Detection of regulatory variation in mouse genes

Functional polymorphism in genes can be classified as coding variation, altering the amino-acid sequence of the encoded protein, or regulatory variation, affecting the level or pattern of expression of the gene. Coding variation can be recognized directly from DNA sequence, and consequently its frequency and characteristics have been extensively described. By contrast, virtually nothing is known about the extent to which gene regulation varies in populations. Yet it is likely that regulatory variants are important in modulating gene function: alterations in gene regulation have been proposed to influence disease susceptibility and to have been the primary substrate for the evolution of species. Here, we report a systematic study to assess the extent of cis-acting regulatory variation in 69 genes across four inbred mouse strains. We find that at least four of these genes show allelic differences in expression level of 1.5-fold or greater, and that some of these differences are tissue specific. The results show that the impact of regulatory variants can be detected at a significant frequency in a genomic survey and suggest that such variation may have important consequences for organismal phenotype and evolution. The results indicate that larger-scale surveys in both mouse and human could identify a substantial number of genes with common regulatory variation.     

Effects of size and temperature on developmental time

Body size and temperature are the two most important variables affecting nearly all biological rates and times. The relationship of size and temperature to development is of particular interest, because during ontogeny size changes and temperature often varies. Here we derive a general model, based on first principles of allometry and biochemical kinetics, that predicts the time of ontogenetic development as a function of body mass and temperature. The model fits embryonic development times spanning a wide range of egg sizes and incubation temperatures for birds and aquatic ectotherms (fish, amphibians, aquatic insects and zooplankton). The model also describes nearly 75% of the variation in post-embryonic development among a diverse sample of zooplankton. The remaining variation is partially explained by stoichiometry, specifically the whole-body carbon to phosphorus ratio. Development in other animals at other life stages is also described by this model. These results suggest a general definition of biological time that is approximately invariant and common to all organisms.     

Dissection of COPI and Arf1 dynamics in vivo and role in Golgi membrane transport

Cytosolic coat proteins that bind reversibly to membranes have a central function in membrane transport within the secretory pathway. One well-studied example is COPI or coatomer, a heptameric protein complex that is recruited to membranes by the GTP-binding protein Arf1. Assembly into an electron-dense coat then helps in budding off membrane to be transported between the endoplasmic reticulum (ER) and Golgi apparatus. Here we propose and corroborate a simple model for coatomer and Arf1 activity based on results analysing the distribution and lifetime of fluorescently labelled coatomer and Arf1 on Golgi membranes of living cells. We find that activated Arf1 brings coatomer to membranes. However, once associated with membranes, Arf1 and coatomer have different residence times: coatomer remains on membranes after Arf1-GTP has been hydrolysed and dissociated. Rapid membrane binding and dissociation of coatomer and Arf1 occur stochastically, even without vesicle budding. We propose that this continuous activity of coatomer and Arf1 generates kinetically stable membrane domains that are connected to the formation of COPI-containing transport intermediates. This role for Arf1/coatomer might provide a model for investigating the behaviour of other coat protein systems within cells.     

Synaptotagmins I and IV promote transmitter release independently of Ca(2+) binding in the C(2)A domain

At nerve terminals, a focal and transient increase in intracellular Ca(2+) triggers the fusion of neurotransmitter-filled vesicles with the plasma membrane. The most extensively studied candidate for the Ca(2+)-sensing trigger is synaptotagmin I, whose Ca(2+)-dependent interactions with acidic phospholipids and syntaxin have largely been ascribed to its C(2)A domain, although the C(2)B domain also binds Ca(2+) (refs 7, 8). Genetic tests of synaptotagmin I have been equivocal as to whether it is the Ca(2+)-sensing trigger of fusion. Synaptotagmin IV, a related isoform that does not bind Ca(2+) in the C(2)A domain, might be an inhibitor of release. We mutated an essential aspartate of the Ca(2+)-binding site of the synaptotagmin I C(2)A domain and expressed it in Drosophila lacking synaptotagmin I. Here we show that, despite the disruption of the binding site, the Ca(2+)-dependent properties of transmission were not altered. Similarly, we found that synaptotagmin IV could substitute for synaptotagmin I. We conclude that the C(2)A domain of synaptotagmin is not required for Ca(2+)-dependent synaptic transmission, and that synaptotagmin IV promotes rather than inhibits transmission.     

Interspecific differences in grass seed imbibition

Seeds from 12 grass species were studied relative to mode of wetting and time of exposure to water to document interspecific differences in imbibition characteristics. Imbibition causes seeds to become wet, and wet seeds are more detectable to consumers than dry seeds. Thus, germination potential and ability to remain undetected by consumers may represent an important trade-off. Seeds wetted for 0-192 h in vials imbibed water at rates equivalent to seeds wetted by contact with wet paper towels pressing against their seed coat, except for seeds of Avena sativa , which weighed more after wetting in 2-mL vials with free water (0.471 g vs. 0.432 g). Seeds from different species imbibed water at different rates. These data show that interspecific variation in imbibition for seeds is high and support an expectation that imbibition potential can interact with detectability to consumers in an evolutionary trade-off.     

Phylogenetic divergence in a desert fish: differentiation of speckled dace within the Bonneville, Lahontan, and upper Snake river basins

Historical events have had a great impact on the biogeography of fishes of western North America. We examined the genetic variation of the speckled dace ( Rhinichthys osculus ) to determine the effects on this species of extensive hydrological changes during the last 10 million years in the Bonneville and Lahontan basins of the Great Basin and the upper Snake River Basin. Eight hundred sixty-nine base pairs of the mitochondrial gene cytochrome b were sequenced from 97 individuals representing 22 populations within these 3 basins, as well as from 2 individuals of longnose dace ( Rhinichthys cataractae ) that served as outgroups. Additionally, 13 speckled dace sequences representing 3 Bonneville populations were used from GenBank. Phylogenetic relationships were reconstructed using maximum parsimony and maximum likelihood criteria. Analysis of molecular variance was used to determine population structure and to estimate the amount of gene flow across the community boundaries. Three distinct clades were reconstructed representing the Lahontan Basin, the northern Bonneville and upper Snake River basins, and the southern Bonneville Basin. Additionally, most of the population structuring was explained by variation among basins (65.33%). Speckled dace demonstrated high genetic variation. As hypothesized, the northern and southern Bonneville specimens formed separate clades; however, the southern Bonneville clade was basal to a sister clade formed by the northern Bonneville/upper Snake River and Lahontan clades. These relationships indicate that Pliocene connections between the Snake, Lahontan, and Bonneville drainages, rather than more recent Pleistocene connections, best explain population structuring in speckled dace.     

Kanab ambersnail and other terrestrial snails in south central Utah

Surveys for succineid snails were conducted to improve genetic and geographical information for the endangered Kanab ambersnail ( Oxyloma haydeni kanabensis Pilsbry) and related taxa within the Succineidae. Surveys were carried out in the Bureau of Land Management Kanab District, at the Grand Staircase Escalante National Monument, on 3 private holdings, and along Highways 89, 12, and 14, all in south central Utah. A population of Kanab ambersnails was known to exist in the region; other populations of Oxyloma were discovered in primarily seep-fed wetlands in Kanab Creek and in tributaries of and wetlands along the Virgin, Sevier, and Escalante rivers in Kane, Garfield, and Piute counties. None of the newly discovered populations was identified as Kanab ambersnail on the basis of anatomical evidence, although one was at the type locale for that species. We list other snail species encountered and discuss the status of the Kanab ambersnail in light of recent genetic research.     

A comparison of mosquito consumption and prey selection between least chub ( Iotichthys phlegethontis ) and western mosquitofish ( Gambusia affinis )

We compared mosquito consumption and prey selection between least chub ( Iotichthys phlegethontis ) and western mosquitofish ( Gambusia affinis ) to determine the potential of least chub as an indigenous replacement for mosquito control in Utah. Mosquito consumption was compared between the 2 species in 2 experiments. The first tested consumption at 3 ratios of pupae and larvae ( Culex sp.; 1:3, 3:4, and 1:1), and the second tested consumption at varying densities of larvae (967 larvae ? m–3 , 1354 larvae ? m–3 , and 2258 larvae ? m–3 [30, 42, and 70 larvae per 31-L tank, respectively]). Western mosquitofish consumed more mosquitoes at lower pupae-to-larvae ratios than least chub, but least chub consumed more mosquitoes as the ratio of pupae to larvae increased. Western mosquitofish consumed significantly more larvae than least chub at all densities. Prey selection was compared between least chub and western mosquitofish, either individually or in intraspecific pairs, when the fish were fed equal abundances of 3 prey items: mosquito larvae, Daphnia magna , and midge larvae ( Chironomid sp.). Least chub consumed significantly fewer total prey items for both the 1- and 2-fish trials; western mosquitofish consumed significantly more individuals of each prey type except for Daphnia magna in the 1-fish trials. Least chub and western mosquitofish demonstrated no selection for prey items, indicating that both fish would consume mosquito larvae at rates relative to abundance. Feeding habits demonstrated in this study indicated that least chub could be a potential replacement for western mosquitofish for mosquito control; however, field studies should be conducted to assess the ability of both species to control mosquitoes in a natural setting.     

Can Townsend's ground squirrels survive on a diet of exotic annuals?

Southwestern Idaho desert shrub-bunchgrass rangeland is being invaded by fire-prone exotic annuals that permanently dominate the landscape following wildfires. This study was undertaken to describe diets of Townsend's ground squirrels ( Spermophilus townsendii idahoensis ) at four study sites with varying degrees of exotic annual invasion to determine if the squirrels could utilize high proportions of exotic annuals in their diets. Townsend's ground squirrels were collected in March and May of 1987 and 1988, and stomach contents were analyzed using a microhistological technique. Grasses comprised 37-87% of Townsend's ground squirrel diets at the four sites. Native species, especially Sandberg's bluegrass ( Poa secunda ), winterfat ( Ceratoides lanata ), big sagebrush ( Artemisia tridentata ) and six-weeks fescue ( Vulpia octoflora ) constituted 7-96% (x = 47.2%) of the diet, whereas exotic species, especially cheatgrass ( Bromus tectorum ), tumbleweed ( Salsola iberica ), and tansymustards ( Descurainia spp.) made up 4-68% (x = 48.0%) of the diet. At each site 2-4 species comprised >90% of the diet. There was no apparent correlation between the importance values of exotic species at a site and their importance in Townsend's ground squirrel diets.     

First episode psychosis with extrapyramidal signs prior to antipsychotic drug treatment

Extrapyramidal movement disorders are common in chronic schizophrenia, and may be an intrinsic feature of the illness as well as related to antipsychotic drug treatment. Similar dysfunctions at illness onset may have implications for outcome, and for under- standing the mechanisms of illness. The objectives were to examine the clinical correlates of pre-treatment movement disorders at first episode of psychosis, and determine associations with neuropsychological function and striatal structure. Never medicated subjects were recruited from consecutive admissions to Early Psychosis Programs with defined catchment areas in Hong Kong, China, and Halifax, Canada. Standardized clinical, neuropsychological and brain imaging assessments were carried out at baseline and following acute and long term treatment with typical or atypical antipsychotic drugs. At the Hong Kong site, we studied 84 subjects with first episode psychosis (n = 10 with EPS). At the Halifax site, we studied 40 subjects with first episode psychosis (n = 17 with EPS), and 23 healthy comparison subjects. Subjects with movement disorders prior to treatment (EPS+) had higher total PANSS scores at baseline (mean elevation 19.9% Hong Kong, P = 0.016; 14.7% Halifax, P = 0.049). In subjects treated with atypical antipsychotics (all Halifax), EPS+ status at baseline predicted more movement disorders at long term follow up (P = 0.0005). In both cohorts, EPS+ subjects had poorer acute symptomatic treatment response assessed with the PANSS (Hong Kong P = 0.005; Halifax P = 0.017). Neuropsychological impairment related to executive dysfunction appeared greater in a small sam- ple of EPS+ subjects (Hong Kong, effect size 0.26-0.27, P < 0.05). Caudate volumes were 4.5% larger in EPS+ compared with EPS-subjects (Halifax P = 0.042), and correlations between striatal volumes and age were different in the EPS+ group. In conclu- sion, pre-treatment EPS is present in a substantial minority of subjects with first episode psychosis, appears to persist at long term follow up, and is associated with poorer response of symptoms to treatment. Selective impairment of executive function and stria- tal enlargement provides evidence of abnormalities of brain function and structure associated with this aspect of early psychosis.