Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum Information About a Microarray Experiment (MIAME), that describes the minimum information required to ensure that microarray data can be easily interpreted and that results derived from its analysis can be independently verified. The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools. With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it.     

Myeloid leukaemia inhibitory factor maintains the developmental potential of embryonic stem cells

Embryonic stem (ES) cells, the totipotent outgrowths of blastocysts, can be cultured and manipulated in vitro and then returned to the embryonic environment where they develop normally and can contribute to all cell lineages. Maintenance of the stem-cell phenotype in vitro requires the presence of a feeder layer of fibroblasts or of a soluble factor, differentiation inhibitory activity (DIA) produced by a number of sources; in the absence of DIA the ES cells differentiate into a wide variety of cell types. We recently noted several similarities between partially purified DIA and a haemopoietic regulator, myeloid leukaemia inhibitory factor (LIF), a molecule which induces differentiation in M1 myeloid leukaemic cells and which we have recently purified, cloned and characterized. We demonstrate here that purified, recombinant LIF can substitute for DIA in the maintenance of totipotent ES cell lines that retain the potential to form chimaeric mice.     

High levels of gene flow in the California vole ( Microtus californicus ) are consistent across spatial scales

Gene flow links the genetic and demographic structures of species. Despite the fact that similar genetic and demographic patterns shape both local population structure and regional phylogeography, the 2 levels of population connectivity are rarely studied simultaneously. Here, we studied gene flow in the California vole ( Microtus californicus ), a small-bodied rodent with limited vagility but high local abundance. Within a 4.86-km 2 preserve in central California, genetic diversity in 6 microsatellites was high, and Bayesian methods indicated a single genetic cluster. However, individual-based genetic analysis detected a clear signal for isolation-by-distance (IBD) and fine-scale population structure. Mitochondrial cytochrome b sequencing revealed 11 unique haplotypes from the one local area where we sequenced 62 individuals. Phylogeographic analysis of these individuals combined with those sampled from the northern geographic range of the species (the range of the species spans western North America from southern Oregon to northern Mexico and is centered geographically within the state of California) again indicated a lack of structure but a signal for IBD. Patterns of gene flow thus are consistent across spatial scales: while dispersal of the California vole is limited across geographic distance, there is nonetheless considerable movement across the landscape. We conclude that in this species, high local population abundances overcome the potential genetic and demographic effects of limited dispersal.     

Foliage age as a factor in food utilization by the western spruce budworm, Choristoneura occidentalis

The influence of current year foliage age on food consumption and utilization by the western spruce budworm, Choristoneura occidentalis (Lepidoptera:Tortricidae), was examined. Larvae were fed immature foliage of Douglas-fir ( Pseudotsuga menziesii var. glauca ), Engelmann spruce ( Picea engelmannii ), and corkbark fir ( Abies lasiocarpa var. arizonica ) in June and August of 1981 and Douglas fir in June and July of 1982. All larvae feeding on early season (June) foliage reached maturity. Larvae feeding on middle (July) and late (August) season foliage died before reaching pupation. Relative growth rate and efficiency of conversion of ingested food decreased with foliage age in both the 1981 and 1982 experiments. Relative consumption rate increased with foliage age in the 1981 and decreased in the 1982 experiment.     

Size, structure, and habitat characteristics of populations of Braya humilis var. humilis (Brassicaceae): an alpine disjunct from Colorado

Size, structure, and habitat characteristics were studied in three populations of Braya humilis var. humilis (C. A. Meyer) Robins, in Gray & Wats. (Brassicaceae), a small, herbaceous perennial of the alpine tundra in central Colorado. There was a significant association between numbers of reproductive, juvenile, and seedling individuals and population location. Plant size within reproductive, juvenile, and seedling size classes varied significantly among three populations. Plots containing Braya had significantly lower total plant cover, a different set of dominant plant species, more rock, bare ground, and less litter than plots without Braya . Braya appears to be restricted to calcareous substrates that experience a moderate level of disturbance, such as solifluction lobes and abandoned roads. Populations are small despite the existence of much potential habitat. Population studies are necessary for active conservation management of Braya .     

Estimates of site potential for Douglas-fir based on site index for several southwestern habitat types

Estimates of site potential for Douglas-fir based on measured site indexes in 450 stands are compared between 10 southwestern habitat types. Significant differences in site potential are found between the habitat types studied.     

Life histories of stoneflies (Plecoptera) in the Rio Conejos of southern Colorado

Thirty-one stonefly species representing eight families were collected during the March 1987 to May 1990 study period. Genera represented by more than one species included Capnia, Utacapnia, Taenionema, Suwallia, Triznaka, Isogenoides, and Isoperla . Peak species richness was recorded on or near the summer solstice in 1988 and 1989. Climatic differences between years were reflected in nymphal development and emergence phenology of most species. New or important corroborative life history data are presented for 11 stonefly species of this assemblage. The hyporheic nymphal development of most cholroperlid species limited the number of early instars sampled and our capacity to interpret voltinism. Limited nymphal data suggested a univoltine-slow cycle for Plumiperla diversa (Frison). Adults of Suwallia pallidula (Banks) and S. wardi (Banks) were present for an extended summer period, but the bulk of their respective emergence times was temporally separated. Isogenoides zionensis Hanson, Pteronarcella badia (Hagen), and Pteronarcys californica Newport were all shown for the first time to have a 9-10 mo egg diapauses, and all three species have a semivoltine life cycle. Skwala Americana (Klápalek) and Isoperla fulva Claassen were further confirmed to have univoltine-slow cycles. Univoltine-fast and univoltine-slow life cycles are reported for the first time in I. phalerata and I. quinquepunctata , respectively. Regression analysis revealed that six of the eight abunduant species had extended emergence patterns (slopes of < 5%/d), while only two had synchronous patterns. Warmer spring and summer temperatures in 1989 increased the slopes for five of the eight species studied, but did not change their synchrony designation. Nine of 11 abundant species advanced their median emergence date in 1989 over 1988. This and the higher slope values are consistent with a hurried nymphal development and narrower emergence period due to the warmer thermal regime of 1989.     

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis. Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding 'higher' Nasutitermes species (which do not contain cellulose-fermenting protozoa) to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important symbiotic functions including H2 metabolism, CO2-reductive acetogenesis and N2 fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-microl environment can be.     

Low beta diversity of herbivorous insects in tropical forests

Recent advances in understanding insect communities in tropical forests have contributed little to our knowledge of large-scale patterns of insect diversity, because incomplete taxonomic knowledge of many tropical species hinders the mapping of their distribution records. This impedes an understanding of global biodiversity patterns and explains why tropical insects are under-represented in conservation biology. Our study of approximately 500 species from three herbivorous guilds feeding on foliage (caterpillars, Lepidoptera), wood (ambrosia beetles, Coleoptera) and fruit (fruitflies, Diptera) found a low rate of change in species composition (beta diversity) across 75,000 square kilometres of contiguous lowland rainforest in Papua New Guinea, as most species were widely distributed. For caterpillars feeding on large plant genera, most species fed on multiple host species, so that even locally restricted plant species did not support endemic herbivores. Large plant genera represented a continuously distributed resource easily colonized by moths and butterflies over hundreds of kilometres. Low beta diversity was also documented in groups with differing host specificity (fruitflies and ambrosia beetles), suggesting that dispersal limitation does not have a substantial role in shaping the distribution of insect species in New Guinea lowland rainforests. Similar patterns of low beta diversity can be expected in other tropical lowland rainforests, as they are typically situated in the extensive low basins of major tropical rivers similar to the Sepik-Ramu region of New Guinea studied here.