Generative probabilistic models for protein-protein interaction networks--the biclique perspective

MOTIVATION: Much of the large-scale molecular data from living cells can be represented in terms of networks. Such networks occupy a central position in cellular systems biology. In the protein-protein interaction (PPI) network, nodes represent proteins and edges represent connections between them, based on experimental evidence. As PPI networks are rich and complex, a mathematical model is sought to capture their properties and shed light on PPI evolution. The mathematical literature contains various generative models of random graphs. It is a major, still largely open question, which of these models (if any) can properly reproduce various biologically interesting networks. Here, we consider this problem where the graph at hand is the PPI network of Saccharomyces cerevisiae. We are trying to distinguishing between a model family which performs a process of copying neighbors, represented by the duplication-divergence (DD) model, and models which do not copy neighbors, with the Barabási-Albert (BA) preferential attachment model as a leading example. RESULTS: The observed property of the network is the distribution of maximal bicliques in the graph. This is a novel criterion to distinguish between models in this area. It is particularly appropriate for this purpose, since it reflects the graph's growth pattern under either model. This test clearly favors the DD model. In particular, for the BA model, the vast majority (92.9%) of the bicliques with both sides ≥4 must be already embedded in the model's seed graph, whereas the corresponding figure for the DD model is only 5.1%. Our results, based on the biclique perspective, conclusively show that a na?ve unmodified DD model can capture a key aspect of PPI networks.     

Genome-based bioprospecting of microbes for new therapeutics

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Highlights? Microbial genomes contain multiple clusters for biosynthesis of chemically diverse compounds. ? Most of such genes remain silent, preventing the respective compounds from being discovered. ? Silent gene clusters can be activated and/or heterologously expressed. ? New microbial hosts and tools are needed to make the abovementioned process efficient. ? Synthetic biology will play a major role in the genome-based drug discovery.     

Enslaved bacteria as new hope for plant biotechnologists

The most distinguishing feature of the plant cell is a DNA-containing organelle that sets plants apart from all other organisms: the chloroplast. Compelling evidence supports an endosymbiotic origin for chloroplasts. According to this theory, chloroplasts are descendants of formerly free-living cyanobacterial ancestors which entered an endosymbiotic relationship with a pre-eukaryotic cell and were ultimately integrated into the metabolism of the host cell. Chloroplasts retain many prokaryotic features and their gene expression system still closely resembles that of their eubacterial ancestors. During the past decade, our knowledge about chloroplast biology has benefited immensely from a most remarkable methodological breakthrough: the development of transformation technologies for chloroplast genomes. Moreover, recent advances in the manipulation of higher plant chloroplast genomes have created unprecedented opportunities for the genetic engineering of plants and promise to overcome many of the problems associated with conventional transgenic technologies. This review describes the state of the art in genetic engineering of higher plant chloroplast genomes and highlights the tremendous potential of these technologies for the biotechnology of the future. Received: 27 January 2000 / Received revision: 15 March 2000 / Accepted: 24 March 2000     

Jawing about TNF: new hope for cherubism

Mutations in the SH3-domain binding protein 2 (SH3BP2) are known to cause a rare childhood disorder called cherubism that is characterized by inflammation and bone loss in the jaw, but the mechanism has remained unclear. In this issue, Ueki et al. (Ueki et al., 2007) now demonstrate that a cherubism mutation activates mouse Sh3bp2 resulting in enhanced production of the cytokine TNF-alpha by myeloid cells, leading to both bone loss and inflammation.     

Poxviral immunomodulatory proteins as new therapeutics for immunocorrection

There are numerous viral proteins known to date to modulate protective responses of their hosts. Representatives of the Poxviridae family have the greatest number of genes coding for proteins, inhibiting inflammatory responses, activities of interferons, regulating immune reactions and other protective mechanisms of macroorganisms, among viruses. This review regards poxviral immunomodulatory proteins--namely, complement-binding proteins, inhibitors of serine proteases, chemokine- and TNF-binding proteins --that were shown to be efficient therapeutics in various animal models of inflammatory and autoimmune diseases. The prospects of their usage in clinical practice for treating human inflammatory and autoimmune disorders are discussed.     

Prohibitin: a potential target for new therapeutics

Prohibitin (PHB) is localized to the mitochondria where it might have a role in the maintenance of mitochondrial function and protection against senescence. There is considerable controversy concerning the function of nuclear-localized PHB. PHB has potential roles as a tumor suppressor, an anti-proliferative protein, a regulator of cell-cycle progression and in apoptosis. PHB might also function as a cell-surface receptor for an as-yet unidentified ligand. Cell-associated PHB in the gastrointestinal tract has been implicated in protection against infection and inflammation and the induction of apoptosis in other tissues. The diverse array of functions of PHB, together with the emerging evidence that its function can be modulated specifically in certain tissues, suggest that targeting PHB would be a useful therapeutic approach for the treatment of variety of disease states, including inflammation, obesity and cancer.     

Development of new RNAi therapeutics

RNAi-mediated gene inactivation has become a cornerstone of the present day gene function studies that are the foundation of mechanism and target based drug discovery and development, which could potentially shorten the otherwise long process of drug development. In particular, the coming of age of "RNAi drug" could provide new promising therapeutics bypassing traditional approaches. However, there are technological hurdles need to overcome and the biological limitations need to consider for achieving effective therapeutics. Major hurdles include the intrinsic poor pharmacokinetic property of siRNA and major biological restrictions include off-target effects, interferon response and the interference with endogenous miRNA. Recent innovations in nucleic acid chemistry, formulations and delivery methods have gradually rendered it possible to develop effective RNAi-based therapeutics. Careful design based on the newest RNAi/miRNA biology can also help to minimize the potential tissue toxicity. If successful with systemic application, RNAi drug will no doubt revolutionize the whole drug development process. This review attempts to describe the progress in this area, including applications in preclinical models and recent favorable experience in a number of human trials of local diseases, along with the discussion on the potential limitations of RNAi therapeutics.     

Placenta-derived stem cells: new hope for cell therapy?

An urgent current need in regenerative medicine is that of identifying a plentiful, safe and ethically acceptable stem cell source for the development of therapeutic strategies to restore functionality in damaged or diseased organs and tissues. In this context, human term placenta represents a prime candidate, as it is available in nearly unlimited supply, is ethically problem-free and easily procured. Placental cells display differentiation capacity toward all three germ layers, while also displaying immunomodulatory effects, therefore supporting the possibility that they could be applied in an allogeneic transplantation setting. Although promising data have been reported to date, further study is required to fully characterize the differentiation potential of placenta-derived cells and to identify their possible clinical applications. Here, we provide a snapshot of current knowledge regarding the potential of cells from the amniotic membrane of human term placenta to address current shortcomings in the field of regenerative medicine.     

Gene profiling for defining targets for new therapeutics in autoimmune diseases

The identification of novel targets for improved diagnosis and pharmaceutical intervention is of critical importance for better treatment of autoimmune diseases in the future. The possibility to measure levels of gene expression for tens of thousands of genes simultaneously and in a quantitative fashion will greatly enhance our knowledge of genes and pathways involved in disease pathogenesis. Initial studies have focused on the gene expression profiling of homogeneous cell populations. Genomic-scale gene expression profiling has also more recently been applied to tissue samples from patients with immunopathologies. The scope of the present review is to discuss recent progress in this field with respect to the identification of novel target molecules.     

AIF-mediated caspase-independent necroptosis: a new chance for targeted therapeutics

Cell death has been initially divided into apoptosis, in which the cell plays an active role, and necrosis, which is considered a passive cell death program. Intense research performed in the last decades has concluded that "programmed" cell death (PCD) is a more complex physiological process than initially thought. Indeed, although in most cases the PCD process is achieved via a family of Cys proteases known as caspases, an important number of regulated PCD pathways do not involve this family of proteases. As a consequence, active forms of PCD are initially referred to as caspase-dependent and caspase-independent. More recent data has revealed that there are also active caspase-independent necrotic pathways defined as necroptosis (programmed necrosis). The existence of necroptotic forms of death was corroborated by the discovery of key executioners such as the kinase RIP1 or the mitochondrial protein apoptosis-inducing factor (AIF). AIF is a Janus protein with a redox activity in the mitochondria and a pro-apoptotic function in the nucleus. We have recently described a particular form of AIF-mediated caspase-independent necroptosis that also implicates other molecules such as PARP-1, calpains, Bax, Bcl-2, histone H2AX, and cyclophilin A. From a therapeutic point of view, the unraveling of this new form of PCD poses a question: is it possible to modulate this necroptotic pathway independently of the classical apoptotic paths? Because the answer is yes, a wider understanding of AIF-mediated necroptosis could theoretically pave the way for the development of new drugs that modulate PCD. To this end, we present here an overview of the current knowledge of AIF and AIF-mediated necroptosis. We also summarize the state of the art in some of the most interesting therapeutic strategies that could target AIF or the AIF-mediated necroptotic pathway.     

MicroRNA therapeutics: a new niche for antisense nucleic acids

MicroRNA molecules (miRNAs) are naturally occurring triggers of the RNA-interference pathway. The first identified miRNA, lin-4, was discovered in Caenorhabditis elegans >20 years ago. What began as a curiosity in this model organism has expanded into almost every area of biology; there are now 326 confirmed miRNA genes in humans and the total is predicted to reach 1000. Each miRNA has the potential to regulate hundreds of mRNAs; therefore, there are likely to be few biological pathways not impacted by miRNA regulation. Recent evidence has suggested that miRNAs might be viable therapeutic targets for a wide range of diseases, including cancer. A recent article by Stoffel and colleagues has demonstrated remarkably effective inhibition of miRNAs in vivo, thus providing an entry point into the promising new arena of miRNA therapeutics.