Routing for analog chip designs at NXP Semiconductors

During the study week 2011 we worked on the question of how to automate certain aspects of the design of analog chips. Here we focused on the task of connecting different blocks with electrical wiring, which is particularly tedious to do by hand. For digital chips there is a wealth of research available for this, as in this situation the amount of blocks makes it hopeless to do the design by hand. Hence, we set our task to finding solutions that are based on the previous research, as well as being tailored to the specific setting given by NXP. This resulted in an heuristic approach, which we presented at the end of the week in the form of a protoype tool. In this report we give a detailed account of the ideas we used, and describe possibilities to extend the approach

SAWdoubler: a program for counting self-avoiding walks

This article presents SAWdoubler, a package for counting the total number Z(N) of self-avoiding walks (SAWs) on a regular lattice by the length-doubling method, of which the basic concept has been published previously by us. We discuss an algorithm for the creation of all SAWs of length N, efficient storage of these SAWs in a tree data structure, and an algorithm for the computation of correction terms to the count Z(2N) for SAWs of double length, removing all combinations of two intersecting single-length SAWs. We present an efficient numbering of the lattice sites that enables exploitation of symmetry and leads to a smaller tree data structure; this numbering is by increasing Euclidean distance from the origin of the lattice. Furthermore, we show how the computation can be parallelised by distributing the iterations of the main loop of the algorithm over the cores of a multicore architecture. Experimental results on the 3D cubic lattice demonstrate that Z(28) can be computed on a dual-core PC in only 1 hour and 40 minutes, with a speedup of 1.56 compared to the single-core computation and with a gain by using symmetry of a factor of 26. We present results for memory use and show how the computation is made to fit in 4 Gbyte RAM. It is easy to extend the SAWdoubler software to other lattices; it is publicly available under the GNU LGPL license.Comment: 29 pages, 3 figure

The Medicago genome provides insight into the evolution of rhizobial symbioses

Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species2. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ~94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa’s genomic toolbo

Molecular aspects of the nitrogen fixing system in pea root nodules

This thesis deals with research on symbiotic nitrogen fixation of Pisumsativum and Rhizobium Leguminosarum. Nitrogen fixation takes place in the Rhizobium bacteroids which are located within root nodule cells. Two important proteins in nitrogen fixation are nitrogenase and leghemoglobin. Nitrogenase, the enzyme that reduces N 2 , is synthesized by Rhizobium. Leghemoglobin, which has a function in the O 2 supply of the bacteroids is synthesized by the plant. The molecular biology of symbiotic nitrogen fixation has hardly been the subject of investigation. The regulation of the synthesis in root nodules of e.g. nitrogenase and leghemoglobin is not at all completely clear.In this thesis some general aspects of nodule formation and the regulation of nitrogenase and leghemoglobin (Lb) synthesis have been studied.General aspectsThe transformation of Rhizobium bacteria into nitrogen fixing bacteroids was studied by investigating the DNA content of bacteroid cells by means of cytofluorometry (chapter I). Furthermore the RNA content and the quality of the RNA of R. leguminosarum (PRE) bacteroids were followed during pea development (chapter IV) and the protein synthesis in bacteroids and in the plant fraction of pea root nodules during nodule development was studied (chapter IV). The regulation of nitrogenase and leghemoglobin synthesis were studied in more detail.Regulation of nitrogenase and Lb synthesisNitrogenase and Lb synthesis were studied by 35SO42-labeling of intact pea plants. Intact pea plants are a rather complicated system to study Lb or nitrogenase synthesis, but in more simple systems like e.g. detached root nodules, nitrogenase and Lb synthesis are repressed. We did not succeed in developing a more simple system suitable for studying nitrogenase or Lb synthesis (chapter VII). The regulation of nitrogenase and Lb synthesis were studied by culturing pea plants under conditions that diminished in vivo nitrogenase activity and by determining nitrogenase and Lb synthesis during nodule formation and development. Growth conditions used to diminish in vivo nitrogenase activity were: 1. the addition of NH4+to the growth medium (chapter II) and 2. waterlogging (chapter III). The synthesis of the two nitrogenase components and Lb during nodule formation and development was studied in two different ways: 1. the synthesis of these three proteins was followed by 35SO42-labeling of pea plants of different ages, and analysis of bacteroid and plant proteins by polyacrylamide gel electrophoresis (chapter IV), 2. the sequence of appearance of the two nitrogenase components and Lb during pea nodule formation was determined with specific radioimmunoassays for these three proteins (chapter V).In principle, turnover of proteins can be an important factor in the regulation of protein composition in the bacteroid or plant fraction of root nodules, e.g. during nodule development or after changes in the environmental conditions. Therefore turnover rates of bacteroid and plant proteins of pea root nodules, especially nitrogenase and Lb, were determined (chapter VI)

Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei

The organization of the eukaryote nucleus into functional compartments arises by self-organization both through specific protein–protein and protein–DNA interactions and non-specific interactions that lead to entropic effects, such as e.g. depletion attraction. While many specific interactions have so far been demonstrated, the contributions of non-specific interactions are still unclear. We used coarse-grained molecular dynamics simulations of previously published models for Arabidopsis thaliana chromatin organization to show that non-specific interactions can explain the in vivo localization of nucleoli and chromocenters. Also, we quantitatively demonstrate that chromatin looping contributes to the formation of chromosome territories. Our results are consistent with the previously published Rosette model for Arabidopsis chromatin organization and suggest that chromocenter-associated loops play a role in suppressing chromocenter clustering

Cloning and characterisation of a maize carotenoid cleavage dioxygenase (ZmCCD1) and its involvement in the biosynthesis of apocarotenoids with various roles in mutualistic and parasitic interactions

Colonisation of maize roots by arbuscular mycorrhizal (AM) fungi leads to the accumulation of apocarotenoids (cyclohexenone and mycorradicin derivatives). Other root apocarotenoids (strigolactones) are involved in signalling during early steps of the AM symbiosis but also in stimulation of germination of parasitic plant seeds. Both apocarotenoid classes are predicted to originate from cleavage of a carotenoid substrate by a carotenoid cleavage dioxygenase (CCD), but the precursors and cleavage enzymes are unknown. A Zea mays CCD (ZmCCD1) was cloned by RT-PCR and characterised by expression in carotenoid accumulating E. coli strains and analysis of cleavage products using GC¿MS. ZmCCD1 efficiently cleaves carotenoids at the 9, 10 position and displays 78% amino acid identity to Arabidopsis thaliana CCD1 having similar properties. ZmCCD1 transcript levels were shown to be elevated upon root colonisation by AM fungi. Mycorrhization led to a decrease in seed germination of the parasitic plant Striga hermonthica as examined in a bioassay. ZmCCD1 is proposed to be involved in cyclohexenone and mycorradicin formation in mycorrhizal maize roots but not in strigolactone formatio

De kracht van de stikstofbinders

Hoogleraar Ken Giller propageert onder Afrikaanse boeren het gebruik van peulvruchten. Die hebben dankzij hulp van bacteriën geen stikstofmeststof nodig. In Wageningen onderzoekt hoogleraar Ton Bisseling de finesses van deze symbiose

Digital learning material for model building in molecular biology

Building models to describe processes forms an essential part of molecular biology research. However, in molecular biology curricula little attention is generally being paid to the development of this skill. In order to provide students the opportunity to improve their model building skills, we decided to develop a number of digital cases about developmental biology. In these cases the students are guided to build a model according to a method that is based on expert analysis and historical data; they first build a simplified model based on the wild-type only and then they extend this model step by step based on experimental results. After each extension, the biological implications of the extension are evaluated. The first case was evaluated three times during a regular course at Wageningen University, The Netherlands and once at the University of Zurich, Switzerland. The analysis of audiotapes revealed that students did indeed engage in the reasoning processes, which are typical for model building. Furthermore, exam results seem to suggest that working with the case indeed facilitates model building in analogical situations and the students judged working with the case positivel

Root developmental programs shape the Medicago truncatula nodule meristem

Nodules on the roots of legume plants host nitrogen-fixing Rhizobium bacteria. Several lines of evidence indicate that nodules are evolutionarily related to roots. We determined whether developmental control of the Medicago truncatula nodule meristem bears resemblance to that in root meristems through analyses of root meristem-expressed PLETHORA genes. In nodules, MtPLETHORA 1 and 2 are preferentially expressed in cells positioned at the periphery of the meristem abutting nodule vascular bundles. Their expression overlaps with an auxin response maximum and MtWOX5, which is a marker for the root quiescent center. Strikingly, the cells in the central part of the nodule meristem have a high level of cytokinin and display MtPLETHORA 3 and 4 gene expression. Nodule-specific knockdown of MtPLETHORA genes results in a reduced number of nodules and/or in nodules in which meristem activity has ceased. Our nodule gene expression map indicates that the nodule meristem is composed of two distinct domains in which different MtPLETHORA gene subsets are expressed. Our mutant studies show that MtPLETHORA genes function redundantly in nodule meristem maintenance. This indicates that Rhizobium has recruited root developmental programs for nodule formation

Restriction of host range by the sym2 allele of Afghan pea is nonspecific for the type of modification at the reducing terminus of nodulation signals

Microbial Biotechnolog