37 results on '"Bergner, Laura"'
Search Results
2. Viral communities in vampire bats : geographical variation and ecological drivers
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Bergner, Laura
- Subjects
599.4 ,QH426 Genetics ,QL Zoology ,QR355 Virology - Abstract
Microbial communities play important roles in organismal and ecosystem health. High throughput sequencing has revolutionized our understanding of host-associated microbial communities, but the viral component of these communities remains poorly characterized relative to microbes such as bacteria, particularly in non-human hosts. This knowledge gap has implications for global health, as viruses originating in wildlife are responsible for recent disease outbreaks in humans and domestic animals. Although studies have identified factors differentiating viral communities between species, we have little understanding of the variability of viral communities within species. Comparative studies of viral communities are therefore necessary to characterize novel taxa and to evaluate the ecological factors influencing intraspecific viral diversity and distribution. Bats are recognized as “special” reservoirs for viruses because they are associated with diverse viral communities and display deep evolutionary relationships with individual viral taxa. Common vampire bats (Desmodus rotundus) represent a particularly interesting system in which to investigate viral communities, as they are obligate blood feeders that interact ecologically with many different host species, providing opportunities for the acquisition of diverse viruses. The overall objective of this thesis was to advance our understanding of intraspecific wildlife-associated viral communities using an established field network of common vampire bat colonies across Peru. Specifically, I developed a novel method for comparative viral community studies, characterized the viral communities of vampire bats, and examined the ecological correlates of vampire bat viral diversity across Peru. Metagenomic sequencing is a promising technique for comparative studies of viral communities in wildlife, but there is a need to first develop standardized methods that can be applied to samples collected in the field. In Chapter 2 I developed a shotgun metagenomic sequencing approach to characterizing viral communities from non-invasive samples. Specifically, I optimized extraction and sequencing protocols using fecal and oropharyngeal swabs collected from common vampire bats in Peru. Two preliminary sequencing runs were performed, the results of which motivated four pilot studies in which I tested how different storage media, nucleic acid extraction procedures, and enrichment steps affect the viral community detected. Metagenomic sequencing revealed viral contamination of fetal bovine serum, a component of viral transport medium, suggesting that swabs should be stored in RNALater or another non-biological medium. Extraction and qPCR tests were performed on swabs inoculated with known concentrations of virus, which revealed that nucleic acid should be directly extracted from swabs rather than from supernatant or pelleted material. Metagenomic sequencing of paired samples was used to test enrichment by ribosomal RNA depletion and light DNAse treatment, which both reduced host and bacterial nucleic acid in samples and improved virus detection. A bioinformatic pipeline was developed specifically for processing vampire bat shotgun viral metagenomic data. Finally, the optimized protocol was applied to twelve pooled samples from seven localities in Peru, and read subsampling demonstrated that the viral communities detected were consistent at commonly attained depths of sequencing. The protocol developed in this chapter enables minimally biased comparative viral community studies in non-invasive samples collected from wildlife. Having a detailed understanding of viral diversity in key wildlife hosts is an important first step in evaluating the risk of zoonotic disease emergence, but we still lack a holistic view of viral communities in many species including vampire bats. In Chapter 3, I used the metagenomic sequencing protocol developed in Chapter 2 to thoroughly characterize viral communities in the saliva and feces of vampire bats captured across Peru. Viruses were detected from a range of natural host groups including vertebrate-associated taxa that were potentially infecting vampire bats, bacteriophages associated with gut bacteria, and plant- or insect-infecting viruses potentially acquired from the environment. There were broad differences between fecal and saliva viral communities, showing evidence of body habitat compartmentalization. Overall, results established that vampire bat viral communities differ between body habitats and suggested that, for the vertebrate-infecting families analyzed, novel viruses mostly fall within bat-specific clades, without evidence of livestock or humans acting as a major source of viral diversity in vampire bats. Interspecific differences in ecological and life history traits are known to impact viral richness in bats, but the factors structuring viral communities within bat species are less well understood. In Chapter 4, I examined the spatial, demographic and environmental correlates of intraspecific viral diversity in vampire bats. Three measures of viral diversity were calculated at the colony level: richness, a novel measure of taxonomic diversity, and community composition. Generalized linear models were then used to test the effects of broad scale and local ecological variables on saliva and fecal viral diversity. The results showed for the first time that ecological variables can influence intraspecific viral diversity. In summary, the work presented in this thesis advances our understanding of wildlife-associated viral communities in an ecologically important bat host. Future directions in comparative wildlife viral metagenomics, as discussed in Chapter 5, will include exploring the determinants of viral communities across host species, environments and time.
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- 2018
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3. ICTV Virus Taxonomy Profile: Kolmioviridae 2024
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Kuhn, Jens H., primary, Babaian, Artem, additional, Bergner, Laura M., additional, Dény, Paul, additional, Glebe, Dieter, additional, Horie, Masayuki, additional, Koonin, Eugene V., additional, Krupovic, Mart, additional, Paraskevopoulou, Sofia, additional, de la Peña, Marcos, additional, Smura, Teemu, additional, and Hepojoki, Jussi, additional
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- 2024
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4. Population genetics, phylogeography and gene flow of mainland and island vampire bat (Desmodus rotundus) populations: an investigation into mainland-island bat movement
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Seetahal, Janine F.R., primary, Streicker, Daniel G., additional, Beerli, Peter, additional, Sahadeo, Nikita, additional, Lemey, Philippe, additional, Sanchez-Vazquez, Manuel J., additional, Broos, Alice, additional, Bergner, Laura, additional, Ramkissoon, Vernie, additional, Mahabir, Ron, additional, Tihul, Praimnauth, additional, Hartley, Dane, additional, Sauers, Astrid Van, additional, Karg, Gianna, additional, Mohammed, Ryan S., additional, Biek, Roman, additional, Oura, Christopher A.L., additional, and Carrington, Christine V.F., additional
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- 2024
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5. Epidemiology and biology of a herpesvirus in rabies endemic vampire bat populations
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Griffiths, Megan E., Bergner, Laura M., Broos, Alice, Meza, Diana K., Filipe, Ana da Silva, Davison, Andrew, Tello, Carlos, Becker, Daniel J., and Streicker, Daniel G.
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- 2020
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6. Developing transmissible vaccines for animal infections.
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Streicker, Daniel G., Griffiths, Megan E., Antia, Rustom, Bergner, Laura, Bowman, Peter, dos Santos de Moraes, Maria Vitoria, Esvelt, Kevin, Famulare, Mike, Gilbert, Amy, He, Biao, Jarvis, Michael A., Kennedy, David A., Kuzma, Jennifer, Wanyonyi, Carolyne Nasimiyu, Remien, Christopher, Rocke, Tonie, Rosenke, Kyle, Schreiner, Courtney, Sheen, Justin, and Simons, David
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- 2024
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7. Optimising predictive models to prioritise viral discovery in zoonotic reservoirs
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Becker, Daniel J, primary, Albery, Gregory F, additional, Sjodin, Anna R, additional, Poisot, Timothée, additional, Bergner, Laura M, additional, Chen, Binqi, additional, Cohen, Lily E, additional, Dallas, Tad A, additional, Eskew, Evan A, additional, Fagre, Anna C, additional, Farrell, Maxwell J, additional, Guth, Sarah, additional, Han, Barbara A, additional, Simmons, Nancy B, additional, Stock, Michiel, additional, Teeling, Emma C, additional, and Carlson, Colin J, additional
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- 2022
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8. Longitudinal deep sequencing informs vector selection and future deployment strategies for transmissible vaccines
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Griffiths, Megan E., primary, Broos, Alice, additional, Bergner, Laura M., additional, Meza, Diana K., additional, Suarez, Nicolas M., additional, da Silva Filipe, Ana, additional, Tello, Carlos, additional, Becker, Daniel J., additional, and Streicker, Daniel G., additional
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- 2022
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9. House Wrens Alter Nest Architecture to Compensate for Cavity Vulnerability
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Stanback, Mark T., Stanbeck, Mark T., Bartholomew, Joseph E., Bergner, Laura M., Cline, Esther L., Helms, Paul I., McGovern, Patrick G., Millican, David M., and Roth, Jeffrey E.
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- 2013
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10. Combining genetic data to identify relatedness among founders in a genetically depauperate parrot, the Kakapo (Strigops habroptilus)
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Bergner, Laura M., Jamieson, Ian G., and Robertson, Bruce C.
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- 2014
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11. Using noninvasive metagenomics to characterize viral communities from wildlife
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Bergner, Laura M., Orton, Richard J., da Silva Filipe, Ana, Shaw, Andrew E., Becker, Daniel J., Tello, Carlos, Biek, Roman, and Streicker, Daniel G.
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virome ,RESOURCE ARTICLES ,Oropharynx ,Biodiversity ,Sequence Analysis, DNA ,Desmodus rotundus ,Molecular and Statistical Advances ,Specimen Handling ,Feces ,Virus Diseases ,Chiroptera ,Peru ,Viruses ,Animals ,Resource Article ,Metagenomics ,microbial community ,shotgun metagenomics - Abstract
Microbial communities play an important role in organismal and ecosystem health. While high‐throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here, we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from noninvasively collected faecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low‐input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNase treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time.
- Published
- 2018
12. Diversification of mammalian deltaviruses by host shifting
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Bergner, Laura M., Orton, Richard J., Broos, Alice, Tello, Carlos, Becker, Daniel J., Carrera, Jorge E., Patel, Arvind H., Biek, Roman, and Streicker, Daniel G.
- Abstract
Hepatitis delta virus (HDV) is an unusual RNA agent that replicates using host machinery but exploits hepatitis B virus (HBV) to mobilize its spread within and between hosts. In doing so, HDV enhances the virulence of HBV. How this seemingly improbable hyper-parasitic lifestyle emerged is unknown, but underpins the likelihood that HDV and related deltaviruses may alter other host-virus interactions. Here, we show that deltaviruses diversify by transmitting between mammalian species. Among 96,695 RNA sequence datasets, deltaviruses infected bats, rodents and an artiodactyl from the Americas, but were absent from geographically overrepresented Old World representatives of each mammalian order, suggesting a relatively recent diversification within the Americas. Consistent with diversification by host shifting, both bat and rodent-infecting deltaviruses were paraphyletic and co-evolutionary modeling rejected co-speciation with mammalian hosts. In addition, a two-year field study showed common vampire bats in Peru were infected by two divergent deltaviruses, indicating multiple introductions to a single host species. One vampire bat-associated deltavirus was detected in the saliva of up to 35% of individuals, formed phylogeographically compartmentalized clades, and infected a sympatric bat, illustrating horizontal transmission within and between species on ecological timescales. Consistent absence of HBV-like viruses in two deltavirus-infected bat species indicated acquisitions of novel viral associations during the divergence of bat and human-infecting deltaviruses. Our analyses support an American zoonotic origin of HDV and reveal prospects for future cross-species emergence of deltaviruses. Given their peculiar life history, deltavirus host shifts will have different constraints and disease outcomes compared to ordinary animal pathogens.
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- 2020
13. Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats
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Bergner, Laura M., primary, Mollentze, Nardus, additional, Orton, Richard J., additional, Tello, Carlos, additional, Broos, Alice, additional, Biek, Roman, additional, and Streicker, Daniel G., additional
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- 2021
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14. Detection of Trypanosoma cruzi in the saliva of diverse neotropical bats
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Bergner, Laura M., primary, Becker, Daniel J., additional, Tello, Carlos, additional, Carrera, Jorge E., additional, and Streicker, Daniel G., additional
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- 2021
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15. Complete Alphacoronavirus genome sequence from common vampire bats in Peru
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Bergner, Laura M., Orton, Richard J., and Streicker, Daniel G.
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Bats host diverse coronaviruses, including taxa capable of pandemic spread in humans. We report the genome of an alphacoronavirus from a neotropical bat species (Desmodus rotundus) in Peru, which contributes to our understanding of bat coronaviruses in nature.
- Published
- 2020
16. Conservative plumage masks extraordinary phylogenetic diversity in the Grallaria rufula (Rufous Antpitta) complex of the humid Andes
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Chesser, R. Terry, Isler, Morton L., Cuervo, Andrés M., Cadena, C. Daniel, Galen, Spencer C., Bergner, Laura M., Fleischer, Robert C., Bravo, Gustavo A., Lane, Daniel F., and Hosner, Peter A.
- Abstract
The Grallaria rufula complex is currently considered to consist of 2 species, G. rufula (Rufous Antpitta) and G. blakei (Chestnut Antpitta). However, it has been suggested that the complex, populations of which occur in humid montane forests from Venezuela to Bolivia, comprises a suite of vocally distinct yet morphologically cryptic species. We sequenced nuclear and mitochondrial DNA for 80 individuals from across the distribution of the complex to determine the extent of genetic variation between and within described taxa. Our results revealed 18 geographically coherent clades separated by substantial genetic divergence: 14 within rufula, 3 within blakei, and 1 corresponding to G. rufocinerea (Bicolored Antpitta), a species with distinctive plumage found to be nested within the complex. Neither G. rufula nor G. blakei as presently defined was monophyletic. Although 6 of the 7 recognized subspecies of G. rufula were monophyletic, several subspecies contained substantial genetic differentiation. Genetic variation was largely partitioned across recognized geographic barriers, especially across deep river valleys in Peru and Colombia. Coalescent modeling identified 17 of the 18 clades as significantly differentiated lineages, whereas analyses of vocalizations delineated 16 biological species within the complex. The G. rufula complex seems unusually diverse even among birds of the humid Andes, a prime location for cryptic speciation; however, the extent to which other dispersal-limited Andean species groups exhibit similar degrees of cryptic differentiation awaits further study.
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- 2020
17. Threatened Freshwater Fishes of the Mediterranean Basin Biodiversity Hotspot: Distribution, extinction risk and the impact of hydropower. Euronatur and Riverwatch
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Freyhof, Jörg, Bergner, Laura, and Ford, Matt
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Mediterranean Basin Biodiversity Hotspot ,Threatened Freshwater Fishes - Abstract
The Mediterranean Basin Biodiversity Hotspot is among the most biologically diverse regions worldwide and renowned for its richness of endemic freshwater species. But the hotspot’s lakes, rivers and wetlands are seriously threatened by an unprecedented boom in hydropower development. As a result, aquatic ecosystems have become increasingly degraded due to construction of dams and other infrastructure, compounded by a range of other threats. Advocates of this flawed development model repeatedly overestimate economic benefits and ignore severe environmental consequences. In particular, the impacts of small (10 MW) hydropower plants are disproportionately high when offset against their minuscule contribution to global energy production. At least 5,269 hydropower plants are already operating in the region, with 202 currently under construction. A further 6,393 are proposed, including 5,962 small projects, while 1,579 exist and 2,091 are planned within the boundaries of national parks, biosphere reserves, and other protected areas. In order to anticipate the biodiversity impact of this widening hydropower infrastructure it is essential to understand where threatened species are distributed. This report presents detailed range maps for all 251 freshwater fish species presently recognised as threatened in the Mediterranean Basin Biodiversity Hotspot alongside an updated evaluation of their respective extinction risks. The results suggest that an alarming 63% of all threatened freshwater fish species have already been driven closer to extinction by existing hydropower plants, with 55% of all Critically Endangered species highly impacted. Should hydroelectric expansion in the region go ahead as planned, 74% of all threatened freshwater fish species will be negatively impacted, with 65% set to decline due to small projects alone. At least seven of these could become globally extinct in the wild as a result. Hydropower projects, particularly small schemes, are therefore the most important driver of potential fish species extinctions in the Mediterranean Basin Biodiversity Hotspot. Impoundments created by dams and other hydroelectric infrastructure are also the key pathway by which non-native fish species, another major cause of freshwater fish declines, enter fluvial ecosystems. Moreover, if the hydroelectric schemes planned in the Mediterranean Basin Biodiversity Hotspot are implemented, nations will be unable to comply with the United Nations 2030 Agenda for Sustainable Development or binding international biodiversity targets agreed by parties to the Convention on Biological Diversity and European Union member states. There is an urgent need to mitigate the escalating ecological damage triggered by the hydropower binge through preservation and restoration of free-flowing rivers. Rapid and significant action underpinned by sound scientific evidence is required to safeguard freshwater ecosystems and the incredibly rich biodiversity they support throughout the region. By improving the state of the natural environment, the impacts of ongoing climate change would also be reduced. It is hoped that this report will help inform nature conservation, governments and policy-makers to make the right political, financial and consumer choices to reverse the trend of freshwater biodiversity decline throughout the Mediterranean Basin Biodiversity Hotspot.
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- 2020
18. Complete Genome Sequence of an Alphacoronavirus from Common Vampire Bats in Peru
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Bergner, Laura M., primary, Orton, Richard J., additional, and Streicker, Daniel G., additional
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- 2020
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19. Temporal patterns of vampire bat rabies and host connectivity in Belize
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Becker, Daniel J., primary, Broos, Alice, additional, Bergner, Laura M., additional, Meza, Diana K., additional, Simmons, Nancy B., additional, Fenton, M. Brock, additional, Altizer, Sonia, additional, and Streicker, Daniel G., additional
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- 2020
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20. Diversification of mammalian deltaviruses by host shifting
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Bergner, Laura M., primary, Orton, Richard J., additional, Broos, Alice, additional, Tello, Carlos, additional, Becker, Daniel J., additional, Carrera, Jorge E., additional, Patel, Arvind H., additional, Biek, Roman, additional, and Streicker, Daniel G., additional
- Published
- 2020
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21. Optimizing predictive models to prioritize viral discovery in zoonotic reservoirs
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Becker, Daniel J., primary, Albery, Gregory F., additional, Sjodin, Anna R., additional, Poisot, Timothée, additional, Bergner, Laura M., additional, Dallas, Tad A., additional, Eskew, Evan A., additional, Farrell, Maxwell J., additional, Guth, Sarah, additional, Han, Barbara A., additional, Simmons, Nancy B., additional, Stock, Michiel, additional, Teeling, Emma C., additional, and Carlson, Colin J., additional
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- 2020
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22. Freshwater fish distribution in the Maghreb: a call to contribute
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Ford, Matthew, primary, Brahimi, Amina, additional, Baikeche, Lyas, additional, Bergner, Laura, additional, Clavero, Miguel, additional, Doadrio, Ignacio, additional, Lopes-Lima, Manuel, additional, Perea, Silvia, additional, Yahyaoui, Ahmed, additional, and Freyhof, Jörg, additional
- Published
- 2020
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23. Demographic and environmental drivers of metagenomic viral diversity in vampire bats
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Bergner, Laura M., primary, Orton, Richard J., additional, Benavides, Julio A., additional, Becker, Daniel J., additional, Tello, Carlos, additional, Biek, Roman, additional, and Streicker, Daniel G., additional
- Published
- 2019
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24. Temporal patterns of vampire bat rabies and host connectivity in Belize.
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Becker, Daniel J., Broos, Alice, Bergner, Laura M., Meza, Diana K., Simmons, Nancy B., Fenton, M. Brock, Altizer, Sonia, and Streicker, Daniel G.
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RABIES ,VAMPIRE bats ,BAT ecology ,VIRUS diseases ,RABIES virus ,SEROPREVALENCE - Abstract
In the Neotropics, vampire bats (Desmodus rotundus) are the main reservoir host for rabies, a highly fatal encephalitis caused by viruses in the genus Lyssavirus. Although patterns of rabies virus exposure and infection have been well studied for vampire bats in South America and Mexico, exploring the ecology of vampire bat rabies in other regions is crucial for predicting risks to livestock and humans. In Belize, rabies outbreaks in livestock have increased in recent years, underscoring the need for systematic data on viral dynamics in vampire bats. In this study, we examine the first three years of a longitudinal study on the ecology of vampire bat rabies in northern Belize. Rabies seroprevalence in bats was high across years (29%–80%), suggesting active and endemic virus circulation. Across two locations, the seroprevalence time series per site were inversely related and out of phase by at least a year. Microsatellite data demonstrated historic panmixia of vampire bats, and mark–recapture detected rare but contemporary inter‐site dispersal. This degree of movement could facilitate spatial spread of rabies virus but is likely insufficient to synchronize infection dynamics, which offers one explanation for the observed phase lag in seroprevalence. More broadly, our analyses suggest frequent transmission of rabies virus within and among vampire bat roosts in northern Belize and highlight the need for future spatiotemporal, phylogenetic and ecological studies of vampire bat rabies in Central America. [ABSTRACT FROM AUTHOR]
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- 2021
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25. Molecular systematics of swifts of the genus Chaetura (Aves: Apodiformes: Apodidae)
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Chesser, R. Terry, primary, Vaseghi, Haley, additional, Hosner, Peter A., additional, Bergner, Laura M., additional, Cortes-Rodriguez, M. Nandadevi, additional, Welch, Andreanna J., additional, and Collins, Charles T., additional
- Published
- 2018
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26. Genetic diversity, infection prevalence, and possible transmission routes of Bartonella spp. in vampire bats
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Becker, Daniel J., primary, Bergner, Laura M., additional, Bentz, Alexandra B., additional, Orton, Richard J., additional, Altizer, Sonia, additional, and Streicker, Daniel G., additional
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- 2018
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27. Demographic and environmental drivers of metagenomic viral diversity in vampire bats.
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Bergner, Laura M., Orton, Richard J., Benavides, Julio A., Becker, Daniel J., Tello, Carlos, Biek, Roman, and Streicker, Daniel G.
- Subjects
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BIOGEOCHEMICAL cycles , *VIRAL ecology , *VIRAL variation , *VAMPIRE bats , *BATS , *MODERN society - Abstract
Viruses infect all forms of life and play critical roles as agents of disease, drivers of biochemical cycles and sources of genetic diversity for their hosts. Our understanding of viral diversity derives primarily from comparisons among host species, precluding insight into how intraspecific variation in host ecology affects viral communities or how predictable viral communities are across populations. Here we test spatial, demographic and environmental hypotheses explaining viral richness and community composition across populations of common vampire bats, which occur in diverse habitats of North, Central and South America. We demonstrate marked variation in viral communities that was not consistently predicted by a null model of declining community similarity with increasing spatial or genetic distances separating populations. We also find no evidence that larger bat colonies host greater viral diversity. Instead, viral diversity follows an elevational gradient, is enriched by juvenile‐biased age structure, and declines with local anthropogenic food resources as measured by livestock density. Our results establish the value of linking the modern influx of metagenomic sequence data with comparative ecology, reveal that snapshot views of viral diversity are unlikely to be representative at the species level, and affirm existing ecological theories that link host ecology not only to single pathogen dynamics but also to viral communities. see also the Perspective by Wille [ABSTRACT FROM AUTHOR]
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- 2020
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28. European Colonization, Not Polynesian Arrival, Impacted Population Size and Genetic Diversity in the Critically Endangered New Zealand Kākāpō
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Bergner, Laura M., primary, Dussex, Nicolas, primary, Jamieson, Ian G., primary, and Robertson, Bruce C., primary
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- 2016
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29. Using noninvasive metagenomics to characterize viral communities from wildlife.
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Biek, Roman, Bergner, Laura M., Orton, Richard J., Streicker, Daniel G., da Silva Filipe, Ana, Shaw, Andrew E., Becker, Daniel J., and Tello, Carlos
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- *
DESMODUS rotundus , *MICROBIAL communities , *METAGENOMICS , *ANIMALS , *ECOSYSTEM dynamics - Abstract
Microbial communities play an important role in organismal and ecosystem health. While high‐throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here, we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from noninvasively collected faecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low‐input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNase treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
30. Identification and characterization of microsatellite loci in two socially complex old world tropical babblers (Family Timaliidae)
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Kaiser, Sara A., primary, Danner, J. E., additional, Bergner, Laura, additional, and Fleischer, Robert C., additional
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- 2015
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31. A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae)
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Sloan, Daniel B., primary, Triant, Deborah A., additional, Forrester, Nicole J., additional, Bergner, Laura M., additional, Wu, Martin, additional, and Taylor, Douglas R., additional
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- 2014
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32. A Novel Predicted Bromodomain-Related Protein Affects Coordination Between Meiosis and Spermiogenesis inDrosophilaand Is Required for Male Meiotic Cytokinesis
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Bergner, Laura M., primary, Hickman, F. Edward, additional, Wood, Kathleen H., additional, Wakeman, Carolyn M., additional, Stone, Hunter H., additional, Campbell, Tessa J., additional, Lightcap, Samantha B., additional, Favors, Sheena M., additional, Aldridge, Amanda C., additional, and Hales, Karen G., additional
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- 2010
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33. A Novel Predicted Bromodomain-Related Protein Affects Coordination Between Meiosis and Spermiogenesis in Drosophila and Is Required for Male Meiotic Cytokinesis.
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Bergner, Laura M., Hickman, Edward F., Wood, Kathleen H., Wakeman, Carolyn M., Stone, Hunter H., Campbell, Tessa J., Lightcap, Samantha B., Favors, Sheena M., Aldridge, Amanda C., and Hales, Karen G.
- Subjects
- *
MEIOSIS , *KARYOKINESIS , *SPERMIOGENESIS in animals , *CYTOKINESIS , *DROSOPHILA melanogaster , *BROMODOMAIN-containing proteins , *CHROMATIN , *MORPHOGENESIS , *INSECTS - Abstract
Temporal coordination of meiosis with spermatid morphogenesis is crucial for successful generation of mature sperm cells. We identified a recessive male sterile Drosophila melanogaster mutant, mitoshell, in which events of spermatid morphogenesis are initiated too early, before meiotic onset. Premature mitochondrial aggregation and fusion lead to an aberrant mitochondrial shell around premeiotic nuclei. Despite successful meiotic karyokinesis, improper mitochondrial localization in mitoshell testes is associated with defective astral central spindles and a lack of contractile rings, leading to meiotic cytokinesis failure. We mapped and cloned the mitoshell gene and found that it encodes a novel protein with a bromodomain-related region. It is conserved in some insect lineages. Bromodomains typically bind to histone acetyl-lysine residues and therefore are often associated with chromatin. The Mitoshell bromodomain-related region is predicted to have an alpha helical structure similar to that of bromodomains, but not all the crucial residues in the ligand-binding loops are conserved. We speculate that Mitoshell may participate in transcriptional regulation of spermatogenesis-specific genes, though perhaps with different ligand specificity compared to traditional bromodomains. [ABSTRACT FROM AUTHOR]
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- 2010
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34. [Untitled]
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Bergner, Laura M., Orton, Richard J., Benavides, Julio A., Becker, Daniel J., Tello, Carlos, Biek, Roman, and Streicker, Daniel G.
- Subjects
0106 biological sciences ,0301 basic medicine ,demography ,wildlife disease ,Ecology (disciplines) ,Environment ,Desmodus rotundus ,Wildlife disease ,infectious diseases ,Communicable Diseases ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Chiroptera ,Genetics ,Animals ,Humans ,elevational gradient ,Human virome ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,virome ,Genetic diversity ,Ecology ,biology ,Host (biology) ,population structure ,Biodiversity ,South America ,15. Life on land ,biology.organism_classification ,From the Cover ,030104 developmental biology ,Metagenomics ,Viruses ,Metagenome ,community assembly ,Species richness ,human activities ,shotgun metagenomics - Abstract
Viruses infect all forms of life and play critical roles as agents of disease, drivers of biochemical cycles and sources of genetic diversity for their hosts. Our understanding of viral diversity derives primarily from comparisons among host species, precluding insight into how intraspecific variation in host ecology affects viral communities or how predictable viral communities are across populations. Here we test spatial, demographic and environmental hypotheses explaining viral richness and community composition across populations of common vampire bats, which occur in diverse habitats of North, Central and South America. We demonstrate marked variation in viral communities that was not consistently predicted by a null model of declining community similarity with increasing spatial or genetic distances separating populations. We also find no evidence that larger bat colonies host greater viral diversity. Instead, viral diversity follows an elevational gradient, is enriched by juvenile‐biased age structure, and declines with local anthropogenic food resources as measured by livestock density. Our results establish the value of linking the modern influx of metagenomic sequence data with comparative ecology, reveal that snapshot views of viral diversity are unlikely to be representative at the species level, and affirm existing ecological theories that link host ecology not only to single pathogen dynamics but also to viral communities., https://doi.org/10.1111/mec.15306
35. Threatened Freshwater Fishes of the Mediterranean Basin Biodiversity Hotspot: Distribution, extinction risk and the impact of hydropower. Euronatur and Riverwatch
- Author
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Freyhof, Jörg, Bergner, Laura, and Ford, Matt
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13. Climate action ,11. Sustainability ,Mediterranean Basin Biodiversity Hotspot ,Threatened Freshwater Fishes ,14. Life underwater ,15. Life on land ,6. Clean water ,12. Responsible consumption - Abstract
The Mediterranean Basin Biodiversity Hotspot is among the most biologically diverse regions worldwide and renowned for its richness of endemic freshwater species. But the hotspot’s lakes, rivers and wetlands are seriously threatened by an unprecedented boom in hydropower development. As a result, aquatic ecosystems have become increasingly degraded due to construction of dams and other infrastructure, compounded by a range of other threats. Advocates of this flawed development model repeatedly overestimate economic benefits and ignore severe environmental consequences. In particular, the impacts of small (10 MW) hydropower plants are disproportionately high when offset against their minuscule contribution to global energy production. At least 5,269 hydropower plants are already operating in the region, with 202 currently under construction. A further 6,393 are proposed, including 5,962 small projects, while 1,579 exist and 2,091 are planned within the boundaries of national parks, biosphere reserves, and other protected areas. In order to anticipate the biodiversity impact of this widening hydropower infrastructure it is essential to understand where threatened species are distributed. This report presents detailed range maps for all 251 freshwater fish species presently recognised as threatened in the Mediterranean Basin Biodiversity Hotspot alongside an updated evaluation of their respective extinction risks. The results suggest that an alarming 63% of all threatened freshwater fish species have already been driven closer to extinction by existing hydropower plants, with 55% of all Critically Endangered species highly impacted. Should hydroelectric expansion in the region go ahead as planned, 74% of all threatened freshwater fish species will be negatively impacted, with 65% set to decline due to small projects alone. At least seven of these could become globally extinct in the wild as a result. Hydropower projects, particularly small schemes, are therefore the most important driver of potential fish species extinctions in the Mediterranean Basin Biodiversity Hotspot. Impoundments created by dams and other hydroelectric infrastructure are also the key pathway by which non-native fish species, another major cause of freshwater fish declines, enter fluvial ecosystems. Moreover, if the hydroelectric schemes planned in the Mediterranean Basin Biodiversity Hotspot are implemented, nations will be unable to comply with the United Nations 2030 Agenda for Sustainable Development or binding international biodiversity targets agreed by parties to the Convention on Biological Diversity and European Union member states. There is an urgent need to mitigate the escalating ecological damage triggered by the hydropower binge through preservation and restoration of free-flowing rivers. Rapid and significant action underpinned by sound scientific evidence is required to safeguard freshwater ecosystems and the incredibly rich biodiversity they support throughout the region. By improving the state of the natural environment, the impacts of ongoing climate change would also be reduced. It is hoped that this report will help inform nature conservation, governments and policy-makers to make the right political, financial and consumer choices to reverse the trend of freshwater biodiversity decline throughout the Mediterranean Basin Biodiversity Hotspot.
36. Using noninvasive metagenomics to characterize viral communities from wildlife.
- Author
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Bergner LM, Orton RJ, da Silva Filipe A, Shaw AE, Becker DJ, Tello C, Biek R, and Streicker DG
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- Animals, Biodiversity, Feces virology, Oropharynx virology, Peru, Virus Diseases virology, Chiroptera virology, Metagenomics methods, Sequence Analysis, DNA methods, Specimen Handling methods, Virus Diseases veterinary, Viruses classification, Viruses genetics
- Abstract
Microbial communities play an important role in organismal and ecosystem health. While high-throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here, we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from noninvasively collected faecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low-input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNase treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time., (2018 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.)
- Published
- 2019
- Full Text
- View/download PDF
37. Efficacy and Biomarker Study of Bevacizumab for Hearing Loss Resulting From Neurofibromatosis Type 2-Associated Vestibular Schwannomas.
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Blakeley JO, Ye X, Duda DG, Halpin CF, Bergner AL, Muzikansky A, Merker VL, Gerstner ER, Fayad LM, Ahlawat S, Jacobs MA, Jain RK, Zalewski C, Dombi E, Widemann BC, and Plotkin SR
- Subjects
- Adolescent, Adult, Aged, Angiogenesis Inhibitors administration & dosage, Drug Administration Schedule, Female, Hearing Loss etiology, Humans, Male, Middle Aged, Neurofibromatosis 2 physiopathology, Neuroma, Acoustic physiopathology, Young Adult, Bevacizumab administration & dosage, Biomarkers, Tumor metabolism, Hearing Loss drug therapy, Hearing Loss metabolism, Neurofibromatosis 2 drug therapy, Neurofibromatosis 2 metabolism, Neuroma, Acoustic drug therapy, Neuroma, Acoustic metabolism
- Abstract
Purpose: Neurofibromatosis type 2 (NF2) is a tumor predisposition syndrome characterized by bilateral vestibular schwannomas (VSs) resulting in deafness and brainstem compression. This study evaluated efficacy and biomarkers of bevacizumab activity for NF2-associated progressive and symptomatic VSs., Patients and Methods: Bevacizumab 7.5 mg/kg was administered every 3 weeks for 46 weeks, followed by 24 weeks of surveillance after treatment with the drug. The primary end point was hearing response defined by word recognition score (WRS). Secondary end points included toxicity, tolerability, imaging response using volumetric magnetic resonance imaging analysis, durability of response, and imaging and blood biomarkers., Results: Fourteen patients (estimated to yield > 90% power to detect an alternative response rate of 50% at alpha level of 0.05) with NF2, with a median age of 30 years (range, 14 to 79 years) and progressive hearing loss in the target ear (median baseline WRS, 60%; range 13% to 82%), were enrolled. The primary end point, confirmed hearing response (improvement maintained ≥ 3 months), occurred in five (36%) of 14 patients (95% CI, 13% to 65%; P < .001). Eight (57%) of 14 patients had transient hearing improvement above the 95% CI for WRS. No patients experienced hearing decline. Radiographic response was seen in six (43%) of 14 target VSs. Three grade 3 adverse events, hypertension (n = 2) and immune-mediated thrombocytopenic purpura (n = 1), were possibly related to bevacizumab. Bevacizumab treatment was associated with decreased free vascular endothelial growth factor (not bound to bevacizumab) and increased placental growth factor in plasma. Hearing responses were inversely associated with baseline plasma hepatocyte growth factor (P = .019). Imaging responses were associated with high baseline tumor vessel permeability and elevated blood levels of vascular endothelial growth factor D and stromal cell-derived factor 1α (P = .037 and .025, respectively)., Conclusion: Bevacizumab treatment resulted in durable hearing response in 36% of patients with NF2 and confirmed progressive VS-associated hearing loss. Imaging and plasma biomarkers showed promising associations with response that should be validated in larger studies., (© 2016 by American Society of Clinical Oncology.)
- Published
- 2016
- Full Text
- View/download PDF
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