Antiviral Protection via RdRP-Mediated Stable Activation of Innate Immunity

For many emerging and re-emerging infectious diseases, definitive solutions via sterilizing adaptive immunity may require years or decades to develop, if they are even possible. The innate immune system offers alternative mechanisms that do not require antigen-specific recognition or a priori knowledge of the causative agent. However, it is unclear whether effective stable innate immune system activation can be achieved without triggering harmful autoimmunity or other chronic inflammatory sequelae. Here, we show that transgenic expression of a picornavirus RNA-dependent RNA polymerase (RdRP), in the absence of other viral proteins, can profoundly reconfigure mammalian innate antiviral immunity by exposing the normally membrane-sequestered RdRP activity to sustained innate immune detection. RdRP-transgenic mice have life-long, quantitatively dramatic upregulation of 80 interferon-stimulated genes (ISGs) and show profound resistance to normally lethal viral challenge. Multiple crosses with defined knockout mice (Rag1, Mda5, Mavs, Ifnar1, Ifngr1, and Tlr3) established that the mechanism operates via MDA5 and MAVS and is fully independent of the adaptive immune system. Human cell models recapitulated the key features with striking fidelity, with the RdRP inducing an analogous ISG network and a strict block to HIV-1 infection. This RdRP-mediated antiviral mechanism does not depend on secondary structure within the RdRP mRNA but operates at the protein level and requires RdRP catalysis. Importantly, despite lifelong massive ISG elevations, RdRP mice are entirely healthy, with normal longevity. Our data reveal that a powerfully augmented MDA5-mediated activation state can be a well-tolerated mammalian innate immune system configuration. These results provide a foundation for augmenting innate immunity to achieve broad-spectrum antiviral protection.     

Characterization of a Prefusion-Specific Antibody That Recognizes a Quaternary,Cleavage-Dependent Epitope on the RSV Fusion Glycoprotein

Prevention efforts for respiratory syncytial virus (RSV) have been advanced due to the recent isolation and characterization of antibodies that specifically recognize the prefusion conformation of the RSV fusion (F) glycoprotein. These potently neutralizing antibodies are in clinical development for passive prophylaxis and have also aided the design of vaccine antigens that display prefusion-specific epitopes. To date, prefusion-specific antibodies have been shown to target two antigenic sites on RSV F, but both of these sites are also present on monomeric forms of F. Here we present a structural and functional characterization of human antibody AM14, which potently neutralized laboratory strains and clinical isolates of RSV from both A and B subtypes. The crystal structure and location of escape mutations revealed that AM14 recognizes a quaternary epitope that spans two protomers and includes a region that undergoes extensive conformational changes in the pre- to postfusion F transition. Binding assays demonstrated that AM14 is unique in its specific recognition of trimeric furin-cleaved prefusion F, which is the mature form of F on infectious virions. These results demonstrate that the prefusion F trimer contains potent neutralizing epitopes not present on monomers and that AM14 should be particularly useful for characterizing the conformational state of RSV F-based vaccine antigens.     

Development and Validation of a Novel Platform-Independent Metastasis Signature in Human Breast Cancer

PurposeThe molecular drivers of metastasis in breast cancer are not well understood. Therefore, we sought to identify the biological processes underlying distant progression and define a prognostic signature for metastatic potential in breast cancer.ResultsWe identified a broad range of metastatic potential that was independent of intrinsic breast cancer subtypes. 146 genes were significantly associated with metastasis progression and were linked to cancer-related biological functions, including cell migration/adhesion, Jak-STAT, TGF-beta, and Wnt signaling. These genes were used to develop a platform-independent gene expression signature (M-Sig), which was trained and subsequently validated on 5 independent cohorts totaling nearly 1800 breast cancer patients with all p-values < 0.005 and hazard ratios ranging from approximately 2.5 to 3. On multivariate analysis accounting for standard clinicopathologic prognostic variables, M-Sig remained the strongest prognostic factor for metastatic progression, with p-values < 0.001 and hazard ratios > 2 in three different cohorts.ConclusionM-Sig is strongly prognostic for metastatic progression, and may provide clinical utility in combination with treatment prediction tools to better guide patient care. In addition, the platform-independent nature of the signature makes it an excellent research tool as it can be directly applied onto existing, and future, datasets.     

Body iron is a contributor to oxidative damage of DNA

The transition metal iron is catalytically highly active in vitro, and not surprisingly, body iron has been suggested to promote oxidative stress in vivo. In the current analysis we studied the association of serum ferritin concentration and serum soluble transferrin receptor concentration with daily urinary 8-hydroxydeoxyguanosine excretion, a marker of oxidative stress, in 48 mildly dyslipidemic men in East Finland. In multivariate linear regression analyses allowing for age, smoking, body mass index and physical exercise, serum ferritin concentration predicted the excretion rate at B = 0.17 (95% CI 0.08-0.26, P = 0.001), and serum soluble transferrin receptor to ferritin concentration ratio (TfR/ferritin) predicted the excretion rate at B = - 0.13 (95% CI - 0.21 to - 0.05, P = 0.002). Our data suggest that body iron contributes to excess oxidative stress already at non-iron overload concentrations in these subjects.     

Plasma ghrelin levels in rainbow trout in response to fasting, feeding and food composition, and effects of ghrelin on voluntary food intake

Ghrelin, a peptide hormone which stimulates growth hormone (GH) release, appetite and adiposity in mammals, was recently identified in fish. In this study, the roles of ghrelin in regulating food intake and the growth hormone (GH)-insulin-like growth factor I (IGF-I) system of rainbow trout (Oncorhynchus mykiss) were investigated in three experiments: 1) Pre- and postprandial plasma levels of ghrelin were measured in relation to dietary composition and food intake through dietary inclusion of radio-dense lead-glass beads, 2) the effect of a single intraperitoneal (i.p.) injection with rainbow trout ghrelin on short-term voluntary food intake was examined and 3) the effect of one to three weeks fasting on circulating ghrelin levels and the correlation with plasma GH and IGF-I levels, growth and lipid content in the liver and muscle was studied. There was no postprandial change in plasma ghrelin levels. Fish fed a normal-protein/high-lipid (31.4%) diet tended to have higher plasma ghrelin levels than those fed a high-protein/low-lipid (14.1%) diet. Plasma ghrelin levels decreased during fasting and correlated positively with specific growth rates, condition factor, liver and muscle lipid content, and negatively with plasma GH and IGF-I levels. An i.p. ghrelin injection did not affect food intake during 12-hours post-injection. It is concluded that ghrelin release in rainbow trout may be influenced by long-term energy status, and possibly by diet composition. Further, in rainbow trout, ghrelin seems to be linked to growth and metabolism, but does not seem to stimulate short-term appetite through a peripheral action.     

Can Reindeer Overabundance Cause a Trophic Cascade?

Abstract The region Finnmark, in northernmost Europe, harbors dense populations of semi-domestic reindeer of which some exhibit characteristics of overabundance. Whereas overabundance is evident in terms of density-dependent reductions in reindeer body mass, population growth and abundance of forage plants, claims have been made that this reindeer overabundance also has caused a trophic cascade. These claims are based on the main premise that reindeer overgrazing negatively impacts small-sized, keystone tundra herbivores. We tested this premise by a large-scale study in which the abundance of small rodents, hares and ptarmigans was indexed across reindeer management districts with strong differences in stocking densities. We examined the scale-dependent relations between reindeer, vegetation and these small-sized herbivores by employing a spatially hierarchical sampling design within the management districts. A negative impact of reindeer on ptarmigan, probably as a result of browsing reducing tall Salix, was indicated. However, small rodents (voles and lemmings), which are usually the keystone herbivores in the plant-based tundra food web, were not negatively impacted. On the contrary, there was a strong positive relationship between small rodents and reindeer, both at the scale of landscape areas and local patches, with characteristics of snow-bed vegetation, suggesting facilitation between Norwegian lemmings and reindeer. We conclude that the recent dampening of the vole and lemming population cycle with concurrent declines of rodent predators in northernmost Europe were not caused by large herbivore overgrazing.     

A resource for understanding and evaluating outcomes of undergraduate field experiences

Undergraduate field experiences (UFEs) are a prominent element of science education across many disciplines; however, empirical data regarding the outcomes are often limited. UFEs are unique in that they typically take place in a field setting, are often interdisciplinary, and include diverse students. UFEs range from courses, to field trips, to residential research experiences, and thereby have the potential to yield a plethora of outcomes for undergraduate participants. The UFE community has expressed interest in better understanding how to assess the outcomes of UFEs. In response, we developed a guide for practitioners to use when assessing their UFE that promotes an evidence‐based, systematic, iterative approach. This essay guides practitioners through the steps of: identifying intended UFE outcomes, considering contextual factors, determining an assessment approach, and using the information gained to inform next steps. We provide a table of common learning outcomes with aligned assessment tools, and vignettes to illustrate using the assessment guide. We aim to support comprehensive, informed assessment of UFEs, thus leading to more inclusive and reflective UFE design, and ultimately improved student outcomes. We urge practitioners to move toward evidence‐based advocacy for continued support of UFEs.     

The food, growth and abundance of five co-existing cyprinids in lake basins of different morphometry and water quality

The food, growth and abundance of five co-existing cyprinid fish species in the eutrophic Lake Hiidenvesi were studied. The diet overlaps within the cyprinid community in shallow lake basins were compared with those in a deep basin, where littoral resources are less available. Roach, bleak and white bream inhabited both the shallow and the deep parts of the lake. Their growth rate was slow, probably due to the low availability of animal food, indicated by the increasing proportion of detritus and plant material in the diets towards the end of the summer. In the deep basin, roach and bleak, contrary to white bream, did not forage on the very abundant invertebrate Chaoborus flavicans, explained by the migration behaviour of C. flavicans. Blue bream, unlike other cyprinids, utilized copepods and had a relatively fast growth rate, but was mostly restricted to the shallow areas. The condition of the bream stock was weak both in terms of growth and abundance. The availability of zoobenthos was low and bream was not able to compete for zooplankton with the more specialized planktivores.     

Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis

Patients with inherited retinal dystrophies (IRDs) were recruited from two understudied populations: Mexico and Pakistan as well as a third well-studied population of European Americans to define the genetic architecture of IRD by performing whole-genome sequencing (WGS). Whole-genome analysis was performed on 409 individuals from 108 unrelated pedigrees with IRDs. All patients underwent an ophthalmic evaluation to establish the retinal phenotype. Although the 108 pedigrees in this study had previously been examined for mutations in known IRD genes using a wide range of methodologies including targeted gene(s) or mutation(s) screening, linkage analysis and exome sequencing, the gene mutations responsible for IRD in these 108 pedigrees were not determined. WGS was performed on these pedigrees using Illumina X10 at a minimum of 30X depth. The sequence reads were mapped against hg19 followed by variant calling using GATK. The genome variants were annotated using SnpEff, PolyPhen2, and CADD score; the structural variants (SVs) were called using GenomeSTRiP and LUMPY. We identified potential causative sequence alterations in 61 pedigrees (57%), including 39 novel and 54 reported variants in IRD genes. For 57 of these pedigrees the observed genotype was consistent with the initial clinical diagnosis, the remaining 4 had the clinical diagnosis reclassified based on our findings. In seven pedigrees (12%) we observed atypical causal variants, i.e. unexpected genotype(s), including 4 pedigrees with causal variants in more than one IRD gene within all affected family members, one pedigree with intrafamilial genetic heterogeneity (different affected family members carrying causal variants in different IRD genes), one pedigree carrying a dominant causative variant present in pseudo-recessive form due to consanguinity and one pedigree with a de-novo variant in the affected family member. Combined atypical and large structural variants contributed to about 20% of cases. Among the novel mutations, 75% were detected in Mexican and 50% found in European American pedigrees and have not been reported in any other population while only 20% were detected in Pakistani pedigrees and were not previously reported. The remaining novel IRD causative variants were listed in gnomAD but were found to be very rare and population specific. Mutations in known IRD associated genes contributed to pathology in 63% Mexican, 60% Pakistani and 45% European American pedigrees analyzed. Overall, contribution of known IRD gene variants to disease pathology in these three populations was similar to that observed in other populations worldwide. This study revealed a spectrum of mutations contributing to IRD in three populations, identified a large proportion of novel potentially causative variants that are specific to the corresponding population or not reported in gnomAD and shed light on the genetic architecture of IRD in these diverse global populations.