Monitoring of gene expression by functional proteomics: response of human lung fibroblast cells to stimulation by endothelin-1.

Proteomic methods have been used to monitor changes in protein synthesis in the first 4 h following stimulation of human lung fibroblasts with endothelin-1. Using pulsed [(35)S]methionine labeling, about 70 proteins with altered protein synthesis could be detected, and the 35 proteins showing the largest changes were identified by mass spectrometry. The observed proteins included unexpected proteins such as Sox5, two isoforms of Rab14, Rab3A, translationally controlled tumor protein, and one protein of previously unknown function. There was a wide range of different kinetic behavior, and groups of functionally linked proteins such as Rab14, nucleophosmin,and cyclin-dependent kinase inhibitor 1B could be detected from similar kinetics. We propose that the functional proteomic methods are competitive with and have some advantages compared to expression profiling methods for monitoring gene expression.     

Non-Canonical Wnt Predominates in Activated Rat Hepatic Stellate Cells,Influencing HSC Survival and Paracrine Stimulation of Kupffer Cells

The Wnt system is highly complex and is comprised of canonical and non-canonical pathways leading to the activation of gene expression. Our aim was to examine changes in the expression of Wnt ligands and regulators during hepatic stellate cell (HSC) transdifferentiation and assess the relative contributions of the canonical and non-canonical Wnt pathways in fibrogenic activated HSC. The expression profile of Wnt ligands and regulators in HSC was not supportive for a major role for β-catenin-dependent canonical Wnt signalling, this verified by inability to induce Topflash reporter activity in HSC even when expressing a constitutive active β-catenin. We detected expression of Wnt5a in activated HSC which can signal via non-canonical mechanisms and showed evidence for non-canonical signalling in these cells involving phosphorylation of Dvl2 and pJNK. Stimulation of HSC or Kupffer cells with Wnt5a regulated HSC apoptosis and expression of TGF-β1 and MCP1 respectively. We were unable to confirm a role for β-catenin-dependent canonical Wnt in HSC and instead propose autocrine and paracrine functions for Wnts expressed by activated HSC via non-canonical pathways. The data warrant detailed investigation of Wnt5a in liver fibrosis.     

Endotoxin tolerance represents a distinctive state of alternative polarization (M2) in human mononuclear cells

Classical (M1) and alternative (M2) polarization of mononuclear cells (MNCs) such as monocyte and macrophages is known to occur in response to challenges within a microenvironment, like the encounter of a pathogen. LPS, also known as endotoxin, is a potent inducer of inflammation and M1 polarization. LPS can also generate an effect in MNCs known as endotoxin tolerance, defined as the reduced capacity of a cell to respond to LPS activation after an initial exposure to this stimulus. Using systems biology approaches in PBMCs, monocytes, and monocyte-derived macrophages involving microarrays and advanced bioinformatic analysis, we determined that gene responses during endotoxin tolerance were similar to those found during M2 polarization, featuring gene and protein expression critical for the development of key M2 MNC functions, including reduced production of proinflammatory mediators, expression of genes involved in phagocytosis, as well as tissue remodeling. Moreover, expression of different metallothionein gene isoforms, known for their role in the control of oxidative stress and in immunomodulation, were also found to be consistently upregulated during endotoxin tolerance. These results demonstrate that after an initial inflammatory stimulus, human MNCs undergo an M2 polarization probably to control hyperinflammation and heal the affected tissue.     

Social experiments in the mesoscale: humans playing a spatial prisoner's dilemma

Background

The evolutionary origin of cooperation among unrelated individuals remains a key unsolved issue across several disciplines. Prominent among the several mechanisms proposed to explain how cooperation can emerge is the existence of a population structure that determines the interactions among individuals. Many models have explored analytically and by simulation the effects of such a structure, particularly in the framework of the Prisoner''s Dilemma, but the results of these models largely depend on details such as the type of spatial structure or the evolutionary dynamics. Therefore, experimental work suitably designed to address this question is needed to probe these issues.

Methods and Findings

We have designed an experiment to test the emergence of cooperation when humans play Prisoner''s Dilemma on a network whose size is comparable to that of simulations. We find that the cooperation level declines to an asymptotic state with low but nonzero cooperation. Regarding players'' behavior, we observe that the population is heterogeneous, consisting of a high percentage of defectors, a smaller one of cooperators, and a large group that shares features of the conditional cooperators of public goods games. We propose an agent-based model based on the coexistence of these different strategies that is in good agreement with all the experimental observations.

Conclusions

In our large experimental setup, cooperation was not promoted by the existence of a lattice beyond a residual level (around 20%) typical of public goods experiments. Our findings also indicate that both heterogeneity and a “moody” conditional cooperation strategy, in which the probability of cooperating also depends on the player''s previous action, are required to understand the outcome of the experiment. These results could impact the way game theory on graphs is used to model human interactions in structured groups.     

Revision of Mecinus heydenii species complex (Curculionidae): integrative taxonomy reveals multiple species exhibiting host specialization

A combined taxonomic, morphological, molecular and biological study revealed that the species presently named Mecinus heydenii is actually composed of five different species: M. heydenii Wencker, 1866; M. raphaelis Baviera & Caldara sp. n., M. laeviceps Tournier, 1873; M. peterharrisi To?evski & Caldara sp. n. and M. bulgaricus Angelov, 1971. These species can be distinguished from each other by a few subtle characteristics, mainly in the shape of the rostrum and body of the penis, and the colour of the integument. The first four species live on different species of Linaria plants, respectively, L. vulgaris (L.) P. Mill., L. purpurea (L.) P. Mill. L. genistifolia (L.) P. Mill. and L. dalmatica (L.) P. Mill., whereas the host plant of M. bulgaricus is still unknown. An analysis of mtCOII gene sequence data revealed high genetic divergence among these species, with uncorrected pairwise distances of 9% between M. heydenii and M. raphaelis, 11.5% between M. laeviceps, M. heydenii and M. raphaelis, while M. laeviceps and M. peterharrisi are approximately 6.3% divergent from each other. Mecinus bulgaricus exhibits even greater divergence from all these species and is more closely related to M. dorsalis Aubé, 1850. Sampled populations of M. laeviceps form three geographical subspecies: M. laeviceps laeviceps, M. laeviceps meridionalis To?evski & Jovi? and M. laeviceps corifoliae To?evski & Jovi?. These subspecies show clear genetic clustering with uncorrected mtDNA COII divergences of approximately 1.4% from each other.     

Monitoring the presence of genetically modified food on the market of the Republic of Croatia

From the beginning of the human race people have been applying different methods to change the genetic material of either plants or animals in order to increase their yield as well as to improve the quality and quantity of food. Genetically modified organism (GMO) means an organism in which the genetic material has been altered in a way that does not occur naturally by mating and/or natural recombination. Analysing the presence of GMO in food is done by detecting the presence of either specific DNA sequences inserted in the genome of transgenic organism, or detecting proteins as a result of the expression of the inserted DNA. In this work food testing for the presence of genetically modified organisms was conducted during the period from 2004 to 2007 in the GMO laboratory of the Croatian National Institute of Public Health. According to the regulations, among the samples in which the presence of GMO was detected, all those which had more than 0.9% of GMO content were either rejected from the border or removed from the market, because such GM food has to be appropriately labelled. Among the food samples which were analysed in 2004: 127 (2.37%) of a total of 1226 samples contained more than 0.9% of GMOs; in 2005 there was only one in 512 (0.20%) samples in total; in 2006 there were 4 out of 404 samples (0.99%), and in 2007: 7 of a total of 655 samples (1.07%) had GMO content above the allowed threshold of 0.9%.     

Molecular Characterization of a Novel Bacteriocin and an Unusually Large Aggregation Factor of <Emphasis Type="Italic">Lactobacillus paracasei</Emphasis> subsp. <Emphasis Type="Italic">paracasei</Emphasis> BGSJ2-8, a Natural Isolate from Homemade Cheese

Screening the collection of natural isolates from semi-hard homemade cheese resulted in isolation and characterization of strain Lactobacillus paracasei subsp. paracasei BGSJ2-8. The strain BGSJ2-8 harbors several important phenotypes, such as bacteriocin production, aggregation phenomenon, and production of proteinase. Bacteriocin SJ was purified by three-step chromatography. Mass spectrometry established molecular mass of the active peptide at 5372 Da. The auto-aggregation phenotype of wild-type (WT) strain was mediated by secreted aggregation-promoting factor (protein of molecular mass > 200 kDa), probably acting in cooperation with other cell surface protein(s). Comparative study of WT and its spontaneous nonaggregating derivative revealed that aggregation factor was responsible for the observed differences in the bacteriocin and proteinase activities. Bacteriocin SJ activity and resistance to different stresses were higher in the presence of aggregating factor. In contrast, proteinase activity was stronger in the nonaggregating derivative.