Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans

Recent studies of mitochondrial DNA (mtDNA) variation in mammals and Drosophila have shown an excess of amino acid variation within species (replacement polymorphism) relative to the number of silent and replacement differences fixed between species. To examine further this pattern of nonneutral mtDNA evolution, we present sequence data for the ND3 and ND5 genes from 59 lines of Drosophila melanogaster and 29 lines of D. simulans. Of interest are the frequency spectra of silent and replacement polymorphisms, and potential variation among genes and taxa in the departures from neutral expectations. The Drosophila ND3 and ND5 data show no significant excess of replacement polymorphism using the McDonald-Kreitman test. These data are in contrast to significant departures from neutrality for the ND3 gene in mammals and other genes in Drosophila mtDNA (cytochrome b and ATPase 6). Pooled across genes, however, both Drosophila and human mtDNA show very significant excesses of amino acid polymorphism. Silent polymorphisms at ND5 show a significantly higher variance in frequency than replacement polymorphisms, and the latter show a significant skew toward low frequencies (Tajima's D = -1.954). These patterns are interpreted in light of the nearly neutral theory where mildly deleterious amino acid haplotypes are observed as ephemeral variants within species but do not contribute to divergence. The patterns of polymorphism and divergence at charge-altering amino acid sites are presented for the Drosophila ND5 gene to examine the evolution of functionally distinct mutations. Excess charge-altering polymorphism is observed at the carboxyl terminal and excess charge-altering divergence is detected at the amino terminal. While the mildly deleterious model fits as a net effect in the evolution of nonrecombining mitochondrial genomes, these data suggest that opposing evolutionary pressures may act on different regions of mitochondrial genes and genomes.      

Immune activation and viral burden in acute disease induced by simian immunodeficiency virus SIVsmmPBj14: correlation between in vitro and in vivo events.

The simian immunodeficiency virus SIVsmmPBj14 (SIV-PBj14) is an atypical lentivirus that causes acute disease and death in pig-tailed macaques and in vitro replicates efficiently in resting macaque lymphocytes and activates and induces proliferation of lymphocytes. The present study was conducted to test the hypothesis that production of large quantities of SIV-PBj14 induces widespread immune activation and elaboration of cytokines which lead directly to the death of infected pig-tailed macaques. Following intravenous inoculation of pig-tailed macaques with SIV-PBj14, acute disease developed and was characterized by high levels of plasma viremia, p27gag antigenemia, tumor necrosis factor alpha, and interleukin-6 (IL-6). All animals died within 10 days of infection, at which time some animals had as many as 100% CD4+ cells in the periphery and lymphoid tissues infected. During the last few days before death, titers of infectious virus in blood increased as much as 10(5)-fold. By using dual-label immunofluorescence assays for detection of cell surface activation markers, both CD4+ and CD8+ lymphocytes were shown to express the IL-2 and transferrin receptors following either in vivo or in vitro infection with SIV-PBj14. Furthermore, in vitro infection of quiescent macaque lymphocytes by SIV-PBj14 was accompanied by proliferation of both CD4+ and CD8+ lymphocyte subsets, as measured by incorporation of [3H]thymidine. Increases in numbers of activated lymphocytes and levels of proinflammatory cytokines in plasma coincided with increased amounts of detectable virus in vivo. Clinical signs of disease and pathologic findings were most consistent with death from a shock-like syndrome, in which acute-phase inflammatory cytokines are known to play a major role. Tumor necrosis factor alpha, IL-2, and IL-6 were detected in some cultures infected with SIV-PBj14, but this finding was not consistent. When cytokines were detected, their concentrations were essentially no different from those found in control cultures infected with SIVsmm9, a prototypic strain from which SIV-PBj14 was derived. The in vivo results suggest a synergistic cycle of activation of lymphocytes and monocytes, elaboration of cytokines, and virus production that accelerates uncontrolled and culminates in death. The observed correlations between in vivo and in vitro activation events following SIV-PBj14 infection validate the use of in vitro studies to clarify lentivirus-lymphocyte interactions that may contribute to the virulence of SIV-PBj14.     

Transient transfection of polarized epithelial monolayers with CFTR and reporter genes using efficacious lipids

Transient transfection of epithelial cells with lipid reagents has been limited because of toxicity and lack of efficacy. In this study, we show that more recently developed lipids transfect nonpolarized human airway epithelial cells with high efficacy and efficiency and little or no toxicity. Because of this success, we hypothesized that these lipids may also allow transient transfection of polarized epithelial monolayers. A panel of reagents was tested for transfer of the reporter gene luciferase (LUC) into polarized monolayers of non-cystic fibrosis (non-CF) and CF human bronchial epithelial cells, MDCK epithelial cell monolayers, and, ultimately, primary non-CF and CF airway epithelial cells. Lipid reagents, which were most successful in initial LUC assays, were also tested for transfer of vectors bearing the reporter gene green fluorescent protein (GFP) and for successful transfection and expression of an epithelial-specific protein, the cystic fibrosis transmembrane conductance regulator (CFTR). Electrophysiological, biochemical, and immunological assays were performed to show successful complementation of an epithelial monolayer with transiently expressed CFTR. We also present findings that help facilitate monolayer formation by these airway epithelial cell lines. Together, these data show that polarized monolayers are transfected transiently with more recently developed lipids, specifically LipofectAMINE PLUS and LipofectAMINE 2000. Transient transfection of epithelial monolayers provides a powerful system in which to express the cDNA of any epithelium-specific protein transiently in a native polarized epithelium to study protein function.     

CD40-mediated activation of NF-kappa B in airway epithelial cells

We have reported previously that airway epithelial cells (AEC) express CD40 and that activation of this molecule stimulates the expression of inflammatory mediators, including the chemokine RANTES (regulated on activation normal T cell expressed and secreted). Because NF-kappaB regulates the expression of many inflammatory mediators, such as RANTES, we utilized CD40-mediated induction of RANTES expression to investigate the mechanisms that underlie CD40-mediated activation of NF-kappaB in AEC. Results demonstrate that, in AEC, intact NF-kappaB sites were required for CD40-mediated activation of the RANTES promoter. To examine activation of NF-kappaB binding directly, electrophoretic mobility shift analyses were performed. These analyses revealed that CD40 ligation stimulated NF-kappaB binding and that the activated NF-kappaB complexes were composed of p65 subunits. Additional studies focused on the CD40-triggered signaling pathways that facilitate NF-kappaB activation. Findings show that CD40 engagement activated the IkappaB kinases IKK-alpha and IKK-beta and stimulated IkappaBalpha phosphorylation. Analyses also examined the role of tumor necrosis factor-associated factor (TRAF) molecules in CD40-mediated NF-kappaB activation within AEC. Stable transfectants expressing wild-type or mutant forms of the cytoplasmic domain of CD40 suggested that TRAF3, but not TRAF2, binding was essential for CD40-mediated RANTES expression. Further studies indicated that exogenous expression of wild-type TRAF3 enhanced activation of the RANTES promoter, whereas exogenous expression of wild-type TRAF2 inhibited this activation; TRAF3-mediated enhancement was dependent upon NF-kappaB. Together, these findings suggest that, in AEC, ligation of CD40 regulates the expression of inflammatory mediators, such as RANTES, via activation of NF-kappaB. Moreover, these results suggest that CD40-mediated signaling in AEC differs with previously reported findings observed in other cell models, such as B lymphocytes.     

Proinflammatory and Th2-derived cytokines modulate CD40-mediated expression of inflammatory mediators in airway epithelia: implications for the role of epithelial CD40 in airway inflammation

Cytokines produced by activated macrophages and Th2 cells within the lung play a key role in asthma-associated airway inflammation. Additionally, recent studies suggest that the molecule CD40 modulates lung immune responses. Because airway epithelial cells can act as immune effector cells through the expression of inflammatory mediators, the epithelium is now considered important in the generation of asthma-associated inflammation. Therefore, the goal of the present study was to examine the effects of proinflammatory and Th2-derived cytokines on the function of CD40 in airway epithelia. The results show that airway epithelial cells express CD40 and that engagement of epithelial CD40 induces a significant increase in expression of the chemokines RANTES, monocyte chemoattractant protein (MCP-1), and IL-8 and the adhesion molecule ICAM-1. Cross-linking epithelial CD40 had no effect on expression of the adhesion molecule VCAM-1. The proinflammatory cytokines TNF-alpha and IL-1beta and the Th2-derived cytokines IL-4 and IL-13 modulated the positive effects of CD40 engagement on inflammatory mediator expression in airway epithelial cells. Importantly, CD40 ligation enhanced the sensitivity of airway epithelial cells to the effects of TNF-alpha and/or IL-1beta on expression of RANTES, MCP-1, IL-8, and VCAM-1. In contrast, neither IL-4 nor IL-13 modified the effects of CD40 engagement on the expression of RANTES, MCP-1, IL-8, or VCAM-1; however, both IL-4 and IL-13 attenuated the effects of CD40 cross-linking on ICAM-1 expression. Together, these findings suggest that interactions between CD40-responsive airway epithelial cells and CD40 ligand+ leukocytes, such as activated T cells, eosinophils, and mast cells, modulate asthma-associated airway inflammation.     

Comparison of Cesium-137 and X-ray Irradiators by Using Bone Marrow Transplant Reconstitution in C57BL/6J Mice

Mice are used extensively in transplantation studies involving bone marrow ablation. Due to the increasing security issues and expenses involved with γ irradiators, self-contained X-ray irradiators have been increasing in popularity. We hypothesized that bone marrow ablation by irradiation of mice with a ¹³⁷Cs irradiator would be comparable to that from an X-ray source irradiator. A lethal-dose curve was obtained by irradiating C57BL/6J mice with 500, 700, 900, and 1100 cGy from either source. These data were used to determine the lethal radiation exposure range for a noncompetitive bone marrow engraftment curve for each source. At 90 d after reconstitution, the bone marrow engraftment curves revealed significant differences between the 2 sources in the establishment of B cell, myeloid, and T cell lineages. Murine B cell reconstitution after exposure to a ¹³⁷Cs source was greater than that after X-ray exposure at each dose level, whereas the converse was true for myeloid cell reconstitution. At the 1050- and 1100-cGy doses, mice irradiated by using the X-ray source demonstrated higher levels of T cell reconstitution but decreased survival compared with mice irradiated with the ¹³⁷Cs source. We concluded that although both sources ablated endogenous bone marrow sufficiently to enable stem cell engraftment, there are distinct physiologic responses that should be considered when choosing the optimal source for use in a study and that irradiation from the ¹³⁷Cs source was associated with lower overall morbidity due to opportunistic infection.Abbreviations: B3, barrier level; B4, barrier level 4; BMT, bone marrow transplantationStudies of hematopoietic stem cell transplantation have evolved over the past 60 y.^1,9 Many preclinical investigations involving cell and gene therapy and hematopoietic stem cell function are performed in mouse models, and techniques such as adoptive cell transfer and bone marrow transplant are commonly used in these studies. Such techniques often require a supralethal dose of irradiation to ensure adequate engraftment with donor cells and subsequent survival. Conventional γ-emitting irradiators (¹³⁷Cs and ⁶⁰Co sources) have been used to deliver myeloablative doses of radiation prior to bone marrow transplantation (BMT). After the terrorist attack of 11 September 11 2001, security measures regarding active radioactive source irradiators have been heightened. In 2005, the US Congress passed the Energy Policy Act, in which the US Nuclear Regulatory Commission was assigned to evaluate and prevent malicious misuse of radioactive materials. As a result, increased security controls were imposed on radioactive material sources and quantities of concern, including shielded active source irradiators.¹⁴ Mandated security measures now include fingerprinting and a criminal-history record check to allow persons unescorted access to various radioactive materials.¹⁵ Background checks and fingerprinting procedures can be time-consuming and present an additional expense that usually is passed on to individual investigators. These enhanced security measures have significantly increased the expense associated with use of these irradiators, and federal regulations as proposed in 10 CFR Part 37 are likely to become more stringent in coming years.¹⁶ This situation has correspondingly led to an increased interest in the use of X-ray irradiators as a substitute for γ-ray sources such as ¹³⁷Cs, and many animal facilities across the country have begun to purchase these units, even though there is no unbiased comparative information regarding the effectiveness of the instruments.In addition to decreased security requirements, X-ray irradiators are substantially less expensive to purchase than are active-source irradiators. After reviewing quotes, we estimate that the initial purchase price of an X-ray irradiator is about one sixth that of a cesium source. These figures do not include the costs of shipping, installation, or disposal of old active-source machines, and thus actual starts up costs are much higher. Annual maintenance as well as annual or semiannual dosimetry assessment costs are relatively comparable between the 2 sources. X-ray irradiators offer an additional financial advantage in that they do not require the strict security measures required for active γ-source irradiators. Given the number of disadvantages for the possession and use of γ-emitting irradiators, the use of X-ray irradiators in research likely will increase in the future.Extensive review of the literature did not reveal any studies in which bone marrow transplantation (BMT) efficiencies, kinetics, or overall responses in mice were compared between ¹³⁷Cs and X-ray irradiators. We hypothesized that both the ¹³⁷Cs and X-ray sources would ablate the bone marrow effectively and allow for comparable donor bone marrow reconstitution, and we sought to compare any differences in cell population engraftment after the use of each source. Recipient hematologic recovery after irradiation and reconstitution with bone marrow was assessed by determining the percentages of B and T lymphocytes and myeloid cells in the peripheral blood at 90 d after engraftment. In light of previously published work, we hypothesized that using the X-ray source before BMT would require a reduced dosage of radiation compared with that for the ¹³⁷Cs source.^4,6,9Historically, lethal-dose curves have been generated to calculate the dose which is lethal for 50% of the irradiated animals (mice, in this case) over a 30-d period (that is, the LD_50:30); this method allows approximation of the radiation sensitivity of a cohort of experimental mice.¹¹ A mouse in which 100% of the bone marrow has been ablated will be unable to recover hematopoietic function and will die. A priori, if the animal dies, one can assume that the minimal lethal dose has been reached or exceeded; conversely, if the mouse survives, the minimal lethal dose was not achieved. Because of the number of mice needed to calculate an accurate LD_50:30, we elected to perform a broad lethal-dose curve (1100 to 500 cGy in 200-cGy increments) to determine the point at which 100% death was reached for both sources. We then used this information as the lower radiation exposure limit for a bone marrow reconstitution curve (refined into 50-cGy increments), thereby allowing us to examine the bone marrow reconstitution response after differing radiation exposures.⁹ There is ample support in the literature for the broad lethal-dose test range chosen in this study.^4,9 Previous work with thymocyte reconstitution after bone marrow ablation has demonstrated that irradiation exposures of approximately 400 cGy are required to establish a population of donor-derived thymocytes in the recipient.⁵ Therefore, we used a dosage test range above 400cGy in the current study. The dose range for this study was 500 to 1100 cGy, and we expected to see morbidity and mortality primarily due to bone marrow failure between 8 and 20 d in the lethal-dose curve.¹²