Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

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Development of a gene-based radiation hybrid map of chicken Chromosome 7 and comparison to human and mouse

To validate the ChickRH6 whole-genome radiation hybrid (WGRH) panel, we constructed a map of chicken Chromosome 7 based on 19 microsatellite markers from the genetic map and 76 ESTs (expressed sequence tags), whose efficient targeted development was made possible by using the ICCARE software. This high-density radiation hybrid (RH) map of a chicken macrochromosome gives us indications on characteristics of ChickRH6. The potential resolution of the panel is 325 kb and the practical resolution of our framework map is 1.3 Mb. Based on these results, a complete framework map of the chicken genome would comprise 1000 markers. The marker order is in good agreement with the genetic map and comparison with the human and mouse sequence maps revealed a number of internal rearrangements.     

Genetic structure of the LXS panel of recombinant inbred mouse strains: a powerful resource for complex trait analysis

The set of LXS recombinant inbred (RI) strains is a new and exceptionally large mapping panel that is suitable for the analysis of complex traits with comparatively high power. This panel consists of 77 strains—more than twice the size of other RI sets— and will typically provide sufficient statistical power (=0.8) to map quantitative trait loci (QTLs) that account for 25% of genetic variance with a genomewide p < 0.05. To characterize the genetic architecture of this new set of RI strains, we genotyped 330 MIT microsatellite markers distributed on all autosomes and the X Chromosome and assembled error-checked meiotic recombination maps that have an average F₂-adjusted marker spacing of 4 cM. The LXS panel has a genetic structure consistent with random segregation and subsequent fixation of alleles, the expected 3–4 × map expansion, a low level of nonsyntenic association among loci, and complete independence among all 77 strains. Although the parental inbred strains—Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS)—were derived originally by selection from an 8-way heterogeneous stock selected for differential sensitivity to sedative effects of ethanol, the LXS panel is also segregating for many other traits. Thus, the LXS panel provides a powerful new resource for mapping complex traits across many systems and disciplines and should prove to be of great utility in modeling the genetics of complex diseases in human populations.(Robert W. Williams and Beth Bennett)These authors contributed equally to this work.     

Basic fibroblast growth factor, neurofilament, and glial fibrillary acidic protein immunoreactivities in the myenteric plexus of the rat esophagus and colon

The enteric nervous system consists of a number of interconnected networks of neuronal cell bodies and fibers as well as satellite cells, the enteric glia. Basic fibroblast growth factor (bFGF) is a mitogen for a variety of mesodermal and neuroectodermal-derived cells and its presence has been described in many tissues. The present work employs immunohistochemistry to analyze neurons and glial cells in the esophageal and colic enteric plexus of the Wistar rat for neurofilament (NF) and glial fibrillary acidic proteins (GFAP) immunoreactivity as well as bFGF immunoreactivity in these cells. Rats were processed for immunohistochemistry; the distal esophagus and colon were opened and their myenteric plexuses were processed as whole-mount preparations. The membranes were immunostained for visualization of NF, GFAP, and bFGF. NF immunoreactivity was seen in neuronal cell bodies of esophageal and colic enteric ganglia. GFAP-immunoreactive enteric glial cells and processes were present in the esophageal and colic enteric plexuses surrounding neuronal cell bodies and axons. A dense net of GFAP-immunoreactive processes was seen in the ganglia and connecting strands of the myenteric plexus. bFGF immunoreactivity was observed in the cytoplasm of the majority of the neurons in the enteric ganglia of esophagus and colon. The two-color immunoperoxidase and immunofluorescence methods revealed bFGF immunoreactivity also in the nucleus of GFAP-positive enteric glial cells. The results suggest that immunohistochemical localization of NF and GFAP may be an important tool in the study of the plasticity in the enteric nervous system. The presence of bFGF in neurons and glia of the myenteric plexus of the esophagus and the colon indicates that this neurotrophic factor may exert autocrine and paracrine actions in the enteric nervous system.     

FGF-2 and S100beta immunoreactivities increase in reactive astrocytes, but not in microglia, in ascending dopamine pathways following a striatal 6-OHDA-induced partial lesion of the nigrostriatal system

Partial lesions were induced in rat midbrain dopamine ascending pathways by intrastriatal injection of 6-hydroxydopamine (6-OHDA), and after two weeks changes were observed in the immunoreactivities of S100beta, a calcium-binding protein, and basic fibroblast growth factor (FGF-2), which is neurotrophic. Semiquantitative microdensitometric image analysis revealed increased intensities of FGF-2 and S100beta immunostaining in putative glial profiles of the ipsilateral neostriatum, pars compacta (SNc) and reticulata (SNr) of the substantia nigra and ventral tegmental area (VTA). Double immunofluorescence and immunoperoxidase procedures, using antibodies against glial fibrillary acidic protein and OX-42, showed that these increased immunoreactivities were restricted to reactive astrocytes; they were not observed in reactive microglia. These results indicate that reactive astrocytes may exert paracrine trophic actions through S100beta and FGF-2 in the midbrain dopamine ascending pathways after striatal 6-OHDA treatment. Interactions between S100beta and FGF-2 may be relevant to neuronal maintenance and repair following dopamine injury.     

Forwarding Group Multicast Protocol (FGMP) for multihop, mobile wireless networks

In this paper we propose a new multicast protocol for multihop mobile wireless networks. Instead of forming multicast trees, a group of nodes in charge of forwarding multicast packets is designated according to members' requests. Multicast is then carried out via “scoped” flooding over such a set of nodes. The forwarding group is periodically refreshed to handle topology/membership changes. Multicast using forwarding group takes advantage of wireless broadcast transmissions and reduces channel and storage overhead, thus improving the performance and scalability. The key innovation with respect to wired multicast schemes like DVMRP is the use of flags rather than upstream/downstream link state, making the protocol more robust to mobility. The dynamic reconfiguration capability makes this protocol particularly suitable for mobile networks. The performance of the proposed scheme is evaluated via simulation and is compared to that of DVMRP and global flooding. This revised version was published online in August 2006 with corrections to the Cover Date.