Lipid packing determines protein-membrane interactions: Challenges for apolipoprotein A-I and high density lipoproteins

Protein and protein-lipid interactions, with and within specific areas in the cell membrane, are critical in order to modulate the cell signaling events required to maintain cell functions and viability. Biological bilayers are complex, dynamic platforms, and thus in vivo observations usually need to be preceded by studies on model systems that simplify and discriminate the different factors involved in lipid-protein interactions. Fluorescence microscopy studies using giant unilamellar vesicles (GUVs) as membrane model systems provide a unique methodology to quantify protein binding, interaction, and lipid solubilization in artificial bilayers. The large size of lipid domains obtainable on GUVs, together with fluorescence microscopy techniques, provides the possibility to localize and quantify molecular interactions. Fluorescence Correlation Spectroscopy (FCS) can be performed using the GUV model to extract information on mobility and concentration. Two-photon Laurdan Generalized Polarization (GP) reports on local changes in membrane water content (related to membrane fluidity) due to protein binding or lipid removal from a given lipid domain. In this review, we summarize the experimental microscopy methods used to study the interaction of human apolipoprotein A-I (apoA-I) in lipid-free and lipid-bound conformations with bilayers and natural membranes. Results described here help us to understand cholesterol homeostasis and offer a methodological design suited to different biological systems.     

Patterns of genetic diversity in colonizing plant species: Nassauvia lagascae var. lanata (Asteraceae: Mutisieae) on Volcan Lonquimay, Chile

The effect of colonization on the distribution of genetic diversity within and among populations in relation to species characteristics remains an open empirical question. The objective of this study was to contrast genetic diversity within and among established and colonizing populations of Nassauvia lagascae var. lanata on Volcán Lonquimay (Araucanía Region, Chile), which erupted on 25 December 1988, and relate genetic diversity to biological characteristics of the populations. We analyzed a total of 240 individuals from 15 populations distributed along the Andes Cordillera using AFLP and obtained a total of 307 AFLP bands, of which 97.7% are polymorphic. Values of population differentiation (F(ST)) did not differ significantly among established and colonizing populations, but colonizing populations did have reduced levels of genetic divergence (as indicated by private and rare bands) and genetic variation (e.g., Shannon index). We conclude that a founder effect through limited numbers of founding propagules derived from nearby source populations has not yet been compensated for by subsequent population growth and migration. Low rates of secondary dispersal via running water, kin-structure within populations, and slow population growth seem to contribute to the slow recovery of genetic diversity.     

Enrichment of ultraconserved elements among genomic imbalances causing mental delay and congenital anomalies

Background

In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required.

Results

We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms.

Conclusions

The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data.     

Recovery of Populus tremuloides seedlings following severe drought causing total leaf mortality and extreme stem embolism

In contrast with other native Populus species in North America, Populus tremuloides (aspen) can successfully establish itself in drought‐prone areas, yet no comprehensive analysis has been performed on the ability of seedlings to withstand and recover from a severe drought resulting in complete leaf mortality. Here, we subjected 4‐month‐old aspen seedlings grown in two contrasting soil media to a progressive drought until total leaf mortality, followed by a rewatering cycle. Stomatal conductance (g_s), photosynthesis and transpiration followed a sigmoid decline with declining fraction of extractable soil water values. Cessation of leaf expansion occurred close to the end of the linear‐decrease phase, when g_s was reduced by 95%. Leaf mortality started after g_s reached the lowest values, which corresponded to a stem–xylem pressure potential (Ψ_xp) of ?2.0 MPa and a percent loss of stem hydraulic conductivity (PLC) of 50%. In plants with 50% leaf mortality, PLC values remained around 50%. Complete leaf mortality occurred at an average stem PLC of 90%, but all seedlings were able to resprout after 6–10 days of being rewatered. Plants decapitated at soil level before rewatering developed root suckers, while those left with a 4‐cm stump or with their stems intact resprouted exclusively from axillary buds. Resprouting was accompanied by recovery of stem hydraulic conductivity, with PLC values around 30%. The percentage of resprouted buds was negatively correlated with the stem %PLC. Thus, the recovery of stem hydraulic conductivity appears as an important factor in the resprouting capacity of aspen seedlings following a severe drought.     

Paraquat-induced oxidative stress response during amphibian early embryonic development

In addition to the endogenous production of reactive oxygen species (ROS) as a result of normal development, amphibian external development often forces embryos to deal with oxidative stress-producing agents present in the environment. Embryos should therefore develop protective systems to reduce ROS toxicity and achieve successful development. The present work was aimed to characterize the effects produced by the widespread-used ROS-generator pesticide Paraquat during early embryonic development in the toad Chaunus arenarum, as well as to get insights into the defense response elicited by amphibian embryos. The approach consisted in generating a sharp and brief oxidative stress condition early during embryonic development to stimulate the cellular mechanisms involved in ROS-antioxidant response. Results revealed that Paraquat-treatment reduced the ability of embryos to develop normally, leading to arrests of development and severe malformations such as tail abnormalities, abdominal edema, reduced head development and curved dorsal structures. Although Paraquat effects were morphologically evident from gastrula stage on, alterations such as chromatin condensation were observed even at blastula stage by histological examinations. Regarding detoxifying enzymes, a significant induction of Mn-superoxide dismutase activity was detected at stages beyond gastrula in embryos surviving Paraquat treatment, suggesting a major role of this enzyme in the antioxidant response during early embryonic development.     

Purification and identification of antibacterial phenolics from Tripodanthus acutifolius leaves

Aims: To perform an activity‐guided purification, identification and quantification of antibacterial compounds from Tripodanthus acutifolius infusion. To validate the antibacterial activity of purified substances. Methods and Results: Bioautographic methods were employed as screening assays for purifying bioactive substances. Purification procedures included sephadex LH‐20 column chromatography and reverse phase HPLC. Identification was achieved by spectroscopic methods (UV‐Vis, MS, NMR and polarimetry) and chromatographic assays (paper chromatography and HPLC). Antibacterial activity was studied by microdilution, colony count and photometric assays, Sytox green stain and transmission electron microscopy (TEM). Four glycoflavonoids (rutin, nicotiflorin, hyperoside and isoquercitrin) and an unusual phenylbutanoid glycoside (tripodantoside) were purified and identified. Tripodantoside was found at 6·59 ± 0·82 g per 100 g of dry leaves. The flavonoids showed bactericidal effect at a concentration of 4 mg ml^?1 against Staphylococcus aureus and Pseudomonas aeruginosa strains from American Type Culture Collection, while tripodantoside was almost four times more active than those compounds, with a minimum bactericidal concentration = 1·024 mg ml^?1 against these strains. Tripodantoside aglycone showed bacteriolytic effects on the assayed strains, causing evident damages on cell wall and membrane, while tripodantoside did not exhibit those effects. Conclusions: The antibacterial activity of T. acutifolius infusion would be partially attributed to the purified glycoflavonoids and mainly to tripodantoside. Significance and Impact: The high extraction yield and the antibacterial activity exhibited by tripodantoside makes this chemical structure of interest to support further studies dealing with chemical modifications to increase the antibacterial activity or to seek another activities.     

Photoreactivation and dark repair in UV-treated microorganisms: effect of temperature

Because of the lack of readily available information about the influence of temperature on microorganism reactivation processes subsequent to inactivation with UV radiation, a series of batch reactivation studies were performed at 5, 10, 15, 20, 25, and 30 degrees C. A special effort was made to model the reactivation process to enable the effect of the temperature variable to be quantified. Because an earlier-proposed kinetic model (K. Kashimada, N. Kamiko, K. Yamamoto, and S. Ohgaki, Water Sci. Technol. 33:261-269, 1996), a first-order saturation type, does not adequately fit the data obtained in experiments of reactivation in conditions of light and darkness, a modification of that model is proposed. The new model, which actually coincides with the classical logistic equation, incorporates two kinetic parameters: the maximum survival ratio (Sm) and the second-order reactivation rate constant (k2). In order to interpret correctly the reactivation occurring in conditions of darkness, a new term for the decay is added to the logistic equation. The new model accurately fits the data obtained in reactivation experiments, permitting the interpretation of the kinetic parameters Sm, k2, and M (for only repair in darkness), where M is mortality, a zero-order decay rate constant, and their relationship with various environmental conditions, such as microbial type, light, and temperature. The parameters Sm and k2 (and M for reactivation in conditions of darkness) show exponential dependence on the reactivating temperature, and it is possible to predict their values and hence the reactivation curve from the equations proposed in this work.     

Trans platinum complexes design: one novel water soluble oxime derivative that contains aliphatic amines in trans configuration

In an attempt to design new antitumoral drugs based on transplatin complexes, we determined the experimental conditions for the preparation of trans-[Pt((CH(3))(2)CNOH)((CH(3))(2)CHNH(2))Cl(2)], and solved the crystal structure. The cytotoxicity of the novel complex, the cis counterpart, cisplatin, and a trans complex with aliphatic amines, as well as the capacity of some of these complexes to cause either apoptotic or necrotic cell death, was comparatively examined in NRK-52E rat renal tubular cells and HepG2 human hepatoma cells. The results indicate that the oxime complex with trans geometry, but not the one with cis geometry, causes death by apoptosis, making the complex potentially suitable for therapeutic purposes. However cytotoxicity values are higher in the case of cis geometry than in trans geometry in both tumoral and non-tumoral cell lines.     

Ultracentrifugation of serum samples allows detection of hepatitis C virus RNA in patients with occult hepatitis C

Occult hepatitis C virus (HCV) infection of patients with abnormal liver function tests of unknown origin who are anti-HCV and serum HCV RNA negative but who have HCV RNA in the liver has been described. As HCV replicates in the liver cells of these patients, it could be that the amount of circulating viral particles is under the detection limit of the most sensitive techniques. To prove this hypothesis, serum samples from 106 patients with occult HCV infection were analyzed. Two milliliters of serum was ultracentrifuged over a 10% sucrose cushion for 17 h at 100,000 x g(av), where av means average, and HCV RNA detection was performed by strand-specific real-time PCR. Out of the 106 patients, 62 (58.5%) had detectable serum HCV RNA levels after ultracentrifugation, with a median load of 70.5 copies/ml (range, 18 to 192). Iodixanol density gradient studies revealed that HCV RNA was positive at densities of 1.03 to 1.04 and from 1.08 to 1.19 g/ml, which were very similar to those found in the sera of patients with classical chronic HCV infection. Antigenomic HCV RNA was found in the livers of 56 of 62 (90.3%) patients with detectable serum HCV RNA levels after ultracentrifugation, compared to 27 of 44 (61.4%) negative patients (P < 0.001). No differences in the median loads of antigenomic HCV RNA between patients with an those without serum HCV RNA (4.5 x 10(4) [range, 7.9 x 10(2) to 1.0 x 10(6)] versus 2.3 x 10(4) [range, 4.0 x 10(2) to 2.2 x 10(5)]) were found. Alanine aminotransferase and gamma-glutamyl transpeptidase levels, liver necroinflammatory activity, and fibrosis did not differ between both groups. In conclusion, HCV RNA can be detected in the sera of patients with occult HCV infection after circulating viral particles are concentrated by ultracentrifugation.     

Conserved changes in envelope function during human immunodeficiency virus type 1 coreceptor switching

We studied the evolution of human immunodeficiency virus type 1 (HIV-1) envelope function during the process of coreceptor switching from CCR5 to CXCR4. Site-directed mutagenesis was used to introduce most of the possible intermediate mutations in the envelope for four distinct coreceptor switch mutants, each with a unique pattern of CCR5 and CXCR4 utilization that extended from highly efficient use of both coreceptors to sole use of CXCR4. Mutated envelopes with some preservation of entry function on either CCR5- or CXCR4-expressing target cells were further characterized for their sensitivity to CCR5 or CXCR4 inhibitors, soluble CD4, and the neutralizing antibodies b12-IgG and 4E10. A subset of mutated envelopes was also studied in direct CD4 or CCR5 binding assays and in envelope-mediated fusion reactions. Coreceptor switch intermediates displayed increased sensitivity to CCR5 inhibitors (except for a few envelopes with mutations in V2 or C2) that correlated with a loss in CCR5 binding. As use of CXCR4 improved, infection mediated by the mutated envelopes became more resistant to soluble CD4 inhibition and direct binding to CD4 increased. These changes were accompanied by increasing resistance to the CXCR4 inhibitor AMD3100. Sensitivity to neutralizing antibody was more variable, although infection of CXCR4-expressing targets was generally more sensitive to neutralization by both b12-IgG and 4E10 than infection of CCR5-expressing target cells. These changes in envelope function were uniform in all four series of envelope mutations and thus were independent of the final use of CCR5 and CXCR4. Decreased CCR5 and increased CD4 binding appear to be common features of coreceptor switch intermediates.