A Parameter for IL-10 and TGF-? Mediated Regulation of HIV-1 Specific T Cell Activation Provides Novel Information and Relates to Progression Markers

HIV replication is only partially controlled by HIV-specific activated effector T cells in chronic HIV infection and strategies are warranted to improve their efficacy. Chronic T cell activation is generally accompanied by regulation of antigen-specific T cell responses which may impair an effective control of chronic infections. The impact of HIV-induced T cell regulation on individual patients’ disease progression is largely unknown, since classical T cell activation assays reflect net activation with regulation as unknown contributing factor. We here explore a quantitative parameter for antigen-induced cytokine-mediated regulation (R_AC) of HIV-specific effector T cell activation by functional antibody-blockade of IL-10 and transforming growth factor-β. HIV Env- and Gag-specific T cell activation and R_AC were estimated in peripheral blood mononuclear cells from 30 treatment-naïve asymptomatic HIV-infected progressors (CD4 count 472/µl, HIV RNA 37500 copies/ml) stimulated with overlapping peptide panels for 6 days. R_AC was estimated from differences in T cell activation between normal and blocked cultures, and related to annual CD4 loss, immune activation (CD38) and microbial translocation (plasma lipopolysaccharides). R_AC was heterogeneously distributed between individual patients and the two HIV antigens. Notably, R_AC did not correlate to corresponding classical activation. Env R_AC correlated with CD38 and CD4 loss rates (r> = 0.37, p = <0.046) whereas classical Gag activation tended to correlate with HIV RNA (r = −0.35, p = 0.06). 14 patients (47%) with low R_AC’s to both Env and Gag had higher CD8 counts (p = 0.014) and trends towards lower annual CD4 loss (p = 0.056) and later start with antiretroviral treatment (p = 0.07) than the others. In contrast, patients with high R_AC to both Env and Gag (n = 8) had higher annual CD4 loss (p = 0.034) and lower CD8 counts (p = 0.014). R_AC to Env and Gag was not predicted by classical activation parameters and may thus provide additional information on HIV-specific immunity. R_AC and other assessments of regulation deserve further in-depth exploration.     

Risk‐sensitive reproductive allocation: fitness consequences of body mass losses in two contrasting environments

For long‐lived organisms, the fitness value of survival is greater than that of current reproduction. Asymmetric fitness rewards suggest that organisms inhabiting unpredictable environments should adopt a risk‐sensitive life history, predicting that it is adaptive to allocate resources to increase their own body reserves at the expense of reproduction. We tested this using data from reindeer populations inhabiting contrasting environments and using winter body mass development as a proxy for the combined effect of winter severity and density dependence. Individuals in good and harsh environments responded similarly: Females who lost large amounts of winter body mass gained more body mass the coming summer compared with females losing less mass during winter. Additionally, females experienced a cost of reproduction: On average, barren females gained more body mass than lactating females. Winter body mass development positively affected both the females' reproductive success and offspring body mass. Finally, we discuss the relevance of our findings with respect to scenarios for future climate change.     

Trehalose lipid biosurfactants produced by the actinomycetes <Emphasis Type="Italic">Tsukamurella spumae</Emphasis> and <Emphasis Type="Italic">T. pseudospumae</Emphasis>

Actinomycetales are known to produce various secondary metabolites including products with surface-active and emulsifying properties known as biosurfactants. In this study, the nonpathogenic actinomycetes Tsukamurella spumae and Tsukamurella pseudospumae are described as producers of extracellular trehalose lipid biosurfactants when grown on sunflower oil or its main component glyceryltrioleate. Crude extracts of the trehalose lipids were purified using silica gel chromatography. The structure of the two trehalose lipid components (TL A and TL B) was elucidated using a combination of matrix-assisted laser desorption/ionization time-of-flight/time-of-flight/tandem mass spectroscopy (MALDI-ToF-ToF/MS/MS) and multidimensional NMR experiments. The biosurfactants were identified as 1-α-glucopyranosyl-1-α-glucopyranosid carrying two acyl chains varying of C4 to C6 and C16 to C18 at the 2′ and 3′ carbon atom of one sugar unit. The trehalose lipids produced demonstrate surface-active behavior and emulsifying capacity. Classified as risk group 1 organisms, T. spumae and T. pseudospumae hold potential for the production of environmentally friendly surfactants.     

Kinetic modeling of rhamnolipid production by Pseudomonas aeruginosa PAO1 including cell density-dependent regulation

The production of rhamnolipid biosurfactants by Pseudomonas aeruginosa is under complex control of a quorum sensing-dependent regulatory network. Due to a lack of understanding of the kinetics applicable to the process and relevant interrelations of variables, current processes for rhamnolipid production are based on heuristic approaches. To systematically establish a knowledge-based process for rhamnolipid production, a deeper understanding of the time-course and coupling of process variables is required. By combining reaction kinetics, stoichiometry, and experimental data, a process model for rhamnolipid production with P. aeruginosa PAO1 on sunflower oil was developed as a system of coupled ordinary differential equations (ODEs). In addition, cell density-based quorum sensing dynamics were included in the model. The model comprises a total of 36 parameters, 14 of which are yield coefficients and 7 of which are substrate affinity and inhibition constants. Of all 36 parameters, 30 were derived from dedicated experimental results, literature, and databases and 6 of them were used as fitting parameters. The model is able to describe data on biomass growth, substrates, and products obtained from a reference batch process and other validation scenarios. The model presented describes the time-course and interrelation of biomass, relevant substrates, and products on a process level while including a kinetic representation of cell density-dependent regulatory mechanisms.     

Involvement of Rad52 in T‐DNA circle formation during Agrobacterium tumefaciens‐mediated transformation of Saccharomyces cerevisiae

Agrobacterium tumefaciens cells carrying a tumour inducing plasmid (Ti‐plasmid) can transfer a defined region of transfer DNA (T‐DNA) to plant cells as well as to yeast. This process of Agrobacterium‐mediated transformation (AMT) eventually results in the incorporation of the T‐DNA in the genomic DNA of the recipient cells. All available evidence indicates that T‐strand transfer closely resembles conjugal DNA transfer as found between Gram‐negative bacteria. However, where conjugal plasmid DNA transfer starts via relaxase‐mediated processing of a single origin of transfer (oriT), the T‐DNA is flanked by two imperfect direct border repeats which are both substrates for the Ti‐plasmid encoded relaxase VirD2. Yeast was used as a model system to investigate the requirements of the recipient cell for the formation of T‐DNA circles after AMT. It was found that, despite the absence of self‐homology on the T‐DNA, the homologous repair proteins Rad52 and Rad51 are involved in T‐DNA circle formation. A model is presented involving the formation of T‐DNA concatemers derived from T‐strands by a process of strand‐transfer catalysed by VirD2. These concatemers are then resolved into T‐DNA circles by homologous recombination in the recipient cell.     

Gender-specific cold responses induce a similar body-cooling rate but different neuroendocrine and immune responses

This study investigated whether there are any gender differences in body-heating strategies during cold stress and whether the immune and neuroendocrine responses to physiological stress differ between men and women. Thirty-two participants (18 men and 14 women) were exposed to acute cold stress by immersion to the manubrium level in 14 °C water. The cold stress continued until rectal temperature (T_RE) reached 35.5 °C or for a maximum of 170 min. The responses to cold stress of various indicators of body temperature, insulation, metabolism, shivering, stress, and endocrine and immune function were compared between men and women. During cold stress, T_RE and muscle and mean skin temperatures decreased in all subjects (P < 0.001). These variables and the T_RE cooling rate did not differ between men and women. The insulative response was greater in women (P < 0.05), whereas metabolic heat production and shivering were greater (P < 0.05) in men. Indicators of cold strain did not differ between men and women, but men exhibited larger changes in the indicators of neuroendocrine (epinephrine level) and in immune (tumor necrosis factor-α level) responses (both P < 0.05). The results of the present study indicated that men exhibited a greater metabolic response and shivering thermogenesis during acute cold stress, whereas women exhibited a greater insulative response. Despite the similar experience of cold strain in men and women, the neuroendocrine and immune responses were larger in men. Contrary to our expectations, the cooling rate was similar in men and women.     

Generation,analysis and functional annotation of expressed sequence tags from the sheepshead minnow (Cyprinodon variegatus)

Background

Genomic islands (GIs) are clusters of alien genes in some bacterial genomes, but not be seen in the genomes of other strains within the same genus. The detection of GIs is extremely important to the medical and environmental communities. Despite the discovery of the GI associated features, accurate detection of GIs is still far from satisfactory.

Results

In this paper, we combined multiple GI-associated features, and applied and compared various machine learning approaches to evaluate the classification accuracy of GIs datasets on three genera: Salmonella, Staphylococcus, Streptococcus, and their mixed dataset of all three genera. The experimental results have shown that, in general, the decision tree approach outperformed better than other machine learning methods according to five performance evaluation metrics. Using J48 decision trees as base classifiers, we further applied four ensemble algorithms, including adaBoost, bagging, multiboost and random forest, on the same datasets. We found that, overall, these ensemble classifiers could improve classification accuracy.

Conclusions

We conclude that decision trees based ensemble algorithms could accurately classify GIs and non-GIs, and recommend the use of these methods for the future GI data analysis. The software package for detecting GIs can be accessed at http://www.esu.edu/cpsc/che_lab/software/GIDetector/.

     

Differential protein profiling of primary versus immortalized human RPE cells identifies expression patterns associated with cytoskeletal remodeling and cell survival

Functional research of retinal pigment epithelium (RPE) most often relies on utilization of RPE-derived cell lines in vitro. However, no studies about similarities and differences of the respective cell lines exist so far. Thus, we here analyze the proteome of the most popular RPE cell lines: ARPE-19 and hTERT and compare their constitutive and de novo synthesized protein expression profiles to human early passage retinal pigment epithelial cells (epRPE) by 2-D electrophoresis and MALDI-TOF peptide mass fingerprinting. In all three cell lines the baseline protein expression pattern corresponded well to the de novo synthesized cellular proteome. However, comparison of the protein profile of epRPE cells with that of hTERT-RPE cells revealed a higher abundance of proteins related to cell migration, adhesion, and extracellular matrix formation, paralleled by a down-regulation of proteins attributed to cell polarization, and showed an altered expression of detoxification enzymes in hTERT-RPE. ARPE-19 cells, however, exhibited a higher abundance of components of the microtubule cytoskeleton and differences in expression of proteins related to proliferation and cell death. epRPE cells, hTERT-RPE, and ARPE-19 therefore may respond differently with respect to certain functional properties, a finding that should prove valuable for future in vitro studies.