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Human coronavirus (HCoV)-NL63 causes respiratory tract infections in humans and uses angiotensin-converting enzyme 2 (ACE2) as a receptor. We sought to establish a mouse model of HCoV-NL63 and determine whether prior rhinovirus (RV)-A1B infection affected HCoV-NL63 replication. HCoV-NL63 was propagated in LLC-MK2 cells expressing human ACE2. RV-A1B was grown in HeLa-H1 cells. C57BL6/J or transgenic mice expressing human ACE2 were infected intranasally with sham LLC-MK2 cell supernatant or 1 × 105 tissue culture infectious dose (TCID50) units HCoV-NL63. Wild-type mice were infected with 1 × 106 plaque-forming units (PFU) RV-A1B. Lungs were assessed for vRNA, bronchoalveolar lavage (BAL) cells, histology, HCoV-NL63 nonstructural protein 3 (nsp3), and host gene expression by next-generation sequencing and qPCR. To evaluate sequential infections, mice were infected with RV-A1B followed by HCoV-NL63 infection 4 days later. We report that hACE2 mice infected with HCoV-NL63 showed evidence of replicative infection with increased levels of vRNA, BAL neutrophils and lymphocytes, peribronchial and perivascular infiltrates, and expression of nsp3. Viral replication peaked 3 days after infection and inflammation persisted 6 days after infection. HCoV-NL63-infected hACE2 mice showed increased mRNA expression of IFNs, IFN-stimulated proteins, and proinflammatory cytokines. Infection with RV-A1B 4 days before HCoV-NL63 significantly decreased both HCoV-NL63 vRNA levels and airway inflammation. Mice infected with RV-A1B prior to HCoV-NL63 showed increased expression of antiviral proteins compared with sham-treated mice. In conclusion, we established a mouse model of HCoV-NL63 replicative infection characterized by relatively persistent viral replication and inflammation. Prior infection with RV-A1B reduced HCoV-NL63 replication and airway inflammation, indicative of viral interference. NEW & NOTEWORTHY: We describe a mouse model of human coronavirus (HCoV) infection. Infection of transgenic mice expressing human angiotensin-converting enzyme 2 (ACE2) with HCoV-NL63 produced a replicative infection with peribronchial inflammation and nonstructural protein 3 expression. Mice infected with RV-A1B 4 days before HCoV-NL63 showed decreased HCoV-NL63 replication and airway inflammation and increased expression of antiviral proteins compared with sham-treated mice. This research may shed light on human coronavirus infections, viral interference, and viral-induced asthma exacerbations. [ABSTRACT FROM AUTHOR]

Background: The factors contributing to the accelerated convergent evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not fully understood. Unraveling the contribution of viral replication in immunocompromised patients is important for the early detection of novel mutations and developing approaches to limit COVID-19. Methods: We deep sequenced SARS-CoV-2 RNA from 192 patients (64% hospitalized, 39% immunosuppressed) and compared the viral genetic diversity within the patient groups of different immunity and hospitalization status. Serial sampling of 14 patients was evaluated for viral evolution in response to antiviral treatments. Results: We identified hospitalized and immunosuppressed patients with significantly higher levels of viral genetic diversity and variability. Further evaluation of serial samples revealed accumulated mutations associated with escape from neutralizing antibodies in a subset of the immunosuppressed patients treated with antiviral therapies. Interestingly, the accumulated viral mutations that arose in this early Omicron wave, which were not common in the patient viral lineages, represent convergent mutations that are prevalent in the later Omicron sublineages, including the XBB, BA.2.86.1 and its descendent JN sublineages. Conclusions: Our results illustrate the importance of identifying convergent mutations generated during antiviral therapy in immunosuppressed patients, as they may contribute to the future evolutionary landscape of SARS-CoV-2. Our study also provides evidence of a correlation between SARS-CoV-2 convergent mutations and specific antiviral treatments. Evaluating high-confidence genomes from distinct waves in the pandemic with detailed patient metadata allows for discerning of convergent mutations that contribute to the ongoing evolution of SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Copyright of Language & Intercultural Communication is the property of Taylor & Francis Ltd and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Language is often used to demonstrate group membership and to establish cultural identity. When the language is not readily available or is at risk, individuals tend to turn to other markers to develop their cultural identity. Using Leximancer for thematic and conceptual analyses of interviews with ten accomplished musicians in Nova Scotia, Canada, we argue that the commitment to learning music and dance may act as a channel to learning Scottish Gaelic, a threatened local heritage language. Drawing on Norton's construct of investment in language learning, we consider the extent to which participants commit to learning the language and the music/dance for their identification to the Gaelic culture. Given that Gaelic music and dance traditions remain healthy, even as the language is declining, the results of our research have significant implications for language revitalisation efforts. [ABSTRACT FROM AUTHOR]

Background Kawasaki disease (KD) is a febrile illness of young childhood that can result in coronary artery aneurysms and death. Coronavirus disease 2019 (COVID-19) mitigation strategies resulted in a marked decrease in KD cases worldwide, supporting a transmissible respiratory agent as the cause. We previously reported a peptide epitope recognized by monoclonal antibodies (MAbs) derived from clonally expanded peripheral blood plasmablasts from 3 of 11 KD children, suggesting a common disease trigger in a subset of patients with KD. Methods We performed amino acid substitution scans to develop modified peptides with improved recognition by KD MAbs. We prepared additional MAbs from KD peripheral blood plasmablasts and assessed MAb characteristics that were associated with binding to the modified peptides. Results We report a modified peptide epitope that is recognized by 20 MAbs from 11 of 12 KD patients. These MAbs predominantly use heavy chain VH3-74 ; two-thirds of VH3-74 plasmablasts from these patients recognize the epitope. The MAbs were nonidentical between patients but share a common complementarity-determining region 3 (CDR3) motif. Conclusions These results demonstrate a convergent VH3-74 plasmablast response to a specific protein antigen in children with KD, supporting one predominant causative agent in the etiopathogenesis of the illness. [ABSTRACT FROM AUTHOR]

Human society is dependent on nature1,2, but whether our ecological foundations are at risk remains unknown in the absence of systematic monitoring of species’ populations3. Knowledge of species fluctuations is particularly inadequate in the marine realm4. Here we assess the population trends of 1,057 common shallow reef species from multiple phyla at 1,636 sites around Australia over the past decade. Most populations decreased over this period, including many tropical fishes, temperate invertebrates (particularly echinoderms) and southwestern Australian macroalgae, whereas coral populations remained relatively stable. Population declines typically followed heatwave years, when local water temperatures were more than 0.5 °C above temperatures in 2008. Following heatwaves5,6, species abundances generally tended to decline near warm range edges, and increase near cool range edges. More than 30% of shallow invertebrate species in cool latitudes exhibited high extinction risk, with rapidly declining populations trapped by deep ocean barriers, preventing poleward retreat as temperatures rise. Greater conservation effort is needed to safeguard temperate marine ecosystems, which are disproportionately threatened and include species with deep evolutionary roots. Fundamental among such efforts, and broader societal needs to efficiently adapt to interacting anthropogenic and natural pressures, is greatly expanded monitoring of species’ population trends7,8.A systematic census at 1,636 sites around Australia from 2008 to 2021 finds that more than 30% of shallow invertebrate species in cool latitudes exhibit a high extinction risk due to declining populations and oceanic barriers, but tropical coral species remain relatively stable. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 Omicron variant is more immune evasive and less virulent than other major viral variants that have so far been recognized1–12. The Omicron spike (S) protein, which has an unusually large number of mutations, is considered to be the main driver of these phenotypes. Here we generated chimeric recombinant SARS-CoV-2 encoding the S gene of Omicron (BA.1 lineage) in the backbone of an ancestral SARS-CoV-2 isolate, and compared this virus with the naturally circulating Omicron variant. The Omicron S-bearing virus robustly escaped vaccine-induced humoral immunity, mainly owing to mutations in the receptor-binding motif; however, unlike naturally occurring Omicron, it efficiently replicated in cell lines and primary-like distal lung cells. Similarly, in K18-hACE2 mice, although virus bearing Omicron S caused less severe disease than the ancestral virus, its virulence was not attenuated to the level of Omicron. Further investigation showed that mutating non-structural protein 6 (nsp6) in addition to the S protein was sufficient to recapitulate the attenuated phenotype of Omicron. This indicates that although the vaccine escape of Omicron is driven by mutations in S, the pathogenicity of Omicron is determined by mutations both in and outside of the S protein.Comparisons of a chimeric recombinant version of SARS-CoV-2, the ancestral SARS-CoV-2 strain and an Omicron isolate show that the attenuated virulence of Omicron is caused by mutations in both the spike protein and nsp6. [ABSTRACT FROM AUTHOR]

The pandemic of SARS-CoV-2 is characterized by the emergence of new variants of concern (VOCs) that supplant previous waves of infection. Here, we describe our investigation of the lineages and host-specific mutations identified in a particularly vulnerable population of predominantly older and immunosuppressed SARS-CoV-2-infected patients seen at our medical center in Chicago during the transition from the Delta to Omicron wave. We compare two primer schemes, ArticV4.1 and VarSkip2, used for short read amplicon sequencing, and describe our strategy for bioinformatics analysis that facilitates identifying lineage-associated mutations and host-specific mutations that arise during infection. This study illustrates the ongoing evolution of SARS-CoV-2 VOCs in our community and documents novel constellations of mutations that arise in individual patients. The ongoing evaluation of the evolution of SARS-CoV-2 during this pandemic is important for informing our public health strategies. [ABSTRACT FROM AUTHOR]

Patient satisfaction is important to patient outcomes. Previous attempts to conceptualize satisfaction have often taken an atheoretical approach and focused on doctors' communication skills. Patients are becoming more active health consumers involved in their health care and current definitions of patient satisfaction may not accurately reflect patient expectations about their health consultations. Earlier research found that meeting patients' emotional needs - through empathy and patient-centered communication - is important to patient satisfaction. New research is needed to explore how those needs can be met given the changing trend in patient behaviors and the focus on patient-centredness. This study employed two communication theories - the Willingness to Communicate Model and Communication Accommodation Theory - to consider both patients' communicative decisions, and the intergroup features of the health context that can influence communicative behaviors. Two hundred and fiftythree patients from health clinics in Canada and Australia described what satisfaction meant to them, and identified what aspects of their health consultation were satisfying (or not), and we investigated their perceptions of doctor's emotional expression. Results suggest that patient perceptions of their participation in the consultation predicts their perceptions of doctor emotional expression, and their satisfaction with the consultation. Patients want both emotional and medical needs met in an environment that balances interpersonal and intergroup communication. Our findings suggest the need to expand current definitions of patient satisfaction, patient-centredness and emotional expression. We discuss the implications of these findings for health practitioners and consider future research that addresses the need for more individualized health care. [ABSTRACT FROM AUTHOR]

To sustainably manage forest biodiversity and monitor changes in species patterning, mapping the spatial distribution of tree species is indispensable. Remote sensing can provide powerful tools for mapping species, but this task is complex in areas with high plant diversity and multi-layered canopies. This paper addresses the issue of classifying wet eucalypt forest plants by examining tree crown segmentation and species classification using different combinations of remote sensing datasets against mapped tree locations. This study explores optimal segmentation parameters for tree crown delineation compared to manually digitized tree crowns. The best segmentation accuracy of 88.71%, resulted from segmenting a combined Minimum Noise Fraction (MNF) dataset derived from hyperspectral imagery (HSI) and a LiDAR-derived Canopy Height Model (CHM). Object-based classification of tree species was performed using a random forest classifier. The fused dataset of MNF and CHM produced the highest overall accuracy of 78.26% for four vegetation classes, while the fused HSI, indices, and CHM performed best (66.67%) with five vegetation classes. However, both approaches had a high overall performance. The CHM contributed to tree crown segmentation and species classification accuracy, and fused datasets were more robust to spatially discriminate wet eucalypt forest species compared to a single dataset. Eucalyptus obliqua was classified with the highest accuracy of 90.86% for four classes using the fused MNF and CHM dataset, and 86.11% for five classes using the fused HSI, indices, and CHM dataset. An important understorey species – the tree fern (Dicksonia antarctica) – was classified with the highest accuracy of 83.54% for four classes using HSI. Therefore, fusing hyperspectral and LiDAR data could classify both the overstorey and dominant understorey species, and thus play a crucial role in identifying forest biological diversity. This approach will be useful for forest managers and ecologists to plan sustainable management of eucalypt forest biodiversity and produce maps for monitoring species of interest. [ABSTRACT FROM AUTHOR]

Forest loss and degradation are the greatest threats to biodiversity worldwide. Rising global wood demand threatens further damage to remaining native forests. Contrasting solutions across a continuum of options have been proposed, yet which of these offers most promise remains unresolved. Expansion of high‐yielding tree plantations could free up forest land for conservation provided this is implemented in tandem with stronger policies for conserving native forests. Because plantations and other intensively managed forests often support far less biodiversity than native forests, a second approach argues for widespread adoption of extensive management, or 'ecological forestry', which better simulates natural forest structure and disturbance regimes – albeit with compromised wood yields and hence a need to harvest over a larger area. A third, hybrid suggestion involves 'Triad' zoning where the landscape is divided into three sorts of management (reserve, ecological/extensive management, and intensive plantation). Progress towards resolving which of these approaches holds the most promise has been hampered by the absence of a conceptual framework and of sufficient empirical data formally to identify the most appropriate landscape‐scale proportions of reserves, extensive, and intensive management to minimize biodiversity impacts while meeting a given level of demand for wood. In this review, we argue that this central challenge for sustainable forestry is analogous to that facing food‐production systems, and that the land sharing–sparing framework devised to establish which approach to farming could meet food demand at least cost to wild species can be readily adapted to assess contrasting forest management regimes. We develop this argument in four ways: (i) we set out the relevance of the sharing–sparing framework for forestry and explore the degree to which concepts from agriculture can translate to a forest management context; (ii) we make design recommendations for empirical research on sustainable forestry to enable application of the sharing–sparing framework; (iii) we present overarching hypotheses which such studies could test; and (iv) we discuss potential pitfalls and opportunities in conceptualizing landscape management through a sharing–sparing lens. The framework we propose will enable forest managers worldwide to assess trade‐offs directly between conservation and wood production and to determine the mix of management approaches that best balances these (and other) competing objectives. The results will inform ecologically sustainable forest policy and management, reduce risks of local and global extinctions from forestry, and potentially improve a valuable sector's social license to operate. [ABSTRACT FROM AUTHOR]

Understanding the effects of logging and fire on forest soil communities is integral to our knowledge of forest ecology and effective resource management. The resulting changes in soil biota have substantial impacts on forest succession and associated ecosystem processes. We quantified bacterial and fungal abundance, diversity and community composition across a logging and burn severity gradient, approximately one month after fire, in temperate wet eucalypt forests in Tasmania, Australia. Using amplicon sequencing and real‐time quantitative PCR of the bacterial 16S rRNA gene and fungal ITS1 region, we demonstrate that (i) burn severity is a strong driver of soil microbial community composition, (ii) logging and high severity burning substantially reduce the biomass and diversity of soil bacteria and fungi, and (iii) the impacts of logging and burning on soil microbial communities are largely restricted to the top 10 cm of soil, with weak impacts on the subsoil. The impacts of disturbance on microbial community composition are greater than the effects of site‐to‐site edaphic differences. Fire also drives more divergence in community composition than logging alone. Key microbial taxa driving differences in severely burnt soils include bacterial genera implicated in plant‐growth promotion and producing antifungal compounds as well as saprotrophic fungi that are also capable of forming ectomycorrhizal associations. Our research suggests that low‐moderate severity burns are important for maintaining diversity and biomass in soil microbial communities but having a range of burn severities across a site contributes to the overall diversity of habitat conditions providing for both microbial and plant diversity. [ABSTRACT FROM AUTHOR]

DNA metabarcoding is an emerging approach for monitoring biodiversity, but uncertainties remain about its capacity to detect subtle differences in invertebrate community composition comparable to those achievable based on conventional morphological identification. In this study, DNA metabarcoding and morphology‐based approaches were compared as tools for investigating whether logging history impacted beetle communities in Tasmanian wet eucalypt forests. We compared 12 unlogged mature forest sites with 12 neighboring regeneration sites that had been logged approximately 55 years previously. The number of species identified based on morphology (173) was close to the number of zero‐radius operational taxonomic units (ZOTUs) identified by DNA metabarcoding of cytochrome c oxidase subunit I (COI, 176) and 16S ribosomal RNA (16S, 156) markers. Subtle but significant differences in beetle species composition between regeneration and unlogged mature forests were captured by both morphology‐based and COI DNA metabarcoding approaches, but not by 16S DNA metabarcoding. Our results support the suitability of mitochondrial COI for studying invertebrate biodiversity. A slight loss of signal compared to the morphology‐based approach may be resolved by developing more comprehensive DNA reference databases. While confirming forest recovery of 48–58 years did not fully restore mature forest beetle communities, we suggest that DNA metabarcoding can be used for monitoring biodiversity and probing subtle differences in community composition. [ABSTRACT FROM AUTHOR]

Background Kawasaki disease (KD) is the leading cause of childhood acquired heart disease in developed nations and can result in coronary artery aneurysms and death. Clinical and epidemiologic features implicate an infectious cause but specific antigenic targets of the disease are unknown. Peripheral blood plasmablasts are normally highly clonally diverse but the antibodies they encode are approximately 70% antigen-specific 1–2 weeks after infection. Methods We isolated single peripheral blood plasmablasts from children with KD 1–3 weeks after onset and prepared 60 monoclonal antibodies (mAbs). We used the mAbs to identify their target antigens and assessed serologic response among KD patients and controls to specific antigen. Results Thirty-two mAbs from 9 of 11 patients recognize antigen within intracytoplasmic inclusion bodies in ciliated bronchial epithelial cells of fatal cases. Five of these mAbs, from 3 patients with coronary aneurysms, recognize a specific peptide, which blocks binding to inclusion bodies. Sera from 5/8 KD patients day ≥ 8 after illness onset, compared with 0/17 infant controls (P  < .01), recognized the KD peptide antigen. Conclusions These results identify a protein epitope targeted by the antibody response to KD and provide a means to elucidate the pathogenesis of this important worldwide pediatric problem. [ABSTRACT FROM AUTHOR]

In recent decades, a paradigm shift in forest management and associated policies has led to greater emphasis on harvest practices that retain mature, overstory trees in forest stands that would otherwise be clear‐cut. While it is often assumed that the maintenance of compositional and structural complexity, such as that achieved through retention forestry approaches, will also mitigate negative impacts to functional diversity, empirical evidence of this relationship is sparse. We examined the effects of an aggregated retention system on taxonomic and functional diversity in a regenerating aspen‐dominated forest. Sampling was conducted along transects arranged to capture the transition from harvested (regenerating) forest to mature, unharvested forest (both intact forest stands and 0.1 ha retention aggregates). We then assessed the magnitude and distance of edge effects on multiple indices of taxonomic and functional diversity as well as functional identity. Twelve years after harvest, the distance and magnitude of edge effects on functional and taxonomic diversity did not differ between the two unharvested patch sizes (intact vs. aggregate); however, intact forest exhibited greater resistance to edge effects and greater depth of edge influence into harvested areas for some traits compared to aggregates. Analyses relying on functional traits were generally applicable across sites within a highly variable forest type, and our results demonstrate the promise of using functional traits to assess management impacts on plant diversity across a landscape. Aggregates maintained some functional attributes associated with interior forest and influenced adjacent regeneration. However, trends in some traits (i.e., shade tolerance and seed mass), particularly in the seedling layer, suggest aggregates of this size provide primarily edge habitat. [ABSTRACT FROM AUTHOR]

Background: Kawasaki disease (KD) is the leading cause of childhood acquired heart disease in developed nations and can result in coronary artery aneurysms and death. Clinical and epidemiologic features implicate an infectious cause but specific antigenic targets of the disease are unknown. Peripheral blood plasmablasts are normally highly clonally diverse but the antibodies they encode are approximately 70% antigen-specific 1-2 weeks after infection.Methods: We isolated single peripheral blood plasmablasts from children with KD 1-3 weeks after onset and prepared 60 monoclonal antibodies (mAbs). We used the mAbs to identify their target antigens and assessed serologic response among KD patients and controls to specific antigen.Results: Thirty-two mAbs from 9 of 11 patients recognize antigen within intracytoplasmic inclusion bodies in ciliated bronchial epithelial cells of fatal cases. Five of these mAbs, from 3 patients with coronary aneurysms, recognize a specific peptide, which blocks binding to inclusion bodies. Sera from 5/8 KD patients day ≥ 8 after illness onset, compared with 0/17 infant controls (P < .01), recognized the KD peptide antigen.Conclusions: These results identify a protein epitope targeted by the antibody response to KD and provide a means to elucidate the pathogenesis of this important worldwide pediatric problem. [ABSTRACT FROM AUTHOR]

Communication between health professionals and patients is an intergroup phenomenon where the health professional has the most power and status. Over the past few decades, there has been a steady increase in the availability to patients of information about healthcare and specific diseases on the Internet. In this paper, we ask whether the use of Internet health information assists patients to manage their consultations with health professionals better and whether it alters the intergroup dynamic by providing a more equal status for patients. In this study 370 participants from Australia and Canada completed a survey that included a 'willingness to communicate with health professionals' scale. They also commented on their use and trust of Internet health information. Thematic analysis suggests that patients' use of Internet health information serves as a broker between patients and their health provider in health consultations. We discuss the implications of these findings for health practitioners as they address how easier Internet access influences patient interactions with health professionals. We consider future research directions these finding provide in explaining communication behaviour in this context. [ABSTRACT FROM AUTHOR]

1. DNA metabarcoding is a cost‐effective species identification approach with great potential to assist entomological ecologists. This review presents a practical guide to help entomological ecologists design their own DNA metabarcoding studies and ensure that sound ecological conclusions can be obtained. 2. The review considers approaches to field sampling, laboratory work, and bioinformatic analyses, with the aim of providing the background knowledge needed to make decisions at each step of a DNA metabarcoding workflow. 3. Although most conventional sampling methods can be adapted to DNA metabarcoding, this review highlights techniques that will ensure suitable DNA preservation during field sampling and laboratory storage. The review also calls for a greater understanding of the occurrence, transportation, and deposition of environmental DNA when applying DNA metabarcoding approaches for different ecosystems. 4. Accurate species detection with DNA metabarcoding needs to consider biases introduced during DNA extraction and PCR amplification, cross‐contamination resulting from inappropriate amplicon library preparation, and downstream bioinformatic analyses. Quantifying species abundance with DNA metabarcoding is in its infancy, yet recent studies demonstrate promise for estimating relative species abundance from DNA sequencing reads. 5. Given that bioinformatics is one of the biggest hurdles for researchers new to DNA metabarcoding, several useful graphical user interface programs are recommended for sequence data processing, and the application of emerging sequencing technologies is discussed. [ABSTRACT FROM AUTHOR]

Coronaviruses (CoVs) are positive-sense RNA viruses that can emerge from endemic reservoirs and infect zoonotically, causing significant morbidity and mortality. CoVs encode an endoribonuclease designated EndoU that facilitates evasion of host pattern recognition receptor MDA5, but the target of EndoU activity was not known. Here, we report that EndoU cleaves the 5′-polyuridines fromnegative-sense viral RNA, termed PUN RNA, which is the product of polyA-templated RNA synthesis. Using a virus containing an EndoU catalytic-inactive mutation, we detected a higher abundance of PUN RNA in the cytoplasm compared to wildtype− infected cells. Furthermore, we found that transfecting PUN RNA into cells stimulates a robust, MDA5-dependent interferon response, and that removal of the polyuridine extension on the RNA dampens the response. Overall, the results of this study reveal the PUN RNA to be a CoV MDA5-dependent pathogen-associated molecular pattern (PAMP). We also establish a mechanism for EndoU activity to cleave and limit the accumulation of this PAMP. Since EndoU activity is highly conserved in all CoVs, inhibiting this activity may serve as an approach for therapeutic interventions against existing and emerging CoV infections. [ABSTRACT FROM AUTHOR]

SARS-coronavirus (CoV) is a zoonotic agent derived from rhinolophid bats, in which a plethora of SARS-related, conspecific viral lineages exist. Whereas the variability of virulence among reservoir-borne viruses is unknown, it is generally assumed that the emergence of epidemic viruses from animal reservoirs requires human adaptation. To understand the influence of a viral factor in relation to interspecies spillover, we studied the papain-like protease (PLP) of SARS-CoV. This key enzyme drives the early stages of infection as it cleaves the viral polyprotein, deubiquitinates viral and cellular proteins, and antagonizes the interferon (IFN) response. We identified a bat SARS-CoV PLP, which shared 86% amino acid identity with SARS-CoV PLP, and used reverse genetics to insert it into the SARS-CoV genome. The resulting virus replicated like SARS-CoV in Vero cells but was suppressed in IFN competent MA-104 (3.7-fold), Calu-3 (2.6-fold) and human airway epithelial cells (10.3-fold). Using ectopically-expressed PLP variants as well as full SARS-CoV infectious clones chimerized for PLP, we found that a protease-independent, anti-IFN function exists in SARS-CoV, but not in a SARS-related, bat-borne virus. This PLP-mediated anti-IFN difference was seen in primate, human as well as bat cells, thus independent of the host context. The results of this study revealed that coronavirus PLP confers a variable virulence trait among members of the species SARS-CoV, and that a SARS-CoV lineage with virulent PLPs may have pre-existed in the reservoir before onset of the epidemic. [ABSTRACT FROM AUTHOR]

Abstract: Maintaining developmental heterogeneity of ecological communities within landscapes is crucial for sustainable native forest management. Consequently, methods to assess forest maturity (i.e. the degree to which the forest contains attributes and supports processes characteristic of late‐successional forests) are valuable for making management decisions. However, no consistent, pragmatic method to quantify maturity that incorporates multiple ecosystem elements is available for many forest systems, including Australian wet eucalypt forests. We draw upon forest community dynamics theory to develop a method to quantify maturity based on forest attributes, and use this method to create two metrics of wet eucalypt forest floristic and structural maturity. We then test the ability of remotely sensed and field‐collected variables to predict these metrics. Both the floristic and structural maturity metrics performed well at capturing underlying trends of forest maturation. Remotely sensed LiDAR (Light Detection and Ranging) and photo‐interpretation data provided estimates of moderate accuracy for both floristic and structural maturity (R2 = .57–.77). Field variables that are relatively efficient and accurate to measure provided greater model accuracy (R2 = .73–.85). Including more complex field variables increased model accuracy to high levels (R2 = .93). Therefore, while maturity predicted from remote‐sensing data enables a useful and accessible large‐scale maturity measure, field indices would provide a more accurate means of assessing maturity at the local stand level. Synthesis and applications. The metrics developed in this study provide a powerful tool for undertaking consistent assessments of wet eucalypt forest maturity. This assessment tool could improve forest management by providing information to optimise practices such as prioritising stands for retention or harvesting, determining the effectiveness of restoration or management practices and monitoring changes in maturity over time. The method could be adapted to any forest system that undergoes well‐defined directional development. [ABSTRACT FROM AUTHOR]

Copyright of Canadian Modern Language Review is the property of University of Toronto Press and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Acoustic recording units (ARUs) have recently been used in place of field observers to survey birds. To test whether data obtained from ARUs and from point counts by a field observer are directly comparable, we surveyed Tasmanian forest birds using these two methods at exactly the same times and places. Data derived from ARUs were similar to those obtained by the field observer without distance constraints for (a) the total numbers of species detected at each of three points, and (b) both the number and composition of species within each of the 13 5-minute surveys at each point. However, data sets obtained by each method comprised more records of certain species, largely because of calls being detected by one method but not by the other. Additional differences between methods arose because ARUs could not detect birds seen by the field observer that were not calling, and ARUs sometimes led to false positive identifications when the person listening to recordings was unable to distinguish mimetic calls from those of the species being mimicked. Because ARUs appeared to detect many calls from beyond 100 m, their use to survey a particular patch of vegetation requires placement (within the vegetation patch) at distances greater than 100 m from the edge of the patch to prevent the inclusion of calls from non-target vegetation. [ABSTRACT FROM AUTHOR]

Abstract: Aims: Bryophyte re‐colonization after disturbance is largely governed by environmental conditions within disturbed forests. In particular, distance to a forest edge is an important predictor of bryophyte community re‐colonization, through either direct constraints, such as dispersal limitation, or indirectly by altering environmental conditions. This study examines a range of factors – environmental, distance to an edge, substrate specific environment or local‐level environment – to determine which are important in the re‐colonization of bryophyte communities after forest harvesting. As bryophyte communities vary with the particular substrate inhabited, responses were examined across four substrates (rock, exposed roots, ground and CWD). Location: Tasmanian southern forests, Australia. Methods: Bryophyte composition was examined on four substrates (ground, coarse wood debris, exposed roots, rocks) within three ages (~7, ~27 and ~45 years post‐disturbance) of harvested wet eucalypt forest. Re‐colonization success of bryophyte communities was determined by comparing communities in regeneration forest to mature forest communities using axis scores from one‐dimensional constrained ordination. The importance of various environmental conditions for re‐colonization success was then modelled. Finally, path analysis was used to determine whether the impact of distance to a forest edge was meditated through its effects on key environmental variables. Results: Multiple environmental factors impacted re‐colonization of mature bryophyte communities. Local‐level conditions such as microclimate (temperature, humidity and VPD) and LAI were the most important in determining re‐colonization across substrates. Path analysis showed that distance to a forest edge had a significant impact on re‐colonization success, but only a relatively small part of this was mediated through its impact on environmental factors. Conclusions: Bryophyte re‐colonization is driven by a combination of microclimate conditions and factors related to distance from a forest edge (most likely dispersal distance). While some substrate‐specific factors impact bryophyte re‐colonization success, the consistent impact of local environmental factors across substrates suggests that harvesting management strategies that develop more ‘mature’ microclimate conditions and increase proximity to nearby mature forest patches will be beneficial for all bryophytes communities. As bryophyte re‐colonization was correlated with temporally dynamic environmental conditions, we suggest that forest age needs to be considered in future work. [ABSTRACT FROM AUTHOR]

Background. Kawasaki disease (KD) is widely viewed as an acute arteritis. However, our pathologic studies show that chronic coronary arteritis can persist long after disease onset and is closely linked with arterial stenosis. Transcriptome profiling of acute KD arteritis tissues revealed upregulation of T lymphocyte, type I interferon, and allograft inflammatory factor-1 (AIF1) genes. We determined whether these immune responses persist in chronic KD arteritis, and we investigated the role of AIF1 in these responses. Methods. Gene expression in chronic KD and childhood control arteries was determined by real-time reverse-transcriptase polymerase chain reaction, and arterial protein expression was determined by immunohistochemistry and immunofluorescence. Allograft inflammatory factor-1 small-interfering ribonucleic acid macrophage treatment was performed to investigate the role of AIF1 in macrophage and T lymphocyte activation. Results. Allograft inflammatory factor-1 protein was highly expressed in stenotic KD arteries and colocalized with the macrophage marker CD68. T lymphocyte and interferon pathway genes were significantly upregulated in chronic KD coronary artery tissues. Alpha interferon-induced macrophage expression of CD80 and major histocompatibility complex class II was dependent on AIF1, and macrophage expression of AIF1 was required for antigen-specific T lymphocyte activation. Conclusions. Allograft inflammatory factor-1, originally identified in posttransplant arterial stenosis, is markedly upregulated in KD stenotic arterial tissues. T lymphocyte and type I interferon responses persist in chronic KD arteritis. Allograft inflammatory factor-1 may play multiple roles linking type I interferon response, macrophage activation, and antigen-specific T lymphocyte activation. These results suggest the likely importance of lymphocyte-myeloid cell cross-talk in the pathogenesis of KD arteritis and can inform selection of new immunotherapies for clinical trials in high-risk KD children. [ABSTRACT FROM AUTHOR]

The present research examines the role of music and dance in motivating Gaelic language learning on Cape Breton Island (Canada). The Gaelic language, once thriving in this context, has declined in use but flourishes in both music and dance. This article presents the results of in-depth interviews (60-90 minutes) with 10 accomplished adult musicians and dancers who described in rich detail connections between traditional music and the Gaelic language. The interview texts were analyzed using Leximancer 4.0, text-mining software that performs an automatic analysis by deriving, in a grounded fashion, the key concepts in a text. Semantic and relational co-occurrence information was extracted using artificial intelligence, producing a map of interrelations among concepts. Three interrelated concepts are introduced to describe community-level motivational processes evident in the interviews: Rooted second language (L2) self, heritage passions, and heritage convictions. The rooted L2 self is defined by connections to place and speakers of the language; heritage passions reflect the development of emotional bonds, core values, and strengths; and heritage convictions capture deep-seated beliefs, attitudes, and mindsets. Elements of both Gardner's notion of integrative motivation and Dörnyei's L2 self system are evident and are considered within Ushioda's (2009) person-in-context relational model, emphasizing the connections among learners and contexts. [ABSTRACT FROM AUTHOR]

The roles that functional traits and/or evolutionary history of species from co-occurring trophic groups have in determining community recovery following disturbance are poorly understood. Functional traits help determine how species interact with their environment, thus functional traits are likely to change with time since logging. However, traits of species may also be phylogenetically constrained depending on their evolutionary history. Because beetles are trophically diverse, the effects of phylogenetic and functional aspects of community recovery can be compared between co-occurring trophic groups., Using a chronosequence of forest ages following logging, we applied a novel combination of functional trait and phylogenetic approaches to assess the extent to which taxonomic, functional and phylogenetic composition recovered after logging, and if these dimensions of composition approached those characteristic of mature forests, for both predators and decomposers/primary consumers. We also examined to what extent functional traits of both trophic groups were phylogenetically conserved., Predator functional composition had recovered ∼45 years after logging, and this recovery preceded taxonomic recovery. Neither taxonomic nor functional composition had recovered for the decomposer/primary consumer communities by this time., In contrast to decomposers/primary consumers, predator community recovery had no distinct phylogenetic signature, yet predator functional traits were more phylogenetically conserved than decomposers/primary consumer functional traits., Trait syndromes that characterise forest recovery stages are identified and provide a basis for future work on community re-assembly following disturbance., We demonstrate differential recovery of co-occurring beetle trophic groups following disturbance. We show that functional and phylogenetic composition may be disconnected from taxonomic composition; highlighting the advantages of integrating understanding of these three potentially independent components of ecological diversity to enable deeper understanding of animal community composition. [ABSTRACT FROM AUTHOR]

Coronaviruses are positive-sense RNA viruses that generate double-stranded RNA (dsRNA) intermediates during replication, yet evade detection by host innate immune sensors. Here we report that coronavirus nonstructural protein 15 (nsp15), an endoribonuclease, is required for evasion of dsRNA sensors. We evaluated two independent nsp15 mutant mouse coronaviruses, designated N15m1 and N15m3, and found that these viruses replicated poorly and induced rapid cell death in mouse bone marrow-derived macrophages. Infection of macrophages with N15m1, which expresses an unstable nsp15, or N15m3, which expresses a catalysis-deficient nsp15, activated MDA5, PKR, and the OAS/RNase L system, resulting in an early, robust induction of type I IFN, PKR-mediated apoptosis, and RNA degradation. Immunofluorescence imaging of nsp15 mutant virus-infected macrophages revealed significant dispersal of dsRNA early during infection, whereas in WT virus-infected cells, the majority of the dsRNA was associated with replication complexes. The loss of nsp15 activity also resulted in greatly attenuated disease in mice and stimulated a protective immune response. Taken together, our findings demonstrate that coronavirus nsp15 is critical for evasion of host dsRNA sensors in macrophages and reveal that modulating nsp15 stability and activity is a strategy for generating liveattenuated vaccines. [ABSTRACT FROM AUTHOR]

Fire and timber harvesting can diminish the extent of older forests in the near term. The amount and configuration of mature and regenerating forest in the landscape (landscape structure) influences habitat suitability for mature-forest-associated species. We applied spatial analysis to describe the landscape structure of three wet eucalypt forest landscapes in south–eastern Australia and used the results from empirical biodiversity studies to frame interpretation of possible impacts on habitat suitability. We determined the extent of structurally mature forest, its reservation status, and the extent to which it may be edge affected. We also assessed how landscape structure potentially impacts the re-establishment of mature-forest-associated species into previously harvested areas through the proximity to (mature forest influence)—and extent of (landscape context)—mature forest in the surrounding landscape. Our analyses were designed to inform forest management initiatives that draw on these landscape-scale concepts. Central Highlands Victoria had less structurally mature eucalypt forest (4%) compared to North West Tasmania (14%) and Southern Forests Tasmania (21%). Detrimental effects of edge influence on structurally mature forest appeared relatively minor. Low levels of mature forest influence combined with low-medium surrounding mature forest cover (landscape context) indicate potential limitations on re-colonisation of coupes by mature-forest-associated species. Our results vindicate the recent shift toward variable retention silviculture and landscape context planning. Our approach to landscape analysis provides a useful framework for other managed forest landscapes. [ABSTRACT FROM AUTHOR]

Reporting progress against targets for international biodiversity agreements is hindered by a shortage of suitable biodiversity data. We describe a cost-effective system involving Reef Life Survey citizen scientists in the systematic collection of quantitative data covering multiple phyla that can underpin numerous marine biodiversity indicators at high spatial and temporal resolution. We then summarize the findings of a continentaland decadal-scale State of the Environment assessment for rocky and coral reefs based on indicators of ecosystem state relating to fishing, ocean warming, and invasive species and describing the distribution of threatened species. Fishing impacts are widespread, whereas substantial warming-related change affected some regions between 2005 and 2015. Invasive species are concentrated near harbors in southeastern Australia, and the threatened-species index is highest for the Great Australian Bight and Tasman Sea. Our approach can be applied globally to improve reporting against biodiversity targets and enhance public and policymakers' understanding of marine biodiversity trends. [ABSTRACT FROM AUTHOR]

Retention harvesting, an approach that intentionally retains legacy features such as mature overstory trees, provides options for achieving ecological objectives. At the same time, retained overstory trees may compete with the nearby recovering understory for resources, and much remains to be learned about potential trade-offs with regeneration objectives, particularly over extended time periods. We assessed the influence of aggregated retention (reserved mature overstory and understory patches) versus intact forest on structure and productivity (standing biomass) of the adjacent woody understory and regeneration 12 years after harvest in northern Minnesota, USA. Each site was dominated by Populus tremuloides Michx., a species that regenerates prolifically via root sprouts following disturbance. Overall, fewer differences than expected occurred between the effects of intact forest and aggregated retention on regeneration, despite the small size (0.1 ha) of aggregates. Instead, harvest status and distance from harvest edge had a greater influence on structure and standing woody biomass. Proximity to aggregates reduced large sapling biomass (all species, combined) relative to open conditions, but only up to 5 m into harvested areas. This suggests the trade-off for achieving productivity objectives might be minimal if managers use retention aggregates in this region to achieve ecological objectives and meet management guidelines. [ABSTRACT FROM AUTHOR]

Timber harvest can adversely affect forest biota. Recent research and application suggest that retention of mature forest elements (retention forestry), including unharvested patches (or aggregates) within larger harvested units, can benefit biodiversity compared to clearcutting. However, it is unclear whether these benefits can be generalized among the diverse taxa and biomes in which retention forestry is practiced. Lack of comparability in methods for sampling and analyzing responses to timber harvest and edge creation presents a challenge to synthesis. We used a consistent methodology (similarly spaced plots or traps along transects) to investigate responses of vascular plants and ground-active beetles to aggregated retention at replicate sites in each of four temperate and boreal forest types on three continents: Douglas-fir forests in Washington, USA; aspen forests in Minnesota, USA; spruce forests in Sweden; and wet eucalypt forests in Tasmania, Australia. We assessed (1) differences in local (plot-scale) species richness and composition between mature (intact) and regenerating (previously harvested) forest; (2) the lifeboating function of aggregates (capacity to retain species of unharvested forest); and whether intact forests and aggregates (3) are susceptible to edge effects and (4) influence the adjacent regenerating forest. Intact and harvested forests differed in composition but not richness of plants and beetles. The magnitude of this difference was generally similar among regions, but there was considerable heterogeneity of composition within and among replicate sites. Aggregates within harvest units were effective at lifeboating for both plant and beetle communities. Edge effects were uncommon even within the aggregates. In contrast, effects of forest influence on adjacent harvested areas were common and as strong for aggregates as for larger blocks of intact forest. Our results provide strong support for the widespread application of aggregated retention in boreal and temperate forests. The consistency of pattern in four very different regions of the world suggests that, for forest plants and beetles, responses to aggregated retention are likely to apply more widely. Our results suggest that through strategic placement of aggregates, it is possible to maintain the natural heterogeneity and biodiversity of mature forests managed for multiple objectives. [ABSTRACT FROM AUTHOR]

Background: Kawasaki Disease (KD) can cause potentially life-threatening coronary arteritis in young children, and has a likely infectious etiology. Transcriptome profiling is a powerful approach to investigate gene expression in diseased tissues. RNA sequencing of KD coronary arteries could elucidate the etiology and the host response, with the potential to improve KD diagnosis and/or treatment. Methods: Deep RNA sequencing was performed on KD (n = 8) and childhood control (n = 7) coronary artery tissues, revealing 1074 differentially expressed mRNAs. Non-human RNA sequences were subjected to a microbial discovery bioinformatics platform, and microbial sequences were analyzed by Metastats for association with KD. Results: T lymphocyte activation, antigen presentation, immunoglobulin production, and type I interferon response were significantly upregulated in KD arteritis, while the tumor necrosis factor α pathway was not differentially expressed. Transcripts from known infectious agents were not specifically associated with KD coronary arteritis. Conclusions: The immune transcriptional profile in KD coronary artery tissues has features of an antiviral immune response such as activated cytotoxic T lymphocyte and type I interferon-induced gene upregulation. These results provide new insights into the pathogenesis of KD arteritis that can guide selection of new immunomodulatory therapies for high-risk KD patients, and provide direction for future etiologic studies. [ABSTRACT FROM AUTHOR]

The articles presented in this special issue bring attention to important sociocultural variables and language strategies present in the ever-changing and complex health care system. These articles were selected from the health communication symposium of the 14th International Conference of Language and Social Psychology held in Hawaii in 2014. The articles each concentrate on different aspects of health communication and employ different theoretical and analytical approaches, but they all call for more education and better interventions to improve relations in the health context and patient care. [ABSTRACT FROM AUTHOR]

By emphasizing the value of health professionals’ communication skills in creating positive health care experiences, researchers have tended to study health communication as an interpersonal encounter. Interactions in the health context, though, are inherently intergroup. Using the language and social psychology approach, this study emphasizes those intergroup features of health communication. We used mixed methods and applied communication accommodation theory and the willingness to communicate construct to the health context. Participants in Canada and Australia (N = 371) were asked about their perceptions of their health consultations. Multiple regression analyses revealed that health communication competence was the best predictor of patient willingness to communicate. Differences between patients’ accounts of positive and negative health care experiences were clearly differentiated by their perceptions of the health professionals’ communication strategies. The potential effects of these strategies on patient participation are discussed. [ABSTRACT FROM AUTHOR]

Gravid traps are commonly used by mosquito control agencies to collect local populations of Culex pipiens, which are then tested for the presence of West Nile virus. Culex pipiens adults disperse a relatively short distance (~2.5 km) from their breeding site, so it can be challenging to position a sufficient number of gravid traps to accurately monitor these mosquitoes in large urban areas. As placement of these traps is often limited to locations out of public?view, the potential for placing these traps belowground in commonly found storm-water catch basins was investigated. We compared the numbers of mosquitoes isolated in the Centers for Disease Control and Prevention (CDC) gravid traps placed aboveground with various types of CDC gravid traps placed in nearby catch basins. We found that the gravid traps placed in catch basins collected significantly fewer Culex pipiens females as compared to the aboveground traps. However, the 2 types of catch basin traps continued to function and collect mosquitoes despite heavy rainfall and runoff, demonstrating their utility for sample collection in an urban setting. The potential advantages and disadvantages of using catch basins for the placement of CDC gravid traps are discussed. [ABSTRACT FROM AUTHOR]

In increasingly fragmented landscapes, it is important to understand how mature forest affects adjacent secondary forest (forest influence). Forest influence on ecological succession of beetle communities is largely unknown. We investigated succession and forest influence using 235 m long transects across boundaries between mature and secondary forest at 15 sites, sampling a chronosequence of three forest age classes (5-10, 23-29, and 42-46 years since clear-cutting) in tall eucalypt forest in Tasmania, Australia. Our results showed that ground-dwelling beetle communities showed strong successional changes, and in the oldest secondary forests, species considered indicators of mature forest had recolonized to abundance levels similar to those observed within adjacent mature forest stands. However, species composition also showed forest influence gradients in all age classes. Forest influence was estimated to extend 13 m and 20 m in the youngest and intermediate-aged secondary forests, respectively. However, the estimated effect extended to at least 176 m in the oldest secondary forest. our environmental modeling suggests that leaf litter, microclimate, and soil variables were all important in explaining the spatial variation in beetle assemblages, and the relative importance of factors varied between secondary forest age classes. Mature-forest beetle communities can recolonize successfully from the edge, and our results provide a basis for land managers to build mature habitat connectivity into forest mosaics typical of production forests. our results also indicate the importance of forest influence in determining potential conservation value of older secondary forest for beetles. [ABSTRACT FROM AUTHOR]

1. New logical and analytical frameworks for studying functional traits have led to major advances in plant and freshwater ecology at local and global scales. The ecological and taxonomic diversity of terrestrial adult beetles ( Coleoptera) means that functional trait approaches should have considerable power to illuminate the function not only of these animals but also of the ecosystems in which they occur. 2. Even though the functional trait concept is not new in ecology, it is still plagued with inconsistencies in methodology and terminology. Plant-based studies have shown that an integrated and relatively consistent functional trait approach facilitates comparisons between studies, and allows the full utility and predictive capacity of trait-based approaches to be realised. 3. This review outlines a logical framework for adult beetle functional trait studies using uniform terminology and methodology similar to those used by plant ecologists. Beetle life-history and ecomorphological trait studies are synthesised and it is shown that a combination of both is analogous to the functional trait approach. A general functional trait list for beetles and potential functional links is outlined, as are potential analysis approaches. A consistent functional trait approach, coupled with advances in molecular techniques, has the capability to provide deeper insights into beetle community assembly and how beetles impact ecosystems and will enable worldwide comparisons and predictions to be made. [ABSTRACT FROM AUTHOR]

Industrial forestry typically leads to a simplified forest structure and altered species composition. Retention of trees at harvest was introduced about 25 years ago to mitigate negative impacts on biodiversity, mainly from clearcutting, and is now widely practiced in boreal and temperate regions. Despite numerous studies on response of flora and fauna to retention, no comprehensive review has summarized its effects on biodiversity in comparison to clearcuts as well as un-harvested forests., Using a systematic review protocol, we completed a meta-analysis of 78 studies including 944 comparisons of biodiversity between retention cuts and either clearcuts or un-harvested forests, with the main objective of assessing whether retention forestry helps, at least in the short term, to moderate the negative effects of clearcutting on flora and fauna., Retention cuts supported higher richness and a greater abundance of forest species than clearcuts as well as higher richness and abundance of open-habitat species than un-harvested forests. For all species taken together (i.e. forest species, open-habitat species, generalist species and unclassified species), richness was higher in retention cuts than in clearcuts., Retention cuts had negative impacts on some species compared to un-harvested forest, indicating that certain forest-interior species may not survive in retention cuts. Similarly, retention cuts were less suitable for some open-habitat species compared with clearcuts., Positive effects of retention cuts on richness of forest species increased with proportion of retained trees and time since harvest, but there were not enough data to analyse possible threshold effects, that is, levels at which effects on biodiversity diminish. Spatial arrangement of the trees (aggregated vs. dispersed) had no effect on either forest species or open-habitat species, although limited data may have hindered our capacity to identify responses. Results for different comparisons were largely consistent among taxonomic groups for forest and open-habitat species, respectively., Synthesis and applications. Our meta-analysis provides support for wider use of retention forestry since it moderates negative harvesting impacts on biodiversity. Hence, it is a promising approach for integrating biodiversity conservation and production forestry, although identifying optimal solutions between these two goals may need further attention. Nevertheless, retention forestry will not substitute for conservation actions targeting certain highly specialized species associated with forest-interior or open-habitat conditions. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus (SARS-CoV) encodes a papain-like protease (PLpro) with both deubiquitinating (DUB) and deISGylating activities that are proposed to counteract the post-translational modification of signaling molecules that activate the innate immune response. Here we examine the structural basis for PLpro's ubiquitin chain and interferon stimulated gene 15 (ISG15) specificity. We present the X-ray crystal structure of PLpro in complex with ubiquitin-aldehyde and model the interaction of PLpro with other ubiquitin-chain and ISG15 substrates. We show that PLpro greatly prefers K48- to K63-linked ubiquitin chains, and ISG15-based substrates to those that are mono-ubiquitinated. We propose that PLpro's higher affinity for K48-linked ubiquitin chains and ISG15 stems from a bivalent mechanism of binding, where two ubiquitin-like domains prefer to bind in the palm domain of PLpro with the most distal ubiquitin domain interacting with a “ridge” region of the thumb domain. Mutagenesis of residues within this ridge region revealed that these mutants retain viral protease activity and the ability to catalyze hydrolysis of mono-ubiquitin. However, a select number of these mutants have a significantly reduced ability to hydrolyze the substrate ISG15-AMC, or be inhibited by K48-linked diubuiquitin. For these latter residues, we found that PLpro antagonism of the nuclear factor kappa-light-chain-enhancer of activated B-cells (NFκB) signaling pathway is abrogated. This identification of key and unique sites in PLpro required for recognition and processing of diubiquitin and ISG15 versus mono-ubiquitin and protease activity provides new insight into ubiquitin-chain and ISG15 recognition and highlights a role for PLpro DUB and deISGylase activity in antagonism of the innate immune response. [ABSTRACT FROM AUTHOR]

In line with global targets agreed under the Convention on Biological Diversity, the number of marine protected areas (MPAs) is increasing rapidly, yet socio-economic benefits generated by MPAs remain difficult to predict and under debate. MPAs often fail to reach their full potential as a consequence of factors such as illegal harvesting, regulations that legally allow detrimental harvesting, or emigration of animals outside boundaries because of continuous habitat or inadequate size of reserve. Here we show that the conservation benefits of 87 MPAs investigated worldwide increase exponentially with the accumulation of five key features: no take, well enforced, old (>10 years), large (>100 km2), and isolated by deep water or sand. Using effective MPAs with four or five key features as an unfished standard, comparisons of underwater survey data from effective MPAs with predictions based on survey data from fished coasts indicate that total fish biomass has declined about two-thirds from historical baselines as a result of fishing. Effective MPAs also had twice as many large (>250 mm total length) fish species per transect, five times more large fish biomass, and fourteen times more shark biomass than fished areas. Most (59%) of the MPAs studied had only one or two key features and were not ecologically distinguishable from fished sites. Our results show that global conservation targets based on area alone will not optimize protection of marine biodiversity. More emphasis is needed on better MPA design, durable management and compliance to ensure that MPAs achieve their desired conservation value. [ABSTRACT FROM AUTHOR]

Forest influence is a type of edge effect that occurs when mature forests affect the recolonisation of adjacent disturbed areas. This can be driven by changes in microclimate conditions near the edge or by an increase in establishment ability with proximity to a propagule source. Bryophyte recolonisation is sensitive to both microclimate and dispersal distance, therefore they are an ideal group to examine how strong forest influence is and over what distance it operates. Responses to forest influence are known to be highly species dependent; therefore, we tested whether distance affects the recolonisation ability of a range of bryophytes. As well as examining a range of species, we tested whether forest influence operated differently on two types of substrate used by bryophytes (logs and ground). For most of the species examined, establishment rates in disturbed forest diminished further away from the mature edge. The influence of unlogged mature forest on bryophyte establishment in harvested forest occurred up to 50m. Species varied in their response to distance, and the relationships with distance were stronger on the ground compared with log substrates. These results support the concept of forest influence, with areas closer to mature forest experiencing more substantial re-establishment. These findings are relevant to conservation of bryophytes in managed native forests. Understanding the ability of species to recolonise after disturbances created by forest harvesting is critical for sustainable forestry. This paper examined how bryophyte recolonisation was impacted by distance to a mature forest. Recolonisation of bryophytes declined with increasing distance to a mature forest and therefore the distance between retained mature forest patches should be considered in the management of forest harvesting. [ABSTRACT FROM AUTHOR]

Species richness has dominated our view of global biodiversity patterns for centuries. The dominance of this paradigm is reflected in the focus by ecologists and conservation managers on richness and associated occurrence-based measures for understanding drivers of broad-scale diversity patterns and as a biological basis for management. However, this is changing rapidly, as it is now recognized that not only the number of species but the species present, their phenotypes and the number of individuals of each species are critical in determining the nature and strength of the relationships between species diversity and a range of ecological functions (such as biomass production and nutrient cycling). Integrating these measures should provide a more relevant representation of global biodiversity patterns in terms of ecological functions than that provided by simple species counts. Here we provide comparisons of a traditional global biodiversity distribution measure based on richness with metrics that incorporate species abundances and functional traits. We use data from standardized quantitative surveys of 2,473 marine reef fish species at 1,844 sites, spanning 133 degrees of latitude from all ocean basins, to identify new diversity hotspots in some temperate regions and the tropical eastern Pacific Ocean. These relate to high diversity of functional traits amongst individuals in the community (calculated using Rao's Q), and differ from previously reported patterns in functional diversity and richness for terrestrial animals, which emphasize species-rich tropical regions only. There is a global trend for greater evenness in the number of individuals of each species, across the reef fish species observed at sites ('community evenness'), at higher latitudes. This contributes to the distribution of functional diversity hotspots and contrasts with well-known latitudinal gradients in richness. Our findings suggest that the contribution of species diversity to a range of ecosystem functions varies over large scales, and imply that in tropical regions, which have higher numbers of species, each species contributes proportionally less to community-level ecological processes on average than species in temperate regions. Metrics of ecological function usefully complement metrics of species diversity in conservation management, including when identifying planning priorities and when tracking changes to biodiversity values. [ABSTRACT FROM AUTHOR]

Immune sera from convalescent patients have been shown to be effective in the treatment of patients infected with Severe Acute Respiratory Syndrome Virus (SARS-CoV) making passive immune therapy with human monoclonal antibodies an attractive treatment strategy for SARS. Previously, using Xenomouse (Amgen British Columbia Inc), we produced a panel of neutralizing Human monoclonal antibodies (HmAbs) that could specifically bind to the ectodomain of the SARS-CoV spike (S) glycoprotein. Some of the HmAbs were S1 domain specific, while some were not. In this study, we describe non-S1 binding neutralizing HmAbs that can specifically bind to the conserved S2 domain of the S protein. However, unlike the S1 specific HmAbs, the S2 specific HmAbs can neutralize pseudotyped viruses expressing different S proteins containing receptor binding domain sequences of various clinical isolates. These data indicate that HmAbs which bind to conserved regions of the S protein are more suitable for conferring protection against a wide range of SARS-CoV variants and have implications for generating therapeutic antibodies or subunit vaccines against other enveloped viruses. [ABSTRACT FROM AUTHOR]

The majority of the world's forests are used for multiple purposes, which often include the potentially conflicting goals of timber production and biodiversity conservation. A scientifically validated management approach that can reduce such conflicts is retention forestry, an approach modeled on natural processes, which emerged in the last 25 years as an alternative to clearcutting. A portion of the original stand is left unlogged to maintain the continuity of structural and compositional diversity. We detail retention forestry's ecological role, review its current practices, and summarize the large research base on the subject. Retention forestry is applicable to all forest Homes, complements conservation in reserves, and represents bottom-up conservation through forest manager involvement. A research challenge is to identify thresholds for retention amounts to achieve desired outcomes. We define key issues for future development and link retention forestry with land-zoning allocation at various scales, expanding its uses to forest restoration and the management of uneven-age forests. [ABSTRACT FROM AUTHOR]

Background: Kawasaki disease is recognized as the most common cause of acquired heart disease in children in the developed world. Clinical, epidemiologic, and pathologic evidence supports an infectious agent, likely entering through the lung. Pathologic studies proposing an acute coronary arteritis followed by healing fail to account for the complex vasculopathy and clinical course. Methodology/Principal Findings: Specimens from 32 autopsies, 8 cardiac transplants, and an excised coronary aneurysm were studied by light (n = 41) and transmission electron microscopy (n = 7). Three characteristic vasculopathic processes were identified in coronary (CA) and non-coronary arteries: acute self-limited necrotizing arteritis (NA), subacute/chronic (SA/C) vasculitis, and luminal myofibroblastic proliferation (LMP). NA is a synchronous neutrophilic process of the endothelium, beginning and ending within the first two weeks of fever onset, and progressively destroying the wall into the adventitia causing saccular aneurysms, which can thrombose or rupture. SA/C vasculitis is an asynchronous process that can commence within the first two weeks onward, starting in the adventitia/perivascular tissue and variably inflaming/ damaging the wall during progression to the lumen. Besides fusiform and saccular aneurysms that can thrombose, SA/C vasculitis likely causes the transition of medial and adventitial smooth muscle cells (SMC) into classic myofibroblasts, which combined with their matrix products and inflammation create progressive stenosing luminal lesions (SA/C-LMP). Remote LMP apparently results from circulating factors. Veins, pulmonary arteries, and aorta can develop subclinical SA/C vasculitis and SA/C-LMP, but not NA. The earliest death (day 10) had both CA SA/C vasculitis and SA/C-LMP, and an "eosinophilictype" myocarditis. Conclusions/Significance: NA is the only self-limiting process of the three, is responsible for the earliest morbidity/ mortality, and is consistent with acute viral infection. SA/C vasculitis can begin as early as NA, but can occur/persist for months to years; LMP causes progressive arterial stenosis and thrombosis and is composed of unique SMC-derived pathologic myofibroblasts. [ABSTRACT FROM AUTHOR]

Viruses have evolved elaborate mechanisms to evade or inactivate the complex system of sensors and signaling molecules that make up the host innate immune response. Here we show that human coronavirus (HCoV) NL63 and severe acute respiratory syndrome (SARS) CoV papain-like proteases (PLP) antagonize innate immune signaling mediated by STING (stimulator of interferon genes, also known as MITA/ERIS/MYPS). STING resides in the endoplasmic reticulum and upon activation, forms dimers which assemble with MAVS, TBK-1 and IKKe, leading to IRF-3 activation and subsequent induction of interferon (IFN). We found that expression of the membrane anchored PLP domain from human HCoV-NL63 (PLP2-TM) or SARS-CoV (PLpro-TM) inhibits STING-mediated activation of IRF-3 nuclear translocation and induction of IRF-3 dependent promoters. Both catalytically active and inactive forms of CoV PLPs co-immunoprecipitated with STING, and viral replicase proteins co-localize with STING in HCoV-NL63-infected cells. Ectopic expression of catalytically active PLP2-TM blocks STING dimer formation and negatively regulates assembly of STING-MAVS-TBK1/IKKe complexes required for activation of IRF-3. STING dimerization was also substantially reduced in cells infected with SARS-CoV. Furthermore, the level of ubiquitinated forms of STING, RIG-I, TBK1 and IRF-3 are reduced in cells expressing wild type or catalytic mutants of PLP2-TM, likely contributing to disruption of signaling required for IFN induction. These results describe a new mechanism used by CoVs in which CoV PLPs negatively regulate antiviral defenses by disrupting the STING-mediated IFN induction. [ABSTRACT FROM AUTHOR]