A natural allele of Nxf1 suppresses retrovirus insertional mutations

Endogenous retroviruses have shaped the evolution of mammalian genomes. Host genes that control the effects of retrovirus insertions are therefore of great interest. The modifier-of-vibrator-1 locus (Mvb1) controls levels of correctly processed mRNA from genes mutated by endogenous retrovirus insertions into introns, including the Pitpn(vb) tremor mutation and the Eya1(BOR) model of human branchiootorenal syndrome. Positional complementation cloning identifies Mvb1 as the nuclear export factor Nxf1, providing an unexpected link between the mRNA export receptor and pre-mRNA processing. Population structure of the suppressive allele in wild Mus musculus castaneus suggests selective advantage. A congenic Mvb1(CAST) allele is a useful tool for modifying gene expression from existing mutations and could be used to manipulate engineered mutations containing retroviral elements.     

Ru2 and Ru encode mouse orthologs of the genes mutated in human Hermansky-Pudlak syndrome types 5 and 6

Hermansky-Pudlak syndrome (HPS) is a genetically heterogeneous disease involving abnormalities of melanosomes, platelet dense granules and lysosomes. Here we have used positional candidate and transgenic rescue approaches to identify the genes mutated in ruby-eye 2 and ruby-eye mice (ru2 and ru, respectively), two 'mimic' mouse models of HPS. We also show that these genes are orthologs of the genes mutated in individuals with HPS types 5 and 6, respectively, and that their protein products directly interact. Both genes are previously unknown and are found only in higher eukaryotes, and together represent a new class of genes that have evolved in higher organisms to govern the synthesis of highly specialized lysosome-related organelles.     

Egg recognition and counting reduce costs of avian conspecific brood parasitism

Birds parasitized by interspecific brood parasites often adopt defences based on egg recognition but such behaviours are puzzlingly rare in species parasitized by members of the same species. Here I show that conspecific egg recognition is frequent, accurate and used in three defences that reduce the high costs of conspecific brood parasitism in American coots. Hosts recognized and rejected many parasitic eggs, reducing the fitness costs of parasitism by half. Recognition without rejection also occurred and some hosts banished parasitic eggs to inferior outer incubation positions. Clutch size comparisons revealed that females combine egg recognition and counting to make clutch size decisions--by counting their own eggs, while ignoring distinctive parasitic eggs, females avoid a maladaptive clutch size reduction. This is clear evidence that female birds use visual rather than tactile cues to regulate their clutch sizes, and provides a rare example of the ecological and evolutionary context of counting in animals.     

Habitat features and predictive habitat modeling for the Colorado chipmunk in southern New Mexico

Two subspecies of Colorado chipmunk (state threatened and federal species of concern) occur in southern New MeXico: Tamias quadrivittatus australis in the Organ Mountains and T. q. oscuraensis in the Oscura Mountains. We developed a GIS model of potentially suitable habitat based on vegetation and elevation features, evaluated site classifications of the GIS model, and determined vegetation and terrain features associated with chipmunk occurrence. We compared GIS model classifications with actual vegetation and elevation features measured at 37 sites. At 60 sites we measured 18 habitat variables regarding slope, aspect, tree species, shrub species, and ground cover. We used logistic regression to analyze habitat variables associated with chipmunk presence/absence. All (100%) 37 sample sites (28 predicted suitable, 9 predicted unsuitable) were classified correctly by the GIS model regarding elevation and vegetation. For 28 sites predicted suitable by the GIS model, 18 sites (64%) appeared visually suitable based on habitat variables selected from logistic regression analyses, of which 10 sites (36%) were specifically predicted as suitable habitat via logistic regression. We detected chipmunks at 70% of sites deemed suitable via the logistic regression models. Shrub cover, tree density, plant proximity, presence of logs, and presence of rock outcrop were retained in the logistic model for the Oscura Mountains; litter, shrub cover, and grass cover were retained in the logistic model for the Organ Mountains. Evaluation of predictive models illustrates the need for multi-stage analyses to best judge performance. Microhabitat analyses indicate prospective needs for different management strategies between the subspecies. Sensitivities of each population of the Colorado chipmunk to natural and prescribed fire suggest that partial burnings of areas inhabited by Colorado chipmunks in southern New Mexico may be beneficial. These partial burnings may later help avoid a fire that could substantially reduce habitat of chipmunks over a mountain range.     

Forecasting time series with increasing seasonal variation

Four options for modeling and forecasting time series data containing increasing seasonal variation are discussed, including data transformations, double seasonal difference models and two kinds of transfer function-type ARIMA models employing seasonal dummy variables. An explanation is given for the typical ARIMA model identification analysis failing to identify double seasonal difference models for this kind of data. A logical process of selecting one option for a particular case is outlined, focusing on issues of linear versus non-linear increasing seasonal variation, and the level of stochastic versus deterministic behavior in a time series. Example models for the various options are presented for six time series, with point forecast and interval forecast comparisons. Interval forecasts from data-transformation models are found to generally be too wide and sometimes illogical in the dependence of their width on the point forecast level. Suspicion that maximum likelihood estimation of ARIMA models leads to excessive indications of unit roots in seasonal moving-average operators is reported.     

Stream temperatures and the elevational distribution of redband trout in southwestern Idaho

During July to September 1994-1995, I examined water temperatures at the lower end of the elevational distribution of redband trout ( Oncorhynchus mykiss gairdneri ) in 4 streams in the Owyhee Mountains in southwestern Idaho. Maximum water temperatures in Castle, Shoofly, Little Jacks, and Big Jacks creeks during low flows during a drought in 1994 ranged from 26.7° C to 29.0° C. Water temperatures fluctuated 9.5-11° C during the 24-h period maximum temperatures were observed. Stream flows at the lower end of Big Jacks and Little Jacks creeks in 1994 were 3 s -1 and subsided underground 50-130 m downstream pools inhabited by trout. Trout were distributed to lower elevations where drainage basin area was larger in 2 of 3 yr ( P 5 km downstream of the lowest pool inhabited by trout in 1995-1996.     

Stinger utilization and predation in the scorpion Paruroctonus boreus

The utilization of the stinger and the predatory technique of the scorpion, Paruroctonus boreus, was studied under laboratory conditions. During the study, 83 feedings were observed. Age of the scorpions and the percentage of prey stung by them were used to classify the scorpions into groups. The scorpions aged 13–61 days always stung prey. After 62 days the scorpions began to selectively utilize the stinger. Utilization declined until it reached 30 percent in the adult stage. The stinger is apparently necessary for prey capture only in the early life stages.       

The Ter mutation in the dead end gene causes germ cell loss and testicular germ cell tumours

In mice, the Ter mutation causes primordial germ cell (PGC) loss in all genetic backgrounds. Ter is also a potent modifier of spontaneous testicular germ cell tumour (TGCT) susceptibility in the 129 family of inbred strains, and markedly increases TGCT incidence in 129-Ter/Ter males. In 129-Ter/Ter mice, some of the remaining PGCs transform into undifferentiated pluripotent embryonal carcinoma cells, and after birth differentiate into various cells and tissues that compose TGCTs. Here, we report the positional cloning of Ter, revealing a point mutation that introduces a termination codon in the mouse orthologue (Dnd1) of the zebrafish dead end (dnd) gene. PGC deficiency is corrected both with bacterial artificial chromosomes that contain Dnd1 and with a Dnd1-encoding transgene. Dnd1 is expressed in fetal gonads during the critical period when TGCTs originate. DND1 has an RNA recognition motif and is most similar to the apobec complementation factor, a component of the cytidine to uridine RNA-editing complex. These results suggest that Ter may adversely affect essential aspects of RNA biology during PGC development. DND1 is the first protein known to have an RNA recognition motif directly implicated as a heritable cause of spontaneous tumorigenesis. TGCT development in the 129-Ter mouse strain models paediatric TGCT in humans. This work will have important implications for our understanding of the genetic control of TGCT pathogenesis and PGC biology.