scholarly journals Untangling mechanisms of crude oil toxicity: Linking gene expression, morphology and PAHs at two developmental stages in a cold-water fish

2021 ◽  
Vol 757 ◽  
pp. 143896
Author(s):  
Elin Sørhus ◽  
Carey E. Donald ◽  
Denis da Silva ◽  
Anders Thorsen ◽  
Ørjan Karlsen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Crude Oil ◽  
Developmental Stages ◽  
Cold Water ◽  
Water Fish ◽  
Oil Toxicity

scholarly journals Untangling mechanisms of crude oil toxicity: linking gene expression, morphology and PAHs at two developmental stages in a cold-water fish

2020 ◽  
Author(s):  
Elin Sørhus ◽  
Carey E. Donald ◽  
Denis da Silva ◽  
Anders Thorsen ◽  
Ørjan Karlsen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Crude Oil ◽  
Developmental Stages ◽  
Cold Water ◽  
Melanogrammus Aeglefinus ◽  
List Type ◽  
Short Term ◽  
Oil Droplet ◽  
Oil Toxicity ◽  
Oil Exposure

AbstractEarly life stages of fish are highly sensitive to crude oil exposure and thus, short term exposures during critical developmental periods could have detrimental consequences for juvenile survival. Here we administered crude oil to Atlantic haddock (Melanogrammus aeglefinus) in short term (3-day) exposures at two developmental time periods: before first heartbeat, from gastrulation to cardiac cone stage (early), and from first heartbeat to one day before hatching (late). A frequent sampling regime enabled us to determine immediate PAH uptake, metabolite formation and gene expression changes. In general, the embryotoxic consequences of an oil exposure were more severe in the early exposure animals. Oil droplet fouling in the highest doses resulted in severe cardiac and craniofacial abnormalities. Gene expression changes of Cytochrome 1 a,b,c and d (cyp1a,b,c,d), Bone morphogenetic protein 10 (bmp10), ABC transporter b1 (abcb1) and Rh-associated G-protein (rhag) were linked to PAH uptake, occurrence of metabolites of phenanthrene and developmental and functional abnormalities. We detected circulation-independent, oil-induced gene expression changes and separated phenotypes linked to proliferation, growth and disruption of formation events at early and late developmental stages. Our study gives an increased knowledge about developmentally dependent effects of crude oil toxicity. Thus, providing more knowledge and detail to new and several existing adverse outcome pathways of crude oil toxicity.Graphical abstractHighlightsOil droplet fouling occurred in the whole water column and increased the oil toxicity.Early exposure resulted in higher PAH uptake due to lower metabolism resulting in more severe abnormalities.A rapid and circulation-indepenent regulation of bmp10 suggested a direct oil-induced effect on calcium homeostasis.Expression of rhag indicated a direct oil-induced effect on osmoregulatory cells and osmoregulation.Severe eye abnormalities especially in the late exposure was linked to inappropriate overexpression of cyp1b in the eyes.

Application of Chemical Herders Do Not Increase Acute Crude Oil Toxicity to Cold-Water Marine Species

2021 ◽  
Author(s):  
Bjørn Henrik Hansen ◽  
Trond Nordtug ◽  
Ida Beathe Øverjordet ◽  
Dag Altin ◽  
Julia Farkas ◽  
...  
Keyword(s):  
Crude Oil ◽  
Cold Water ◽  
Marine Species ◽  
Oil Toxicity

The Role of Temperature and Heterotrophism in Determining Crude Oil Toxicity

1975 ◽  
Vol 10 (1) ◽  
pp. 73-83
Author(s):  
J.E.S. Graham ◽  
T.C. Hutchinson
Keyword(s):  
Crude Oil ◽  
Aqueous Extract ◽  
Chlorella Vulgaris ◽  
Nutrient Medium ◽  
General Pattern ◽  
Growth Stimulation ◽  
Aqueous Extracts ◽  
Chlamydomonas Eugametos ◽  
Wide Range ◽  
Oil Toxicity

Abstract Crude oil spills are increasingly likely to occur from drilling, pumping and transportation activities as oil development proceeds at a rapid pace. These spills may occur over the wide range of climatic conditions which obtain in Canada. Little is known of oil toxicity at different temperatures; consequently, laboratory studies were made of the variability of the toxicity of aqueous extracts of a Norman Wells crude oil to freshwater algae over the temperature range 5°C to 35°C. Two unicellular green algae were studied: Chlamydomonas eugametos and Chlorella vulgaris. Their response (measured by cell numbers) varied with temperature and species. Whereas Chlamydomonas eugametos showed a general pattern of growth inhibition by oil at all temperatures with maximum inhibition at 25°C, Chlorella vulgaris showed general growth stimulation by oil with maximum stimulation at 25°C, this temperature was chosen for all further experimentation. All experiments were done using unialgal cultures and sterile technique. Cells were grown in 50 ml of nutrient medium (BBM) in 125 ml Erlenmeyer flasks. Such flasks allow gas exchange and permit loss of volatile hydrocarbons. Aqueous extracts were made by slowly stirring 5% crude oil with the nutrient medium for six hours using a magnetic mixer. The extract was then allowed to sit for two to four hours before the lower fraction was drawn off for use. Experiments were carried out in controlled environment chambers (±2°C) with a twelve hour light-dark cycle. All further experiments used a similar methodology. (Note: Chlamydomonas eugametos experiments were carried out on a rotary shaker at 125 rpm.) An attempt was made to determine the reason for the remarkable stimulation in growth of Chlorella vulgaris #29 at 25°C. This organism has been described in the literature as heterotrophic. Thus three reasons for stimulation seemed possible: 1. heterotrophic uptake of hydrocarbons directly from solution; 2. heterotrophic uptake of organic compounds formed or released by microbial breakdown of hydrocarbons (the aqueous extract of crude was not sterile); or 3. the use of CO2 released to solution by microbial respiration. The original experiment was repeated in the dark at 20°C to determine if stimulation still occurred. It did not, since cells exposed to the aqueous extract decreased in numbers. However, after two weeks the cells were illuminated and even though experimental flasks started off with depleted populations, they outgrew the control cells within two weeks. This suggested that if stimulation was related to heterotrophism, it must, at least in this case, have been the unusual case of photoheterotrophism. The reasons for this stimulation of growth are currently under investigation. Several methods are being employed to investigate the suspected heterotrophism. Experiments will be done to determine whether light energy is essential to the stimulation. Two varieties of Chlorella vulgaris, i.e. #29 and #260 are heterotrophic and autotrophic respectively, are to be used in experiments. Sterile aqueous extracts made by pressure ultrafiltration will be used. These experiments should determine whether algal growth stimulation is related to heterotrophism or whether microbial degradation of hydrocarbons is the real source of stimulation. Although the toxicity of crude oil may be rapidly ameliorated by physical and/or biological phenomena, one must still be aware of the possibility of a large input of organic carbon causing extensive eutrophication. Thus both toxicity and eutrophication will cause a selection, in terms of survival, in a natural environment. It is evident that although an oil spill may not totally destroy an ecosystem, it will certainly alter its natural composition considerably.

scholarly journals Integrative Modelling of Gene Expression and Digital Phenotypes to Describe Senescence in Wheat

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 909
Author(s):  
Anyela Valentina Camargo Rodriguez
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Computational Modelling ◽  
Plant Morphology ◽  
Reproductive Organs ◽  
Biological Trait ◽  
Cereal Grain ◽  
Plant Level

Senescence is the final stage of leaf development and is critical for plants’ fitness as nutrient relocation from leaves to reproductive organs takes place. Although senescence is key in nutrient relocation and yield determination in cereal grain production, there is limited understanding of the genetic and molecular mechanisms that control it in major staple crops such as wheat. Senescence is a highly orchestrated continuum of interacting pathways throughout the lifecycle of a plant. Levels of gene expression, morphogenesis, and phenotypic development all play key roles. Yet, most studies focus on a short window immediately after anthesis. This approach clearly leaves out key components controlling the activation, development, and modulation of the senescence pathway before anthesis, as well as during the later developmental stages, during which grain development continues. Here, a computational multiscale modelling approach integrates multi-omics developmental data to attempt to simulate senescence at the molecular and plant level. To recreate the senescence process in wheat, core principles were borrowed from Arabidopsis Thaliana, a more widely researched plant model. The resulted model describes temporal gene regulatory networks and their effect on plant morphology leading to senescence. Digital phenotypes generated from images using a phenomics platform were used to capture the dynamics of plant development. This work provides the basis for the application of computational modelling to advance understanding of the complex biological trait senescence. This supports the development of a predictive framework enabling its prediction in changing or extreme environmental conditions, with a view to targeted selection for optimal lifecycle duration for improving resilience to climate change.

scholarly journals Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuping Li ◽  
Xiaoju Liang ◽  
Xuguo Zhou ◽  
Yu An ◽  
Ming Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stage ◽  
Reference Genes ◽  
Developmental Stages ◽  
Individual Factors ◽  
Congeneric Species ◽  
Spatio Temporal ◽  
The Stability ◽  
Different Tissues ◽  
Selection Of

AbstractGlycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.

scholarly journals Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity

2021 ◽  
Vol 22 (12) ◽  
pp. 6556
Author(s):  
Junjun Huang ◽  
Xiaoyu Li ◽  
Xin Chen ◽  
Yaru Guo ◽  
Weihong Liang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abc Transporters ◽  
Developmental Stages ◽  
Aluminum Toxicity ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Purifying Selection ◽  
Biotic Stresses ◽  
Genome Wide ◽  
New Germplasm

ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.

scholarly journals A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Aliki Xanthopoulou ◽  
Javier Montero-Pau ◽  
Belén Picó ◽  
Panagiotis Boumpas ◽  
Eleni Tsaliki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cucurbita Pepo ◽  
Developmental Stages ◽  
Lateral Roots ◽  
Expression Patterns ◽  
Male Flower ◽  
Differentially Expressed ◽  
Gene Expression Atlas ◽  
Summer Squash ◽  
Expression Atlas

Abstract Background Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity. Conclusions These findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. This comprehensive gene expression atlas is expected not only to provide a global view of gene expression patterns in all major tissues in C. pepo but to also serve as a valuable resource for functional genomics and gene discovery in Cucurbitaceae.

scholarly journals Microencapsulation of oil droplets using cold water fish gelatine/gum arabic complex coacervation by membrane emulsification

2013 ◽  
Vol 53 (1) ◽  
pp. 362-372 ◽  
Author(s):  
Emma Piacentini ◽  
Lidietta Giorno ◽  
Marijana M. Dragosavac ◽  
Goran T. Vladisavljević ◽  
Richard G. Holdich
Keyword(s):  
Cold Water ◽  
Gum Arabic ◽  
Complex Coacervation ◽  
Oil Droplets ◽  
Membrane Emulsification ◽  
Water Fish
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