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

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

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

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

Exploring Fear of Cancer Recurrence in a sample of heterogeneous distressed cancer patients with and without a psychiatric disorder

Fear of Cancer Recurrence (FCR) is a concern among cancer patients. Recent insights suggest that FCR should be viewed as a distinct syndrome. However, few studies have explored its overlap with psychiatric morbidity. We examined this overlap in a sample of distressed cancer patients. Self-referred patients (n = 245) were assessed with the Structured Clinical Interview for DSM-IV-TR Axis-I disorders and the Fear of Cancer Recurrence Inventory-Short Form. Proportions of patients with and without a psychiatric disorder meeting validated cut-offs for screening and clinically relevant FCR were compared. The prevalence of psychiatric disorders was 36%. Clinically relevant FCR was found in 198 patients (81%). Patients with a current psychiatric disorder reported clinically relevant FCR more frequently (89%) compared to those with no disorder (77%). Of patients reporting clinically relevant FCR, the majority (61%) did not additionally meet the criteria for a psychiatric disorder. These findings suggest that there should be particular attention for patients with elevated levels of FCR, warranting FCR-specific treatment. Trial registry number Clinicaltrials.gov NCT0213851

Towards device-size atomistic models of amorphous silicon

The atomic structure of amorphous materials is believed to be well described by the continuous random network model. We present an algorithm for the generation of large, high-quality continuous random networks. The algorithm is a variation of the "sillium" approach introduced by Wooten, Winer, and Weaire. By employing local relaxation techniques, local atomic rearrangements can be tried that scale almost independently of system size. This scaling property of the algorithm paves the way for the generation of realistic device-size atomic networks.Comment: 7 pages, 3 figure

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

One-Step Agrobacterium Mediated Transformation of Eight Genes Essential for Rhizobium Symbiotic Signaling Using the Novel Binary Vector System pHUGE

Advancement in plant research is becoming impaired by the fact that the transfer of multiple genes is difficult to achieve. Here we present a new binary vector for Agrobacterium tumefaciens mediated transformation, pHUGE-Red, in concert with a cloning strategy suited for the transfer of up to nine genes at once. This vector enables modular cloning of large DNA fragments by employing Gateway technology and contains DsRED1 as visual selection marker. Furthermore, an R/Rs inducible recombination system was included allowing subsequent removal of the selection markers in the newly generated transgenic plants. We show the successful use of pHUGE-Red by transferring eight genes essential for Medicago truncatula to establish a symbiosis with rhizobia bacteria as one 74 kb T-DNA into four non-leguminous species; strawberry, poplar, tomato and tobacco. We provide evidence that all transgenes are expressed in the root tissue of the non-legumes. Visual control during the transformation process and subsequent marker gene removal makes the pHUGE-Red vector an excellent tool for the efficient transfer of multiple genes