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- Pertoldi, Cino, et al.
(författare)
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On the brink between extinction and persistence
- 2008
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Ingår i: Biology Direct. - : Springer Science and Business Media LLC. - 1745-6150. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- The nature of size fluctuations is crucial in forecasting future population persistence, independently of whether the variability stems from external forces or from the dynamics of the population renewal process. The risk of intercepting zero is highly dependent on the way the variance of the population size relates to its mean. The minimum population size required for a population not to go extinct can be determined by a scaling equation relating the variance to the arithmetic mean. By the use of a derived expression for the harmonic mean defined by the parameters of the scaling equation we show how it is possible to separate the domains of persistence from those of extinction and to facilitate the identification of populations on the brink of extinction.
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| 3. |
- Chang, W.-J., et al.
(författare)
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Intron Evolution and Information processing in the DNA polymerase alpha gene in spirotrichous ciliates : A hypothesis for interconversion between DNA and RNA deletion
- 2007
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Ingår i: Biology Direct. - : Springer Science and Business Media LLC. - 1745-6150. ; 2, s. 6-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The somatic DNA molecules of spirotrichous ciliates are present as linear chromosomes containing mostly single-gene coding sequences with short 5' and 3' flanking regions. Only a few conserved motifs have been found in the flanking DNA. Motifs that may play roles in promoting and/or regulating transcription have not been consistently detected. Moreover, comparing subtelomeric regions of 1,356 end-sequenced somatic chromosomes failed to identify more putatively conserved motifs. RESULTS: We sequenced and compared DNA and RNA versions of the DNA polymerase alpha (pol alpha) gene from nine diverged spirotrichous ciliates. We identified a G-C rich motif aaTACCGC(G/C/T) upstream from transcription start sites in all nine pol alpha orthologs. Furthermore, we consistently found likely polyadenylation signals, similar to the eukaryotic consensus AAUAAA, within 35 nt upstream of the polyadenylation sites. Numbers of introns differed among orthologs, suggesting independent gain or loss of some introns during the evolution of this gene. Finally, we discuss the occurrence of short direct repeats flanking some introns in the DNA pol alpha genes. These introns flanked by direct repeats resemble a class of DNA sequences called internal eliminated sequences (IES) that are deleted from ciliate chromosomes during development. CONCLUSIONS: Our results suggest that conserved motifs are present at both 5' and 3' untranscribed regions of the DNA pol alpha genes in nine spirotrichous ciliates. We also show that several independent gains and losses of introns in the DNA pol alpha genes have occurred in the spirotrichous ciliate lineage. Finally, our statistical results suggest that proven introns might also function in an IES removal pathway. This could strengthen a recent hypothesis that introns evolve into IESs, explaining the scarcity of introns in spirotrichs. Alternatively, the analysis suggests that ciliates might occasionally use intron splicing to correct, at the RNA level, failures in IES excision during developmental DNA elimination.
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| 4. |
- Hintze, Arend, Professor, et al.
(författare)
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Modularity and anti-modularity in networks with arbitrary degree distribution
- 2010
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Ingår i: Biology Direct. - : Springer Science and Business Media LLC. - 1745-6150. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Background: Much work in systems biology, but also in the analysis of social network and communication and transport infrastructure, involves an in-depth analysis of local and global properties of those networks, and how these properties relate to the function of the network within the integrated system. Most often, systematic controls for such networks are difficult to obtain, because the features of the network under study are thought to be germane to that function. In most such cases, a surrogate network that carries any or all of the features under consideration, while created artificially and in the absence of any selective pressure relating to the function of the network being studied, would be of considerable interest.Results: Here, we present an algorithmic model for growing networks with a broad range of biologically and technologically relevant degree distributions using only a small set of parameters. Specifying network connectivity via an assortativity matrix allows us to grow networks with arbitrary degree distributions and arbitrary modularity. We show that the degree distribution is controlled mainly by the ratio of node to edge addition probabilities, and the probability for node duplication. We compare topological and functional modularity measures, study their dependence on the number and strength of modules, and introduce the concept of anti-modularity: a property of networks in which nodes from one functional group preferentially do not attach to other nodes of that group. We also investigate global properties of networks as a function of the network's growth parameters, such as smallest path length, correlation coefficient, small-world-ness, and the nature of the percolation phase transition. We search the space of networks for those that are most like some well-known biological examples, and analyze the biological significance of the parameters that gave rise to them.Conclusions: Growing networks with specified characters (degree distribution and modularity) provides the opportunity to create surrogates for biological and technological networks, and to test hypotheses about the processes that gave rise to them. We find that many celebrated network properties may be a consequence of the way in which these networks grew, rather than a necessary consequence of how they work or function.Reviewers: This article was reviewed by Erik van Nimwegen, Teresa Przytycka (nominated by Claus Wilke), and Leonid Mirny. For the full reviews, please go to the Reviewer's Comments section. © 2010 Hintze and Adami; licensee BioMed Central Ltd.
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| 5. |
- Krishnamurthy, Supriya, et al.
(författare)
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The stochastic behavior of a molecular switching circuit with feedback
- 2007
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Ingår i: Biology Direct. - : Springer Science and Business Media LLC. - 1745-6150. ; 2, s. 13-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit consists of a kinase and phosphatase acting on multiple sites of a substrate that, contingent on its modification state, catalyzes its own phosphorylation and, in a symmetric scenario, dephosphorylation. The symmetric case is viewed as a cartoon of conflicting feedback that could result from antagonistic pathways impinging on the state of a shared component. Results: Multisite phosphorylation is sufficient for bistable behavior under feedback even when catalysis is linear in substrate concentration, which is the case we consider. We compute the phase diagram, fluctuation spectrum and large-deviation properties related to switch memory within a statistical mechanics framework. Bistability occurs as either a first- order or second-order nonequilibrium phase transition, depending on the network symmetries and the ratio of phosphatase to kinase numbers. In the second-order case, the circuit never leaves the bistable regime upon increasing the number of substrate molecules at constant kinase to phosphatase ratio. Conclusion: The number of substrate molecules is a key parameter controlling both the onset of the bistable regime, fluctuation intensity, and the residence time in a switched state. The relevance of the concept of memory depends on the degree of switch symmetry, as memory presupposes information to be remembered, which is highest for equal residence times in the switched states.
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| 10. |
- Sazonova, EV, et al.
(författare)
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A link between mitotic defects and mitotic catastrophe: detection and cell fate
- 2021
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Ingår i: Biology direct. - : Springer Science and Business Media LLC. - 1745-6150. ; 16:1, s. 25-
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Tidskriftsartikel (refereegranskat)abstract
- Although the phenomenon of mitotic catastrophe was first described more than 80 years ago, only recently has this term been used to explain a mechanism of cell death linked to delayed mitosis. Several mechanisms have been suggested for mitotic catastrophe development and cell fate. Depending on molecular perturbations, mitotic catastrophe can end in three types of cell death, namely apoptosis, necrosis, or autophagy. Moreover, mitotic catastrophe can be associated with different types of cell aging, the development of which negatively affects tumor elimination and, consequently, reduces the therapeutic effect. The effective triggering of mitotic catastrophe in clinical practice requires induction of DNA damage as well as inhibition of the molecular pathways that regulate cell cycle arrest and DNA repair. Here we discuss various methods to detect mitotic catastrophe, the mechanisms of its development, and the attempts to use this phenomenon in cancer treatment.
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