Molecular characterization of common fragile sites as a strategy to discover cancer susceptibility genes

The cytogenetic hypothesis that common fragile sites (cFSs) are hotspots of cancer breakpoints is increasingly supported by recent data from whole-genome profiles of different cancers. cFSs are components of the normal chromosome structure that are particularly prone to breakage under conditions of replication stress. In recent years, cFSs have become of increasing interest in cancer research, as they not only appear to be frequent targets of genomic alterations in progressive tumors, but also already in precancerous lesions. Despite growing evidence of their importance in disease development, most cFSs have not been investigated at the molecular level and most cFS genes have not been identified. In this review, we summarize the current data on molecularly characterized cFSs, their genetic and epigenetic characteristics, and put emphasis on less-studied cFS genes as potential contributors to cancer development.     

CAS directly interacts with vinculin to control mechanosensing and focal adhesion dynamics

Focal adhesions are cellular structures through which both mechanical forces and regulatory signals are transmitted. Two focal adhesion-associated proteins, Crk-associated substrate (CAS) and vinculin, were both independently shown to be crucial for the ability of cells to transmit mechanical forces and to regulate cytoskeletal tension. Here, we identify a novel, direct binding interaction between CAS and vinculin. This interaction is mediated by the CAS SRC homology 3 domain and a proline-rich sequence in the hinge region of vinculin. We show that CAS localization in focal adhesions is partially dependent on vinculin, and that CAS–vinculin coupling is required for stretch-induced activation of CAS at the Y410 phosphorylation site. Moreover, CAS–vinculin binding significantly affects the dynamics of CAS and vinculin within focal adhesions as well as the size of focal adhesions. Finally, disruption of CAS binding to vinculin reduces cell stiffness and traction force generation. Taken together, these findings strongly implicate a crucial role of CAS–vinculin interaction in mechanosensing and focal adhesion dynamics.     

Modelling and knowledge transfer in complexity science

I analyse the construction and transfer of models in complexity science. Thereby, I introduce a distinction between (i) vertical model construction, which is based on knowledge about a specific target system, (ii) horizontal model construction, which is based on the alteration of an existing model and therefore does not require any references to a specific target system; and (iii) the transfer of models, which consists of the assignment of an existing model to a new target system. I argue that, in complexity science, all three of those modelling activities take place. Furthermore, I show that these activities can be divided into two general categories: (i) the creation of a repository of models without specific target systems, which have been created by large-scale horizontal construction; and (ii) the transfer of these models to particular target systems in the natural sciences, which can also be followed by an extension of the transferred model through vertical construction of adaptions and additions to its dynamics. I then argue that this interplay of different modelling activities in complexity science provides a mechanism for the transfer of knowledge between different scientific fields. It is also crucial to the interdisciplinary nature of complexity science.     

A newly-discovered Cd-hyperaccumulator Solanum nigrum L.

Phytoremediation emerged in early the 1980s is animportant technology for remedying contaminated sites.One of the most promising phytoremediation technologiesis phytoextraction using hyperaccumulators to removeheavy metals from contaminated soils. The ter…     

A stomatin-domain protein essential for touch sensation in the mouse

Touch and mechanical pain are first detected at our largest sensory surface, the skin. The cell bodies of sensory neurons that detect such stimuli are located in the dorsal root ganglia, and subtypes of these neurons are specialized to detect specific modalities of mechanical stimuli. Molecules have been identified that are necessary for mechanosensation in invertebrates but so far not in mammals. In Caenorhabditis elegans, mec-2 is one of several genes identified in a screen for touch insensitivity and encodes an integral membrane protein with a stomatin homology domain. Here we show that about 35% of skin mechanoreceptors do not respond to mechanical stimuli in mice with a mutation in stomatin-like protein 3 (SLP3, also called Stoml3), a mammalian mec-2 homologue that is expressed in sensory neurons. In addition, mechanosensitive ion channels found in many sensory neurons do not function without SLP3. Tactile-driven behaviours are also impaired in SLP3 mutant mice, including touch-evoked pain caused by neuropathic injury. SLP3 is therefore indispensable for the function of a subset of cutaneous mechanoreceptors, and our data support the idea that this protein is an essential subunit of a mammalian mechanotransducer.     

Common nonsynonymous variants in PCSK1 confer risk of obesity

Mutations in PCSK1 cause monogenic obesity. To assess the contribution of PCSK1 to polygenic obesity risk, we genotyped tag SNPs in a total of 13,659 individuals of European ancestry from eight independent case-control or family-based cohorts. The nonsynonymous variants rs6232, encoding N221D, and rs6234-rs6235, encoding the Q665E-S690T pair, were consistently associated with obesity in adults and children (P = 7.27 x 10(-8) and P = 2.31 x 10(-12), respectively). Functional analysis showed a significant impairment of the N221D-mutant PC1/3 protein catalytic activity.     

Integrating mechanistic explanations through epistemic perspectives

Talk of levels is ubiquitous in philosophy, especially in the context of mechanistic explanations spanning multiple levels. The mechanistic conception of levels, however, does not allow for the kind of integration needed to construct such multi-level mechanistic explanations integrating observations from different scientific domains. To address the issues arising in this context, I build on a certain perspectival aspect inherent in the mechanistic view. Rather than focusing on compositionally related levels of mechanisms, I suggest analyzing the situation in terms of epistemic perspectives researchers take when making scientific observations. Characterizing epistemic perspectives along five dimensions allows for a systematic analysis of the relations the scientific observations made from these different epistemic perspectives. This, in turn, provides a solid foundation for integrating the mechanistic explanations that are based on the scientific observations in question.     

HIV-1 adaptation to NK-cell-mediated immune pressure

Natural killer (NK) cells have an important role in the control of viral infections, recognizing virally infected cells through a variety of activating and inhibitory receptors. Epidemiological and functional studies have recently suggested that NK cells can also contribute to the control of HIV-1 infection through recognition of virally infected cells by both activating and inhibitory killer immunoglobulin-like receptors (KIRs). However, it remains unknown whether NK cells can directly mediate antiviral immune pressure in vivo in humans. Here we describe KIR-associated amino-acid polymorphisms in the HIV-1 sequence of chronically infected individuals, on a population level. We show that these KIR-associated HIV-1 sequence polymorphisms can enhance the binding of inhibitory KIRs to HIV-1-infected CD4(+) T cells, and reduce the antiviral activity of KIR-positive NK cells. These data demonstrate that KIR-positive NK cells can place immunological pressure on HIV-1, and that the virus can evade such NK-cell-mediated immune pressure by selecting for sequence polymorphisms, as was previously described for virus-specific T cells and neutralizing antibodies. NK cells might therefore have a previously underappreciated role in contributing to viral evolution.     

Intestinal epithelial barrier and mucosal immunity

Both innate immunity and mucosal surfaces provide the first line of defence against mucosal infections. Innate immunity is a universal and evolutionarily conserved form of host defence that senses microbial organisms. Recent advances in the field of immunology are due mainly to the discovery of the role of Toll-like receptors (TLRs), which recognize conserved microbial molecules. TLR stimulation induces specific patterns of gene expression that lead to the shaping of innate and adaptive immunity. Since mucosal tissues are colonized by innocuous microflora and challenged by infectious pathogens, activation of TLRs in epithelial and lamina propria cells must be tightly controlled to avoid inappropriate signalling that might lead to mucosal inflammation. This review aims to highlight novel insight on the molecules, pathways and gene expression networks associated with microbial recognition by TLRs and mucosal immunity.