A central role for Bid in granzyme B-induced apoptosis

Granzyme B, a protease released from cytotoxic lymphocytes, has been proposed to induce target cell death by cleaving and activating the pro-apoptotic Bcl-2 family member Bid. It has also been proposed that granzyme B can induce target cell death by activating caspases directly, by cleaving caspase substrates, and/or by cleaving several non-caspase substrates. The relative importance of Bid in granzyme B-induced cell death has therefore remained unclear. Here we report that cells isolated from various tissues of Bid-deficient mice were resistant to granzyme B-induced cell death. Consistent with the proposed role of Bid in regulating mitochondrial outer membrane permeabilization, cytochrome c remained in the mitochondria of Bid-deficient cells treated with granzyme B. Unlike wild type cells, Bid-deficient cells survived and were then able to proliferate normally, demonstrating the critical role for Bid in mediating granzyme B-induced apoptosis.     

Life Cycle Assessment Software: Selection Can Impact Results

When software is used to facilitate life cycle assessments (LCAs), the implicit assumption is that the results obtained are not a function of the choice of software used. LCAs were done in both SimaPro and GaBi for simplified systems of creation and disposal of 1 kilogram each of four basic materials (aluminum, corrugated board, glass, and polyethylene terephthalate) to determine whether there were significant differences in the results. Data files and impact assessment methodologies (Impact 2002, ReCiPe, and TRACI 2) were ostensibly identical (although there were minor variations in the available ReCiPe version between the programs that were investigated). Differences in reported impacts of greater than 20% for at least one of the four materials were found for 9 of the 15 categories in Impact 2002+, 7 of the 18 categories in ReCiPe, and four of the nine categories in TRACI. In some cases, these differences resulted in changes in the relative rankings of the four materials. The causes of the differences for 14 combinations of materials and impact categories were examined by tracing the results back to the life cycle inventory data and the characterization factors in the life cycle impact assessment (LCIA) methods. In all cases examined, a difference in the characterization factors used by the two programs was the cause of the differing results. As a result, when these software programs are used to inform choices, the result can be different conclusions about relative environmental preference that are functions purely of the software implementation of LCIA methods, rather than of the underlying data.     

Body temperature and basking behaviour of Nile crocodiles (Crocodylus niloticus) during winter

The ability to thermoregulate in reptilians is often through behavioural modification. We investigated body temperature (T_b) patterns during winter in the amphibious Nile crocodile (Crocodylus niloticus) and its relationship to basking behaviour at the St. Lucia Crocodile Centre, St. Lucia, South Africa. It was found that crocodiles had no daily plateaus in T_b but rather continuous oscillations in T_b within a range of mean minimum T_b 18.8–19.6 °C to mean maximum T_b 26.9–29.2 °C. Crocodile T_b increased during the day, usually after 10:00 irrespective of body size. Behavioural data showed that the crocodiles usually left the water to bask around 10:00. It is suggested that basking behaviour is important for elevating T_b rather than attaining a preferred T_b. The increased T_b may allow them to perform optimally when they return to water. The basking occurrence has management implications as it suggests that the best time to conduct aerial censuses of the St. Lucia crocodiles is during winter after 10:00 when most of the individuals are basking and hence most easily seen.     

The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer

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Kinase-dependent Regulation of Inositol 1,4,5-Trisphosphate-dependent Ca2+ Release during Oocyte Maturation

Fertilization induces a species-specific Ca²⁺ transient with specialized spatial and temporal dynamics, which are essential to temporally encode egg activation events such as the block to polyspermy and resumption of meiosis. Eggs acquire the competence to produce the fertilization-specific Ca²⁺ transient during oocyte maturation, which encompasses dramatic potentiation of inositol 1,4,5-trisphosphate (IP₃)-dependent Ca²⁺ release. Here we show that increased IP₃ receptor (IP₃R) sensitivity is initiated at the germinal vesicle breakdown stage of maturation, which correlates with maturation promoting factor (MPF) activation. Extensive phosphopeptide mapping of the IP₃R resulted in ∼70% coverage and identified three residues, Thr-931, Thr-1136, and Ser-114, which are specifically phos pho ryl a ted during maturation. Phospho-specific antibody analyses show that Thr-1136 phos pho ryl a tion requires MPF activation. Activation of either MPF or the mitogen-activated protein kinase cascade independently, functionally sensitizes IP₃-dependent Ca²⁺ release. Collectively, these data argue that the kinase cascades driving meiotic maturation potentiates IP₃-dependent Ca²⁺ release, possibly trough direct phos pho ryl a tion of the IP₃R.Egg activation refers to the cellular and molecular events that take place immediately following fertilization, transitioning the zygote into embryogenesis. In vertebrates, egg activation encompasses the block to polyspermy and the completion of oocyte meiosis, which is coupled to the extrusion of the second polar body. Interestingly, in all sexually reproducing organisms tested to date the cellular events associated with egg activation are Ca²⁺-dependent (1). Importantly the Ca²⁺ signal at fertilization encodes the progression of these cellular events in a defined temporal sequence that ensures a functional egg-to-embryo transition (2, 3). The first order of business for the fertilized egg is to block polyspermy, which could be lethal to the embryo. This presents a particularly difficult problem for the large Xenopus oocyte. Therefore, this species employs a fast and slow blocks to polyspermy, both of which are Ca²⁺-dependent (4). In addition, the Ca²⁺ release wave at fertilization releases the metaphase II cytostatic factor-dependent arrest in Xenopus oocytes. As is the case in other vertebrates, Xenopus eggs arrest at metaphase of meiosis II, an event that marks the completion of maturation.Therefore, Ca²⁺ dynamics at fertilization initiate and temporally encode critical cellular events for the egg-to-embryo transition. Specificity in Ca²⁺ signaling is encoded to a large extent in the spatial, temporal, and amplitude features of the Ca²⁺ signal. This endows Ca²⁺ signaling with its versatility and specificity, where in the same cell Ca²⁺ signals can mediate distinct cellular responses (5, 6).Ca²⁺ signaling pathways and intracellular organelles remodel during oocyte maturation, a complex cellular differentiation that prepares the egg for fertilization and egg activation (7, 8). In Xenopus the activity and distribution of multiple essential Ca²⁺-transporting proteins is modulated dramatically during oocyte maturation (8). Functional studies and mathematical modeling support the conclusion that the two critical determinants of Ca²⁺ signaling remodeling during Xenopus oocyte maturation are the internalization of the plasma-membrane Ca²⁺-ATPase, and the sensitization of inositol 1,4,5-trisphosphate (IP₃)²-dependent Ca²⁺ release (9–11). Indeed Ca²⁺ release from intracellular stores through the IP₃ receptor (IP₃R) represents the primary source for the initial Ca²⁺ rise at fertilization in vertebrates (12–14). The sensitivity of IP₃-dependent Ca²⁺ release is enhanced during maturation (10, 15). The IP₃R physically clusters during maturation (9, 16), and this is associated with functional clustering of elementary Ca²⁺ release events (10). IP₃R clustering is important for the slow and continuous nature of Ca²⁺ wave propagation in Xenopus eggs (10). In fact the potentiation of IP₃-dependent Ca²⁺ release is a hallmark of Ca²⁺ signaling differentiation during oocyte maturation in several vertebrate and invertebrate species (17–19). However, the mechanisms underlying enhanced IP₃-dependent Ca²⁺ release are not well understood.An attractive mechanism to explain increased IP₃R sensitivity during oocyte maturation is phosphorylation, given the critical role kinase cascades play in the initiation and progression of the meiotic cell cycle. Furthermore, the affinity of the IP₃R increases during mitosis apparently due to direct phosphorylation by maturation-promoting factor (MPF) (20, 21). In contrast, in starfish eggs, although the increase in Ca²⁺ release was dependent on MPF activation, MPF does not directly phosphorylate the IP₃R, but rather it appears to mediate its effect through the actin cytoskeleton (22, 23). More recently, the MAPK cascade has been shown to be important for shaping Ca²⁺ dynamics in mouse eggs (24). Together, these results argue that phosphorylation plays an important role in the sensitization of IP₃-dependent Ca²⁺ release during M-phase.Xenopus oocyte maturation is initiated by steroids that appear to act on a cell surface receptor (25). An important kinase cascade activated during maturation is the MAPK cascade that is initiated through the accumulation of Mos (Fig. 1A). This cascade culminates in the inhibition of Myt1, which phosphorylates and inhibits MPF. MPF is the key regulator of entry into M-phase and is composed of a Ser/Thr kinase subunit (cdk1) and cyclin B as a regulatory subunit. In addition, activation of Cdc25C is essential for oocyte maturation, because it represents the rate-limiting step in MPF activation (26). Cdc25C is phosphorylated by polo-like kinase through unknown upstream steps. In this work we analyze the functional regulation and phosphorylation pattern of the IP₃R during oocyte maturation to better understand the role of cell cycle kinases in modulating IP₃-dependent Ca²⁺ release.Open in a separate windowFIGURE 1.IP₃-dependent Ca²⁺ release dynamics during maturation. A, kinase cascades driving Xenopus oocyte maturation. B, oocytes were injected with caged-IP₃ and Oregan Green 1,2-bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid tetrakis 1 before imaging. Maturation was induced with progesterone, and cells were collected at different time points as indicated. Cells were imaged in line scan mode on a Zeiss LSM510 with the near UV 450 nm laser continuously on, at low intensity to produce a slow gradual IP₃ rise. After imaging each cell was lysed and analyzed individually for the activation state of MAPK and MPF. MPF was assayed using an anti-phospho-Tyr-15-cdk1 antibody (arrow). Dephosphorylation is indicative of MPF activation. MAPK activation was detected using a phospho-specific MAPK antibody (arrowhead). Tubulin was the loading control (dash). C, percent of cells at each time point that either exhibit no release for the duration of the line scan (No Rel., black), puffs only (puffs, green), puffs followed by a wave (Puff-Wave, blue), or only a Ca²⁺ wave (Wave, red). For each time point n = 11–23 cells. D, amplitude of the first peak during the line scan as compared with the maximal Ca²⁺ signal. Mean ± S.E. (n = 9–18). E, latency until the first Ca²⁺ signal (Time to first peak) as compared with the time required to reach maximal signal (Time to Max). Mean ± S.E. (n = 9–18). For C–E: oocytes (Ooc); cells treated with progesterone that have not undergone GVBD at 2 or more hours after progesterone (p > 2); cells at GVBD and up to 0.5 h after GVBD (GVBD 0–0.5); cells from 0.5 to 2.5 h after GVBD (GVBD 0.5–2.5); fully mature eggs at 3 or more hours after GVBD (>3 egg).     

Neutralization-Sensitive R5-Tropic Simian-Human Immunodeficiency Virus SHIV-2873Nip,Which Carries env Isolated from an Infant with a Recent HIV Clade C Infection

Human immunodeficiency virus clade C (HIV-C) accounts for >56% of all HIV infections worldwide. To investigate vaccine safety and efficacy in nonhuman primates, a pathogenic, R5-tropic, neutralization-sensitive simian-human immunodeficiency virus (SHIV) carrying HIV-C env would be desirable. We have constructed SHIV-2873Ni, an R5-tropic SHIV carrying a primary pediatric HIV-C env gene isolated from a 2-month-old Zambian infant, who died within 1 year of birth. SHIV-2873Ni was constructed using SHIV-1157ipd3N4 (R. J. Song, A. L. Chenine, R. A. Rasmussen, C. R. Ruprecht, S. Mirshahidi, R. D. Grisson, W. Xu, J. B. Whitney, L. M. Goins, H. Ong, P. L. Li, E. Shai-Kobiler, T. Wang, C. M. McCann, H. Zhang, C. Wood, C. Kankasa, W. E. Secor, H. M. McClure, E. Strobert, J. G. Else, and R. M. Ruprecht. J. Virol. 80:8729-8738, 2006) as the backbone, since the latter contains additional NF-κB sites in the long terminal repeats to enhance viral replicative capacity. The parental virus, SHIV-2873Ni, was serially passaged through five rhesus monkeys (RMs); SHIV-2873Nip, the resulting passaged virus, was reisolated from the fourth recipient about 1 year postinoculation. SHIV-2873Nip was replication competent in RM peripheral blood mononuclear cells of all random donors tested and was exclusively R5 tropic, and its env gene clustered with HIV-C by phylogenetic analysis; its high sensitivity to neutralization led to classification as a tier 1 virus. Indian-origin RMs were inoculated by different mucosal routes, resulting in high peak viral RNA loads. Signs of virus-induced disease include depletion of gut CD4⁺ T lymphocytes, loss of memory T cells in blood, and thrombocytopenia that resulted in fatal cerebral hemorrhage. SHIV-2873Nip is a highly replication-competent, mucosally transmissible, pathogenic R5-tropic virus that will be useful to study viral pathogenesis and to assess the efficacy of immunogens targeting HIV-C Env.Currently, 33 million people are living with human immunodeficiency virus (HIV)/AIDS (www.unaids.org), and the majority of them live in sub-Saharan Africa and South and Southeast Asia, including China and India, where HIV subtype C (HIV-C) circulates in >90% of the HIV-infected population (UNAIDS) (50). This distribution makes HIV-C the most prevalent subtype in the global pandemic, accounting for >56% of all HIV infections worldwide (www.unaids.org). Globally, HIV is one of the leading causes of childhood morbidity and mortality. Children account for 20% of all HIV-related deaths, 7% of individuals living with HIV, and 16% of new infections annually (reviewed in references 26, 29, and 38). In sub-Saharan Africa, HIV-C is responsible for approximately 50% of all infections, and a significant number of infections are in infants and children. HIV transmission from infected mothers to their infants is the primary mode of infection in children and can occur in utero, intrapartum, or postnatally through breast milk. The use of antiretroviral drugs has successfully reduced the rate of HIV infection in infants in the developed world to approximately 1%; nevertheless, such regimens have only recently become available in many of the developing nations where mother-to-child transmission of HIV is most significant (reviewed in references 26 and 38).Simian-human immunodeficiency viruses (SHIVs) are chimeric viruses that contain HIV envelope genes in the simian immunodeficiency virus (SIV) backbone. They have been used in a wide range of studies investigating lentiviral pathogenesis, antiviral immunity, virus-host interactions, mucosal transmission, and vaccine and drug efficacy (20). However, the majority of current SHIV strains utilize envelope genes derived from HIV clade B strains, which represent fewer than 10% of all global infections. Therefore, the available SHIV chimeras do not reflect the genetic diversity of the HIV epidemic, which is dominated by non-B clades, especially by HIV-C. Only a few studies have focused on developing anti-clade C Env vaccines (25, 27, 44, 49), with one efficacy study in primate models (44). To investigate lentiviral pathogenesis as well as anti-HIV-C vaccine safety and efficacy in nonhuman primate models, a pathogenic, CCR5-restricted, clade C SHIV (SHIV-C) would be very useful.Previously, we have generated an R5-tropic SHIV-C, SHIV-1157i (6, 51), which carries env from a 6-month-old Zambian infant born to an HIV-positive mother. During prospective long-term follow-up, this infant turned out to be a long-term nonprogressor who has remained asymptomatic at 8 years of age (61). The rhesus monkey (RM)-adapted strain, SHIV-1157ip, was pathogenic and has caused AIDS in several monkeys thus far, but with a relatively low rate of disease progression. AIDS developed in RMs between 127 and 300 weeks postinoculation (17a). A late virus was reisolated and engineered to contain extra NF-κB sites in the long terminal repeats (LTRs) (51); follow-up times for monkeys infected with this late form are not yet sufficient to assess development to AIDS, although signs of disease have developed. A possible explanation is that the env gene used to construct the original SHIV-1157i is an important determinant of the disease progression rate. The fact that the env gene was derived from a long-term nonprogressor may be linked to the relatively slow disease progression we observed in RMs infected with SHIV carrying the corresponding env gene.We sought to test whether constructing an R5-tropic SHIV with an env gene derived from a rapid progressor would give rise to a more virulent R5-tropic SHIV-C. Although HIV- or SIV-infected individuals with either typical rates of disease progression or long-term nonprogression have been studied extensively, few reports were focused on the virologic and immunologic characteristics of patients with rapid disease progression (9, 22). Patients who progress to AIDS within 1 to 2 years from the time of infection have been identified among infants and adults (7, 13, 34, 35, 46), with a higher frequency in infant populations. These patients demonstrate rapid loss of CD4⁺ T cells and lack potent cellular and humoral immune responses.Here we report the construction of SHIV-2873Ni, a chimera that carries env of an R5-tropic HIV-C strain isolated from a rapid progressor, a 2-month-old Zambian baby who died of AIDS-related disease within 1 year of birth. SHIV-2873Ni was serially passaged through five RMs; SHIV-2873Nip, the passaged virus, was reisolated and characterized from the fourth recipient about 1 year postinoculation when signs of disease were manifest. The RM-adapted virus caused T-cell depletion within a few months postinoculation.     

Synergy between DNA polymerases increases polymerase chain reaction inhibitor tolerance in forensic DNA analysis

The success rate of diagnostic polymerase chain reaction (PCR) analysis is lowered by inhibitory substances present in the samples. Recently, we showed that tolerance to PCR inhibitors in crime scene saliva stains can be improved by replacing the standard DNA polymerase AmpliTaq Gold with alternative DNA polymerase-buffer systems (Hedman et al., BioTechniques 47 (2009) 951-958). Here we show that blending inhibitor-resistant DNA polymerase-buffer systems further increases the success rate of PCR for various types of real crime scene samples showing inhibition. For 34 of 42 “inhibited” crime scene stains, the DNA profile quality was significantly improved using a DNA polymerase blend of ExTaq Hot Start and PicoMaxx High Fidelity compared with AmpliTaq Gold. The significance of the results was confirmed by analysis of variance. The blend performed as well as, or better than, the alternative DNA polymerases used separately for all tested sample types. When used separately, the performance of the DNA polymerases varied depending on the nature of the sample. The superiority of the blend is discussed in terms of complementary effects and synergy between the DNA polymerase-buffer systems.