Effective energy function for proteins in lipid membranes

A simple extension of the EEF1 energy function to heterogeneous membrane-aqueous media is proposed. The extension consists of (a) development of solvation parameters for a nonpolar phase using experimental data for the transfer of amino acid side-chains from water to cyclohexane, (b) introduction of a heterogeneous membrane-aqueous system by making the reference solvation free energy of each atom dependent on the vertical coordinate, (c) a modification of the distance-dependent dielectric model to account for reduced screening of electrostatic interactions in the membrane, and (d) an adjustment of the EEF1 aqueous model in light of recent calculations of the potential of mean force between amino acid side-chains in water. The electrostatic model is adjusted to match experimental observations for polyalanine, polyleucine, and the glycophorin A dimer. The resulting energy function (IMM1) reproduces the preference of Trp and Tyr for the membrane interface, gives reasonable energies of insertion into or adsorption onto a membrane, and allows stable 1-ns MD simulations of the glycophorin A dimer. We find that the lowest-energy orientation of melittin in bilayers varies, depending on the thickness of the hydrocarbon layer.     

Partitioning evapotranspiration fluxes from a Colorado grassland using stable isotopes: Seasonal variations and ecosystem implications of elevated atmospheric CO2

The stable isotopic composition of soil water is controlled by precipitation inputs, antecedent conditions, and evaporative losses. Because transpiration does not fractionate soil water isotopes, the relative proportions of evaporation and transpiration can be estimated using a simple isotopic mass balance approach. At our site in the shortgrass steppe in semi-arid northeastern Colorado, ¹⁸O values of soil water were almost always more enriched than those of precipitation inputs, owing to evaporative losses. The proportion of water lost by evaporation (E/ET) during the growing season ranged from nil to about 40% (to >90% in the dormant season), and was related to the timing of precipitation inputs. The sum of transpiration plus evaporation losses estimated by isotopic mass balance were similar to actual evapotranspiration measured from a nearby Bowen ratio system. We also investigated the evapotranspiration response of this mixed C₃/C₄ grassland to doubled atmospheric [CO₂] using Open-Top Chambers (OTC). Elevated atmospheric [CO₂] led to increased soil-water conservation via reduced stomatal conductance, despite greater biomass growth. We used a non-invasive method to measure the ¹⁸O of soil CO₂ as a proxy for soil water, after establishing a strong relationship between ¹⁸O of soil CO₂ from non-chambered control (NC) plots and ¹⁸O of soil–water from an adjacent area of native grassland. Soil–CO₂ ¹⁸O values showed significant treatment effects, particularly during a dry summer: values in ambient chambers (AC) were more enriched than in NC and elevated chamber (EC) plots. During the dry growing season of 2000, transpiration from the EC treatment was higher than from AC and lower than from NC treatments, but during 2001, transpiration was similar on all three treatments. Slightly higher evaporation rates from AC than either EC or NC treatments in 2000 may have resulted from increased convection across the soil surface from the OTC blowers, combined with lower biomass and litter cover on the AC treatment. Transpiration-use efficiency, or the amount of above-ground biomass produced per mm water transpired, was always greatest on EC and lowest on NC treatments.     

Expression and production of bioactive human interleukin-18 in transgenic tobacco plants

The cDNA of human interleukin-18 (hIL-18) was successfully inserted into the genome of tobacco plant, Nicotiana tabacum cv. NC-89, using Agrobacterium tumefaciens-mediated transformation. Insertion and translation of hIL-18 in transformants were confirmed by PCR, ELISA, and Western blot, respectively. The transformed extracts contained the recombinant hIL-18 protein up to 0.05% of total soluble protein. Activity of the recombinant hIL-18 in plant cells was confirmed by the induction of IFN- on IL-18-responsive J6-1 cells by the extracts obtained from the transformants. The expression level of hIL-18 (351 ng g^–1 tobacco tissue) obtained in the present study may be sufficient to induce responses/effects in vivo.     

OsSEND-1: a new RAD2 nuclease family member in higher plants

A novel endonuclease, a new member of the RAD2 nuclease family, has been identified from the higher plant, rice (Oryza sativa L. cv. Nipponbare), and designated as OsSEND-1. The open reading frame of the OsSEND-1 cDNA encoded a predicted product of 641 amino acid residues with a molecular weight of 69.9 kDa. The encoded protein showed a relatively high degree of sequence homology with the RAD2 nuclease family proteins, especially RAD2 nuclease, but it differed markedly from FEN-1, XPG or HEX1/EXO1. The N- and I-domains in the family were highly conserved in the OsSEND-1 sequence. The protein was much smaller than XPG, but larger than HEX1/EXO1 and FEN-1. The genome sequence was composed of 14 exons, and was localized at the almost terminal region of the short arm of chromosome 8. Northern blotting and in situ hybridization analyses demonstrated preferential expression of OsSEND-1 mRNA in proliferating tissues such as meristem. The mRNA level of OsSEND-1 was induced by UV and DNA-damaging agent such as MMS or H₂O₂, indicating that OsSEND-1 has some roles in the repair of many types of damaged DNA. The recombinant peptide showed endonuclease activity.     

Identification of metastasis-associated proteins by proteomic analysis and functional exploration of interleukin-18 in metastasis

Very little is currently known about mechanisms underlying cancer metastasis. In the present study, metastasis-associated proteomes were separated and identified by comparative proteomic analysis, and the metastasis-related function of candidate protein interleukin-18 (IL-18) was further elucidated. First, a pair of highly and poorly metastatic sublines (termed PLA801D and PLA801C, respectively), originating from the same parental PLA801 cell line, was identified by spontaneous tumorigenicity and metastasis in vivo and characterized by metastatic phenotypes analysis in vitro. Subsequently, a proteomic approach was used to compare the protein expression profiles between PLA801C and PLA801D sublines. Eleven proteins were identified and further verified by one-dimensional Western blotting, Northern blot and/or semiquantitative reverse transciptase polymerase chain reaction analysis. Compared with those in poorly metastatic PLA801C subline, cytokeratin 18, tissue transglutaminase, Rho GDP-dissociation inhibitor 1, tropomyosin, fibroblast type, IL-18 and annexin I were significantly up-regulated, while protein disulfide isomerase, heat shock protein 60, peroxiredoxin 1, chlorine intracellular channel protein 1 (CLI1) and creatine kinase, B chain were significantly down-regulated in the highly metastatic PLA801D subline. Intriguingly, all the identified candidate proteins except for CLI1 have been shown to be somehow associated with distinct aspects of tumor metastasis such as cell growth, motility, invasion, adhesion, apoptosis and tumor immunity, etc. Considering that IL-18 was present in highly metastatic PLA801D but absent in poorly metastatic PLA801C, the association of IL-18 with metastasis was further elucidated by introducing IL-18 sense/IL-18 antisense into PLA801C/PLA801D sublines simultaneously. The results demonstrated that ectopically expressed IL-18 promoted cell motility in vitro and down-regulated E-cadherin expression of PLA801C transfectants, while IL-18 antisense remarkably decreased cell invasion potency in vitro and notably increased E-cadherin expression of PLA801D transfectants, indicating that IL-18 might play a role in metastasis by inhibiting E-cadherin expression.     

Recombinant expression of Munc18c in a baculovirus system and interaction with syntaxin4

Two protein families that are critical for vesicle transport are the Syntaxin and Munc18/Sec1 families of proteins. These two molecules form a high affinity complex and play an essential role in vesicle docking and fusion. Munc18c was expressed as an N-terminally His-tagged fusion protein from recombinant baculovirus in Sf9 insect cells. His-tagged Munc18c was purified to homogeneity using both cobalt-chelating affinity chromatography and gel filtration chromatography. With this simple two-step protocol, 3.5 mg of purified Munc18c was obtained from a 1L culture. Further, the N-terminal His-tag could be removed by thrombin cleavage while the tagged protein was bound to metal affinity resin. Recombinant Munc18c produced in this way is functional, in that it forms a stable complex with the SNARE interacting partner, syntaxin4. Thus we have developed a method for producing and purifying large amounts of functional Munc18c--both tagged and detagged--from a baculovirus expression system. We have also developed a method to purify the Munc18c:syntaxin4 complex. These methods will be employed for future functional and structural studies.     

A Simple Method for Preparation of 18α-Glycyrrhetinic Acid and Its Derivatives

Treatment of 18-glycyrrhizic acid with a methanolic solution of HCl resulted in 1 : 1 mixture of methyl esters of 18- and 18-glycyrrhetinic acids. Benzoylation of the mixture led to methyl esters of 3-benzoyl-18-glycyrrhetinic acid and 3-benzoyl-18-glycyrrhetinic acid, which were separated by chromatography on silica gel. 18-Glycyrrhetinic acid was prepared by alkaline hydrolysis of methyl 3-benzoyl-18-glycyrrhetinate and was further used for the syntheses of 3-keto-18-glycyrrhetinic acid and methyl esters of 18-glycyrrhetinic acid and 3-keto-18-glycyrrhetinic acid.     

Regional variations in intestinal brush border membrane fluidity and function during diabetes and the role of oxidative stress and non-enzymatic glycation

The physical state (fluidity) of lipids modulates the activities of several membrane bound enzymes and transport proteins. Alteration of brush border membrane (BBM) fluidity is one of the several changes exhibited by the small intestine during diabetes. In the present study, an investigation of the diabetes induced regional changes in fluidity, oxidative damage, non-enzymatic glycation as well as the activities and the kinetic parameters of the enzymes alkaline phosphatase and -glutamyl transpeptidase was carried out on the intestinal BBM. At the end of 6 weeks of diabetes, significant increases in the extent of both oxidative damage and non-enzymatic glycation were observed along the length of the intestine along with a simultaneous decrease in membrane fluidity. A significant correlation between the decrease in BBM fluidity and increase in non-enzymatic glycation was observed in the duodenum and jejunum. Additionally regional variations in the activities and kinetic parameters of both the enzymes were observed.     

Evaluation of triterpenols and sterols as organic matter biomarkers in a mangrove ecosystem in northern Brazil

Mangrove leaves, sediment, and excrementfrom the mangrove crab Ucidescordatus from the coastal areas of theBragança peninsula in North Brazil wereanalysed to determine suitable biomarkersfor mangrove-derived organic matter. Leavesof Rhizophora mangle (red mangrove),the dominant species in the area, werecharacterised by high amounts of-amyrin, germanicol, taraxerol, andlupeol. Avicennia germinans (blackmangrove) mainly contained betulin, lupeol,and -sitosterol, whereas significantquantities of -sitosterol and lupeolwere typical of Laguncularia racemosa(white mangrove), the locally leastabundant species. Except for betulin, theexcrement of U. cordatus containedall of the above substances, but moststrongly reflected the triterpenolsignature of R. mangle leaves, thepredominant diet of this crab. Surfacesediments from various mangrove locationshad relatively uniform compositions thatpossibly reflect tidal mixing. Sedimentextracts were dominated by taraxerol andcontained smaller amounts of-amyrin, germanicol, and lupeol.Only sediments in a marsh area, dominatedby Sporobolus virginicus (seashoredropseed) and Eleocharis sp. (spikerush), revealed a differentbiomarker distribution. Core samples ofsubrecent sediment (up to 4000 ¹⁴C yrBP), for which previous pollen analysisindicated vegetation dominated bymangroves, had compositions similar to thatof the surface sediment. Taraxerol was themain component in the examined mangrovesediments and may be a marker for mangrovematter in this region, although analysis ofplant material did not unequivocallysupport this. Germanicol is suggested to bea biomarker for organic matter from R.mangle in North Brazil. It was detected inolder sediments, and was not significantlyaffected by ingestion by land crabs.     

Patterns of ribosomal gene variation in elite commercial chicken pure line populations

The nucleolus organizer region (NOR) encodes the tandemly repeated 18S, 5.8S and 28S ribosomal (r) RNA genes. The NORs of broiler and layer commercial chicken pure lines were studied to establish the type and extent of genetic variation at this important locus. The parameters studied were gene copy number, repeat size, and diversity of NOR-types. The populations were organized into three groups for analysis including brown-egg broiler (13 lines), brown-egg layer (six lines), and white-egg layer (eight lines). The ribosomal gene copy number average of the white-egg layer populations was significantly lower (329 genes) than that of the brown-egg layers (372 genes); the brown-egg broiler ribosomal gene average was intermediate (350 genes). The white-egg layer populations exhibited a ribosomal repeat unit average size of 36 kb, significantly different from the brown-egg layer and brown-egg broiler average repeat unit size of 32.5 and 33.9 kb, respectively. NOR array size was similar among the three groups (6 mb). The brown-egg broiler populations exhibited polymorphic NOR patterns, intra- and interline, whereas the white-egg layer populations were essentially monomorphic for NOR-type; brown-egg layers exhibited an intermediate level of NOR diversity. Some NOR array characteristics may be a function of breed origin as brown-egg commercial populations, both broilers and layers, have similar breed origins and exhibited similarities for predominant repeat unit size as compared with white-egg layer populations. However, the finding that brown-egg broiler lines typically exhibit a greater number of segregating NOR-types than brown-egg layer lines suggests that the selection schemes of broiler vs. layer pure line populations may also have influenced the degree of variation at this gene complex.