The Old-Javanese Rāmāyaṇa Kakawin

Indonesi

Pelvi-ureteric obstruction

In chapter 1 the history of pelvi-ureteric junction obstruction (PUJO) is described. In the past (Hippocrates and Tulp) this condition was recognized but it was not until the 17th century that the first operations were performed in order to drain the kidney or to remove stones. The first nephrectomy was described by Simon (1862). ... Zie: Summary

The genome sequence of hairy root Rhizobium rhizogenes strain LBA9402: bioinformatics analysis suggests the presence of a new opine system in the agropine Ri plasmid

We report here the complete genome sequence of the Rhizobium rhizogenes (formerly Agrobacterium rhizogenes) strain LBA9402 (NCPPB1855rifR), a pathogenic strain causing hairy root disease. To assemble a complete genome, we obtained short reads from Illumina sequencing and long reads from Oxford Nanopore Technology sequencing. The genome consists of a 3,958,212 bp chromosome, a 2,005,144 bp chromid (secondary chromosome) and a 252,168 bp Ri plasmid (pRi1855), respectively. The primary chromosome was very similar to that of the avirulent biocontrol strain K84, but the chromid showed a 724 kbp deletion accompanied by a large 1.8 Mbp inversion revealing the dynamic nature of these secondary chromosomes. The sequence of the agropine Ri plasmid was compared to other types of Ri and Ti plasmids. Thus, we identified the genes responsible for agropine catabolism, but also a unique segment adjacent to the TL region that has the signature of a new opine catabolic gene cluster including the three genes that encode the three subunits of an opine dehydrogenase. Our sequence analysis also revealed a novel gene at the very right end of the TL-DNA, which is unique for the agropine Ri plasmid. The protein encoded by this gene was most related to the succinamopine synthases of chrysopine and agropine Ti plasmids and thus may be involved in the synthesis of the unknown opine that can be degraded by the adjacent catabolic cluster. The available sequence will facilitate the use of R. rhizogenes and especially LBA9402 in both the laboratory and for biotechnological purposes.Plant science

Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid

Background The Agrobacterium strain AB2/73 has a unique host range for the induction of crown gall tumors, and contains an exceptionally large, over 500 kbp mega Ti plasmid. We used whole genome sequencing to fully characterize and comparatively analyze the complex genome of strain AB2/73, including its Ti plasmid and virulence factors. Results We obtained a high-quality, full genomic sequence of AB2/73 by a combination of short-read Illumina sequencing and long-read Nanopore sequencing. The AB2/73 genome has a total size of 7,266,754 bp with 59.5% GC for which 7012 genes (6948 protein coding sequences) are predicted. Phylogenetic and comparative genomics analysis revealed that strain AB2/73 does not belong to the genus Agrobacterium, but to a new species in the genus Rhizobium, which is most related to Rhizobium tropici. In addition to the chromosome, the genome consists of 6 plasmids of which the largest two, of more than 1 Mbp, have chromid-like properties. The mega Ti plasmid is 605 kbp in size and contains two, one of which is incomplete, repABC replication units and thus appears to be a cointegrate consisting of about 175 kbp derived from an unknown Ti plasmid linked to 430 kbp from another large plasmid. In pTiAB2/73 we identified a complete set of virulence genes and two T-DNAs. Besides the previously described T-DNA we found a larger, second T-DNA containing a 6b-like onc gene and the acs gene for agrocinopine synthase. Also we identified two clusters of genes responsible for opine catabolism, including an acc-operon for agrocinopine degradation, and genes putatively involved in rideopine catabolism. The plasmid also harbours tzs, iaaM and iaaH genes for the biosynthesis of the plant growth regulators cytokinin and auxin. Conclusions The comparative genomics analysis of the high quality genome of strain AB2/73 provided insight into the unusual phylogeny and genetic composition of the limited host range Agrobacterium strain AB2/73. The description of its unique genomic composition and of all the virulence determinants in pTiAB2/73 will be an invaluable tool for further studies into the special host range properties of this bacterium.Plant science

Characterization of the Agrobacterium octopine-cucumopine catabolic plasmid pAtAg67

Microbial Biotechnolog

Species literacy: the perception and cultural portrayal of animals

In his dissertation Michiel Hooykaas outlines the results of six empirical research projects focused at biodiversity awareness in the Netherlands, specifically people’s knowledge about animals. Providing insight into people’s perception of animal biodiversity is valuable both from a scientific perspective and from the perspective of conservation, as biodiversity loss continues and the relationship between humans and nature is under increasing pressure. The first part of this thesis focuses on species literacy, a newly coined concept that stands for broad and in-depth knowledge about species. Quantitative research projects are described that established the level of species literacy in professionals and laypeople. The second part of this thesis explores the portrayal of animals in cultural products aimed at children. Quantitative content analyses were used to examine the image of animal biodiversity conveyed by two product categories: picture books and clothes. The patterns uncovered in cultural portrayals of animals mirrored the knowledge patterns found in the first part of the dissertation. Animal groups well known by people predominated children’s fashion and picture books, while others were portrayed less frequently and in less specific manners. The revealed patterns imply that Dutch laypeople currently miss out on enriching experiences with biodiversity, and they hold important implications for conservation. The third and final part of this thesis explores, from the perspective of biodiversity communicators, the potential to connect people with biodiversity in places that are becoming increasingly urbanized. As such, promising avenues to foster species literacy and engage people with biodiversity are distilled.Science Communication and Societ

The translocated virulence protein VirD5 causes DNA damage and mutation during Agrobacterium-mediated transformation of yeast

Plant sciencesMicrobial Biotechnolog