Spatial proximity of translocation-prone gene loci in human lymphomas

Cancer cells frequently have disease-specific chromosome rearrangements. It is poorly understood why translocations between chromosomes recur at specific breakpoints in the genome. Here we provide evidence that higher-order spatial genome organization is a contributing factor in the formation of recurrent translocations. We show that MYC, BCL and immunoglobulin loci, which are recurrently translocated in various B-cell lymphomas, are preferentially positioned in close spatial proximity relative to each other in normal B cells. Loci in spatial proximity are non-randomly positioned towards the nuclear interior in normal B cells. This locus proximity is the consequence of higher-order genome structure rather than a property of individual genes. Our results suggest that the formation of specific translocations in human lymphomas, and perhaps other tissues, is determined in part by higher-order spatial organization of the genome.     

Dax1 is required for testis determination

The orphan nuclear receptor, Dax1, was originally proposed to act as an 'anti-testis' factor. We find, however, that Nr0b1 (also called Dax1 and Ahch, which encodes Dax1) is in fact required for testis differentiation.     

Wnt proteins are lipid-modified and can act as stem cell growth factors

Wnt signalling is involved in numerous events in animal development, including the proliferation of stem cells and the specification of the neural crest. Wnt proteins are potentially important reagents in expanding specific cell types, but in contrast to other developmental signalling molecules such as hedgehog proteins and the bone morphogenetic proteins, Wnt proteins have never been isolated in an active form. Although Wnt proteins are secreted from cells, secretion is usually inefficient and previous attempts to characterize Wnt proteins have been hampered by their high degree of insolubility. Here we have isolated active Wnt molecules, including the product of the mouse Wnt3a gene. By mass spectrometry, we found the proteins to be palmitoylated on a conserved cysteine. Enzymatic removal of the palmitate or site-directed and natural mutations of the modified cysteine result in loss of activity, and indicate that the lipid is important for signalling. The purified Wnt3a protein induces self-renewal of haematopoietic stem cells, signifying its potential use in tissue engineering.     

Systematic variation in gene expression patterns in human cancer cell lines

We used cDNA microarrays to explore the variation in expression of approximately 8,000 unique genes among the 60 cell lines used in the National Cancer Institute's screen for anti-cancer drugs. Classification of the cell lines based solely on the observed patterns of gene expression revealed a correspondence to the ostensible origins of the tumours from which the cell lines were derived. The consistent relationship between the gene expression patterns and the tissue of origin allowed us to recognize outliers whose previous classification appeared incorrect. Specific features of the gene expression patterns appeared to be related to physiological properties of the cell lines, such as their doubling time in culture, drug metabolism or the interferon response. Comparison of gene expression patterns in the cell lines to those observed in normal breast tissue or in breast tumour specimens revealed features of the expression patterns in the tumours that had recognizable counterparts in specific cell lines, reflecting the tumour, stromal and inflammatory components of the tumour tissue. These results provided a novel molecular characterization of this important group of human cell lines and their relationships to tumours in vivo.     

Insights into SCF ubiquitin ligases from the structure of the Skp1-Skp2 complex

F-box proteins are members of a large family that regulates the cell cycle, the immune response, signalling cascades and developmental programmes by targeting proteins, such as cyclins, cyclin-dependent kinase inhibitors, IkappaBalpha and beta-catenin, for ubiquitination (reviewed in refs 1-3). F-box proteins are the substrate-recognition components of SCF (Skp1-Cullin-F-box protein) ubiquitin-protein ligases. They bind the SCF constant catalytic core by means of the F-box motif interacting with Skp1, and they bind substrates through their variable protein-protein interaction domains. The large number of F-box proteins is thought to allow ubiquitination of numerous, diverse substrates. Most organisms have several Skp1 family members, but the function of these Skp1 homologues and the rules of recognition between different F-box and Skp1 proteins remain unknown. Here we describe the crystal structure of the human F-box protein Skp2 bound to Skp1. Skp1 recruits the F-box protein through a bipartite interface involving both the F-box and the substrate-recognition domain. The structure raises the possibility that different Skp1 family members evolved to function with different subsets of F-box proteins, and suggests that the F-box protein may not only recruit substrate, but may also position it optimally for the ubiquitination reaction.     

On local realism and commutativity

James D. Malley and Arthur Fine have argued that interest in noncontextual hidden variable theories is misplaced because at bottom such theories are simply attempts to turn noncommuting quantities into commuting ones. We disagree and argue that the issues are richer and more complex.     

Regional and seasonal diet of the Western Burrowing Owl in south central Nevada

We examined diets of Western Burrowing Owls ( Athene cunicularia hypugaea ) based on contents of pellets and large prey remains collected year-round at burrows in each of the 3 regions in south central Nevada (Mojave Desert, Great Basin Desert, and Transition region). The most common prey items, based on percent frequency of occurrence, were crickets and grasshoppers, beetles, rodents, sun spiders, and scorpions. The most common vertebrate prey was kangaroo rats ( Dipodomys spp.). True bugs (Hemiptera), scorpions, and western harvest mice ( Reithrodontomys megalotis ) occurred most frequently in pellets from the Great Basin Desert region. Kangaroo rats ( Dipodomys spp.) and pocket mice (Perognathinae) were the most important vertebrate prey items in the Transition and Mojave Desert regions, respectively. Frequency of occurrence of any invertebrate prey was high (>80%) in samples year-round but dropped in winter samples, with scorpions and sun spiders exhibiting the steepest declines. Frequency of occurrence of any vertebrate prey peaked in spring samples, was intermediate for winter and summer samples, and was lowest in fall samples. With the possible exception of selecting for western harvest mice in the Great Basin Desert region, Western Burrowing Owls in our study appeared to be opportunistic foragers with a generalist feeding strategy.     

Timing, distribution, and abundance of kokanees spawning in a Lake Tahoe tributary

We counted kokanee spawners and carcasses every 1-7 days from mid-September through mid-November in 1991 and 1992 in Taylor Creek, a tributary to Lake Tahoe, California-Nevada. Less than 1% of the spawning run entered Taylor Creek before flow from Fallen Leaf Lake was increased on 2 October 1991; in 1992 the peak occurred on 30 September or 1 October after flows increased on 29 September. In both years spawners concentrated in the middle three of five stream reaches below the impassable Fallen Leaf Lake dam. From tab-and-recovery experiments, the average longevity of male spawners in the stream was 3.5 days in 1991 and 2.8 days in 1992, whereas the average female longevity was 2.0 days in 1991 and 2.3 days in 1992. Observed carcasses accounted for less than 10% of spawners counted, suggesting removal by scavengers or high predation on prespawners. An estimated 1928 males and 1309 females spawned in 1991, and 8021 males and 8712 females spawned in 1992. Our estimate of 3237 spawners in 1991 compared favorably to our estimate of 3520 ± 1474 prespawners staging in Lake Tahoe in mid-September. An index of kokanee abundance in Lake Tahoe has historically been based on 1-day surveys every 1 November since 1960; however, estimated total spawner abundance was 19 times higher than the annual index of 158 spawners in 1991, 141 times higher than the index count of 100 spawners in 1992. The index count and mean fork lengths of spawners (278 ± 10 mm [2 SE] for males, and 248 ± 3 mm for females) in 1991 and 1992 were the lowest on record.     

Arthropod community dynamics in undisturbed and intensively managed mountain brush habitats

The population dynamics and decomposition activities of litter arthropods in an unmanaged sagehrush/bitterbrush habitat in southeastern Wyoming were assessed in 1986. The effects of sagebrush/bitterbrush management practices on litter arthropod communities and the role of these communities in decomposition were also assessed. Insecticide applications were used to selectively exclude arthropods in order to determine the ecological impact of these detritivores. Application of a herbicide, 2,4-D, was associated with increased arthropod populations for 30 days following treatment. Mowing increased arthropod densities at two different times, 10-30 days and 50 days post treatment, perhaps as a result of functional and numerical responses by litter arthropods. Elimination of arthropods from otherwise undisturbed shrub habitats by the use of broad-spectrum insecticides reduced the rate of litter decomposition during the growing season, indicating that these organisms play an important role in decomposition and nutrient cycling.