A Natural Genetic Variant of Granzyme B Confers Lethality to a Common Viral Infection

Many immune response genes are highly polymorphic, consistent with the selective pressure imposed by pathogens over evolutionary time, and the need to balance infection control with the risk of auto-immunity. Epidemiological and genomic studies have identified many genetic variants that confer susceptibility or resistance to pathogenic micro-organisms. While extensive polymorphism has been reported for the granzyme B (GzmB) gene, its relevance to pathogen immunity is unexplored. Here, we describe the biochemical and cytotoxic functions of a common allele of GzmB (GzmB^W) common in wild mouse. While retaining ‘Asp-ase’ activity, GzmB^W has substrate preferences that differ considerably from GzmB^P, which is common to all inbred strains. In vitro, GzmB^W preferentially cleaves recombinant Bid, whereas GzmB^P activates pro-caspases directly. Recombinant GzmB^W and GzmB^P induced equivalent apoptosis of uninfected targets cells when delivered with perforin in vitro. Nonetheless, mice homozygous for GzmB^W were unable to control murine cytomegalovirus (MCMV) infection, and succumbed as a result of excessive liver damage. Although similar numbers of anti-viral CD8 T cells were generated in both mouse strains, GzmB^W-expressing CD8 T cells isolated from infected mice were unable to kill MCMV-infected targets in vitro. Our results suggest that known virally-encoded inhibitors of the intrinsic (mitochondrial) apoptotic pathway account for the increased susceptibility of GzmB^W mice to MCMV. We conclude that different natural variants of GzmB have a profound impact on the immune response to a common and authentic viral pathogen.     

Metabolic Reprogramming during Purine Stress in the Protozoan Pathogen Leishmania donovani

The ability of Leishmania to survive in their insect or mammalian host is dependent upon an ability to sense and adapt to changes in the microenvironment. However, little is known about the molecular mechanisms underlying the parasite response to environmental changes, such as nutrient availability. To elucidate nutrient stress response pathways in Leishmania donovani, we have used purine starvation as the paradigm. The salvage of purines from the host milieu is obligatory for parasite replication; nevertheless, purine-starved parasites can persist in culture without supplementary purine for over three months, indicating that the response to purine starvation is robust and engenders parasite survival under conditions of extreme scarcity. To understand metabolic reprogramming during purine starvation we have employed global approaches. Whole proteome comparisons between purine-starved and purine-replete parasites over a 6–48 h span have revealed a temporal and coordinated response to purine starvation. Purine transporters and enzymes involved in acquisition at the cell surface are upregulated within a few hours of purine removal from the media, while other key purine salvage components are upregulated later in the time-course and more modestly. After 48 h, the proteome of purine-starved parasites is extensively remodeled and adaptations to purine stress appear tailored to deal with both purine deprivation and general stress. To probe the molecular mechanisms affecting proteome remodeling in response to purine starvation, comparative RNA-seq analyses, qRT-PCR, and luciferase reporter assays were performed on purine-starved versus purine-replete parasites. While the regulation of a minority of proteins tracked with changes at the mRNA level, for many regulated proteins it appears that proteome remodeling during purine stress occurs primarily via translational and/or post-translational mechanisms.     

Engagement of NKG2D on Bystander Memory CD8 T Cells Promotes Increased Immunopathology following Leishmania major Infection

One of the hallmarks of adaptive immunity is the development of a long-term pathogen specific memory response. While persistent memory T cells certainly impact the immune response during a secondary challenge, their role in unrelated infections is less clear. To address this issue, we utilized lymphocytic choriomeningitis virus (LCMV) and Listeria monocytogenes immune mice to investigate whether bystander memory T cells influence Leishmania major infection. Despite similar parasite burdens, LCMV and Listeria immune mice exhibited a significant increase in leishmanial lesion size compared to mice infected with L. major alone. This increased lesion size was due to a severe inflammatory response, consisting not only of monocytes and neutrophils, but also significantly more CD8 T cells. Many of the CD8 T cells were LCMV specific and expressed gzmB and NKG2D, but unexpectedly expressed very little IFN-γ. Moreover, if CD8 T cells were depleted in LCMV immune mice prior to challenge with L. major, the increase in lesion size was lost. Strikingly, treating with NKG2D blocking antibodies abrogated the increased immunopathology observed in LCMV immune mice, showing that NKG2D engagement on LCMV specific memory CD8 T cells was required for the observed phenotype. These results indicate that bystander memory CD8 T cells can participate in an unrelated immune response and induce immunopathology through an NKG2D dependent mechanism without providing increased protection.     

Non-invasive assessment of embryonic sex in cattle by metabolic fingerprinting of in vitro culture medium

The objective of this work was to determine whether metabolic fingerprinting of spent bovine embryo culture media using Fourier transform infrared spectroscopy (FTIR) correlates with embryonic sex. Embryos were produced in vitro from oocytes collected from cows slaughtered in an abattoir. Day-6 embryos were individually cultured in synthetic oviduct fluid for 24 h, prior to the time (Day-7) intended for embryo transfer or cryopreservation. Culture medium was analyzed by FTIR. Embryos were sexed by a PCR procedure based on amelogenin gene amplification or transferred to a recipient and sex observed at birth. Media samples from embryos diagnosed as male (n = 47) or female (n = 70) were individually collected and evaluated using FTIR. The spectra obtained were analyzed according to metabolomic profile of embryo culture media and embryonic sex. The discrimination capability of the classifiers was assessed for accuracy, sensitivity (female), sensitivity (male) and area under the ROC curve (AUC). Performance of sex prediction (%) was high within early blastocysts + blastocysts (74.4 ± 10.2, accuracy; 0.749 ± 0.099, AUC) and excellent for expanded blastocysts (86.0 ± 12.6, accuracy; 0.898 ± 0.094, AUC). A combination of metabolomic and bioinformatic analysis provides a non-invasive mean of embryonic sex analysis.     

Domain Compositions and Fullerene Aggregation Govern Charge Photogeneration in Polymer/Fullerene Solar Cells

The complex microstructure of organic semiconductor mixtures continues to obscure the connection between the active layer morphology and photovoltaic device performance. For example, the ubiquitous presence of mixed phases in the active layer of polymer/fullerene solar cells creates multiple morphologically distinct interfaces which are capable of exciton dissociation or charge recombination. Here, it is shown that domain compositions and fullerene aggregation can strongly modulate charge photogeneration at ultrafast timescales through studies of a model system, mixtures of a low band‐gap polymer, poly[(4,4′‐bis(2‐ethylhexyl)dithieno[3,2‐b:2′,3′‐d]germole)‐2,6‐diyl‐alt‐(2,1,3‐benzothia‐diazole)‐4,7‐diyl], and [6,6]‐phenyl‐C₇₁‐butyric acid methyl ester. Structural characterization using energy‐filtered transmission electron microscopy (EFTEM) and resonant soft X‐ray scattering shows similar microstructures even with changes in the overall film composition. Composition maps generated from EFTEM, however, demonstrate that compositions of mixed domains vary significantly with overall film composition. Furthermore, the amount of polymer in the mixed domains is inversely correlated with device performance. Photoinduced absorption studies using ultrafast infrared spectroscopy demonstrate that polaron concentrations are highest when mixed domains contain the least polymer. Grazing‐incidence X‐ray scattering results show that larger fullerene coherence lengths are correlated to higher polaron yields. Thus, the purity of the mixed domains is critical for efficient charge photogeneration because purity modulates fullerene aggregation and electron delocalization.     

Crossing the line: increasing body size in a trans-Wallacean lizard radiation (Cyrtodactylus,Gekkota)

The region between the Asian and Australian continental plates (Wallacea) demarcates the transition between two differentiated regional biotas. Despite this striking pattern, some terrestrial lineages have successfully traversed the marine barriers of Wallacea and subsequently diversified in newly colonized regions. The hypothesis that these dispersals between biogeographic realms are correlated with detectable shifts in evolutionary trajectory has however rarely been tested. Here, we analyse the evolution of body size in a widespread and exceptionally diverse group of gekkotan lizards (Cyrtodactylus), and show that a clade that has dispersed eastwards and radiated in the Australopapuan region appears to have significantly expanded its body size ‘envelope’ and repeatedly evolved gigantism. This pattern suggests that the biotic composition of the proto-Papuan Archipelago provided a permissive environment in which new colonists were released from evolutionary constraints operating to the west of Wallacea.     

Bacterial genome replication at subzero temperatures in permafrost

Microbial metabolic activity occurs at subzero temperatures in permafrost, an environment representing ∼25% of the global soil organic matter. Although much of the observed subzero microbial activity may be due to basal metabolism or macromolecular repair, there is also ample evidence for cellular growth. Unfortunately, most metabolic measurements or culture-based laboratory experiments cannot elucidate the specific microorganisms responsible for metabolic activities in native permafrost, nor, can bulk approaches determine whether different members of the microbial community modulate their responses as a function of changing subzero temperatures. Here, we report on the use of stable isotope probing with ¹³C-acetate to demonstrate bacterial genome replication in Alaskan permafrost at temperatures of 0 to −20 °C. We found that the majority (80%) of operational taxonomic units detected in permafrost microcosms were active and could synthesize ¹³C-labeled DNA when supplemented with ¹³C-acetate at temperatures of 0 to −20 °C during a 6-month incubation. The data indicated that some members of the bacterial community were active across all of the experimental temperatures, whereas many others only synthesized DNA within a narrow subzero temperature range. Phylogenetic analysis of ¹³C-labeled 16S rRNA genes revealed that the subzero active bacteria were members of the Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes and Proteobacteria phyla and were distantly related to currently cultivated psychrophiles. These results imply that small subzero temperature changes may lead to changes in the active microbial community, which could have consequences for biogeochemical cycling in permanently frozen systems.