Find research datasets worth reusing

opencc-by-4.0Oct 2024View details →

CTD and biogeochemical data from a phytoplankton bloom in the North Pacific Subtropical Gyre in summer 2022 (PARAGON II expedition)

CTD and biogeochemical data from a phytoplankton bloom in the North Pacific Subtropical Gyre in August 2022 (PARAGON II expedition) aboard the R/V Kilo Moana (KM2209).

opencc-zeroDec 2014View details →

Data from: Genome-wide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus)

Harmful algal blooms (HABs), which can be lethal in marine species and cause illness in humans, are increasing worldwide. In the Gulf of Mexico, HABs of Karenia brevis produce neurotoxic brevetoxins that cause large-scale marine mortality events. The long history of such blooms, combined with the potentially severe effects of exposure, may have produced a strong selective pressure for evolved resistance. Advances in next-generation sequencing, in particular genotyping-by-sequencing, greatly enable the genomic study of such adaptation in natural populations. We used restriction site-associated DNA (RAD) sequencing to investigate brevetoxicosis resistance in common bottlenose dolphins (Tursiops truncatus). To improve our understanding of the epidemiology and aetiology of brevetoxicosis and the potential for evolved resistance in an upper trophic level predator, we sequenced pools of genomic DNA from dolphins sampled from both coastal and estuarine populations in Florida and during multiple HAB-associated mortality events. We sequenced 129 594 RAD loci and analysed 7431 single nucleotide polymorphisms (SNPs). The allele frequencies of many of these polymorphic loci differed significantly between live and dead dolphins. Some loci associated with survival showed patterns suggesting a common genetic-based mechanism of resistance to brevetoxins in bottlenose dolphins along the Gulf coast of Florida, but others suggested regionally specific mechanisms of resistance or reflected differences among HABs. We identified candidate genes that may be the evolutionary target for brevetoxin resistance by searching the dolphin genome for genes adjacent to survival-associated SNPs.

opencc-zeroDec 2014View details →

Data from: Fish sound production in the presence of harmful algal blooms in the eastern Gulf of Mexico

This paper presents the first known research to examine sound production by fishes during harmful algal blooms (HABs). Most fish sound production is species-specific and repetitive, enabling passive acoustic monitoring to identify the distribution and behavior of soniferous species. Autonomous gliders that collect passive acoustic data and environmental data concurrently can be used to establish the oceanographic conditions surrounding sound-producing organisms. Three passive acoustic glider missions were conducted off west-central Florida in October 2011, and September and October 2012. The deployment period for two missions was dictated by the presence of red tide events with the glider path specifically set to encounter toxic Karenia brevis blooms (a.k.a red tides). Oceanographic conditions measured by the glider were significantly correlated to the variation in sounds from six known or suspected species of fish across the three missions with depth consistently being the most significant factor. At the time and space scales of this study, there was no detectable effect of red tide on sound production. Sounds were still recorded within red tide-affected waters from species with overlapping depth ranges. These results suggest that the fishes studied here did not alter their sound production nor migrate out of red tide-affected areas. Although these results are preliminary because of the limited measurements, the data and methods presented here provide a proof of principle and could serve as protocol for future studies on the effects of algal blooms on the behavior of soniferous fishes. To fully capture the effects of episodic events, we suggest that stationary or vertically profiling acoustic recorders and environmental sampling be used as a complement to glider measurements.

opencc-zeroAug 2021View details →

Impact of upwelling on phytoplankton blooms and hypoxia along the Chinese coast in the East China Sea

This study evaluates the rarely observed phenomenon of the simultaneous occurrences of phytoplankton blooms, hypoxia, and upwelling along the Zhejiang coast in the East China Sea. Results show that the upwelling uplifted bottom water to 5–10 m below the surface. In the upwelling region, phytoplankton blooms (Chl a = 10.9 μg L−1) occurred and hypoxia or low-oxygen appeared below the surface water. High concentrations of nitrate and phosphate were regenerated in the hypoxic regions, corresponding with mean values (± SD) of 16.9 (± 1.5) and 0.90 (± 0.14) μM, respectively. The upwelling expanded the region of hypoxic water, which nearly reached the surface, thereby increasing the threat to marine life. In addition to fluvial nutrients, the upwelling of water with high nutrient levels, especially phosphates, can enhance phytoplankton blooms. The results suggest that hypoxia can become more severe due to further decomposition of bloom-derived organic matter after blooms crash.

opencc-zeroSep 2021View details →

Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom

Production and use of proteins is under strong selection in microbes, but it is unclear how proteome-level traits relate to ecological strategies. We identified and quantified proteomic traits of eukaryotic microbes and bacteria through an Antarctic phytoplankton bloom using in situ metaproteomics. Different taxa, rather than different environmental conditions, formed distinct clusters based on their ribosomal and photosynthetic proteomic proportions, and we propose that these characteristics relate to ecological differences. We defined and used a proteomic proxy for regulatory cost, which showed that SAR11 had the lowest regulatory cost of any taxa we observed at our summertime Southern Ocean study site. Haptophytes had lower regulatory cost than diatoms, which may underpin haptophyte-to-diatom bloom progression in the Ross Sea. We were able to make these proteomic trait inferences by assessing various sources of bias in metaproteomics, providing practical recommendations for researchers in the field. We have quantified several proteomic traits (ribosomal and photosynthetic proteomic proportions, regulatory cost) in eukaryotic and bacterial taxa, which can then be incorporated into trait-based models of microbial communities that reflect resource allocation strategies.

opencc-by-4.0Oct 2021View details →

Large diatom bloom off the Antarctic Peninsula during cool conditions associated with the 2015/2016 El Niño: data availability

This dataset contains the results of phytoplankton chemotaxonomic groups derived from the HPLC/CHEMTAX analysis. The data were collected during the late spring and mid-late summer (November, January and February, respectively) of 2015/2016 along the Northern Antarctic Peninsula. This dataset includes an additional content in respect to diatom biomass proportion, collected between 2008-2017 during the late summer (February) along the Northern Antarctic Peninsula. The indices used in the study are also presented.

opencc-zeroNov 2022View details →

Diazotrophy modulates cyanobacteria stoichiometry through functional traits that determine bloom magnitude and toxin production

Harmful cyanobacterial blooms are an increasing threat to water quality. The interactions between two eco-physiological functional traits of cyanobacteria, diazotrophy (nitrogen (N)-fixation) and N-rich cyanotoxin synthesis, have never been examined in a stoichiometric explicit manner. We explored how a gradient of resource N:phosphorus (P) affects the biomass, N, P stoichiometry, light-harvesting pigments, and cylindrospermopsin production in a N-fixing cyanobacterium, Aphanizomenon. Low N:P Aphanizomenon cultures produced the same biomass as populations grown in high N:P cultures. The biomass accumulation determined by carbon, indicated low N:P Aphanizomenon cultures did not have a N-fixation growth tradeoff, in contrast to some other diazotrophs that maintain stoichiometric N homeostasis at the expense of growth. However, N-fixing Aphanizomenon populations produced less particulate cylindrospermopsin and had undetectable dissolved cylindrospermopsin compared to non-N-fixing populations. The pattern of low to high cyanotoxin cell quotas across an N:P gradient in the diazotrophic cylindrospermopsin producer is similar to the cyanotoxin cell quota response in non-diazotrophic cyanobacteria. We suggest that diazotrophic cyanobacteria may be characterized into two broad functional groups, the N-storage-strategists and the growth-strategists, which use N-fixation differently and may determine patterns of bloom magnitude and toxin production in nature.

opencc-by-4.0Aug 2022View details →

Dataset of Usability and Acceptance of Alboom: A Crowd-Based Early Warning System for Harmful Algal Blooms

Alboom is a crowd-based smartphone application and database system to record, store, analyze, share, and provide early warning information regarding harmful algal blooms (HABs). Similar to other participatory-based applications, the willingness of community members to be actively involved is paramount to the success of the application implementation. The dataset is the investigation results of usability and acceptance of Alboom. The questionnaires were built using an augmented technology acceptance model (TAM) to identify factors that affect the continual use intention of the application. In addition to the native TAM variables, such as perceived ease of use and usefulness as well as attitude, other factors, including HAB awareness, social influence, and reward, were also studied. Furthermore, the usability factor was also examined, specifically using the System Usability Scale (SUS) approach.

opencc-zeroJan 2023View details →

High capacity for a dietary specialist consumer population to cope with increasing cyanobacterial blooms

We present a common-garden experiment to study the feeding plasticity of a key deposit-feeder in the Baltic Sea, a low diversity system presenting a good model for studying local adaptations. Based on the latitudinal gradient in phytoplankton blooms, with a single diatom bloom (high nutritional quality) in the north and a diatom bloom followed by cyanobacteria bloom (low nutritional quality) in the south, we expected populations of the amphipod Monoporeia affinis to be dietary specialists in the north and generalists in the south. We tested this hypothesis using a combination of stable isotope tracers, trophic niche analyses, and various endpoints of growth and health status. We found that the toxin-producing cyanobacteria, when mixed with diatoms, were efficiently incorporated and used for growth by both populations. However, contrary to the expectations, the feeding plasticity was more pronounced in the northern population, indicating genetically-based divergence and suggesting that this population is capable of ecological adaptation to the climate-induced northward cyanobacteria expansion in this system. Results provide important understandings for adaptations to increasing cyanobacteria in a future warming world in both limnic and marine ecosystems by invertebrates, but are likely widely applicable to other consumers where questions on adaptations to altered food quality.

opencc-by-4.0Dec 2022View details →

Supplementary Data for "The impetus for bloom of Mesozoic terrestrial ecosystems in northern China: Insights from volcanic nutrient and harmful element delivery" in GRL.

Supplementary data tables for Ma et al. (2023) associated with the paper entitled "The impetus for bloom of Mesozoic terrestrial ecosystems in northern China: Insights from volcanic nutrient and harmful element delivery" published in GRL.

opencc-zeroJun 2023View details →

Data for: Biochemical properties of naturally occurring human bloom helicase variants

Bloom syndrome helicase (BLM) is a RecQ-family helicase implicated in a variety of cellular processes, including DNA replication, DNA repair, and telomere maintenance. Mutations in human BLM cause Bloom syndrome (BS), an autosomal recessive disorder that leads to myriad negative health impacts including a predisposition to cancer. BS-causing mutations in BLM often negatively impact BLM ATPase and helicase activity. While BLM mutations that cause BS have been well characterized both in vitro and in vivo, there are other less studied BLM mutations that exist in the human population that do not lead to BS. Two of these non-BS mutations, encoding BLM P868L and BLM G1120R, when homozygous, increase sister chromatid exchanges in human cells. To characterize these naturally occurring BLM mutant proteins in vitro, we purified the BLM catalytic core with either the P868L or G1120R substitution. We also purified a BLM K869A K870A mutant protein, which alters a lysine-rich loop proximal to the P868 residue. We found that BLM P868L and BLM G1120R were both able to hydrolyze ATP, bind diverse DNA substrates, and unwind G-quadruplex and duplex DNA structures. Molecular dynamics simulations suggest that the P868L substitution weakens the DNA interaction with the winged-helix domain of BLM and alters the orientation of lobe 1 of the ATPase domain. Because BLM P868L and BLM G1120R retain helicase function in vitro, it is likely that the increased genome instability is caused by specific impacts of the mutant proteins in vivo. Interestingly, we found that BLM K869A K870A has diminished ATPase activity compared to wild-type BLM, weakened binding to duplex DNA structures, and less robust helicase activity. Thus, the lysine-rich loop may have an important role in ATPase activity and specific binding and DNA unwinding functions in BLM.

Fig. 6 in Biosynthesis and emission of methyl hexanoate, the major constituent of floral scent of a night-blooming water lily Victoria cruziana

Fig. 6. Gene expression pattern of VcSABATH1 (A) and VcSABATH3 (B) in four different parts of V. cruziana flowers. Gene transcript levels were measured using RT-qPCR with VcGADPH (glyceraldehyde-3-phosphate dehydrogenase) gene as the internal control. The reactions were performed with three biological repeats, and the data was calculated by 2 ΔΔCT method. The highest levels of expression for each gene were arbitrarily set as 1.0. Different letters denote statistically significant differences among the means according to ANOVA analysis (P <0.05).

Fig. 7 in Biosynthesis and emission of methyl hexanoate, the major constituent of floral scent of a night-blooming water lily Victoria cruziana

Fig. 7. The phylogenetic analysis of VcSABATHs with the SABATH genes identified from N. corolata, non-seed and model species. 39 full-length proteins starting with "Os" are from rice, 24 proteins starting with "At" are from Arabidopsis, seven full-length proteins starting with "NC" are from Nymphaea colorata, five proteins starting with "Pa" are from Picea abies, three proteins starting with "Pt" are from poplar and three proteins starting with "Vc" are from V. cruziana. IAMT: indole-3-acetic acid MT; SAMT: salicylic acid MT; JAMT: jasmonic acid MT; GAMT: gibberellic acid MT; BSMT: benzoic acid/salicylic acid MT; FAMT: farnesoic acid MT. PpSABATH1 from the moss Physcomitrella patterns (Zhao et al., 2012) was used as an outgroup. Bootstrap values of 50 % or higher are indicated. The water lily-specific cluster was shaded.

Fig. 5 in Biosynthesis and emission of methyl hexanoate, the major constituent of floral scent of a night-blooming water lily Victoria cruziana

Fig. 5. GC chromatogram of product of methyltransferase enzyme assays for VcSABATH1-3. The assay conducted with proteins expressed in E. coli with pET32a without any gene insert (empty vector) was used as a negative control. Also shown was the GC chromatogram of the authentic standard methyl hexanoate. Hexanoic acid was used as substrate. While no product was detected from the VcSABATH2 assay, both VcSABATH1 and VcSABATH3 catalyzed the formation of methyl hexanoate (peak 1).

Fig. 4 in Biosynthesis and emission of methyl hexanoate, the major constituent of floral scent of a night-blooming water lily Victoria cruziana

Fig. 4. Multiple sequence alignment of VcSABATHs with selected known SABATHs. Conserved residues are in shade with the more conserved the darker. Residues indicated with "&" are S-adenosyl-L-methionine-binding residues. Residues indicated with "*" are residues that interact with the carboxyl moiety of substrate. CbSAMT, Clarkia breweri salicylic acid methyltransferase (accession No. AAF00108.1); NcDEMT, Nymphaea colorata decanoic acid methyltransferase (accession No. NC11G0120830).

Fig. 3 in Biosynthesis and emission of methyl hexanoate, the major constituent of floral scent of a night-blooming water lily Victoria cruziana

Fig. 3. Emission dynamic of floral volatiles from V. cruziana flowers during two consecutive days of blooming and closing. A, representative flower at four stages during blooming. B, the emission dynamics of total volatiles. C, the emission dynamcis of benzenoids. D. the emission dynamics of methyl hexanoate. Different letters denote statistically significant differences among the means according to ANOVA analysis (P <0.05).

Fig. 1 in Biosynthesis and emission of methyl hexanoate, the major constituent of floral scent of a night-blooming water lily Victoria cruziana

Fig. 1. The identification of volatiles emitted from the flowers of V. cruziana. A, the chromatogram of the volatile emission from the flower during the first bloom. The four peaks were identified as methyl hexanoate (peak 1), benzyl alcohol (peak 2), benzyl 2-methylbutanoate (peak 3), and benzyl tiglate (peak 4). IS stands for internal standard, nonyl acetate. B, chromatogram of three authentic compounds. Peak a1: methyl hexanoate; peak a2: benzyl alcohol (peak 2); peak a3: benzyl tiglate. C. mass spectrum of three compounds from flowers (peaks 1, 2 and 4) and their corresponding authentic standard (peaks a1, a2 and a3).

Fig. 2 in Biosynthesis and emission of methyl hexanoate, the major constituent of floral scent of a night-blooming water lily Victoria cruziana

Fig. 2. Emission of floral volatiles from different of parts of V. cruziana flowers. Intact fully opened flowers were separated into petals, pistils, sepals and stamen, which were subject to headspace collection and GC-MS analysis. In addition to total volatiles (VOCs), the emissions of methyl hexanoate and benzenoids were analyzed separately.