Initial sequencing and comparative analysis of the mouse genome

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.     

The tyrosine phosphatase SHP-1 negatively regulates cytotrophoblast proliferation in first-trimester human placenta by modulating EGFR activation

Insulin-like growth factors (IGFs) influence placental cell (cytotrophoblast) kinetics. We recently reported that the protein tyrosine phosphatase (PTP) SHP-2 positively regulates IGF actions in the placenta. In other systems, the closely related PTP, SHP-1, functions as a negative regulator of signaling events but its role in the placenta is still unknown. We examined the hypothesis that SHP-1 negatively regulates IGF actions in the human placenta. Immunohistochemical (IHC) analysis demonstrated that SHP-1 is abundant in cytotrophoblast. SHP-1 expression was decreased in first-trimester placental explants using siRNA; knockdown did not alter IGF-induced proliferation but it significantly enhanced proliferation in serum-free conditions, revealing that placental growth is endogenously regulated. Candidate regulators were determined by using antibody arrays, Western blotting, and IHC to examine the activation status of multiple receptor tyrosine kinases (RTKs) in SHP-1-depleted explants; amongst the alterations observed was enhanced activation of EGFR, suggesting that SHP-1 may interact with EGFR to inhibit proliferation. The EGFR tyrosine kinase inhibitor PD153035 reversed the elevated proliferation seen in the absence of SHP-1. This study demonstrates a role for SHP-1 in human trophoblast turnover and establishes SHP-1 as a negative regulator of EGFR activation. Targeting placental SHP-1 expression may provide therapeutic benefits in common pregnancy conditions with abnormal trophoblast proliferation.     

Characterizing a first occurrence of bison deposits in southeastern Nevada

Late Holocene bison bones eroding from the badlands topography of Cathedral Gorge State Park in southeastern Nevada have been identified as the remains of Bison and date between approximately 400 and 850 years old. The bones were originally thought to be turn-of-the-century cattle and then early bison, so park personnel had need to solve this interpretive problem. A multidisciplinary team sought information on archaeology, geomorphology, paleontology, and paleoenvironment to document the 1st established occurrence of bison in this part of Nevada and to develop a hypothesis explaining their demise.     

Non-B DNA structure-induced genetic instability and evolution

Repetitive DNA motifs are abundant in the genomes of various species and have the capacity to adopt non-canonical (i.e., non-B) DNA structures. Several non-B DNA structures, including cruciforms, slipped structures, triplexes, G-quadruplexes, and Z-DNA, have been shown to cause mutations, such as deletions, expansions, and translocations in both prokaryotes and eukaryotes. Their distributions in genomes are not random and often co-localize with sites of chromosomal breakage associated with genetic diseases. Current genome-wide sequence analyses suggest that the genomic instabilities induced by non-B DNA structure-forming sequences not only result in predisposition to disease, but also contribute to rapid evolutionary changes, particularly in genes associated with development and regulatory functions. In this review, we describe the occurrence of non-B DNA-forming sequences in various species, the classes of genes enriched in non-B DNA-forming sequences, and recent mechanistic studies on DNA structure-induced genomic instability to highlight their importance in genomes.     

Observations on the developmental biology of Cicindela arenicola Rumpp (Coleoptera: Cicindelidae)

Cicindela arenicola Rumpp is being considered for threatened and endangered status by the U.S. Fish and Wildlife Service. Little is known about the developmental biology of this species. Adults of C. arenicola were active from April through late June and late August through early November, but generally they were not on the surface when temperatures were below 19 C or above 45 C, or when conditions were windy, cloudy, or rainy. Mating and egg-laying occurred only during the spring. Five size classes (1-,2-,3-,4-, and 5-mm diameters) of larval burrow openings were observed. Burrows of 5 mm had a mean depth of 42.23 ± 8.81 cm (1 S.D.). Larvae of C. arenicola were active from April through June and late September through mid-November. Developmental times and larval size were affected by food supplementation. Nearly all food-supplemented, 1-mm, first instars molted to larger second instars of3-mm diameter. Most nonsupplemented larvae spent several months as 2-mm second instars before growing to 3 mm in diameter. Food-supplemented larvae reached the third instar in approximately 13 months, while nonsupplemented larvae took slightly over two years to reach this stage. Development from egg to adult was estimated at two years for food-supplemented larvae and three and one-half to four years for nonsupplemented larvae. Cattle had a significant effect on larval mortality. A high percentage (76-80%) of larval C. arenicola that were stepped on by cattle never reopened their burrows. Only 14% of undisturbed larvae never reopened their burrows. Approximately 15% of 150 larvae marked in 1988 reopened burrows in 1989.     

Geography of exotic plants adjacent to campgrounds, Yellowstone National Park, USA

Eleven campgrounds in Yellowstone National Park were studied to determine the geography of 10 specific exotic plant species adjacent to campgrounds. Exotics were found in only 6 campgrounds. Six species were found at Mammoth campground, a low-elevation, dry site with year-round use. Only 2 species were found in the other 5 campgrounds. Exotics decreased with distance from Mammoth campground out to 6 m and then increased, suggesting a spread in their distribution. Significant associations were found between exotic presence and both open and closed canopies and low levels of disturbance. Generally, exotics decreased with an increase in cover of other vegetation forms. Five species were found most frequently in big sagebrush habitat types.     

Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence strategies to kill its host. U. maydis belongs to the group of biotrophic parasites (the smuts) that depend on living tissue for proliferation and development. Here we report the genome sequence for a member of this economically important group of biotrophic fungi. The 20.5-million-base U. maydis genome assembly contains 6,902 predicted protein-encoding genes and lacks pathogenicity signatures found in the genomes of aggressive pathogenic fungi, for example a battery of cell-wall-degrading enzymes. However, we detected unexpected genomic features responsible for the pathogenicity of this organism. Specifically, we found 12 clusters of genes encoding small secreted proteins with unknown function. A significant fraction of these genes exists in small gene families. Expression analysis showed that most of the genes contained in these clusters are regulated together and induced in infected tissue. Deletion of individual clusters altered the virulence of U. maydis in five cases, ranging from a complete lack of symptoms to hypervirulence. Despite years of research into the mechanism of pathogenicity in U. maydis, no 'true' virulence factors had been previously identified. Thus, the discovery of the secreted protein gene clusters and the functional demonstration of their decisive role in the infection process illuminate previously unknown mechanisms of pathogenicity operating in biotrophic fungi. Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens.     

Dynamic assembly of silent chromatin during thymocyte maturation

Considerable knowledge has been gained from temporal analyses of molecular events culminating in gene activation, but technical hurdles have hindered comparable studies of gene silencing. Here we describe the temporal assembly of silent chromatin at the mouse terminal transferase gene (Dntt), which is silenced and repositioned to pericentromeric heterochromatin during thymocyte maturation. Silencing was nucleated at the Dntt promoter by the ordered deacetylation of histone H3 at Lys9 (H3-Lys9), loss of methylation at H3-Lys4 and acquisition of methylation at H3-Lys9, followed by bidirectional spreading of each event. Deacetylation at H3-Lys9 coincided with pericentromeric repositioning, and neither of these early events required de novo protein synthesis. CpG methylation increased primarily in mature T cells that had left the thymus. A transformed thymocyte line supported reversible inactivation of Dntt without repositioning. In these cells, histone modification changes were nucleated at the promoter but did not spread. These results provide a foundation for elucidating the mechanisms of silent chromatin assembly during development.