Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes

The cytidine deaminase AID hypermutates immunoglobulin genes but can also target oncogenes, leading to tumorigenesis. The extent of AID's promiscuity and its predilection for immunoglobulin genes are unknown. We report here that AID interacted broadly with promoter-proximal sequences associated with stalled polymerases and chromatin-activating marks. In contrast, genomic occupancy of replication protein A (RPA), an AID cofactor, was restricted to immunoglobulin genes. The recruitment of RPA to the immunoglobulin loci was facilitated by phosphorylation of AID at Ser38 and Thr140. We propose that stalled polymerases recruit AID, thereby resulting in low frequencies of hypermutation across the B cell genome. Efficient hypermutation and switch recombination required AID phosphorylation and correlated with recruitment of RPA. Our findings provide a rationale for the oncogenic role of AID in B cell malignancy.

[Early genetic testing in nephrology - a diagnostic aid in ambiguous clinical situations]

Despite a growing number of identified genetic causes of monogenetic disorders, early molecular testing is rarely applied in daily nephrologic practice. In selected cases and to answer specific questions, molecular testing however can be helpful for the specialist. The future significance of genetic testing most likely lies in the area of individual risk profiling for polygenetic disorders. The basis for this testing however has yet to be established.

Surgery for the bone-anchored hearing aid

This review covers the surgery for the bone-anchored hearing aid (Baha(®)). PREOPERATIVE WORKUP: A review of the indications and preoperative diagnostics shows that best results are generally obtained in patients with conductive or mixed hearing loss rehabilitation when surgery is not applicable or has failed and in patients that suffer from single-sided deafness. An audiogram must confirm that the bone conduction hearing is within the inclusion criteria. A computed tomography scan is performed in cases of malformation to assure sufficient bone thickness at the site of screw implantation.

Surgical planning tool for robotically assisted hearing aid implantation

PURPOSE : For the facilitation of minimally invasive robotically performed direct cochlea access (DCA) procedure, a surgical planning tool which enables the surgeon to define landmarks for patient-to-image registration, identify the necessary anatomical structures and define a safe DCA trajectory using patient image data (typically computed tomography (CT) or cone beam CT) is required. To this end, a dedicated end-to-end software planning system for the planning of DCA procedures that addresses current deficiencies has been developed. METHODS :    Efficient and robust anatomical segmentation is achieved through the implementation of semiautomatic algorithms; high-accuracy patient-to-image registration is achieved via an automated model-based fiducial detection algorithm and functionality for the interactive definition of a safe drilling trajectory based on case-specific drill positioning uncertainty calculations was developed. RESULTS :    The accuracy and safety of the presented software tool were validated during the conduction of eight DCA procedures performed on cadaver heads. The plan for each ear was completed in less than 20 min, and no damage to vital structures occurred during the procedures. The integrated fiducial detection functionality enabled final positioning accuracies of [Formula: see text] mm. CONCLUSIONS :    Results of this study demonstrated that the proposed software system could aid in the safe planning of a DCA tunnel within an acceptable time.

A second generation radiation hybrid map to aid the assembly of the bovine genome sequence

BACKGROUND: Several approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from technical deficiencies or lack of statistical support to distinguish between alternative orders of loci. The accuracy of the genome maps could be improved, in principle, if information from different sources was combined to produce integrated maps. The publicly available bovine genomic sequence assembly with 6x coverage (Btau_2.0) is based on whole genome shotgun sequence data and limited mapping data however, it is recognised that this assembly is a draft that contains errors. Correcting the sequence assembly requires extensive additional mapping information to improve the reliability of the ordering of sequence scaffolds on chromosomes. The radiation hybrid (RH) map described here has been contributed to the international sequencing project to aid this process. RESULTS: An RH map for the 30 bovine chromosomes is presented. The map was built using the Roslin 3000-rad RH panel (BovGen RH map) and contains 3966 markers including 2473 new loci in addition to 262 amplified fragment-length polymorphisms (AFLP) and 1231 markers previously published with the first generation RH map. Sequences of the mapped loci were aligned with published bovine genome maps to identify inconsistencies. In addition to differences in the order of loci, several cases were observed where the chromosomal assignment of loci differed between maps. All the chromosome maps were aligned with the current 6x bovine assembly (Btau_2.0) and 2898 loci were unambiguously located in the bovine sequence. The order of loci on the RH map for BTA 5, 7, 16, 22, 25 and 29 differed substantially from the assembled bovine sequence. From the 2898 loci unambiguously identified in the bovine sequence assembly, 131 mapped to different chromosomes in the BovGen RH map. CONCLUSION: Alignment of the BovGen RH map with other published RH and genetic maps showed higher consistency in marker order and chromosome assignment than with the current 6x sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.

The cytidine deaminases AID and APOBEC-1 exhibit distinct functional properties in a novel yeast selectable system

Activation-induced cytidine deaminase (AID) is indispensable for immunoglobulin maturation by somatic hypermutations and class switch recombination and is supposed to deaminate cytidines in DNA, while its homolog APOBEC-1 edits apolipoprotein (apo) B mRNA by cytidine deamination. We studied the editing activity of APOBEC-1 and AID in yeast using the selectable marker Gal4 linked to its specific inhibitor protein Gal80 via an apo B cassette (Gal4-C) or via the variable region of a mouse immunoglobulin heavy chain gene (Gal4-VH). Expression of APOBEC-1 induced C to U editing in up to 15% of the Gal4-C transcripts, while AID was inactive in this reaction even in the presence of the APOBEC-1 complementation factor. After expression of APOBEC-1 as well as AID approximately 10(-3) of yeast cells survived low stringency selection and expressed beta-galactosidase. Neither AID nor APOBEC-1 mutated the VH sequence of Gal4-VH, and consequently the yeast colonies did not escape high stringent selection. AID, however, induced frequent plasmid recombinations that were only rarely observed with APOBEC-1. In conclusion, AID cannot substitute APOBEC-1 to edit the apo B mRNA, and the expression of AID in yeast is not sufficient for the generation of point mutations in a highly transcribed Gal4-VH sequence. Cofactors for AID induced somatic hypermutations of immunoglobulin variable regions, that are present in B cells and a variety of non-B cells, appear to be missing in yeast. In contrast to APOBEC-1, AID alone does not exhibit an intrinsic specificity for its target sequences.

Stochastic rank correlation: a robust merit function for 2D/3D registration of image data obtained at different energies

In this article, the authors evaluate a merit function for 2D/3D registration called stochastic rank correlation (SRC). SRC is characterized by the fact that differences in image intensity do not influence the registration result; it therefore combines the numerical advantages of cross correlation (CC)-type merit functions with the flexibility of mutual-information-type merit functions. The basic idea is that registration is achieved on a random subset of the image, which allows for an efficient computation of Spearman's rank correlation coefficient. This measure is, by nature, invariant to monotonic intensity transforms in the images under comparison, which renders it an ideal solution for intramodal images acquired at different energy levels as encountered in intrafractional kV imaging in image-guided radiotherapy. Initial evaluation was undertaken using a 2D/3D registration reference image dataset of a cadaver spine. Even with no radiometric calibration, SRC shows a significant improvement in robustness and stability compared to CC. Pattern intensity, another merit function that was evaluated for comparison, gave rather poor results due to its limited convergence range. The time required for SRC with 5% image content compares well to the other merit functions; increasing the image content does not significantly influence the algorithm accuracy. The authors conclude that SRC is a promising measure for 2D/3D registration in IGRT and image-guided therapy in general.

Can the World Trade Organization Ensure that International Food Aid is Genuine?

The Doha Round negotiation mandate proposes to minimise trade distortions and commercial displacement under the cover of international food aid, without preventing genuine food aid from reaching people in need. This paper presents problematic aspects of food aid for trade and competition, an overview of the international governance of food aid, and the present rules on food aid embodied in Article 10.4 of the WTO Agreement on Agriculture. The latest available Draft Modalities for Agriculture (December 2008) are seen as an only halfway successful implementation of the Doha mandate. A new text with better targeted disciplines and a political food aid commitment as part of the Doha Round Final Act are proposed in the conclusions.