| 1. |
- Hoencamp, Claire, et al.
(författare)
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3D genomics across the tree of life reveals condensin II as a determinant of architecture type
- 2021
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 372:6545, s. 984-989
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Tidskriftsartikel (refereegranskat)abstract
- We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.
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| 2. |
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| 3. |
- Behringer, H., et al.
(författare)
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Brownian dynamics simulations with hard-body interactions : Spherical particles
- 2012
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 137:16, s. 164108-
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Tidskriftsartikel (refereegranskat)abstract
- A novel approach to account for hard-body interactions in (overdamped) Brownian dynamics simulations is proposed for systems with non-vanishing force fields. The scheme exploits the analytically known transition probability for a Brownian particle on a one-dimensional half-line. The motion of a Brownian particle is decomposed into a component that is affected by hard-body interactions and into components that are unaffected. The hard-body interactions are incorporated by replacing the affected component of motion by the evolution on a half-line. It is discussed under which circumstances this approach is justified. In particular, the algorithm is developed and formulated for systems with space-fixed obstacles and for systems comprising spherical particles. The validity and justification of the algorithm is investigated numerically by looking at exemplary model systems of soft matter, namely at colloids in flow fields and at protein interactions. Furthermore, a thorough discussion of properties of other heuristic algorithms is carried out.
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| 4. |
- Heldt, G., et al.
(författare)
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Approach to combine electron-beam lithography and two-photon polymerization for enhanced nano-channels in network-based biocomputation devices
- 2018
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Ingår i: 34th European Mask and Lithography Conference. - : SPIE. - 9781510621213 ; 10775
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Konferensbidrag (refereegranskat)abstract
- Although conventional computer technology made a huge leap forward in the past decade, a vast number of computational problems remain inaccessible due to their inherently complex nature. One solution to deal with this computational complexity is to highly parallelize computations and to explore new technologies beyond semiconductor computers. Here, we report on initial results leading to a device employing a biological computation approach called network-based biocomputation (NBC). So far, the manufacturing process relies on conventional Electron Beam Lithography (EBL). However we show first promising results expanding EBL patterning to the third dimension by employing Two-Photon Polymerization (2PP). The nanofabricated structures rely on a combination of physical and chemical guiding of the microtubules through channels. Microtubules travelling through the network make their way through a number of different junctions. Here it is imperative that they do not take wrong turns. In order to decrease the usage of erroneous paths in the network a transition from planar 2-dimensional (mesh structure) networks to a design in which the crossing points of the mesh extend into the 3rd dimension is made. EBL is used to fabricate the 2D network structure whereas for the 3D-junctions 2PP is used. The good adaptation of the individual technologies allows for the possibility of a future combination of the two complementary approaches.
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| 5. |
- Singh, Umashankar, et al.
(författare)
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Different Molecular Mechanisms Underlie Placental Overgrowth Phenotypes Caused by Interspecies Hybridization, Cloning, and Esx1 Mutation
- 2004
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Ingår i: Developmental Dynamics. - : Wiley. - 1058-8388 .- 1097-0177. ; 230:1, s. 149-164
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Tidskriftsartikel (refereegranskat)abstract
- To obtain a deeper insight into the genes and gene networks involved in the development of placentopathies, we have assessed global gene expression in three different models of placental hyperplasia caused by interspecies hybridization (IHPD), cloning by nuclear transfer, and mutation of the Esx1 gene, respectively. Comparison of gene expression profiles of approximately 13,000 expressed sequence tags (ESTs) identified specific subsets of genes with changed expression levels in IHPD, cloned, and Esx1 mutant placentas. Of interest, only one gene of known function and one EST of unknown function were found common to all three placentopathies; however, a significant number of ESTs were common to IHPD and cloned placentas. In contrast, only one gene was shared between IHPD and Esx1 mutant, and cloned and Esx1 mutant placentas, respectively. These genes common to different abnormal placental growth genotypes are likely to be important in the occurrence of placentopathy.
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| 6. |
- Tian, Geng, et al.
(författare)
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Expression and function of the LIM homeobox containing genes Lhx3 and Lhx4 in the mouse placenta
- 2008
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Ingår i: Developmental Dynamics. - : Wiley. - 1058-8388 .- 1097-0177. ; 237:5, s. 1517-1525
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Tidskriftsartikel (refereegranskat)abstract
- The LIM homeobox containing genes of the LIM-3 group, Lhx3 and Lhx4, are critical for normal development. Both genes are involved in the formation of the pituitary and the motoneuron system and loss of either gene causes perinatal lethality. Previous studies had shown that Lhx3 is overexpressed in hyperplastic placentas of mouse interspecies hybrids. To determine the role of LHX3 in the mouse placenta, we performed expression and function analyses. Our results show that Lhx3 exhibits specific spatial and temporal expression in the mouse placenta. However, deletion of Lhx3 does not produce a placental phenotype. To test whether this is due to functional substitution by Lhx4, we performed a phenotype analysis of Lhx3-/-; Lhx4-/- double-mutant placentas. A subset of Lhx3-/-; Lhx4-/- placentas exhibited abnormal structure of the labyrinth. However, absence of both LIM-3 genes did not interfere with placental transport nor consistently with expression of target genes such as Gnrhr. Thus, LHX3 and LHX4 appear to be dispensable for placental development and function.
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