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Article ; Online: Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta.

Matriano, Danielle M / Alegado, Rosanna A / Conaco, Cecilia

2021 Volume 11, Issue 1, Page(s) 5993

Abstract: Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible ... ...

Abstract	Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome-evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.
MeSH term(s)	Choanoflagellata/classification ; Choanoflagellata/genetics ; Computational Biology/methods ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Genomics/methods ; Molecular Sequence Annotation ; Phylogeny
Language	English
Publishing date	2021-03-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-85259-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta

Danielle M. Matriano / Rosanna A. Alegado / Cecilia Conaco

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 11

Abstract: Abstract Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its ... ...

Abstract	Abstract Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome—evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Spheres of Hope, Packets of Doom: the Good and Bad of Outer Membrane Vesicles in Interspecies and Ecological Dynamics.

Lynch, Jonathan B / Alegado, Rosanna A

Journal of bacteriology

2017 Volume 199, Issue 15

Abstract: Outer membrane vesicles (OMVs) are proteoliposome nanoparticles ubiquitously produced by Gram-negative bacteria. Typically bearing a composition similar to those of the outer membrane and periplasm of the cells from which they are derived, OMVs package ... ...

Abstract	Outer membrane vesicles (OMVs) are proteoliposome nanoparticles ubiquitously produced by Gram-negative bacteria. Typically bearing a composition similar to those of the outer membrane and periplasm of the cells from which they are derived, OMVs package an array of proteins, lipids, and nucleic acids. Once considered inconsequential by-products of bacterial growth, OMVs have since been demonstrated to mediate cellular stress relief, promote horizontal gene transfer and antimicrobial activity, and elicit metazoan inflammation. Recently, OMVs have gained appreciation as critical moderators of interorganismal dynamics. In this review, we focus on recent progress toward understanding the functions of OMVs with regard to symbiosis and ecological contexts, and we propose potential avenues for future OMV studies.
MeSH term(s)	Animals ; Bacterial Proteins/metabolism ; Gram-Negative Bacteria/physiology ; Host-Pathogen Interactions ; Lipid Metabolism ; Nucleic Acids/metabolism ; Secretory Vesicles/metabolism ; Symbiosis
Chemical Substances	Bacterial Proteins ; Nucleic Acids
Language	English
Publishing date	2017-08-01
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00012-17
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Article ; Online: Systemic racial disparities in funding rates at the National Science Foundation.

Chen, Christine Yifeng / Kahanamoku, Sara S / Tripati, Aradhna / Alegado, Rosanna A / Morris, Vernon R / Andrade, Karen / Hosbey, Justin

eLife

2022 Volume 11

Abstract: Concerns about systemic racism at academic and research institutions have increased over the past decade. Here, we investigate data from the National Science Foundation (NSF), a major funder of research in the United States, and find evidence for ... ...

Abstract	Concerns about systemic racism at academic and research institutions have increased over the past decade. Here, we investigate data from the National Science Foundation (NSF), a major funder of research in the United States, and find evidence for pervasive racial disparities. In particular, white principal investigators (PIs) are consistently funded at higher rates than most non-white PIs. Funding rates for white PIs have also been increasing relative to annual overall rates with time. Moreover, disparities occur across all disciplinary directorates within the NSF and are greater for research proposals. The distributions of average external review scores also exhibit systematic offsets based on PI race. Similar patterns have been described in other research funding bodies, suggesting that racial disparities are widespread. The prevalence and persistence of these racial disparities in funding have cascading impacts that perpetuate a cumulative advantage to white PIs across all of science, technology, engineering, and mathematics.
MeSH term(s)	Engineering ; Immunotherapy ; Systemic Racism
Language	English
Publishing date	2022-11-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.83071
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Article ; Online: Bacterial lipopolysaccharide induces settlement and metamorphosis in a marine larva.

Freckelton, Marnie L / Nedved, Brian T / Cai, You-Sheng / Cao, Shugeng / Turano, Helen / Alegado, Rosanna A / Hadfield, Michael G

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 119, Issue 18, Page(s) e2200795119

Abstract: How larvae of the many phyla of marine invertebrates find places appropriate for settlement, metamorphosis, growth, and reproduction is an enduring question in marine science. Biofilm-induced metamorphosis has been observed in marine invertebrate larvae ... ...

Abstract	How larvae of the many phyla of marine invertebrates find places appropriate for settlement, metamorphosis, growth, and reproduction is an enduring question in marine science. Biofilm-induced metamorphosis has been observed in marine invertebrate larvae from nearly every major marine phylum. Despite the widespread nature of this phenomenon, the mechanism of induction remains poorly understood. The serpulid polychaete Hydroides elegans is a well established model for investigating bacteria-induced larval development. A broad range of biofilm bacterial species elicit larval metamorphosis in H. elegans via at least two mechanisms, including outer membrane vesicles (OMVs) and complexes of phage-tail bacteriocins. We investigated the interaction between larvae of H. elegans and the inductive bacterium Cellulophaga lytica, which produces an abundance of OMVs but not phage-tail bacteriocins. We asked whether the OMVs of C. lytica induce larval settlement due to cell membrane components or through delivery of specific cargo. Employing a biochemical structure–function approach with a strong ecological focus, the cells and OMVs produced by C. lytica were interrogated to determine the class of the inductive compounds. Here, we report that larvae of H. elegans are induced to metamorphose by lipopolysaccharide produced by C. lytica. The widespread prevalence of lipopolysaccharide and its associated taxonomic and structural variability suggest it may be a broadly employed cue for bacterially induced larval settlement of marine invertebrates.
MeSH term(s)	Animals ; Bacteria ; Biofilms ; Invertebrates/physiology ; Larva/physiology ; Lipopolysaccharides/pharmacology ; Metamorphosis, Biological/physiology
Chemical Substances	Lipopolysaccharides
Language	English
Publishing date	2022-04-25
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2200795119
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Article ; Online: A relational framework for microbiome research with Indigenous communities.

Bader, Alyssa C / Van Zuylen, Essie M / Handsley-Davis, Matilda / Alegado, Rosanna A / Benezra, Amber / Pollet, Rebecca M / Ehau-Taumaunu, Hanareia / Weyrich, Laura S / Anderson, Matthew Z

Nature microbiology

2023 Volume 8, Issue 10, Page(s) 1768–1776

Abstract: Ethical practices in human microbiome research have failed to keep pace with scientific advances in the field. Researchers seeking to 'preserve' microbial species associated with Indigenous groups, but absent from industrialized populations, have largely ...

Abstract	Ethical practices in human microbiome research have failed to keep pace with scientific advances in the field. Researchers seeking to 'preserve' microbial species associated with Indigenous groups, but absent from industrialized populations, have largely failed to include Indigenous people in knowledge co-production or benefit, perpetuating a legacy of intellectual and material extraction. We propose a framework centred on relationality among Indigenous peoples, researchers and microbes, to guide ethical microbiome research. Our framework centres accountability to flatten historical power imbalances that favour researcher perspectives and interests to provide space for Indigenous worldviews in pursuit of Indigenous research sovereignty. Ethical inclusion of Indigenous communities in microbiome research can provide health benefits for all populations and reinforce mutually beneficial partnerships between researchers and the public.
MeSH term(s)	Humans ; Population Groups ; Microbiota
Language	English
Publishing date	2023-09-28
Publishing country	England
Document type	Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-023-01471-2
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Article ; Online: Bacterial influences on animal origins.

Alegado, Rosanna A / King, Nicole

Cold Spring Harbor perspectives in biology

2014 Volume 6, Issue 11, Page(s) a016162

Abstract: Animals evolved in seas teeming with bacteria, yet the influences of bacteria on animal origins are poorly understood. Comparisons among modern animals and their closest living relatives, the choanoflagellates, suggest that the first animals used ... ...

Abstract	Animals evolved in seas teeming with bacteria, yet the influences of bacteria on animal origins are poorly understood. Comparisons among modern animals and their closest living relatives, the choanoflagellates, suggest that the first animals used flagellated collar cells to capture bacterial prey. The cell biology of prey capture, such as cell adhesion between predator and prey, involves mechanisms that may have been co-opted to mediate intercellular interactions during the evolution of animal multicellularity. Moreover, a history of bacterivory may have influenced the evolution of animal genomes by driving the evolution of genetic pathways for immunity and facilitating lateral gene transfer. Understanding the interactions between bacteria and the progenitors of animals may help to explain the myriad ways in which bacteria shape the biology of modern animals, including ourselves.
MeSH term(s)	Animals ; Bacteria/genetics ; Bacteria/metabolism ; Biological Evolution ; Cell Adhesion ; Choanoflagellata/genetics ; Choanoflagellata/physiology ; Eukaryota/genetics ; Eukaryota/physiology ; Phagocytosis ; Phylogeny ; Signal Transduction
Language	English
Publishing date	2014-10-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ISSN	1943-0264
ISSN (online)	1943-0264
DOI	10.1101/cshperspect.a016162
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Systemic racial disparities in funding rates at the National Science Foundation

Christine Yifeng Chen / Sara S Kahanamoku / Aradhna Tripati / Rosanna A Alegado / Vernon R Morris / Karen Andrade / Justin Hosbey

eLife, Vol

2022 Volume 11

Abstract	Concerns about systemic racism at academic and research institutions have increased over the past decade. Here, we investigate data from the National Science Foundation (NSF), a major funder of research in the United States, and find evidence for pervasive racial disparities. In particular, white principal investigators (PIs) are consistently funded at higher rates than most non-white PIs. Funding rates for white PIs have also been increasing relative to annual overall rates with time. Moreover, disparities occur across all disciplinary directorates within the NSF and are greater for research proposals. The distributions of average external review scores also exhibit systematic offsets based on PI race. Similar patterns have been described in other research funding bodies, suggesting that racial disparities are widespread. The prevalence and persistence of these racial disparities in funding have cascading impacts that perpetuate a cumulative advantage to white PIs across all of science, technology, engineering, and mathematics.
Keywords	National Science Foundation ; funding ; racial disparities ; systemic racism ; equity ; diversity ; and inclusion ; meta-research ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	306
Language	English
Publishing date	2022-11-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Response of diatom-associated bacteria to host growth state, nutrient concentrations, and viral host infection in a model system.

Baker, Lydia J / Alegado, Rosanna A / Kemp, Paul F

Environmental microbiology reports

2016 Volume 8, Issue 5, Page(s) 917–927

Abstract: Diatoms are photosynthetic unicellular eukaryotes found ubiquitously in aquatic systems. Frequent physical associations with other microorganisms such as bacteria may influence diatom fitness. The predictability of bacterial-diatom interactions is ... ...

Abstract	Diatoms are photosynthetic unicellular eukaryotes found ubiquitously in aquatic systems. Frequent physical associations with other microorganisms such as bacteria may influence diatom fitness. The predictability of bacterial-diatom interactions is hypothesized to depend on availability of nutrients as well as the physiological state of the host. Biotic and abiotic factors such as nutrient levels, host growth stage and host viral infection were manipulated to determine their effect on the ecological succession of bacterial communities associated with a single cell line of Chaetoceros sp. KBDT20; this was assessed using the relative abundance of bacterial phylotypes based on 16S rDNA sequences. A single bacterial family, Alteromonadaceae, dominated the attached-bacterial community (84.0%), with the most prevalent phylotypes belonging to the Alteromonas and Marinobacter genera. The taxa comprising the other 16% of the attached bacterial assemblage include Alphaproteobacteria, Betaproteobacteria, Bacilli, Deltaproteobacteria, other Gammaproteobacteria and Flavobacteria. Nutrient concentration and host growth stage had a statistically significant effect on the phylogenetic composition of the attached bacteria. It was inferred that interactions between attached bacteria, as well as the inherent stochasticity mediating contact may also contribute to diatom-bacterial associations.
Language	English
Publishing date	2016-09-09
Publishing country	United States
Document type	Journal Article
ISSN	1758-2229
ISSN (online)	1758-2229
DOI	10.1111/1758-2229.12456
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Article: Introduced Mangroves along the Coast of Moloka‘i, Hawai‘i may Represent Novel Habitats for Megafaunal Communities

Nakahara, Bryan A. / Demopoulos, Amanda W. J. / Rii, Yoshimi M. / Alegado, Rosanna A. / Fraiola, Kauaoa M. S. / Smith, Craig R.

Pacific science. 2021 July 1, v. 75, no. 2

2021

Abstract: Mangrove forests are prevalent along tropical/subtropical coastlines and provide valuable ecosystem services including coastline stabilization, storm impact reduction, and enhanced coastal productivity. However, mangroves were absent from the Hawaiian ... ...

Abstract	Mangrove forests are prevalent along tropical/subtropical coastlines and provide valuable ecosystem services including coastline stabilization, storm impact reduction, and enhanced coastal productivity. However, mangroves were absent from the Hawaiian Islands and their introduction to Moloka‘i in 1902 has provided an opportunity to examine their unique influence on coastal landscapes. Previous studies indicate an inability of native detritivores to utilize tannin-rich substrates, yielding poor cycling of mangrove-derived detritus in Hawaiian tidal zones. We hypothesize that in addition to altering detrital inputs, introduced mangroves facilitate the persistence of introduced species in the Hawaiian coastal zone by providing novel habitat for juvenile megafauna. To determine whether mangrove-dominated tidal zones harbor megafaunal assemblages distinct from open sandflats, we sampled in two mangrove (M1 and M2) and two adjacent sandflat (S1 and S2) sites along the southern coast of Moloka‘i, where the most mature mangrove forests occur in Hawai‘i. There were no statistical differences in total abundances between M1 and M2 or S1 and S2; therefore, results from individual deployments were pooled across the sites in order to conduct between-habitat (mangrove vs. sandflat) comparisons. Our mangrove study site had significantly higher abundances of megafauna, including several shrimp and crab species, compared to the sandflat site. The community composition within the mangrove site differed from the sandflat site, including higher abundances of non-native mangrove crabs (Scylla serrata), as well as native fish Bathygobius cocosensis and crustaceans (Thalamita crenata, Palaemon pacificus, P. debilis) than in the sandflat site, indicating that the mangrove site may provide niches for both invasive and native species. In addition, mean body length for several similar species was smaller in the mangrove site than in the sandflat site, suggesting that these mangroves may be providing a habitat for juvenile species. While our study was spatially limited to two mangrove and two adjacent sandflat sites, our results suggest that introduced mangroves in Moloka‘i may support small-bodied, native, and non-native megafauna, influencing coastal Hawaiian trophic dynamics. Our case study provides a baseline for megafaunal fish and invertebrate communities present prior to non-native mangrove removal as well as for monitoring potential community changes following expansion of mangrove habitats due to climate change.
Keywords	Palaemon ; Scylla serrata ; body length ; case studies ; climate change ; coasts ; community structure ; crabs ; detritivores ; detritus ; fauna ; fish ; indigenous species ; introduced species ; juveniles ; shrimp ; storms
Language	English
Dates of publication	2021-0701
Size	p. 205-223.
Publishing place	University of Hawai'i Press
Document type	Article
ZDB-ID	2053522-3
ISSN	1534-6188 ; 0030-8870
ISSN (online)	1534-6188
ISSN	0030-8870
DOI	10.2984/75.2.4
Database	NAL-Catalogue (AGRICOLA)

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