Asymmetric and symmetric stem-cell divisions in development and cancer

Much has been made of the idea that asymmetric cell division is a defining characteristic of stem cells that enables them to simultaneously perpetuate themselves (self-renew) and generate differentiated progeny. Yet many stem cells can divide symmetrically, particularly when they are expanding in number during development or after injury. Thus, asymmetric division is not necessary for stem-cell identity but rather is a tool that stem cells can use to maintain appropriate numbers of progeny. The facultative use of symmetric or asymmetric divisions by stem cells may be a key adaptation that is crucial for adult regenerative capacity.     

A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC

The proteins encoded by the classical HLA class I and class II genes in the major histocompatibility complex (MHC) are highly polymorphic and are essential in self versus non-self immune recognition. HLA variation is a crucial determinant of transplant rejection and susceptibility to a large number of infectious and autoimmune diseases. Yet identification of causal variants is problematic owing to linkage disequilibrium that extends across multiple HLA and non-HLA genes in the MHC. We therefore set out to characterize the linkage disequilibrium patterns between the highly polymorphic HLA genes and background variation by typing the classical HLA genes and >7,500 common SNPs and deletion-insertion polymorphisms across four population samples. The analysis provides informative tag SNPs that capture much of the common variation in the MHC region and that could be used in disease association studies, and it provides new insight into the evolutionary dynamics and ancestral origins of the HLA loci and their haplotypes.     

Such small hands: the roles of centrins/caltractins in the centriole and in genome maintenance

Centrins are small, highly conserved members of the EF-hand superfamily of calcium-binding proteins that are found throughout eukaryotes. They play a major role in ensuring the duplication and appropriate functioning of the ciliary basal bodies in ciliated cells. They have also been localised to the centrosome, which is the major microtubule organising centre in animal somatic cells. We describe the identification, cloning and characterisation of centrins in multiple eukaryotic species. Although centrins have been implicated in centriole biogenesis, recent results have indicated that centrosome duplication can, in fact, occur in the absence of centrins. We discuss these data and the non-centrosomal functions that are emerging for the centrins. In particular, we discuss the involvement of centrins in nucleotide excision repair, a process that repairs the DNA lesions that are induced primarily by ultraviolet irradiation. We discuss how centrin may be involved in these diverse processes and contribute to nuclear and cytoplasmic events.     

Reproductive ecology of Dusky Flycatchers in montane meadows of the central Sierra Nevada

Avian species with expansive ranges or those that occupy more than one vegetative association may vary in aspects of their life histories across their ranges. The distribution of Dusky Flycatchers encompasses a variety of vegetative associations, including riparian communities. However, much of the literature on this species details studies conducted in upland areas. Our objectives were to describe the breeding ecology and fecundity of Dusky Flycatchers nesting in montane meadows of the central Sierra Nevada, California. We monitored 36 territories and located 37 Dusky Flycatcher nests in 8 meadows. Average clutch size was 3.9 eggs. Egg laying, incubation, and nestling stages were 4, 15.4, and 16.4 days, respectively. Eighteen nests successfully fledged young, with an average of 3.3 fledglings per successful nest. Nest success was 43% and nest predation was the leading cause of nest failure. Estimated annual fecundity was 1.62 fledglings per pair; however, because all renesting attempts were not located, this should be viewed as the minimum annual fecundity. Dusky Flycatchers we monitored may have had higher fecundity than those nesting in upland areas because riparian areas often have higher arthropod abundances. While the importance of riparian conservation to riparian-obligate bird species is obvious, our study indicates that these areas also may be of value to Dusky Flycatchers that breed in riparian areas and upland areas.     

Behavioral activities and breeding success of Willow Flycatchers in the Sierra Nevada

Observing survival and how individuals allocate time can provide insight into a species' ability to tolerate environmental constraints. We studied the Willow Flycatcher ( Empidonax trallii ) in the Sierra Nevada to determine if there were behavioral differences between pairs that successfully produced offspring and those that did not. This information will advance understanding of why these birds are declining in the Sierra Nevada and contribute to recommendations that may help to conserve them. We studied birds in 13 meadows in 2000 and 2001 using continuous focal-animal observations. Of the 43 territories we observed, 11 were occupied by males who never paired with a female, leaving 32 pairs for analysis. Of the 32 pairs, 13 were successful at breeding on their 1st attempt, and 9 pairs failed at their initial try but were successful on their 2nd breeding attempt. Throughout the breeding season, Willow Flycatchers spent 77%-78% of the day loafing during territory establishment and nest building, and loafing reached a low of 49% of the time budget during the nestling stage. Unsuccessful pairs spent on average 34% more time perching than their successful counterparts, while successful pairs spent on average 48% more of their time on the nest than unsuccessful pairs. Willow Flycatchers doubled the time spent foraging during the nestling phase because they had to meet the daily intake requirements for their young and themselves. Our results suggest that birds that spent more time on the nest and less time vocalizing had a significantly higher probability of successfully producing young because they were able to protect nests from predators, nest parasites, and inclement weather.     

Closing gaps in the human genome with fosmid resources generated from multiple individuals

The human genome sequence has been finished to very high standards; however, more than 340 gaps remained when the finished genome was published by the International Human Genome Sequencing Consortium in 2004. Using fosmid resources generated from multiple individuals, we targeted gaps in the euchromatic part of the human genome. Here we report 2,488,842 bp of previously unknown euchromatic sequence, 363,114 bp of which close 26 of 250 euchromatic gaps, or 10%, including two remaining euchromatic gaps on chromosome 19. Eight (30.7%) of the closed gaps were found to be polymorphic. These sequences allow complete annotation of several human genes as well as the assignment of mRNAs. The gap sequences are 2.3-fold enriched in segmentally duplicated sequences compared to the whole genome. Our analysis confirms that not all gaps within 'finished' genomes are recalcitrant to subcloning and suggests that the paired-end-sequenced fosmid libraries could prove to be a rich resource for completion of the human euchromatic genome.     

Fine-scale structural variation of the human genome

Inversions, deletions and insertions are important mediators of disease and disease susceptibility. We systematically compared the human genome reference sequence with a second genome (represented by fosmid paired-end sequences) to detect intermediate-sized structural variants >8 kb in length. We identified 297 sites of structural variation: 139 insertions, 102 deletions and 56 inversion breakpoints. Using combined literature, sequence and experimental analyses, we validated 112 of the structural variants, including several that are of biomedical relevance. These data provide a fine-scale structural variation map of the human genome and the requisite sequence precision for subsequent genetic studies of human disease.