Whole Genome Amplification for Sequencing and Applications in Conservation Genetics

Abstract: We describe a method for rapidly amplifying whole genomes via a Phi29 DNA polymerase-mediated strand displacement reaction (SDR). Genomic amplification products derived from the SDR reaction resulted in high quantities of DNA suitable for polymerase chain reaction (PCR) amplification and sequencing of mitochondrial genomes. Control region sequences of DNA derived directly from PCR amplicons of extracted DNA were identical to those derived from PCR amplification of SDR genomic DNA. Effective SDR amplification and subsequent sequencing was successful across tissues sources ranging in age from 1 year to 19 years. Strand replacement reaction genomic amplification offers a means of obtaining large quantities of DNA from small amounts of tissue.     

Salivary alpha amylase and salivary cortisol response to fluid consumption in exercising athletes

The objective of the study was to examine salivary biomarker response to fluid consumption in exercising athletes. Exercise induces stress on the body and salivary alpha amylase (sAA) and salivary cortisol are useful biomarkers for activity in the sympathoadrenal medullary system and the hypothalamic pituitary adrenal axis which are involved in the stress response. Fifteen college students were given 150 ml and 500 ml of water on different days and blinded to fluid condition. The exercise protocol was identical for both fluid conditions using absolute exercise intensities ranging from moderate to high. Saliva was collected prior to exercise, post moderate and post high intensities and analyzed by Salimetrics assays. Exercise was significant for sAA with values different between pre-exercise (85 ± 10 U · ml⁻¹) and high intensity (284 ± 30 U · ml⁻¹) as well as between moderate intensity (204 ± 32 U · ml⁻¹) and high intensity. There was no difference in sAA values between fluid conditions at either intensity. Exercise intensity and fluid condition were each significant for cortisol. Cortisol values were different between pre-exercise (0.30 ± 0.03 ug · dL⁻¹) and high intensity (0.45 ± 0.05 ug · dL⁻¹) as well as between moderate intensity (0.33 ± 0.04 ug · dL⁻¹) and high intensity. Moderate exercise intensity cortisol was lower in the 500 ml condition (0.33 ± 0.03 ug · dL⁻¹) compared with the 150 ml condition (0.38 ± 0.03 ug · dL⁻¹). This altered physiological response due to fluid consumption could influence sport performance and should be considered. In addition, future sport and exercise studies should control for fluid consumption.     

Abnormal locomotion in rats after bilateral intrastriatal injection of kainic acid.

The locomotion changes, after bilateral injection of kainic acid into the striata, are characterized by increased swing time and decreased stance time. This may be analogous to the locomotion pattern in patients with Huntington's Disease.     

Major changes in forest carbon and nitrogen cycling caused by declining sulphur deposition

Sulphur (S) and nitrogen (N) deposition are important drivers of the terrestrial carbon (C) and N cycling. We analyzed changes in C and N pools in soil and tree biomass at a highly acidified spruce site in the Czech Republic during a 15 year period. Total S deposition decreased from 5 to 1.1 g m^?2 yr^?1 between 1995 and 2009, whereas bulk N deposition did not change. Over the same period, C and N pools in the Oa horizon declined by 116 g C and 4.2 g N m^?2 yr^?1, a total decrease of 47% and 42%, respectively. This loss of C and N probably originated from organic matter (OM) that had accumulated during the period of high acid deposition when litter decomposition was suppressed. The loss of OM from the Oa horizon coincided with a substantial leaching (1.3 g N m^?2 yr^?1 at 90 cm) in the 1990s to almost no leaching (<0.02 g N m^?2 yr^?1) since 2006. Forest floor net N mineralization also decreased. This had consequences for spruce needle N concentration (from 17.1 to 11.4 mg kg^?1 in current needles), an increase in litterfall C/N ratio (from 51 to 63), and a significant increase in the Oi + Oe horizon C/N ratio (from 23.4 to 27.3) between 1994 and 2009/2010. Higher forest growth and lower canopy defoliation was observed in the 2000s compared to the 1990s. Our results demonstrate that reducing S deposition has had a profound impact on forest organic matter cycling, leading to a reversal of historic ecosystem N enrichment, cessation of nitrate leaching, and a major loss of accumulated organic soil C and N stocks. These results have major implications for our understanding of the controls on both N saturation and C sequestration in forests, and other ecosystems, subjected to current or historic S deposition.     

不同退化阶段高寒草甸土壤化学计量特征

为了阐明不同退化阶段高寒草甸土壤的化学计量特征,沿着高寒草甸退化的梯度选取了原生嵩草草甸、轻度退化草甸和严重沙化草甸,测定了高寒草甸退化过程中不同深度土壤的有机碳、全氮、全磷和全钾含量。结果表明:随着高寒草甸的退化,0～100cm土壤的有机碳、全氮、全磷和全钾含量以及碳氮比、碳磷比、碳钾比、氮磷比、氮钾比和磷钾比均呈降低趋势,且土壤有机碳对高寒草甸退化的敏感性最高,全氮、全磷和全钾的敏感性依次降低,表层20cm的土壤有机碳和全氮可作为表征高寒草甸退化程度最敏感的土壤养分指标。另外,随着草甸的退化,土壤的有机碳、全氮、全磷和全钾含量及其化学计量比的垂直分布明显不同:随着土壤深度的增加,原生嵩草草甸和轻度退化草甸的土壤有机碳、全氮和全磷含量以及碳氮比、碳磷比、碳钾比、氮磷比、氮钾比和磷钾比在0～40cm范围内锐减,在40cm以下缓慢降低并趋于稳定;而沙化草甸土壤的有机碳、全氮、全磷和全钾及其化学计量比随着土壤深度的增加保持不变。     

Activin A stimulates IkappaB-alpha/NFkappaB and RANK expression for osteoclast differentiation,but not AKT survival pathway in osteoclast precursors

Recent studies have reported that activin A enhances osteoclastogenesis in cultures of mouse bone marrow cells stimulated with receptor activator of nuclear factor-kappaB ligand (RANKL) and macrophage colony-stimulating factor (M-CSF). However, the exact mechanisms by which activin A functions during osteoclastogenesis are not clear. RANKL stimulation of RANK/TRAF6 signaling increases nuclear factor-kappaB (NFkappaB) nuclear translocation and activates the Akt/PKB cell survival pathway. Here we report that activin A alone activates IkappaB-alpha, and stimulates nuclear translocation of NFkappaB and receptor activator of nuclear factor-kappaB (RANK) expression for osteoclastogenesis, but not Akt/PKB survival signal transduction including BAD and mammalian target of rapamycin (mTOR) for survival in osteoclast precursors in vitro. Activin A alone failed to activate Akt, BAD, and mTOR by immunoblotting, and it also failed to prevent apoptosis in osteoclast precursors. While activin A activated IkappaB-alpha and induced nuclear translocation of phosphorylated-NFkappaB, and it also enhanced RANK expression in osteoclast precursors. Moreover, activin A enhanced RANKL- and M-CSF-stimulated nuclear translocation of NFkappaB. Our data suggest that activin A enhances osteoclastogenesis treated with RANKL and M-CSF via stimulation of RANK, thereby increasing the RANKL stimulation. Activin A alone activated the NFkappaB pathway, but not survival in osteoclast precursors in vitro, but it is, thus, insufficient as a sole stimulus to osteoclastogenesis.     

The cell survival signal Akt is differentially activated by PDGF-BB, EGF, and FGF-2 in osteoblastic cells

Stimulation of osteoblast survival signals may be an important mechanism of regulating bone anabolism. Protein kinase B (PKB/Akt), a serine-threonine protein kinase, is a critical regulator of normal cell growth, cell cycle progression, and cell survival. In this study we have investigated the signaling pathways activated by growth factors PDGF-BB, EGF, and FGF-2 and determined whether PDGF-BB, EGF, and FGF-2 activated Akt in human or mouse osteoblastic cells. The results demonstrated that both ERK1 and ERK2 were activated by FGF-2 and PDGF-BB. Activation of ERK1 and ERK2 by PDGF-BB and FGF-2 was inhibited by PD 098059 (100 microM), a specific inhibitor of MEK. Wortmannin (500 nM), a specific inhibitor of phosphatidylinositol 3-kinase ( PI 3-K), inhibited the activation of ERK1 and ERK2 by PDGF-BB but not by FGF-2 suggesting that PI 3-K mediated the activation of ERK MAPK pathway by PDGF-BB but not by FGF-2. Rapamycin, an inhibitor of p70 S6 protein kinase and a downstream target of ERK1/2 and PI 3-K, did not affect the activation of ERK1 and ERK2 by the growth factors. Furthermore, our results demonstrated that Akt, a downstream target of PI 3-K, was activated by PDGF-BB but not by FGF-2. Akt activation by PDGF-BB was inhibited by PI 3-kinase inhibitor LY294002. Rapamycin had no effect on Akt activation. Epidermal growth factor (EGF) also activated Akt in osteoblastic cells which was inhibited by LY294002 but not by rapamycin. Taken together, our data for the first time revealed that the activation of ERK1/2 by PDGF-BB is mediated by PI 3-K, and secondly, Akt is activated by PDGF-BB and EGF but not by FGF-2 in human and mouse osteoblastic cells. These results are of critical importance in understanding the role of these growth factors in apoptosis and cell survival. PDGF-BB and EGF but not FGF-2 may stimulate osteoblast cell survival.     

Gelsolin deficiency blocks podosome assembly and produces increased bone mass and strength

Osteoclasts are unique cells that utilize podosomes instead of focal adhesions for matrix attachment and cytoskeletal remodeling during motility. We have shown that osteopontin (OP) binding to the alpha(v)beta(3) integrin of osteoclast podosomes stimulated cytoskeletal reorganization and bone resorption by activating a heteromultimeric signaling complex that includes gelsolin, pp(60c-src), and phosphatidylinositol 3'-kinase. Here we demonstrate that gelsolin deficiency blocks podosome assembly and alpha(v)beta(3)-stimulated signaling related to motility in gelsolin-null mice. Gelsolin-deficient osteoclasts were hypomotile due to retarded remodeling of the actin cytoskeleton. They failed to respond to the autocrine factor, OP, with stimulation of motility and bone resorption. Gelsolin deficiency was associated with normal skeletal development and endochondral bone growth. However, gelsolin-null mice had mildly abnormal epiphyseal structure, retained cartilage proteoglycans in metaphyseal trabeculae, and increased trabecular thickness. With age, the gelsolin-deficient mice expressed increased trabecular and cortical bone thickness producing mechanically stronger bones. These observations demonstrate the critical role of gelsolin in podosome assembly, rapid cell movements, and signal transduction through the alpha(v)beta(3) integrin.     

Conditional Over-Expression of Estrogen Receptor Alpha in a Transgenic Mouse Model

Attempts to delineate the mechanisms of estrogen action have promoted the creation of several estrogen receptor alpha (ER) mouse models in the past decade. These traditional models are limited by the fact that the receptors are either absent or present throughout all stages of development. The purpose of this work was to develop a conditional transgenic model that would provide an in vivo method of controlling the spatial and temporal regulation of ER expression. The tetracycline responsive system was utilized. Three lines of transgenic mice carrying a transgene composed of the coding sequence for murine ER placed under the regulatory control of a tet operator promoter (tet-op) were generated. These three lines of tet-op-mER mice were each mated to an established line of transgenic mice expressing a tetracycline-dependent transactivator protein (tTA) from the mouse mammary tumor virus-long terminal repeat (MMTV-LTR). Double transgenic MMTV-tTA/tet-op-mER mice were produced. All three lines demonstrated dominant gain of ER shown by RT-PCR, immunoprecipitation, and immunohistochemistry. Transgene-specific ER was expressed in numerous tissues including the mammary gland, salivary gland, testis, seminal vesicle, and epididymis. Expression was silenced by administration of doxycycline in the drinking water. This model can be utilized to evaluate the consequences of ER dominant gain in targeted tissues at specific times during development. In this study dominant gain of ER was associated with a reduction in epididymal/vas deferens and seminal vesicle weights consistent with the proposed action of ER on fluid transport in the male reproductive tract. Combining this model with other dominant gain and gene knockout mouse models will be useful for testing effects of ER action in combination with specific gene products and to evaluate if developmental and stage-specific expression of ER can rescue identified phenotypes in gene knockout mice.