47 research outputs found
Science Communication Portfolio
Document describes the theory and practice of verbal and written science communication strategies, and provides an example portfolio on the topic of sea level rise.Are you working on a research manuscript, grant, annual report, or project summary that requires technical language? Do you feel that your finding, if communicated properly, could be useful to people beyond your professional network? This communication-training document for scientists is designed to help you do just that – on your own time and for a variety of verbal and written communication styles. We also provide an example portfolio on the topic of sea level rise for reference.Center for Microbial Oceanography: Research and Education (NSF #0424599, Wood-Charlson); Union of Concerned Scientists (Varga
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Initiation of coral/algal symbioses : the role of cell surface lectin/glycan interactions in recognition and specificity
Mutualistic associations between cnidarians, such as corals, and photosynthetic
dinoflagellate algae provide the trophic and structural foundation of coral reef
ecosystems. In many cases, this intracellular mutualism is highly specific and must be
established anew for each generation of host corals. The ability to maintain partner
specificity across generations implies that cellular mechanisms play a role in interpartner
recognition. In other mutualisms where these recognition mechanisms have
been studied, lectin/glycan interactions have been shown to function in inter-partner
recognition during the onset of a stable symbiosis. However, for the majority of
symbioses, including the cnidarian/dinoflagellate mutualism, cellular recognition
mechanisms that mediate the onset of symbiosis remain largely unknown. How do
larval corals and their symbiotic algae discriminate between their preferred partner and
other hosts or microbes during the onset of symbiosis? I hypothesized that cell surface
lectin/glycan interactions act as one mechanism of recognition and specificity during
initial contact between the partners.
Chapter one reviews the biology of cnidarian/algal symbioses and discusses the
literature to date concerning molecular mechanisms of recognition and specificity
during the onset of cnidarian/algal symbioses and how the cnidarian/algal system
compares with other horizontally-transmitted mutualisms. Chapter two and three explore the role of algal cell surface glycans during the onset of
symbiosis between the Hawai'ian solitary coral Fungia scutaria and its dinoflagellate
symbiont, Symbiodinium clade C1f. To determine whether lectin/glycan interactions
function during infection, I modified the glycans on the cell surface of algal symbionts
(C1f and C31, found in nature in adult F. scutaria and Montipora capitata,
respectively), introduced the modified symbionts to F. scutaria larvae, and then
looked for changes in infection success. After cell surface modification, infection rates
of native C1f algae decreased. In contrast, cell surface modification of non-native C31
algae resulted in higher infection rates compared to unmodified, control C31 algae.
These data suggest that the algal cell surface signals to the host F. scutaria larvae
identifying it as either a native C1f symbiont or non-native C31 algae.
These chapters also investigate the variability of glycans present on the cell surface of
several closely-related clade C symbionts to determine if each algal subclade contains
a unique cell surface glycan profile. I found that cell surface glycan profiles were
different for each symbiont tested, supporting their classification into different
subclades. I hypothesize that this subclade specific glycan profile creates the cell
surface signal that identifies the symbiont to its host coral.
Chapter four describes the complex array of C-type lectins, a type of glycan receptor,
in the anemone Nematostella vectensis genome. The diversity of glycan profiles on
symbiont cell surfaces and C-type lectins in cnidarians suggests that these interactions
could relay a signal for recognition and specificity between symbiotic partners.
Chapter five concludes with a brief discussion that places my results in the context of
cnidarian innate immunity and parallels between the onset of mutualistic symbioses
and the process of infection in parasitic relationships. I close by suggesting future
experiments that continue to explore the role of cell surface lectin/glycan interaction in
recognition and specificity during the onset of cnidarian/algal symbioses
CRISPR-Cas defense system and potential prophages in cyanobacteria associated with the coral black band disease
Understanding how pathogens maintain their virulence is critical to developing tools to mitigate disease in animal populations. We sequenced and assembled the first draft genome of Roseofilum reptotaenium AO1, the dominant cyanobacterium underlying pathogenicity of the virulent coral black band disease (BBD), and analyzed parts of the BBD-associated Geitlerinema sp. BBD_1991 genome in silico. Both cyanobacteria are equipped with an adaptive, heritable clustered regularly interspaced short palindromic repeats (CRISPR)-Cas defense system type I-D and have potential virulence genes located within several prophage regions. The defense system helps to prevent infection by viruses and mobile genetic elements via identification of short fingerprints of the intruding DNA, which are stored as templates in the bacterial genome, in so-called CRISPRs. Analysis of CRISPR target sequences (protospacers) revealed an unusually high number of self-targeting spacers in R. reptotaenium AO1 and extraordinary long CRIPSR arrays of up to 260 spacers in Geitlerinema sp. BBD_1991. The self-targeting spacers are unlikely to be a form of autoimmunity; instead these target an incomplete lysogenic bacteriophage. Lysogenic virus induction experiments with mitomycin C and UV light did not reveal an actively replicating virus population in R. reptotaenium AO1 cultures, suggesting that phage functionality is compromised or excision could be blocked by the CRISPR-Cas system. Potential prophages were identified in three regions of R. reptotaenium AO1 and five regions of Geitlerinema sp. BBD_1991, containing putative BBD relevant virulence genes, such as an NAD-dependent epimerase/dehydratase (a homolog in terms of functionality to the third and fourth most expressed gene in BBD), lysozyme/metalloendopeptidases and other lipopolysaccharide modification genes. To date, viruses have not been considered to be a component of the BBD consortium or a contributor to the virulence of R. reptotaenium AO1 and Geitlerinema sp. BBD_(1)991. We suggest that the presence of virulence genes in potential prophage regions, and the CRISPR-Cas defense systems are evidence of an arms race between the respective cyanobacteria and their bacteriophage predators. The presence of such a defense system likely reduces the number of successful bacteriophage infections and mortality in the cyanobacteria, facilitating the progress of BBD
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kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase
Microbial genome annotation is the process of identifying structural and functional elements in DNA sequences and subsequently attaching biological information to those elements. DRAM is a tool developed to annotate bacterial, archaeal, and viral genomes derived from pure cultures or metagenomes. DRAM goes beyond traditional annotation tools by distilling multiple gene annotations to genome level summaries of functional potential. Despite these benefits, a downside of DRAM is the requirement of large computational resources, which limits its accessibility. Further, it did not integrate with downstream metabolic modeling tools that require genome annotation. To alleviate these constraints, DRAM and the viral counterpart, DRAM-v, are now available and integrated with the freely accessible KBase cyberinfrastructure. With kb_DRAM users can generate DRAM annotations and functional summaries from microbial or viral genomes in a point-and-click interface, as well as generate genome-scale metabolic models from DRAM annotations.Availability and implementationFor kb_DRAM users, the kb_DRAM apps on KBase can be found in the catalog at https://narrative.kbase.us/#catalog/modules/kb_DRAM. For kb_DRAM users, a tutorial workflow with all documentation is available at https://narrative.kbase.us/narrative/129480. For kb_DRAM developers, software is available at https://github.com/shafferm/kb_DRAM
The Importance of Sharing Data in Systems Biology
Systems biology research spans a range of biological scales and science domains, and often requires a collaborative effort to collect and share data so that integration is possible. However, sharing data effectively is a challenging task that requires effort and alignment between collaborative partners, as well as coordination between organizations, repositories, and journals. As a community of systems biology researchers, we must get better at efficiently sharing data, and ensuring that shared data comes with the recognition and citations it deserves
Sharing Science thru Storytelling (2017 Aquatic Sciences)
Slides from a science communication workshop presented at 2017 Aquatic Sciences meeting in Honolulu, Hawai'i (1 March 2017). <br
Implication of the host TGF beta pathway in the onset of symbiosis between larvae of the coral Fungia scutaria and the dinoflagellate Symbiodinium sp (clade C1f)
Dinoflagellate-cnidarian associations form both the trophic and structural foundation of coral-reef ecosystems. Previous studies have highlighted the role of host innate immunity in regulation of these partnerships. This study reveals the presence of a transforming growth factor beta (TGF beta) in the coral Fungia scutaria that clusters with TGF beta sensu stricto (ss) from other animals. In functional studies of F. scutaria larvae, we show that (1) TGF beta ss mRNA is expressed during early stages of development prior to the onset of symbiosis; (2) apparent interference of the TGF beta pathway impairs the onset of symbiosis; and (3) this effect is associated with an increase of cytotoxic nitric oxide secretion, an immune response. This work highlights the importance of the TGF beta pathway in early life-history stages of corals by suggesting that its inhibition impacts the onset of symbiosis
CRISPR-Cas defense system and potential prophages in cyanobacteria associated with the coral black band disease
Understanding how pathogens maintain their virulence is critical to developing tools to mitigate disease in animal populations. We sequenced and assembled the first draft genome of Roseofilum reptotaenium AO1, the dominant cyanobacterium underlying pathogenicity of the virulent coral black band disease (BBD), and analyzed parts of the BBD-associated Geitlerinema sp. BBD_1991 genome in silico. Both cyanobacteria are equipped with an adaptive, heritable clustered regularly interspaced short palindromic repeats (CRISPR)-Cas defense system type I-D and have potential virulence genes located within several prophage regions. The defense system helps to prevent infection by viruses and mobile genetic elements via identification of short fingerprints of the intruding DNA, which are stored as templates in the bacterial genome, in so-called CRISPRs. Analysis of CRISPR target sequences (protospacers) revealed an unusually high number of self-targeting spacers in R. reptotaenium AO1 and extraordinary long CRIPSR arrays of up to 260 spacers in Geitlerinema sp. BBD_1991. The self-targeting spacers are unlikely to be a form of autoimmunity; instead these target an incomplete lysogenic bacteriophage. Lysogenic virus induction experiments with mitomycin C and UV light did not reveal an actively replicating virus population in R. reptotaenium AO1 cultures, suggesting that phage functionality is compromised or excision could be blocked by the CRISPR-Cas system. Potential prophages were identified in three regions of R. reptotaenium AO1 and five regions of Geitlerinema sp. BBD_1991, containing putative BBD relevant virulence genes, such as an NAD-dependent epimerase/dehydratase (a homolog in terms of functionality to the third and fourth most expressed gene in BBD), lysozyme/metalloendopeptidases and other lipopolysaccharide modification genes. To date, viruses have not been considered to be a component of the BBD consortium or a contributor to the virulence of R. reptotaenium AO1 and Geitlerinema sp. BBD_(1)991. We suggest that the presence of virulence genes in potential prophage regions, and the CRISPR-Cas defense systems are evidence of an arms race between the respective cyanobacteria and their bacteriophage predators. The presence of such a defense system likely reduces the number of successful bacteriophage infections and mortality in the cyanobacteria, facilitating the progress of BBD