involved in force generation at the atomic level, the structure and dynamics of the C‐terminal region of TnI remains controversial. This domain of TnI is highly flexible, and it has been proposed that this intrinsically disordered region (IDR) regulates contraction via a “fly‐casting” mechanism. Different structures have been presented for this region using different methodologies: a single α‐helix, a “mobile domain” containing a small β‐sheet, an unstructured region, and a two helix segment. To investigate whether this IDR has in fact any nascent structure, we have constructed a skeletal TnC‐TnI chimera that contains the N‐domain of TnC (1–90), a short linker (GGAGG), and the C‐terminal region of TnI (97–182) and have acquired ¹⁵N NMR relaxation data for this chimera. We compare the experimental relaxation parameters with those calculated from molecular dynamic simulations using four models based upon the structural studies. Our experimental results suggest that the C‐terminal region of TnI does not contain any defined secondary structure, supporting the “fly‐casting” mechanism. We interpret the presence of a “plateau” in the ¹⁵N NMR relaxation data as being an intrinsic property of IDRs. We also identified a more rigid adjacent region of TnI that has implications for muscle performance under ischemic conditions. Proteins 2011. © 2011 Wiley‐Liss, Inc.     

Seasonal dynamic of plant phenophases in Beijing—A case study in Beijing Botanical Garden北大核心CSCD

Aims Seasonality is the typical characteristic of plant landscape in Beijing, including seasonal dynamics of plant phenology. We analyzed the seasonal changes in phenology of 120 deciduous trees in Beijing Botanical Garden, with additional efforts on an innovative methodology in studying plant phenology. Methods Based on the standards of the Chinese Phenological Observation Method, three-level Phenological Code (a, b, and c) was used to recode the phenology data. Our data analysis was performed with “pentad” (5-day period) in 24 Solar Terms. Analytical methods include a frequency distribution method to explore the division of phenophases and their dynamic constitution. The frequency distribution statistics in SPSS 20.0 were applied to explore the temporal dynamics in occurrence time and duration for different types of phenophases. Important findings We found that: The division of phenological seasons and their phenological constitution as: 6th–19th pentad for Spring, with 54.03% of the whole phenophases that are featured with sprouting, leaf spreading and flowering; 20th–45th pentad for Summer, with 12.95% of phenophases that include conclusions of leaf spreading for all trees, intensive fruiting, fewer flowering, and autumn-leaf scenery in late summer; 46th–59th pentad for Autumn, with 27.19% of the phenophases that are characterized with leaf discoloration and defoliation, some fruiting, and very few flowering; and 60th pentad for Winter, with 0.6% of phenophases that are all constituted with defoliation. The temporal distribution pattern of different kinds of phenophases is as follows. The leaf-unfolding phenophases span from 3rd to 23rd pentad and averagely last for 3.27 pentads, with Sorbaria kirilowii as one of the earliest leaf-unfolding species. The leaf coloration phenophases happen between 40th –63rd pentad, with Tilia mongolica and Armeniaca sibirica as the earliest species to show fall-color leaf. The autumn-leaf duration lasts for 8.2 pentads in average, with Euonymus alatus and Sambucus williamsii as the typical species that show longer leaf duration. The leaf period averagely lasts for 44.2 pentads, with Abelia chinensis, Salix matsudana and Kerria japonica holding the longest leaf time. The flowering-type phenophases happen during 1st–53rd pentad, with 8th–23rd pentad as the best ornamental period, and three species (Chimonanthus praecox, Jasminum nudiflorum and Ulmus pumila) as the earliest blooming species and Elsholtzia stauntoni as the last one to bloom. The flowering period lasts for 6.7 pentads in average, with Sorbaria kirilowii, Hibiscus syriacus and Lagerstroemia indica showing the longest flowering time. The fruiting-type phenophases happen between 8th–59th pentad, with Ulmus pumila and Lonicera fragrantissima as the earliest species for fruit maturation. The fruiting duration averagely lasts for 29.0 pentads, and those species that do not lose fruits during the winter and some other species with longer fruit holding period though falling fruits completely in winter such as Viburnum melanocarpum and Physocarpus opulifolius ‘Luteus’ have longer ornamental time of fruit scenery. Compared with a counterpart research in the 1980s, this study reveals that spring in 2017 came earlier by a pentad than that 30 years ago while autumn came later by 3 pentads; additionally, autumn duration shortened by 2 pentads while summer duration prolonged by 4 pentads, resulting in larger differences between the duration of the four seasons. © Chinese Journal of Plant Ecology.     

渤海浮游动物群落生态特点Ⅲ.部分浮游动物数量分布和季节变动

用1959年全国海洋普查中网浮游动物标本,分析渤海水母类,枝角类,糠虾,毛虾和幼虫类的数量分布和季节变化,结果表明,水母类以近岸低盐种为主,主要出现在莱州湾,渤海湾和辽东湾近岸水域,冬季出现的种类较少,优势种为八斑芮氏水母;夏季种类较多,优势种为半球杯水母和嵊山多胃水母等,鸟喙尖头蚤为近岸高温低盐种,主要出现在莱州湾,数量在6月份达到最大值,箭虫是海主要肉食性种类之一,其数量高峰期出现在9月份,长住囊虫的季节变化呈双峰型变化,第1次数量高峰出现在5月份,第2次数量高峰出现在8月份。该种大部分时间主要分布在莱州湾,渤海湾和辽东湾近岸水域,渤海出现的糠虾有长额刺糠虾和漂浮囊糠虾,其中长额否则糠虾受温度的影响较小,在春,夏秋,各有一个数量高峰;漂浮囊糠虾在秋末数量明显增加,这两种糠虾主要分布在渤海湾和辽东湾近岸水域。／三叶针尾涟虫属于低温种类,主要出现在秋季和冬季,细长脚绒属夏季高温种,在6,7月份数量较高,该种的分布受盐度影响比较大,主要出现在受黄海海流影响的谪盐水域,数量较大的幼虫有桡足类的六肢幼体,多毛类海稚虫科的幼体,以壳类幼体和腹足类幼体,其中桡足类六肢幼体和海稚虫科的幼体在5月份出现较多,腹足类幼体在6．7月份数量较高,双壳类幼体在8月份数量较高。     

北京小龙门森林生态系统定位站土壤螨类的垂直分布和季节变动

通过对小龙门森林生态系统定位站栎树林中所设立的5个土壤动物采样点,进行每月1次的土壤取样调查(从1993年4月到1994年1月),,对各土层中螨类的垂直分布和季节变动进行调查分析、结果显示土壤螨类无论是个体数量还是相对丰度,都具有明显的表聚性特点,85％的土壤螨类皆出现于枯枝落叶层和0～5cm的土层。土壤螨类的季节变动调查显示,在枯枝落叶层,土壤螨类有显著的季节变动,且高峰值出现在1993年10月,在10～15cm的土层中,土壤螨类也有相对显著的季节变动,但它的高峰值出现在1994年1月,而在0～5cm和5～10cm的2个土层中,土壤螨类的数量在各个月份之间没有显著的差异。     

Chemical and optical changes in freshwater dissolved organic matter exposed to solar radiation

We studied the chemical and optical changes inthe dissolved organic matter (DOM) from twofreshwater lakes and a Sphagnum bog afterexposure to solar radiation. Stable carbonisotopes and solid-state ¹³C-NMR spectraof DOM were used together with optical andchemical data to interpret results fromexperimental exposures of DOM to sunlight andfrom seasonal observations of two lakes innortheastern Pennsylvania. Solar photochemicaloxidation of humic-rich bog DOM to smaller LMWcompounds and to DIC was inferred from lossesof UV absorbance, optical indices of molecularweight and changes in DOM chemistry. Experimentally, we observed a 1.2 enrichment in ¹³$C and a 47% loss in aromaticC functionality in bog DOM samples exposed tosolar UVR. Similar results were observed inthe surface waters of both lakes. In latesummer hypolimnetic water in humic LakeLacawac, we observed 3 to 4.5enrichments in ¹³C and a 30% increase inaromatic C relative to early spring valuesduring spring mixing. These changes coincidedwith increases in molecular weight and UVabsorbance. Anaerobic conditions of thehypolimnion in Lake Lacawac suggest thatmicrobial metabolism may be turning overallochthonous C introduced during springmixing, as well as autochthonous C. Thismetabolic activity produces HMW DOM during thesummer, which is photochemically labile andisotopically distinct from allochthonous DOM orautochthonous DOM. These results suggest bothphotooxidation of allochthonous DOM in theepilimnion and autotrophic production of DOM bybacteria in the hypolimnion cause seasonaltrends in the UV absorbance of lakes.