Burrowing activities of kangaroo rats and patterns in plant species dominance at a shortgrass steppe-desert grassland ecotone

Abstract. Our objective was to evaluate the effects of burrowing activities by banner-tail kangaroo rats (Dipodomys spectabilis Merriam) on plant community structure and species dominance for two patch types at the ecotone between shortgrass steppe and desert grassland in New Mexico, USA. 10 mounds produced by kangaroo rats were selected in patches dominated by Bouteloua gracilis (the dominant in shortgrass steppe communities) and 10 mounds were selected in patches dominated by B. eriopoda (the dominant in Chihuahuan desert grasslands). Plant cover and density by species were sampled from three locations associated with each mound: the mound proper, the edge of the mound in the transition area, and the off-mound vegetation. Similar cover of B. eriopoda for the edges of mounds in both patch types indicates the ability of this species to respond to animal disturbances regardless of the amount of cover in the surrounding undisturbed vegetation. By contrast, cover of B. gracilis was low for all mounds and mound edges in patches dominated by this species. Much higher cover of B. eriopoda on mound edges compared to the undisturbed vegetation in B. gracilis-dominated patches indicates that kangaroo rats have important positive effects on this species. Lower cover of perennial grasses and higher cover of forbs, shrubs, and succulents on the edges of mounds in B. eriopoda-dominated patches compared to patches dominated by B. gracilis indicate the importance of surrounding vegetation to plant responses on disturbed areas. Our results show that kangaroo rats have important effects on both species dominance and composition for different patch types, and may provide a mechanism for small-scale dominance patterns at an ecotone; thus providing further support for their role as keystone species in desert grasslands.     

Geographic patterns of simulated establishment of two Bouteloua species: implications for distributions of dominants and ecotones

Abstract. Our overall objective was to use a soil water model to predict spatial patterns in germination and establishment of two important perennial C₄-bunchgrasses across the North American shortgrass steppe and desert grassland regions. We also predicted changes in establishment patterns under climate change scenarios. Bouteloua gracilis dominates the shortgrass steppe from northeastern Colorado to southeastern New Mexico. Bouteloua eriopoda dominates desert grasslands in central and southern New Mexico. Germination and establishment for each species were predicted at 16 sites along the gradient using a daily time step, multi-layer soil water model (SOILWAT) to determine the percentage of years that temperature and soil water criteria for germination and establishment were met. Percentage of years with predicted establishment decreased from north to south for B. gracilis, but increased from north to south for B. eriopoda, comparable to observed dominance patterns. The 95 % confidence interval around the point at which simulated establishment were equal for the two species was near the location of the shortgrass steppe-desert grassland ecotone where both species are abundant. The intersection in percentage of years with establishment for the two species was predicted to move further north when climate was scaled using three Global Circulation Models (GCMs), indicating a possible northward expansion of B. eriopoda. Our results suggest that recruitment by seed may be an important process in determining, at least in part, the geographic distribution of these two species. Changes in climate that affect establishment constraints could result in shifts of species dominance that may or may not be accompanied by changes in species composition.     

Genetic identification of endogenous polytropic proviruses by using recombinant inbred mice.

Forty-seven endogenous polytropic murine viruses (Pmv) were identified by examination of proviral-cellular DNA junction fragment segregation in recombinant inbred (RI) mice. Most Pmv loci were found in more than one of the seven RI progenitor strains analyzed, but only four were present in all strains. Chromosomal assignments for 41 Pmv loci were determined by comparing their RI strain distribution patterns with those of known genetic markers. Pmv loci were found dispersed throughout the genome, with chromosomes 1, 3, 4, 5, 7, 11, 12, 15, and 16 each carrying three or more proviruses. Linkage analysis in the AKXD RI set suggested that the gene encoding mink cell focus-forming virus resistance (Rcmfr) of DBA/2J mice is probably not a Pmv provirus. It was also deduced that no single, AKR/J-specific Pmv provirus is required as an env gene donor for thymomagenic mink cell focus-forming viruses. In addition, a Pmv provirus was very closely associated with the albino mutation on chromosome 7.     

Quantitative Determination and Location of Newly Synthesized Virus-Specific Ribonucleic Acid in Chicken Cells Infected with Rous Sarcoma Virus

A sensitive and quantitative nucleic acid hybridization assay for the detection of radioactively labeled avian tumor virus-specific RNA in infected chicken cells has been developed. In our experiments we made use of the fact that DNA synthesized by virions of avian myeloblastosis virus in the presence of actinomycin D (AMV DNA) is complementary to at least 35% of the sequences of 70S RNA from the Schmidt-Ruppin strain (SRV) of Rous sarcoma virus. Annealing of radioactive RNA (either SRV RNA or RNA extensively purified from SRV-infected chicken cells) with AMV DNA followed by ribonuclease digestion and Sephadex chromatography yielded products which were characterized as avian tumor virus-specific RNA-DNA hybrids by hybridization competition with unlabeled 70S AMV RNA, equilibrium density-gradient centrifugation in Cs(2)SO(4) gradients, and by analysis of their ribonucleotide composition. The amount of viral RNA synthesized during pulse labeling with (3)H-uridine could be quantitated by the addition of an internal standard consisting of (32)P-labeled SRV RNA prior to purification and hybridization. This quantitative assay was used to determine that, in SRV-infected chicken cells labeled for increasing lengths of time with (3)H-uridine, labeled viral RNA appeared first in a nuclear fraction, then in a cytoplasmic fraction, and still later in mature virions. This observation is consistent with the hypothesis that RNA tumor virus RNA is synthesized in the nucleus of infected cells.     

Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy

HIV persists during antiretroviral therapy (ART) as integrated proviruses in cells descended from a small fraction of the CD4+ T cells infected prior to the initiation of ART. To better understand what controls HIV persistence and the distribution of integration sites (IS), we compared about 15,000 and 54,000 IS from individuals pre-ART and on ART, respectively, with approximately 395,000 IS from PBMC infected in vitro. The distribution of IS in vivo is quite similar to the distribution in PBMC, but modified by selection against proviruses in expressed genes, by selection for proviruses integrated into one of 7 specific genes, and by clonal expansion. Clones in which a provirus integrated in an oncogene contributed to cell survival comprised only a small fraction of the clones persisting in on ART. Mechanisms that do not involve the provirus, or its location in the host genome, are more important in determining which clones expand and persist.     

Endogenous FGF‐2 is critically important in PTH anabolic effects on bone

Parathyroid hormone (PTH) increases fibroblast growth factor receptor‐1 (FGFR1) and fibroblast growth factor‐2 (FGF‐2) expression in osteoblasts and the anabolic response to PTH is reduced in Fgf2?/? mice. This study examined whether candidate factors implicated in the anabolic response to PTH were modulated in Fgf2?/? osteoblasts. PTH increased Runx‐2 protein expression in Fgf2+/+ but not Fgf2?/? osteoblasts. By immunocytochemistry, PTH treatment induced nuclear accumulation of Runx‐2 only in Fgf2+/+ osteoblasts. PTH and FGF‐2 regulate Runx‐2 via activation of the cAMP response element binding proteins (CREBs). Western blot time course studies showed that PTH increased phospho‐CREB within 15 min that was sustained for 24 h in Fgf2+/+ but had no effect in Fgf2?/? osteoblasts. Silencing of FGF‐2 in Fgf2+/+ osteoblasts blocked the stimulatory effect of PTH on Runx‐2 and CREBs phosphorylation. Studies of the effects of PTH on proteins involved in osteoblast precursor proliferation and apoptosis showed that PTH increased cyclinD1‐cdk4/6 protein in Fgf2+/+ but not Fgf2?/? osteoblasts. Interestingly, PTH increased the cell cycle inhibitor p21/waf1 in Fgf2?/? osteoblasts. PTH increased Bcl‐2/Bax protein ratio in Fgf2+/+ but not Fgf2?/? osteoblasts. In addition PTH increased cell viability in Fgf2+/+ but not Fgf2?/? osteoblasts. These data suggest that endogenous FGF‐2 is important in PTH effects on osteoblast proliferation, differentiation, and apoptosis. Reduced expression of these factors may contribute to the reduced anabolic response to PTH in the Fgf2?/? mice. Our results strongly indicate that the anabolic PTH effect is dependent in part on FGF‐2 expression. J. Cell. Physiol. 219: 143–151, 2009. © 2008 Wiley‐Liss, Inc.     

Functional consequences of the RNase H2A subunit mutations that cause Aicardi-Goutieres syndrome

Mutations in the three genes encoding the heterotrimeric RNase H2 complex cause Aicardi-Goutières Syndrome (AGS). Our mouse RNase H2 structure revealed that the catalytic RNase H2A subunit interfaces mostly with the RNase H2C subunit that is intricately interwoven with the RNase H2B subunit. We mapped the positions of AGS-causing RNase H2A mutations using the mouse RNase H2 structure and proposed that these mutations cause varied effects on catalytic potential. To determine the functional consequences of these mutations, heterotrimeric human RNase H2 complexes containing the RNase H2A subunit mutations were prepared, and catalytic efficiencies and nucleic acid binding properties were compared with the wild-type (WT) complex. These analyses reveal a dramatic range of effects with mutations at conserved positions G37S, R186W, and R235Q, reducing enzymatic activities and substrate binding affinities by as much as a 1000-fold, whereas mutations at non-conserved positions R108W, N212I, F230L, T240M, and R291H reduced activities and binding modestly or not at all. All mutants purify as three-subunit complexes, further supporting the required heterotrimeric structure in eukaryotic RNase H2. These kinetic properties reveal varied functional consequences of AGS-causing mutations in the catalytic RNase H2A subunit and reflect the complex mechanisms of nuclease dysfunction that include catalytic deficiencies and altered protein-nucleic acid interactions relevant in AGS.     

Ribonuclease-Sensitive Deoxyribonucleic Acid Polymerase Activity in Uninfected Rat Cells and Rat Cells Infected with Rous Sarcoma Virus

Rat cells infected with the B77 strain of avian sarcoma virus [R(B77) cells] produced no virus-like particles but contained information for the production of infectious B77 virus. (3)H-labeled deoxyribonucleic acid (DNA) product of the B77 virus endogenous DNA polymerase system was used to determine the relative amounts of B77 virus-specific ribonucleic acid (RNA) in B77 virus-infected chicken and R(B77) cells. R(B77) cells were found to contain much less B77 virus RNA than did B77 virus-infected chicken cells. Ribonuclease-sensitive DNA polymerase activity was present in high-speed pellet fractions from Nonidet extracts of B77 virus-infected rat cells. Similar preparations from some uninfected rat cells contained lesser amounts of a similar ribonuclease-sensitive DNA polymerase activity. The endogenous template for the DNA polymerase activity in high-speed pellet fractions from R(B77) cells was not related to B77 virus RNA or to RNA of a rat C-type virus. The DNA product of the endogenous DNA polymerase in high-speed pellet fractions of R(B77) cells hybridized to a small extent with RNA from the same fraction and to a similar extent with RNA from uninfected rat cells.     

Isotype switching of an immunoglobulin heavy chain transgene occurs by DNA recombination between different chromosomes

Transgenic mice carrying an immunoglobulin mu heavy chain transgene exhibit isotype switching of the transgene. We have now characterized the mechanism of transgene switching in these mice. The site of mu transgene insertion in one transgenic line has been localized to chromosome 5 using a series of polymorphic endogenous retroviruses as genetic markers in backcross mice. The endogenous immunoglobulin heavy chain locus resides on mouse chromosome 12, which shows that transgene isotype switching can occur between two different chromosomes even though normal antibody gene switching has generally been thought to occur within one chromosome. We find that transgene isotype switching involves interchromosomal DNA recombination, and our data suggest that the same enzymatic mechanisms mediate both normal isotype switch recombination and interchromosomal transgene switching. Our findings also support the notion that the isotype switching mechanism can induce chromosomal translocations such as observed for the c-myc gene in some B cell tumors.