Panhandle PCR strategy to amplify MLL genomic breakpoints in treatment-related leukemias

Panhandle PCR amplifies genomic DNA with known 5′ and unknown 3′ sequences from a template with an intrastrand loop schematically shaped like a pan with a handle. We used panhandle PCR to clone MLL genomic breakpoints in two pediatric treatment-related leukemias. The karyotype in a case of treatment-related acute lymphoblastic leukemia showed the t(4;11)(q21;q23). Panhandle PCR amplified the translocation breakpoint at position 2158 in intron 6 in the 5′ MLL breakpoint cluster region (bcr). The karyotype in a case of treatment-related acute myeloid leukemia was normal, but Southern blot analysis showed a single MLL gene rearrangement. Panhandle PCR amplified the breakpoint at position 1493 in MLL intron 6. Screening of somatic cell hybrid and radiation hybrid DNAs by PCR and reverse transcriptase-PCR analysis of the leukemic cells indicated that panhandle PCR identified a fusion of MLL intron 6 with a previously uncharacterized sequence in MLL intron 1, consistent with a partial duplication. In both cases, the breakpoints in the MLL bcr were in Alu repeats, and there were Alu repeats in proximity to the breakpoints in the partner DNAs, suggesting that Alu sequences were relevant to these rearrangements. This study shows that panhandle PCR is an effective method for cloning MLL genomic breakpoints in treatment-related leukemias. Analysis of additional pediatric cases will determine whether breakpoint distribution deviates from the predilection for 3′ distribution in the bcr that has been found in adult cases.

The delayed resurgence of equatorial forests after the Permian–Triassic ecologic crisis

In conjunction with the Permian–Triassic ecologic crisis ≈250 million years ago, massive dieback of coniferous vegetation resulted in a degradation of terrestrial ecosystems in Europe. A 4- to 5-million-year period of lycopsid dominance followed, and renewed proliferation of conifers did not occur before the transition between Early and Middle Triassic. We document this delayed re-establishment of equatorial forests on the basis of palynological data. The reconstructed pattern of vegetational change suggests that habitat restoration, migration, and evolutionary processes acted synergistically, setting the stage for successional replacement of lycopsid dominants by conifers within a period of ≈0.5 million years.

Predicting species diversity in tropical forests

A fundamental question in ecology is how many species occur within a given area. Despite the complexity and diversity of different ecosystems, there exists a surprisingly simple, approximate answer: the number of species is proportional to the size of the area raised to some exponent. The exponent often turns out to be roughly 1/4. This power law can be derived from assumptions about the relative abundances of species or from notions of self-similarity. Here we analyze the largest existing data set of location-mapped species: over one million, individually identified trees from five tropical forests on three continents. Although the power law is a reasonable, zeroth-order approximation of our data, we find consistent deviations from it on all spatial scales. Furthermore, tropical forests are not self-similar at areas ≤50 hectares. We develop an extended model of the species-area relationship, which enables us to predict large-scale species diversity from small-scale data samples more accurately than any other available method.