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Sharkipedia: Elasmobranch Traits and Trends Global Database

Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2020-10-20
Abstract: 

Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone. Originally inspired by FishBase, our databases are modelled after Coral Traits database and the RAM legacy database. The key aspects of our initiative were established with the central tenet of facilitating research on chondrichthyans, and are built on three main principles: (1) being completely web-based open- access and queryable for use by all researchers, (2) quality control and assurance by experts in the field and traceability of every measurement to its original references, and (3) regular updates association with International Union for the Conservation of Nature (IUCN) Red List Assessment workshops of focal species.

Document type: 
Preprint
File(s): 

Resource Pulses Increase the Diversity of Successful Competitors in a Multi-Species Stream Fish Assemblage

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2020-09-18
Abstract: 

Food resources are often patchily distributed through space and time and are classified as resource pulses when hyperabundant. Resource pulses can benefit growth, reproduction, and abundance of various consumers. Yet, it is relatively unknown how such resources are partitioned among competing consumers and how this is influenced by the magnitude of the pulse. Here, we examined how the magnitude of a pulsed resource influences resource partitioning among diverse sizes and species of consumers in a natural setting over small spatial and temporal scales. We focused on salmon egg subsidies to stream fish consumers. We experimentally added different quantities of pink salmon eggs to five meter long experimental stream sections. Egg additions spanned three orders of magnitude from 6 to 3575 eggs. Stream fish (egg consumers) were captured and gastric lavaged at each experimental section to determine how many eggs each individual fish consumed. We modeled taxon‐specific individual egg consumption as a function of egg availability, individual mass, community composition, number of competitors, and stream velocity using hurdle models in a Bayesian framework. We found that there were diminishing returns for increasing egg abundance increasing egg consumption (i.e., type II functional response) for individual size classes of fish, but that higher egg numbers were needed to benefit diverse consumers. Top models indicated that egg availability and individual fish characteristics (size and taxon) drove egg consumption, while community characteristics (species composition and number of competitors) were not supported. Our results suggest that resource pulses can provide rare opportunities for less dominant sizes and species of fish to consume abundant resources. The current paradigm in the stream fish literature suggests that stream fish communities are structured by dominance hierarchies; however, dominance hierarchies may be less influential where pulsed resources comprise a large portion of the resource base.

Document type: 
Article
File(s): 

Identification of Three Monofunctional Diterpene Synthases with Specific Enzyme Activities Expressed during Heartwood Formation in Western Redcedar (Thuja plicata) Trees

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2020-08-12
Abstract: 

Upon harvest, Western redcedar (WRC; Thuja plicata) trees have a high incidence and extent of heartwood rot. While monoterpenoids and lignans have been linked to rot resistance in this species, other specialized metabolites, such as diterpenes, are likely to contribute to rot resistance. Here we report the cloning and functional assessment of three putative diterpene synthase (TpdiTPS) genes expressed during heartwood formation in WRC. The predicted proteins of the three genes lack either of the two catalytically independent active sites typical of most diTPS, indicating monofunctional rather than bifunctional activity. To identify potential catalytic activities of these proteins, we expressed them in genetically engineered Escherichia coli strains that produce four potential substrates, geranylgeranyl diphosphate (GGDP), ent, syn, and normal stereoisomers of copalyl diphosphate (CDP). We found that TpdiTPS3 used GGDP to produce CDP. TpdiTPS2 used normal CDP to produce levopimaradiene. TpdiTPS1 showed stereoselectivity as it used normal CDP to produce sandaracopimaradiene and syn-CDP to produce syn-stemod-13(17)-ene. These genes and protein enzymatic activities have not been previously reported in WRC and provide an opportunity to assess their potential roles in heartwood rot resistance in this economically important species.

Document type: 
Article
File(s): 

Change in Sediment Features and the Macroinvertebrate Community Within an Estuarine Ecosystem Two Years Post‐restoration

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2020-07-30
Abstract: 

Our objective was to assess the response of an estuarine ecosystem to restoration efforts, two years post‐restoration. Sediment attributes of particle size distribution (PSD), %LOI, water content and amounts of fine wood debris (FWD), and the macroinvertebrate community were compared among three sites, two reference and the recently restored site. The restored region had been previously used as a log sorting facility. As indicated by PSD, the restored site showed signs of recovery. However, the macroinvertebrate community had still not responded to restoration efforts. Sediments of reference sites were comprised of fine sand, and the macroinvertebrate community was dominated by Macoma spp. By contrast, at the restored site, sediments were mainly comprised of silt followed by fine sand, Macoma spp. was absent, and the main macroinvertebrate was Glycera americana, a polychaeta characteristic of disturbed regions. The restored site still contained significance amounts of FWD as compared to the two reference sites attributed to its previous use. Although still early in its recovery stage, active restoration did have a positive effect and will have likely kick started the region toward recovery and further follow‐up in five years is recommended.

Document type: 
Article
File(s): 

Run‐Of‐River Dams as a Barrier to the Movement of a Stream‐Dwelling Amphibian

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2020-08-06
Abstract: 

Human activities frequently create structures that alter the connectivity among habitats or act as barriers to the natural movement of animals. Movement allows individuals to access different habitats, connect life history stages, and maintain genetic diversity. Here, we evaluated whether run‐of‐river (RoR) hydropower projects, an emerging renewable energy source in British Columbia, interrupt the longitudinal connectivity among larval stream amphibians, by altering larval rearing densities, with possible repercussions on growth and survival. In three watersheds, we tested for differences in the average upstream and downstream density of larval coastal tailed frog (Ascaphus truei), as well as changes to their longitudinal distribution upstream of the dams, as would be expected if RoR dams or their headponds act as barriers to the natural downstream drift of larvae. We found a 60% decrease in larval densities downstream compared to upstream of dams, consistent with RoR dams interrupting the natural pattern of downstream A. truei drift. Larval densities in the first 10 m above RoR headponds were 3 times higher compared to 100 m upstream, and when expressed in terms of relative abundance, we find a similar pattern, with between 2.5 and 3 times more larvae in the first 10 m above of the headpond than expected if larvae followed a uniform distribution. Our results are consistent with the hypothesis that RoR dams alter the spatial connectivity of A. truei larvae, leading to an accumulation of larvae directly above the dam, with unknown consequences for larval growth and survival. Our findings suggest caution is warranted when interpreting before–after monitoring studies that are often used to evaluate the impact of dams, whereby we find that reductions in downstream densities could be due to interruptions of downstream movement as opposed to direct mortality.

Document type: 
Article
File(s): 

Hermaphroditism in Marijuana (Cannabis sativa L.) Inflorescences – Impact on Floral Morphology, Seed Formation, Progeny Sex Ratios, and Genetic Variation

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2020-06-25
Abstract: 

Cannabis sativa L. (hemp, marijuana) produces male and female inflorescences on different plants (dioecious) and therefore the plants are obligatory out-crossers. In commercial production, marijuana plants are all genetically female; male plants are destroyed as seed formation reduces flower quality. Spontaneously occurring hermaphroditic inflorescences, in which pistillate flowers are accompanied by formation of anthers, leads to undesired seed formation; the mechanism for this is poorly understood. We studied hermaphroditism in several marijuana strains with three objectives: (i) to compare the morphological features of this unique phenotype with normal male flowers; (ii) to assess pollen and seed viability from hermaphroditic flowers; and (iii) to assess the effect of hermaphroditism on progeny male:female (sex) ratios and on genetic variation using molecular methods. The morphological features of anthers, pollen production and germination in hermaphroditic flowers and in staminate inflorescences on male plants were compared using light and scanning electron microscopy. Seeds produced on hermaphroditic plants and seeds derived from cross-fertilization were germinated and seedlings were compared for gender ratios using a PCR-based assay as well as for the extent of genetic variation using six ISSR primers. Nei’s index of gene diversity and Shannon’s Information index were compared for these two populations. The morphology of anthers and pollen formation in hermaphroditic inflorescences was similar to that in staminate flowers. Seedlings from hermaphroditic seeds, and anther tissues, showed a female genetic composition while seedlings derived from cross-fertilized seeds showed a 1:1 male:female sex expression ratio. Uniquely, hermaphroditic inflorescences produced seeds which gave rise only to genetically female plants. In PCR assays, a 540 bp size fragment was present in male and female plants, while a 390 bp band was uniquely associated with male plants. Sequence analysis of these fragments revealed the presence of Copia-like retrotransposons within the C. sativa genome which may be associated with the expression of male or female phenotype. In ISSR analysis, the percentage of polymorphic loci ranged from 44 to 72% in hermaphroditic and cross-fertilized populations. Nei’s index of gene diversity and Shannon’s Information index were not statistically different for both populations. The extent of genetic variation after one generation of selfing in the progeny from hermaphroditic seed is similar to that in progeny from cross-fertilized seeds.

Document type: 
Article
File(s): 

Quantifying Biodiversity Trade-Offs In The Face Of Widespread Renewable and Unconventional Energy Development

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2020-05-05
Abstract: 

The challenge of balancing biodiversity protection with economic growth is epitomized by the development of renewable and unconventional energy, whose adoption is aimed at stemming the impacts of global climate change, yet has outpaced our understanding of biodiversity impacts. We evaluated the potential conflict between biodiversity protection and future electricity generation from renewable (wind farms, run-of-river hydro) and non-renewable (shale gas) sources in British Columbia (BC), Canada using three metrics: greenhouse gas (GHG) emissions, electricity cost, and overlap between future development and conservation priorities for several fish and wildlife groups - small-bodied vertebrates, large mammals, freshwater fish – and undisturbed landscapes. Sharp trade-offs in global versus regional biodiversity conservation exist for all energy technologies, and in BC they are currently smallest for wind energy: low GHG emissions, low-moderate overlap with top conservation priorities, and competitive energy cost. GHG emissions from shale gas are 1000 times higher than those from renewable sources, and run-of-river hydro has high overlap with conservation priorities for small-bodied vertebrates. When all species groups were considered simultaneously, run-of-river hydro had moderate overlap (0.56), while shale gas and onshore wind had low overlap with top conservation priorities (0.23 and 0.24, respectively). The unintended cost of distributed energy sources for regional biodiversity suggest that trade-offs based on more diverse metrics must be incorporated into energy planning.

Document type: 
Article
File(s): 

Use of Sediment Dwelling Bivalves to Biomonitor Plastic Particle Pollution in Intertidal Regions; A Review And Study

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2020-05-22
Abstract: 

We explore the possibility of using the varnish (Nutallia obscurata) and Manila (Venerupis philippinarum) clams as biomonitors of microplastics (MPs) pollution. A short review is first provided on the use of bivalves for biomonitoring MPs in aquatic ecosystems. From the conclusions drawn from our review we determine if the sediment dwelling varnish and Manila clam could possibly be good choices for this purpose. We sampled 8 intertidal sites located within two distinct regions of coastal British Columbia, Burrard Inlet (5 sites) and Baynes Sound (3 sites). Each intertidal region had its own particular use; within Burrard Inlet, BMP a heavily used marine park, CP, EB, J, and AP, popular local beaches, and within Baynes Sound, Met and NHB, two intertidal regions heavily exploited by the shellfish industry and RU an intertidal region with limited aquaculture activity. Microfragments were recovered from bivalves collected from all intertidal regions except for AP. Microspheres were recovered primarily from bivalves sampled from Baynes Sound at NHB where high numbers of spheres within sediments had previously been reported. BMP and Met had the highest number of particles present within individual clams which were predominantly high density polyethylene (HDPE) and a polypropylene composite (PPC). Both polymers are extensively used by the shellfish industry in all gear types, as well as in industrial and recreational marine activities. The spatial distribution of recovered MPs was indicative of the anthropogenic use of the intertidal region suggesting these bivalves, for microfragments and microspheres, may be suitable as biomonitors and could prove to be useful tools for determining whether reduction policies for plastics use are having a positive effect on their release into marine environments.

Document type: 
Article
File(s): 

Cyclophilin A Controls Salmonella Internalization Levels and is Present at E. coli Actin‐Rich Pedestals

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2018-10-12
Abstract: 

Salmonella enterica serovar Typhimurium (S. Typhimurium), enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) commandeer the actin cytoskeleton of their host cells as a crucial step in their infectious processes. These pathogens depend on the injection of their own effectors directly into target host cells in order to usurp cellular signaling pathways that lead to morphological actin rearrangements in those cells. Here we show that the PPIase Cyclophilin A (CypA) is a novel component of S. Typhimurium-induced membrane ruffles and functions to restrict bacterial invasion levels, as in cells depleted of CypA, bacterial loads increase. We also demonstrate that CypA requires the EPEC effector Tir as well as pedestal formation for its recruitment to bacterial attachment sites and that its presence at pedestals also holds during EHEC infections. Finally, we demonstrate that CypA is found at lamellipodia; actin-rich structures at the leading edge of motile cells. Our findings further establish CypA as a component of dynamic actin-rich structures formed during bacterial infections and within cells in general.

Document type: 
Article
File(s): 

Listeria Monocytogenes Hijacks CD147 to Ensure Proper Membrane Protrusion Formation and Efficient Bacterial Dissemination

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2019-05-10
Abstract: 

Efficient cell-to-cell transfer of Listeria monocytogenes (L. monocytogenes) requires the proper formation of actin-rich membrane protrusions. To date, only the host proteins ezrin, the binding partner of ezrin, CD44, as well as cyclophilin A (CypA) have been identified as crucial components for L. monocytogenes membrane protrusion stabilization and, thus, efficient cell-to-cell movement of the microbes. Here, we examine the classical binding partner of CypA, CD147, and find that this membrane protein is also hijacked by the bacteria for their cellular dissemination. CD147 is enriched at the plasma membrane surrounding the membrane protrusions as well as the resulting invaginations generated in neighboring cells. In cells depleted of CD147, these actin-rich structures appear similar to those generated in CypA depleted cells as they are significantly shorter and more contorted as compared to their straighter counterparts formed in wild-type control cells. The presence of malformed membrane protrusions hampers the ability of L. monocytogenes to efficiently disseminate from CD147-depleted cells. Our findings uncover another important host protein needed for L. monocytogenes membrane protrusion formation and efficient microbial dissemination.

Document type: 
Article
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