In this study, a mechanistically motivated kinetic extension of the Local Effect Model was pro- posed. Based on a dynamical simulation of DSB induction by ion radiation and a bi-phasic repair of iDSB and cDSB, consistent time-dose-L E T effects are obtained. Furthermore, the kinetic LEM has been shown to provide an accurate description of experimental data. Thus, it should be ex- pected that the LEM can be used for predictions of the cellularresponse to ion radiation with an arbitrary schedule and to simultaneously gain insight into potentially underlying cellular me- chanisms. In the discussion it was explained that referring to the LEM, it might be advantageous to account for time effects in heavy ion radiotherapy when treatment sessions are prolonged. Furthermore, with regard to radiation protection, the LEM suggests that for endpoints that are closely related to cell survival probabilities, a reduction of radiation effects should not be ex- pected in the limit of low doses and dose-rates. For an extrapolation from high-dose and dose rate to low-dose and dose-rate, a variety of factors have to be accounted for when the accuracy of predictions is the aim. Finally, in connection with the kinetic GLOBLE model, the LEM con- stitutes a universal tool for the assessment of radiation effects caused by photons and ions with varying L E T and with protracted or fractionated dose delivery schedule.
Abstract: Astronauts are exposed to considerable doses of space radiation during long-term space missions. As complete shielding of the highly energetic particles is impracticable, the cellularresponse to space-relevant radiation qualities has to be understood in order to develop countermeasures and to reduce radiation risk uncertainties. The transcription factor Nuclear Factor κB (NF-κB) plays a fundamental role in the immune response and in the pathogenesis of many diseases. We have previously shown that heavy ions with a linear energy transfer (LET) of 100–300 keV/µm have a nine times higher potential to activate NF-κB compared to low-LET X-rays. Here, chemical inhibitor studies using human embryonic kidney cells (HEK) showed that the DNA damage sensor Ataxia telangiectasia mutated (ATM) and the proteasome were essential for NF-κB activation in response to X-rays and heavy ions. NF-κB’s role in cellular radiation response was determined by stable knock-down of the NF-κB subunit RelA. Transfection of a RelA short-hairpin RNA plasmid resulted in higher sensitivity towards X-rays, but not towards heavy ions. Reverse Transcriptase real-time quantitative PCR (RT-qPCR) showed that after exposure to X-rays and heavy ions, NF-κB predominantly upregulates genes involved in intercellular communication processes. This process is strictly NF-κB dependent as the response is completely absent in RelA knock-down cells. NF-κB’s role in the cellular radiation response depends on the radiation quality.
For improvement of cancer therapy, studies with several cancer cells and with various heavy ions, especially carbon ions, had been performed. In a microarray analysis of oral SqCC cells, 84 genes were identified that were modulated by carbon and neon ion (LET ~75 keV/μm) irradiation at all doses (1, 4, and 7 Gy) ( 165 ). Among these genes, three genes (TGFBR2, SMURF2, and BMP7) were found to be involved in the transforming growth factor β signaling pathway and two genes (CCND1 and E2F3) in the cell-cycle G1/S checkpoint regulation pathway. The relevance of these results for normal tissues cells or non-cancer cell lines has to be determined. In normal skin tissue, low doses (0.01 and 1 Gy) of IR resulted in transient alterations in the expression of genes involved in DNA and tissue remodeling, cell-cycle transition, and inflammation (TNF, interleukins) ( 166 ), suggesting an involvement of the NF-κB pathway, the main inflammatory pathway, in the cellularresponse to IR. As exposure to accelerated argon ions (95 MeV/n Ar, LET 271 keV/μm) resulted in strong activation of NF-κB in human cells ( 167 ), the RBE for NF-κB activation by heavy ions of differ- ent LET was determined ( 158 ). NF-κB-dependent gene induction after exposure to heavy ions was detected in stably transfected human 293 reporter cells. For comparison, cells were exposed to 150 kV X-rays. The maximal biologic effect ranged between 70 and 300 keV/μm. Argon ions (271 keV/μm) had the maximal potency (RBE ~9) to activate NF-κB-dependent gene expression in HEK cells. The effect of carbon ions was less pronounced and comparable the activation observed after X-ray exposure ( 168 ). Inhibition of ATM resulted in complete abolishment of NF-κB activation by X-rays and heavy ions. Therefore, NF-κB activation in response to heavy ions is ATM dependent and seems to be mediated by a nuclear signal from the damaged DNA as described for the genotoxin-induced NF-κB subpathway.
can be due to receptor’s lower activation as shown from the phosphorylation of IRb.
Here we presented a method for constructing extended pathways that start at the receptor level and via a complex intracellular signalling pathway identify those mechanisms that drive cellularresponse. Because of the nature of response data - where detailed mechan- isms are sparse and not easily searchable via text mining approaches- we used a data-driven approach to link intracellular activity to cellular responses via non-cano- nical edges. Those edges, together with well-defined intracellular pathways, were used for the construction of the “generic map” which is finally optimised to match high-throughput protein data. The resulting extended pathways revealed intracellular mechanisms that are responsible for the release of 22 cytokines and correlate well with a large body of literature that pinpoint at STATs and NFB as major drivers of inflammatory sti- muli. More importantly, comparison between cell types shows significant differences that lead to survival advan- tages of the HCC cells. Our results constitute a proof- of-principle for construction of “extended pathways” that are capable of linking pathway activity to diverse
can be due to receptor ’s lower activation as shown from the phosphorylation of IRb.
Here we presented a method for constructing extended pathways that start at the receptor level and via a complex intracellular signalling pathway identify those mechanisms that drive cellularresponse. Because of the nature of response data - where detailed mechan- isms are sparse and not easily searchable via text mining approaches- we used a data-driven approach to link intracellular activity to cellular responses via non-cano- nical edges. Those edges, together with well-defined intracellular pathways, were used for the construction of the “generic map” which is finally optimised to match high-throughput protein data. The resulting extended pathways revealed intracellular mechanisms that are responsible for the release of 22 cytokines and correlate well with a large body of literature that pinpoint at STATs and NF B as major drivers of inflammatory sti- muli. More importantly, comparison between cell types shows significant differences that lead to survival advan- tages of the HCC cells. Our results constitute a proof-
Cells were exposed to heavy ions in a broad range of LET (0.3 - 9674 keV/µm) at the heavy ion accelerators GSI, Darmstadt, Germany, GANIL, Caen, France or HIMAC, Japan. X-rays were used as reference radiation. Survival was determined by the colony forming ability test. The relative biological effectiveness (RBE) of reduction of cellular survival was calculated for each radiation quality. Cell cycle progression was quantified by flow cytometry of propidium-iodide stained cells. Mineralization of extracellular matrix was determined by Alizarin Red Staining (ARS). DNA double strand breaks and their repair were visualized by H2AX staining. Gene expression was analysed by reverse transcriptase quantitative real time PCR (RT-qPCR). Activation of Nuclear Factor B (NF-B) was determined by means of a NF-B reporter cell line (HEK-pNF-B-d2EGFP/Neo L2). The role of NF-B in the cellularresponse to space-relevant radiation qualities was investigated by stable transfection with a short hairpin RNA plasmid targeting p65 for NF-B knockdown.
acute effects and late radiation risks for the astronaut and thereby enabling long-term human space flight, the cellular radiation response to densely ionizing radiation needs to be better understood. The biological effectiveness of accelerated heavy ions (which constitute the biologically most important radiation type in space) with high linear energy transfer (LET) for effecting DNA damage response pathways as a gateway to cell death or survival is of major concern not only for space missions but also for new regimes of tumor radiotherapy.
Staphylococcal alpha-toxin is an archetypal killer protein that homo-oligomerizes in target cells to create small transmembrane pores. The membrane-perforating beta-barrel motif is a conserved attack element of cytolysins of Gram-positive and Gram-negative bacteria. Following the recognition that nucleated cells can survive membrane permeabilization, a profile of abundant transcripts was obtained in transiently perforated keratinocytes. Several immediate early genes were found to be upregulated, reminiscent of the cellularresponse to growth factors. Cell cycle analyses revealed doubling of S + G2/M phase cells 26 h post toxin treatment. Determination of cell counts uncovered that after an initial drop, numbers increased to exceed the controls after 2 days. A non-lytic alpha-toxin mutant remained without effect. The alpha-toxin pore is too small to allow egress of cytosolic growth factors, and evidence was instead obtained for growth signalling via the epidermal growth factor receptor (EGFR). Inhibition of the EGFR or of EGFR-proligand- processing blocked the mitogenic effect of alpha-toxin. Western blots with phospho-specific antibodies revealed activation of the EGFR, and of the adapter protein Shc. Immediate early response and proliferation upon transient plasma membrane pore formation by bacterial toxins may represent a novel facet of the complex interaction between pathogen and host.
This possibility can be excluded in humans as cells with complex aneuploidy proliferate comparably to diploid cell, but still exhibit the transcriptional aneuploidy response pattern (Dürrbaum et al, 2014). In human, a unique ESR transcriptional signature has not been described so far. However, the transcriptional changes caused by several stress-inducing conditions have been compared with the aneuploidy response (Dürrbaum et al, 2014). Specifically, the transcriptional profiles of HCT116 cultured in the presence of low or high glucose, hypotoxic conditions, hydrogen peroxide, nitric oxide, hydroxyurea, actinomycin D or bafilomycin A1 were analyzed. A similarity has only been observed when comparing the transcriptional response triggered by aneuploidy and the transcriptional response triggered by treatment with actinomycin D or bafilomycin A1. These evidences suggest that the response to aneuploidy differs from the response to common stress stimuli, but there is a partial overlap with conditions that interferes with autophagy (bafilomycin A1) or transcription (actinomycin D). Moreover, the transcriptome and proteome changes induced by aneuploidy partially resemble the cellularresponse to protein folding deficiency (Donnelly et al, 2014). Comparison between transcriptome of aneuploid cells and transcriptome of hepatocellular carcinoma cells after HSF1 depletion display strong similarity in both the upregulated and downregulated pathways. A partial overlap was observed also when comparing the proteome changes of aneuploid cells and proteome changes of HeLa cells treated with Hsp90 inhibitors for 24 hours. In this case, a stronger similarity was found in the downregulated pathways, including DNA and RNA metabolism and cell cycle progression, whereas the upregulated pathways did not show strong similarity. Taken together, a presence of extra DNA in human cells induces a stress response that resemble the one observed upon interference with protein degradation and folding, thus suggesting that the conserved global deregulation is partially caused by an aneuploidy-dependent proteotoxic stress.
A two-dimensional cross-sectional model is thus used for all levels of detail to save computation time. The simplest implementation (variant 1) that is able to differentiate between the two structural elements and to reproduce the deformation behaviour of the structure consists of rigid line elements for cell sides, which are interlinked by flexible point elements representing the hinges. Basing on this reduced level of detail, which is used for the initial computation of a PACS structure, the investigation of the concept’s potentials is processed. In order to enhance the quality of the structural model and to eliminate sources for variances, it is expanded and supplemented by additional structural mechanisms. Depending on the underlying assumptions behind the calculations and the according level of detail that is used for the modelling of the structure, five possible variants are deduced and specified in Table 2-3. The variants 1 to 3 are part of the following chapters and implemented with the AVW (see chapter 2.1.1), variant 4 is exemplary and gives a prospect to the future work and variant 5 is covered by FEM computations. Already the lowest level of accuracy, variant 1, provides the possibility for shape optimization and to compute deformations and stresses. In this case, both the cell side bending (𝐸𝐼) and its longitudinal stiffness (𝐸𝐴) are assumed to be infinite. The hinges possess infinitesimal bending stiffness and concentrate locally at the crossover of cell sides. The bending stiffness of the related flexure hinges is implemented in variant 2. Variant 3 additionally includes the eccentricity of the hinge elements, which is inevitable for the herein investigated PACS with flexure hinges. The illustrations within Table 2-3 show a symbolic representation of the structural model. The thickness distribution for hinges and cell sides that is shown for variant 5 is exemplary and only illustrates the necessary difference of hinge and cell side thicknesses for ensuring the flexure hinges’ functionality. Dynamic loads and the dynamic structural response on a change of loads are not considered in any of the herein presented computations. The properties of each implemented design variant are discussed in the following. The evaluation of the accuracy of the different modelling types is presented subsequently.
Although the modeling of cell behavior in fibrous gels is beyond the scope of this work our model suggests that at low cell density structure forma- tion is largely independent of the exact material properties (as long as they are isotropic) and one expects alignment of cells into short strings or rings, with- out long-ranged correlation between strings because of the effective screening of elastic signals in the horizontal direction with respect to the string’s axis. For dipoles in 3D positioned on a simple cubic lattice, simulations show that the optimal state exhibits a similar transition between effectively isotropic and aligned structures as a function of Poisson ratio as in 2D. In incompressible substrates (ν = 0.5), we find a hedgehog-like structure, where all dipoles at the corners point to the cube’s center, see Fig. 5.13(a), while for ν = 0 spon- taneous symmetry breaking along a principal lattice lattice vector occurs, see Fig. 5.13(b). For (isotropic) hydrogels typically ν = 0.5, and we therefore do not expect cells to spontaneously align due to elastic interactions in gels with isotropic material properties. However, anisotropic gel properties, e.g. caused by an alignment of collagen fibers, favor cell alignment because the elasticity along the fibers is expected to be larger than in the transverse direction. In this case, cellular traction forces could further stabilize cell alignment by putting fibers under tension. We indeed observe a similar effect in our simulations, when an elastic anisotropy is induced by external strain, see Fig. 5.13(c). The picture shows a snapshot of a Monte Carlo simulations of 100 hard spheres with an elastic dipole moment at their center, where we allowed for both ori- entational and positional degrees of freedom (T ? = 2). In the simulation, we
Among others the following questions are investigated: Which prop- erties of the local transition function are necessary and sufficient for the global transition function to be equivariant under translations (com- mute with the induced action on global configurations)? Is the com- position of global transition functions itself a global transition function and if it is, of which cellular automaton (see chapter 1)? Can global transition functions be pulled or pushed onto quotients, products, re- strictions, and extensions of their cell spaces and if they can, how do the corresponding cellular automata change (see chapter 2)? Are global transition functions for a well chosen topology (or uniformity) on the set of global configurations characterised by equivariance under transla- tions and (uniform) continuity? Is the inverse of a bijective global tran- sition function itself a global transition function (see chapter 3)? On which cell spaces are global transition functions surjective if and only if they are pre-injective (see chapter 5)? How can such cell spaces be char- acterised (see chapter 4)? Can these questions be answered for restric- tions of global transition functions to translation invariant and compact subsets of the set of global configurations (see chapters 6 and 7)? Is there an optimal-time algorithm for the firing squad synchronisation problem on (continuous) graph-shaped cell spaces (see chapter 8)? equivariance and composition
Z. Naturforsch. 53c, 6 7 0 -6 7 6 (1998); received April 20, 1998
Cortex, Memory Networks, Recurrent Model, Active Short-Term Memory, Nonhuman Primate
One example of “emergence“ is the development, as a result of neural ontogeny and living experience, of cortical networks capable of representing and retaining cognitive information. A large body of evidence from neuropsychology, electrophysiology and neuroimaging indi cates that so-called working memory and long-term memory share the same neural substrate in the cerebral cortex. That substrate consists in a system of widespread, overlapping and hierarchically organized networks of cortical neurons. In this system, any neuron or group of neurons can be part of many networks, and thus many memories. Working memory is the temporary activation of one such network of long-term memory for the purpose of executing an action in the near future. The activation of the network may be brought about by stimuli that by virtue of prior experience are in some manner associated with the cognitive content of the network, including the response of the organism to those stimuli. The mechanisms by which the network stays activated are presumed to include the recurrent re-entry of impulses through associated neuronal assemblies of the network. Consistent with this notion is the following evidence: ( 1) working memory depends on the functional integrity of cortico-corti- cal connective loops; and (2) during working memory, remarkable similarities - including “attractor behavior” - have been observed between firing patterns in real cortex and in an artificial recurrent network.
Bunde and Havlin (1994) collected a number of examples and application for these con- cepts in natural sciences. In a strict mathematical sense fractals do not have a characteristical length scale. This means if one sees a picture of a fractal where 1 cm represents 10 km and another picture of the same fractal, where 1 cm represents 0.01 cm one can not relate either of the pictures to the used scale. However, in most natural patterns this is only true for all scales but for a good range of scales, because all natural things have a finite maximal size while the smallest (biologically relevant) scale is reached with molecules. Cellular aggregates have a fi- nite size, so for lengths larger than this size the single cell yields a characteristic length-scale. On scales smaller than the size of a single cell the fractal properties are not applicable.
High water content hydrogels are an attractive material for developing artificial biomimetic ECM as they can meet a range of architectural characteristics and mechanics relevant for many soft tissues . Hydrogels are water swellable, yet water insoluble, crosslinked networks that provide the embedded cells with a highly hydrated environment permeable for oxygen, nutrients and cellular wastes [6‐8]. Hydrogel matrices for in vitro applications include a variety of naturally derived proteins and polysaccharides (e.g. collagen, fibrin), as well as synthetic polymers (e.g. poly(ethylene glycol) (PEG), polylactide, polyacrylamide) (for review see references [9‐12] and Chapter 3). While natural materials have an inherent bioactivity and are commonly degradable by cellular enzymes, synthetic materials also have potential for in vivo applications as their properties can be readily tailored with specific, desirable biochemical or mechanical properties. Many synthetic hydrogels are formed under mild, cytocompatible conditions and can be modified to display specific cell adhesive ligands or degradation sites. Moreover, variations in the synthetic gels’ compliance can be achieved by adjusting the crosslinking density [9, 10]. Hydrogels based on PEG in particular have attracted interest as synthetic ECM analogs in different tissue engineering applications and have been widely explored as substrates for cell encapsulation. Various types of cells, such as osteoblasts, smooth muscle cells and chondrocytes were shown to survive, grow and proliferate in differently modified PEG matrices [11‐14].
In recent years, there has been an increasing interest in the concept of cellular covers of groups. The notion of A-cellular objects in the category of groups was ﬁrst introduced in . Many initially signiﬁcant results were later published in 2007 by E. D. Farjoun, R. G¨ obel and Y. Segev . They mainly studied cellular covers of nilpotent groups and ﬁnite groups, and also some properties of groups inherited by their cellular covers. It was observed in this paper that cellular covers of nilpotent groups of class n are nilpotent of class n as well, in particular, cellular covers of abelian groups are abelian, see [7, pp. 62–63, Theorem 1.4]. This shows that the variety of nilpotent groups of class n is closed under taking cellular covers as well as the variety A p of
The overall response to tumor radiation therapy results from direct radiation damage and indirect bystander effects (RIBE) mediated by secreted molecules and paracrine transfer of short-lived mediators. RIBE can have both detrimental and protective actions on cancerous as well as healthy tissues. Nuclear Factor κB (NF-κB), which governs immune responses, is a prime candidate for mediating RIBE. NF- κB also modulates DNA repair while promoting cellular survival as part of the DNA damage response. After exposure to ionizing radiation NF- κB is activated in directly targeted and non-targeted bystander cells. We tested the hypothesis that the NF-κB status is relevant for induction of RIBE, using a mouse embryonal fibroblasts (MEF) knock-out variant that is unable to activate NF- κB (NF-κB essential modulator knock-out (NEMO ko)).
In untreated cells no differences were detected in p53 dynamics among cells equi- librated at temperatures below and at normotherm 37 ◦ C. With increasing tem- perature, one could observe an effect on the p53 dynamics, even in the absence of DNA damage induced by radiation. At 39 ◦ C a minor increase in the p53 level could be detected. Surprisingly at 41 ◦ C p53 accumulates significantly. Within the first 6 h of the experiments the nuclear p53 level increases constantly and remains elevated for the complete time course of the experiment (Fig. 12.2 (E)). On aver- age the p53 level accumulates in non-irradiated cells at 41 ◦ C to around 60 % of the first observed canonical pulse, detected as response to radiation at 37 ◦ C. Cells irradiated with 10Gy exhibit a much more complex picture. Pulse dura- tion and pulse frequency are correlated with temperature in the range from 33 ◦ C to 39 ◦ C. The lower the temperature the slower pulses appear (Fig. 12.2 (A-D)). Pulses were asynchronous and heterogeneous across the population equilibrated at different temperatures. Therefore, pulses appear damped in the median p53 level in the different cell populations irradiated and equilibrated between 33 ◦ C to 39 ◦ C. At 41 ◦ C a surprising non-canonical response as detected for the non-irradiated cells was observed. Instead of pulsatile dynamics, a strong accumulation within the first 6 hours was detected ensued by a slow decrease over the following hours monitored in the experiment. The p53 accumulates much stronger than what had been observed at other temperatures and reaches levels around 1.5 fold than the average amplitude of the first pulse at 37 ◦ C. After 24h the p53 level is similar in irradiated and non-irradiated cells grown at 41 ◦ C.
Learning and memory refers to the ability of the brain to encode, store and retrieve information. It is widely believed that this striking capability relies on the plastic nature of the neuronal network that allows the brain to adapt and rewire itself in response to experience. Patterns of synaptic activity can persistently modify the strength of synaptic transmission (synaptic strength) in an input-specific manner in a phenomenon termed synaptic plasticity. The concept of synaptic plasticity was first introduced by Donald Hebb nearly 60 years ago: ‘When an axon of cell A is near enough to excite cell B and repeatedly or persistently takes part in firing it, some growth process or metabolic changes takes place in one or both cells such that A’s efficiency, as one of the cells firing B, is increased’ (Hebb 1949). However, it took more than twenty years until the first experimental evidence of synaptic plasticity was provided experimentally. In 1973, Bliss and Lømo discovered that high synaptic activity can result in a persistent increase of synaptic strength, a phenomenon refered to as long-term potentiation (LTP) (Bliss and Lomo 1973). LTP proved to have a functionally opposing counterpart: Long-term depression (LTD), the activity-dependent, input-specific decrease of synaptic strength (Lynch 1977). LTP and LTD are the most extensively studied experimental paradigms of synaptic plasticity and occur in a wide range of species. Indeed, most synapses studied in the brain so far have the ability to undergo LTP and LTD (Cooke and Bliss 2006), and a large body of data reports their importance for learning and memory in vivo. To date, LTP and LTD are believed to be cellular correlates of learning and memory.