A neutralizing single-domain antibody that targets the trimer interface of the human metapneumovirus fusion protein

IMPORTANCE

Human metapneumovirus (hMPV) is an important respiratory pathogen for which no licensed antivirals or vaccines exist. Single-domain antibodies represent promising antiviral biologics that can be easily produced and formatted. We describe the isolation and detailed characterization of two hMPV-neutralizing single-domain antibodies that are directed against the fusion protein F. One of these single-domain antibodies broadly neutralizes hMPV A and B strains, can prevent proteolytic maturation of F, and binds to an epitope in the F trimer interface. This suggests that hMPV pre-F undergoes trimer opening or "breathing" on infectious virions, exposing a vulnerable site for neutralizing antibodies. Finally, we show that this single-domain antibody, fused to a human IgG1 Fc, can protect cotton rats against hMPV replication, an important finding for potential future clinical applications.

Elicitation of pneumovirus-specific B cell responses by a prefusion-stabilized respiratory syncytial virus F subunit vaccine

Respiratory syncytial virus (RSV) is a substantial cause of morbidity and mortality globally. A candidate RSV prefusion (pre-F)-stabilized subunit vaccine, DS-Cav1, has previously been shown to elicit potent and durable neutralizing activity in a phase 1 clinical trial in healthy adults. Here, we used fluorescently labeled probes and flow cytometry to evaluate the antigen specificity and phenotype of RSV F-specific B cells longitudinally after DS-Cav1 immunization. Peripheral blood mononuclear cells (PBMCs) collected at time points before the first immunization through the end of the trial at 44 weeks were assessed by flow cytometry. Our data demonstrate a rapid increase in the frequency of pre-F-specific IgG⁺ and IgA⁺ B cells after the first immunization and a modest increase after a second immunization at week 12. Nearly all F-specific B cells down-regulated CD21 and up-regulated the proliferation marker CD71 after the first immunization, with less pronounced activation after the second immunization. Memory B cells (CD27⁺CD21⁺) specific for pre-F remained elevated above baseline at 44 weeks after vaccination. DS-Cav1 vaccination also activated human metapneumovirus (HMPV) cross-reactive B cells capable of binding prefusion-stabilized HMPV F protein and increased HMPV F-binding antibodies and neutralizing activity for HMPV in some participants. In summary, vaccination with RSV pre-F resulted in the expansion and activation of RSV and HMPV F-specific B cells that were maintained above baseline for at least 10 months and could contribute to long-term pneumovirus immunity.

Structural basis for ultrapotent antibody-mediated neutralization of human metapneumovirus

Human metapneumovirus (hMPV) is a leading cause of morbidity and hospitalization among children worldwide, however, no vaccines or therapeutics are currently available for hMPV disease prevention and treatment. The hMPV fusion (F) protein is the sole target of neutralizing antibodies. To map the immunodominant epitopes on the hMPV F protein, we isolated a panel of human monoclonal antibodies (mAbs), and the mAbs were assessed for binding avidity, neutralization potency, and epitope specificity. We found the majority of the mAbs target diverse epitopes on the hMPV F protein, and we discovered multiple mAb binding approaches for antigenic site III. The most potent mAb, MPV467, which had picomolar potency, was examined in prophylactic and therapeutic mouse challenge studies, and MPV467 limited virus replication in mouse lungs when administered 24 h before or 72 h after viral infection. We determined the structure of MPV467 in complex with the hMPV F protein using cryo-electron microscopy to a resolution of 3.3 Å, which revealed a complex novel prefusion-specific epitope overlapping antigenic sites II and V on a single protomer. Overall, our data reveal insights into the immunodominant antigenic epitopes on the hMPV F protein, identify a mAb therapy for hMPV F disease prevention and treatment, and provide the discovery of a prefusion-specific epitope on the hMPV F protein.

Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins

The human metapneumovirus (hMPV) fusion (F) protein is essential for viral entry and is a key target of neutralizing antibodies and vaccine development. The prefusion conformation is thought to be the optimal vaccine antigen, but previously described prefusion F proteins expressed poorly and were not well stabilized. Here, we use structures of hMPV F to guide the design of 42 variants containing stabilizing substitutions. Through combinatorial addition of disulfide bonds, cavity-filling substitutions, and improved electrostatic interactions, we describe a prefusion-stabilized F protein (DS-CavEs2) that expresses at 15 mg/L and has a melting temperature of 71.9 °C. Crystal structures of two prefusion-stabilized hMPV F variants reveal that antigenic surfaces are largely unperturbed. Importantly, immunization of mice with DS-CavEs2 elicits significantly higher neutralizing antibody titers against hMPV A1 and B1 viruses than postfusion F. The improved properties of DS-CavEs2 will advance the development of hMPV vaccines and the isolation of therapeutic antibodies.

The degree to which the conformation of the human metapneumovirus fusion (F) protein affects immunogenicity has been debated. Here, Hsieh et al. engineer prefusion-stabilized F variants with enhanced thermostability that elicit higher neutralizing antibody titers in mice than postfusion F.

A general pattern of trade-offs between ecosystem resistance and resilience to tropical cyclones

Tropical cyclones drive coastal ecosystem dynamics, and their frequency, intensity, and spatial distribution are predicted to shift with climate change. Patterns of resistance and resilience were synthesized for 4138 ecosystem time series from n = 26 storms occurring between 1985 and 2018 in the Northern Hemisphere to predict how coastal ecosystems will respond to future disturbance regimes. Data were grouped by ecosystems (fresh water, salt water, terrestrial, and wetland) and response categories (biogeochemistry, hydrography, mobile biota, sedentary fauna, and vascular plants). We observed a repeated pattern of trade-offs between resistance and resilience across analyses. These patterns are likely the outcomes of evolutionary adaptation, they conform to disturbance theories, and they indicate that consistent rules may govern ecosystem susceptibility to tropical cyclones.

Availability and assessment of microplastic ingestion by marsh birds in Mississippi Gulf Coast tidal marshes

Millions of tons of plastic enter the environment every year, where much of it concentrates in environmental sinks such as tidal marshes. With prior studies documenting harm to marine fauna caused by this plastic pollution, the need to understand how this novel type of pollution affects estuarine fauna is great. Yet, research on the fate and uptake of plastic pollutants in estuarine ecosystems is sparse. Therefore, we quantified plastic prevalence and ingestion by two species of resident marsh bird, Clapper Rails (Rallus crepitans) and Seaside Sparrows (Ammospiza maritima), in coastal marsh ecosystems within Mississippi. We detected microplastics (plastics smaller than 5 mm) in 64% of marsh sediment samples, 83% of Clapper Rail and 69% of Seaside Sparrow proventriculus samples. Dominant types of microplastics detected in sediment and bird samples were fibers. This study provides the first evidence of microplastic ingestion by marsh birds and its distribution in coastal marshes within Mississippi.

Vaccination with prefusion-stabilized respiratory syncytial virus fusion protein induces genetically and antigenically diverse antibody responses

An effective vaccine for respiratory syncytial virus (RSV) is an unrealized public health goal. A single dose of the prefusion-stabilized fusion (F) glycoprotein subunit vaccine (DS-Cav1) substantially increases serum-neutralizing activity in healthy adults. We sought to determine whether DS-Cav1 vaccination induces a repertoire mirroring the pre-existing diversity from natural infection or whether antibody lineages targeting specific epitopes predominate. We evaluated RSV F-specific B cell responses before and after vaccination in six participants using complementary B cell sequencing methodologies and identified 555 clonal lineages. DS-Cav1-induced lineages recognized the prefusion conformation of F (pre-F) and were genetically diverse. Expressed antibodies recognized all six antigenic sites on the pre-F trimer. We identified 34 public clonotypes, and structural analysis of two antibodies from a predominant clonotype revealed a common mode of recognition. Thus, vaccination with DS-Cav1 generates a diverse polyclonal response targeting the antigenic sites on pre-F, supporting the development and advanced testing of pre-F-based vaccines against RSV.

Suptavumab for the Prevention of Medically Attended Respiratory Syncytial Virus Infection in Preterm Infants

BACKGROUND

Respiratory syncytial virus (RSV) is a major cause of childhood medically attended respiratory infection (MARI).

METHODS

We conducted a randomized, double-blind, placebo-controlled phase 3 trial in 1154 preterm infants of 1 or 2 doses of suptavumab, a human monoclonal antibody that can bind and block a conserved epitope on RSV A and B subtypes, for the prevention of RSV MARI. The primary endpoint was proportion of subjects with RSV-confirmed hospitalizations or outpatient lower respiratory tract infection (LRTI).

RESULTS

There were no significant differences between primary endpoint rates (8.1%, placebo; 7.7%, 1-dose; 9.3%, 2-dose). Suptavumab prevented RSV A infections (relative risks, .38; 95% confidence interval [CI], .14-1.05 in the 1-dose group and .39 [95% CI, .14-1.07] in the 2-dose group; nominal significance of combined suptavumab group vs placebo; P = .0499), while increasing the rate of RSV B infections (relative risk 1.36 [95% CI, .73-2.56] in the 1-dose group and 1.69 [95% CI, .92-3.08] in the 2-dose group; nominal significance of combined suptavumab group vs placebo; P = .12). Sequenced RSV isolates demonstrated no suptavumab epitope changes in RSV A isolates, while all RSV B isolates had 2-amino acid substitution in the suptavumab epitope that led to loss of neutralization activity. Treatment emergent adverse events were balanced across treatment groups.

CONCLUSIONS

Suptavumab did not reduce overall RSV hospitalizations or outpatient LRTI because of a newly circulating mutant strain of RSV B. Genetic variation in circulating RSV strains will continue to challenge prevention efforts.

CLINICAL TRIALS REGISTRATION

NCT02325791. https://clinicaltrials.gov/ct2/show/NCT02325791.

Highly Conserved Molecular Features in IgLONs Contrast Their Distinct Structural and Biological Outcomes

Neuronal growth regulator 1 (NEGR1) and neurotrimin (NTM) are abundant cell-surface proteins found in the brain and form part of the IgLON (Immunoglobulin LSAMP, OBCAM, Neurotrimin) family. In humans, NEGR1 is implicated in obesity and mental disorders, while NTM is linked to intelligence and cognitive function. IgLONs dimerize homophilically and heterophilically, and they are thought to shape synaptic connections and neural circuits by acting in trans (spanning cellular junctions) and/or in cis (at the same side of a junction). Here, we reveal homodimeric structures of NEGR1 and NTM. They assemble into V-shaped complexes via their Ig1 domains, and disruption of the Ig1-Ig1 interface abolishes dimerization in solution. A hydrophobic ridge from one Ig1 domain inserts into a hydrophobic pocket from the opposing Ig1 domain producing an interaction interface that is highly conserved among IgLONs but remarkably plastic structurally. Given the high degree of sequence conservation at the interaction interface, we tested whether different IgLONs could elicit the same biological effect in vivo. In a small-scale study administering different soluble IgLONs directly into the brain and monitoring feeding, only NEGR1 altered food intake significantly. Taking NEGR1 as a prototype, our studies thus indicate that while IgLONs share a conserved mode of interaction and are able to bind each other as homomers and heteromers, they are structurally plastic and can exert unique biological action.

Investigating the role of organic carbon amendments and microbial denitrification gene abundance in nitrogen removal from experimental agricultural drainage ditches with low-grade weirs

Low-grade weirs placed within agricultural drainage ditches in the Lower Mississippi Alluvial Valley can be used as a management practice to enhance nitrogen removal. The addition of organic carbon amendments within ditches that contain weirs could further increase nitrogen removal. Through repeated trials, changes in NO 3 - -N concentration between inflow and outflow were variable in the ditch without weirs, while only decreases in concentration were observed in ditches with weirs. Significant differences in NO 3 - -N concentrations were observed between treatments, with greater removal of NO 3 - -N observed in dissolved organic carbon treatments compared to control and particulate organic carbon treatments. At medium- and high-flow rates, respectively, dissolved organic carbon treatments resulted in greater NO 3 - -N concentration decreases of 31.6% and 27.1% compared to 19% and 11.6% in particulate organic carbon treatments and 18.6% and 17.2% in control treatments. Significant effects of weirs and sampling date on nirS, nirK, nosZ, and 16S rRNA gene abundances were observed. Observed increases in NO 3 - -N removal with organic carbon amendments, provides support for continued investigation on improving the efficacy of organic carbon amendments as a best management practice for NO 3 - -N removal in agricultural drainage ditches. PRACTITIONER POINTS: Dissolved organic carbon amendments increased nitrate-nitrogen removal. Only decreases in nitrate-nitrogen concentration were observed in ditches with weirs. Increasing flow rate did not affect nitrate-nitrogen removal. Abundance of denitrification-performing microbes likely did not affect N removal. Lack of anaerobic soil conditions and short residence time reduced nitrate-N removal.

A Research Framework to Integrate Cross-Ecosystem Responses to Tropical Cyclones

Tropical cyclones play an increasingly important role in shaping ecosystems. Understanding and generalizing their responses is challenging because of meteorological variability among storms and its interaction with ecosystems. We present a research framework designed to compare tropical cyclone effects within and across ecosystems that: a) uses a disaggregating approach that measures the responses of individual ecosystem components, b) links the response of ecosystem components at fine temporal scales to meteorology and antecedent conditions, and c) examines responses of ecosystem using a resistance–resilience perspective by quantifying the magnitude of change and recovery time. We demonstrate the utility of the framework using three examples of ecosystem response: gross primary productivity, stream biogeochemical export, and organismal abundances. Finally, we present the case for a network of sentinel sites with consistent monitoring to measure and compare ecosystem responses to cyclones across the United States, which could help improve coastal ecosystem resilience.

Data of soil, vegetation and bird species found on double-crested cormorant colonies in the southeastern United States

This data article provides the methods and procedures followed to collect and analyse soil, vegetation and bird data on three different treatment islands in Guntersville Reservoir, Alabama. Samples were collected from randomly selected plot points from islands that were placed into three different treatment types: Colony (currently occupied by Double-crested Cormorants) (Phalacrocorax auritus; n = 5), Historic (historically occupied by cormorants and currently abandoned; n = 3) and Reference (never occupied by cormorants; n = 4). We compared vegetation and tree metrics such as structure and diversity, as well as soil chemistry and bird diversity and communities among islands within Guntersville Reservoir. These data document for the first time that we are aware of the long-term effects of soil chemistry changes, vegetation changes, and impacts to avian diversity, in temperate forest ecosystems, by cormorant colonies. All data is associated with the recent article by Veum et al. [1] and provided here as raw data.

Redescription of Eimeria megabubonis Upton, Campbell, Weigel & McKown, 1990 (Apicomplexa: Emeriidae) from the great horned owl Bubo virginianus (Gmelin)

While nine nominal species of Eimeria Schneider, 1875 have been described from strigiform birds, molecular sequence data are not available for any of these species. In the present study, oöcysts of a coccidian were isolated by faecal flotation from the lower intestinal contents of an opportunistically collected, recently deceased great horned owl Bubo virginianus (Gmelin), sporulated in potassium dichromate, and subjected to morphological and molecular characterisation. Comparisons of morphological data with previous accounts of Eimeria spp. from owls were consistent with Eimeria megabubonis Upton, Campbell, Weigel & McKown, 1990. Novel molecular data for the 18S ribosomal RNA gene region and the mitochondrial cytochrome c oxidase subunit 1 gene are provided. The results of phylogenetic analysis based on concatenated sequence data from these regions are presented and implications for the evolutionary history of Eimeria are discussed.

Machine learning of large-scale spatial distributions of wild turkeys with high-dimensional environmental data

Species distribution modeling often involves high-dimensional environmental data. Large amounts of data and multicollinearity among covariates impose challenges to statistical models in variable selection for reliable inferences of the effects of environmental factors on the spatial distribution of species. Few studies have evaluated and compared the performance of multiple machine learning (ML) models in handling multicollinearity. Here, we assessed the effectiveness of removal of correlated covariates and regularization to cope with multicollinearity in ML models for habitat suitability. Three machine learning algorithms maximum entropy (MaxEnt), random forests (RFs), and support vector machines (SVMs) were applied to the original data (OD) of 27 landscape variables, reduced data (RD) with 14 highly correlated covariates being removed, and 15 principal components (PC) of the OD accounting for 90% of the original variability. The performance of the three ML models was measured with the area under the curve and continuous Boyce index. We collected 663 nonduplicated presence locations of Eastern wild turkeys (Meleagris gallopavo silvestris) across the state of Mississippi, United States. Of the total locations, 453 locations separated by a distance of ≥2 km were used to train the three ML algorithms on the OD, RD, and PC data, respectively. The remaining 210 locations were used to validate the trained ML models to measure ML performance. Three ML models had excellent performance on the RD and PC data. MaxEnt and SVMs had good performance on the OD data, indicating the adequacy of regularization of the default setting for multicollinearity. Weak learning of RFs through bagging appeared to alleviate multicollinearity and resulted in excellent performance on the OD data. Regularization of ML algorithms may help exploratory studies of the effects of environmental factors on the spatial distribution and habitat suitability of wildlife.

Morphological, Molecular, and Histopathological Data for Sebekia mississippiensis Overstreet, Self, and Vliet, 1985 (Pentastomida: Sebekidae) in the American Alligator, Alligator mississippiensis Daudin, and the Spotted Gar, Lepisosteus oculatus Winchell

Novel molecular data from both mitochondrial ( cytochrome c oxidase subunit 1) and ribosomal regions ( 18S, ITS1-5.8S, ITS2, and 28S) are provided for Sebekia mississippiensis Overstreet, Self, & Vliet, 1985 , a pentastome infecting the American alligator, Alligator mississippiensis Daudin, 1801, and the spotted gar, Lepisosteus oculatus Winchell, 1864. Adult and nymphal pentastomes are described from the lungs and liver of the type host, A. mississippiensis, collected from Mississippi, while additional nymphs are described from the esophageal lining of L. oculatus specimens collected from Louisiana. This sequencing data will facilitate more accurate identification of various life cycle stages of S. mississippiensis, enabling future work to resolve many ambiguities in the literature regarding this species. Additionally, histopathological data are provided from both the definitive and intermediate hosts.

Morphological, molecular and phylogenetic characterisation of Eimeria macyi Wheat, 1975 (Apicomplexa: Eimeriidae) in the eastern red bat Lasiurus borealis (Müller) from Mississippi, USA

In November 2017, oöcysts of the coccidian Eimeria macyi Wheat, 1975 were isolated from the faeces of a single eastern red bat Lasiurus borealis Müller in Lowndes County, Mississippi, USA. Sporulated oöcysts, morphologically consistent with previous accounts of E. macyi in other chiropterans, were spherical to sub-spherical in shape with a highly mamillated outer wall that appears bi-layered. Oöcysts allowed to sporulate in 2.5% potassium dichromate at ambient temperature (c.23°C) for 7 days were 17-25 × 15-20 (20.7 × 17.9) µm. Micropyle and oöcyst residuum were absent with one to two polar granules scattered among sporocysts. The four ovoid sporocysts were 7-12 × 6-8 (9.9 × 7.1) µm. Stieda bodies were prominent and sub-Stieda bodies were present. Two sporozoites were reflexed within each sporocyst. Nuclear 18S rRNA gene, plastid 23S rRNA gene and mitochondrial cytochrome c oxidase subunit 1 (cox1) gene were sequenced from sporulated oöcysts and compared to other molecular data of Eimeria spp. from rodent and chiropteran hosts. No sequence data in the NCBI database matched E. macyi. Phylogenetic analyses of the sequence data of the 18S rRNA and 23S rRNA genes placed E. macyi within a clade containing Eimeria spp. from rodents and basal to a clade populated by sequences derived from Eimeria spp. of rodents and bats. This account represents a new host record of E. macyi in an eastern red bat and a new geographic locality. Additionally, the cox1 sequence data of Eimeria macyi represents the first mitochondrial sequence of an Eimeria sp. in bats.

Management Practices Used in Agricultural Drainage Ditches to Reduce Gulf of Mexico Hypoxia

Agricultural non-point sources of nutrients and sediments have caused eutrophication and other water quality issues in aquatic and marine ecosystems, such as the annual occurrence of hypoxia in the Gulf of Mexico. Management practices have been implemented adjacent to and in agricultural drainage ditches to promote their wetland characteristics and functions, including reduction of nitrogen, phosphorus, and sediment losses downstream. This review: (1) summarized studies examining changes in nutrient and total suspended solid concentrations and loads associated with management practices in drainage ditches (i.e., riser and slotted pipes, two-stage ditches, vegetated ditches, low-grade weirs, and organic carbon amendments) with emphasis on the Lower Mississippi Alluvial Valley, (2) quantified management system effects on nutrient and total suspended solid concentrations and loads and, (3) identified information gaps regarding water quality associated with these management practices and research needs in this area. In general, management practices used in drainage ditches at times reduced losses of total suspended solids, N, and P. However, management practices were often ineffective during storm events that were uncommon and intense in duration and volume, although these types of events could increase in frequency and intensity with climate change. Studies on combined effects of management practices on drainage ditch water quality, along with research towards improved nutrient and sediment reduction efficiency during intense storm events are urgently needed.

Alligator wrestling: morphological, molecular, and phylogenetic data on Odhneriotrema incommodum (Leidy, 1856) (Digenea: Clinostomidae) from Alligator mississippiensis Daudin, 1801 in Mississippi, USA

Based on specimens collected from harvested American alligator Alligator mississippiensis Daudin, 1801 in Mississippi, USA, novel molecular data for both nuclear ribosomal genes (18S, ITS1-5.8S, ITS2, and 28S) and mitochondrial genes (cytochrome c oxidase subunit 1 and nicotinamide adenine dinucleotide dehydrogenase subunit 1) are provided for Odhneriotrema incommodum (Leidy, 1856), a trematode of the family Clinostomidae Lühe, 1901 infecting A. mississippiensis and the Florida spotted gar Lepisosteus platyrhincus DeKay, 1842. This represents the first sequencing data available for the genus Odhneriotrema and the subfamily Nephrocephalinae Travassos, 1928. Additionally, the results of phylogenetic analyses, additional morphometric data, a photomicrograph, and a line drawing supporting the present identification of O. incommodum are provided. These data will aid in elucidating the life cycle of O. incommodum through molecular identification of larval stages as well as understanding the evolutionary history of Clinostomidae and its subfamilies. Implications for the currently accepted organization of the Clinostomidae are discussed.

Potential Implications of Approaches to Climate Change on the Clean Water Rule Definition of "Waters of the United States"

The 1972 Clean Water Act was passed to protect chemical, physical, and biological integrity of United States' waters. The U.S. Environmental Protection Agency and U.S. Army Corps of Engineers codified a new "waters of the United States" rule on June 29, 2015, because several Supreme Court case decisions caused confusion with the existing rule. Climate change could affect this rule through connectivity between groundwater and surface waters; floodplain waters and the 100-year floodplain; changes in jurisdictional status; and sea level rise on coastal ecosystems. Four approaches are discussed for handling these implications: (1) "Wait and see"; (2) changes to the rule; (3) use guidance documents; (4) Congress statutorily defining "waters of the United States." The approach chosen should be legally defensible and achieved in a timely fashion to provide protection to "waters of the United States" in proactive consideration of scientifically documented effects of climate change on aquatic ecosystems.

Geographic distribution of selected elements in the livers of polar bears from Greenland, Canada and the United States

To assess geographic distributions of elements in the Arctic we compared essential and non-essential elements in the livers of polar bears (Ursus maritimus) collected from five regions within Canada in 2002, in Alaska between 1994 and 1999 and from the northwest and east coasts of Greenland between 1988 and 2000. As, Hg, Pb and Se varied with age, and Co and Zn with gender, which limited spatial comparisons across all populations to Cd, which was highest in Greenland bears. Collectively, geographic relationships appeared similar to past studies with little change in concentration over time in Canada and Greenland for most elements; Hg and Se were higher in some Canadian populations in 2002 as compared to 1982 and 1984. Concentrations of most elements in the polar bears did not exceed toxicity thresholds, although Cd and Hg exceeded levels correlated with the formation of hepatic lesions in laboratory animals.