scholarly journals Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences

2020 ◽  
Vol 17 (23) ◽  
pp. 6145-6162
Author(s):  
Jeffrey M. Dick ◽  
Miao Yu ◽  
Jingqiang Tan
Keyword(s):  
Environmental Conditions ◽  
Microbial Mats ◽  
Compositional Analysis ◽  
Protein Sequences ◽  
Hyperosmotic Stress ◽  
Chemical Compositions ◽  
Salinity Gradients ◽  
Gene And Protein Expression ◽  
The Baltic ◽  
The Impact

Abstract. Prediction of the direction of change of a system under specified environmental conditions is one reason for the widespread utility of thermodynamic models in geochemistry. However, thermodynamic influences on the chemical compositions of proteins in nature have remained enigmatic despite much work that demonstrates the impact of environmental conditions on amino acid frequencies. Here, we present evidence that the dehydrating effect of salinity is detectable as chemical differences in protein sequences inferred from (1) metagenomes and metatranscriptomes in regional salinity gradients and (2) differential gene and protein expression in microbial cells under hyperosmotic stress. The stoichiometric hydration state (nH2O), derived from the number of water molecules in theoretical reactions to form proteins from a particular set of basis species (glutamine, glutamic acid, cysteine, O2, H2O), decreases along salinity gradients, including the Baltic Sea and Amazon River and ocean plume, and decreases in particle-associated compared to free-living fractions. However, the proposed metric does not respond as expected for hypersaline environments. Analysis of data compiled for hyperosmotic stress experiments under controlled laboratory conditions shows that differentially expressed proteins are on average shifted toward lower nH2O. Notably, the dehydration effect is stronger for most organic solutes compared to NaCl. This new method of compositional analysis can be used to identify possible thermodynamic effects in the distribution of proteins along chemical gradients at a range of scales from microbial mats to oceans.

scholarly journals Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences

2020 ◽  
Author(s):  
Jeffrey M. Dick ◽  
Miao Yu ◽  
Jingqiang Tan
Keyword(s):  
Compositional Analysis ◽  
Protein Sequences ◽  
Hyperosmotic Stress ◽  
Differentially Expressed ◽  
Chemical Compositions ◽  
Chemical Gradients ◽  
Salinity Gradients ◽  
Gene And Protein Expression ◽  
The Baltic ◽  
The Impact

Abstract. Thermodynamic influences on the chemical compositions of proteins in nature have remained enigmatic despite much work that demonstrates the impact of environmental conditions on amino acid frequencies. Here, we present evidence that the dehydrating effect of salinity is detectable as chemical differences in protein sequences inferred from (1) metagenomes and metatranscriptomes in regional salinity gradients and (2) differential gene and protein expression in microbial cells under hyperosmotic stress. The stoichiometric hydration state (nH2O), derived from the number of water molecules in theoretical reactions to form proteins from a particular set of basis species (glutamine, glutamic acid, cysteine, O2, H2O), decreases along salinity gradients including the Baltic Sea and Amazon River and ocean plume and in particle-associated compared to free-living fractions. However, the proposed metric does not behave as expected for hypersaline environments. Analysis of data compiled for hyperosmotic stress experiments under controlled laboratory conditions shows that differentially expressed proteins, as well as proteins coded by differentially expressed transcripts, are on average shifted toward lower nH2O. Notably, the dehydration effect is stronger for most organic solutes compared to NaCl. This new method of compositional analysis can be used to identify possible thermodynamic effects in the distribution of proteins along chemical gradients at a range of scales from biofilms to oceans.

scholarly journals Distinct trends in chemical composition of proteins from metagenomes in redox and salinity gradients

2020 ◽  
Author(s):  
Jeffrey M. Dick ◽  
Miao Yu ◽  
Jingqiang Tan
Keyword(s):  
Water Molecules ◽  
Chemical Compositions ◽  
Carbon Oxidation ◽  
The Baltic Sea ◽  
Chemical Gradients ◽  
Salinity Gradients ◽  
Hydration State ◽  
Thermodynamic Effects ◽  
The Baltic ◽  
The Impact

ABSTRACTThermodynamic influences on the chemical compositions of proteins have remained enigmatic despite much work that demonstrates the impact of environmental conditions on amino acid frequencies. Here, we show that the dehydrating effect of salinity is apparent in protein sequences inferred from metagenomes and metatranscriptomes. The stoichiometric hydration state (nH2O), derived from the number of water molecules in theoretical reactions to form proteins from a particular set of basis species (glutamine, glutamic acid, cysteine, O2, H2O), decreases along salinity gradients including the Baltic Sea, Amazon River and ocean plume, and other samples from freshwater and marine environments. Analysis of other metagenomic datasets shows that differences in carbon oxidation state, rather than stoichiometric hydration state, are a stronger indicator of redox gradients than salinity gradients. These compositional metrics can help to identify thermodynamic effects in the distribution of proteins along chemical gradients at scales from geologic systems to cells.

The impact of climate change on the adaptation of marine fish in the Baltic Sea

2005 ◽  
Vol 62 (7) ◽  
pp. 1492-1500 ◽  
Author(s):  
Evald Ojaveer ◽  
Margers Kalejs
Keyword(s):  
Climate Change ◽  
Baltic Sea ◽  
Marine Fish ◽  
Environmental Conditions ◽  
Oxygen Deficiency ◽  
Marine Species ◽  
Production Cycle ◽  
The Baltic Sea ◽  
The Baltic ◽  
The Impact

Abstract The biota in the Baltic Sea has formed under wide variations in environmental conditions induced by climate change since the last glaciation. Areas of the Baltic Sea display marked differences in salinity, oxygen content and temperature of water layers, timing of the peak production cycle, and other basic environmental conditions. Some of the most important adaptations of marine fish to the conditions in the Baltic Sea facilitate reproduction at low and changeable salinity and oxygen deficiency in deeper layers, and enhance the survival of their offspring in early stages of development. In sea herring, flounder, cod, and other late immigrants (which probably colonized the Baltic after the Ancylus stage), abundant year classes occur in periods of higher salinity. During periods of low salinity, the abundance and spatial distribution of marine species is reduced. Probable earlier immigrants (e.g. gulf herring) are less dependent on saltwater inflows, but they depend more on local processes. The success of marine species in different areas of the Baltic Sea has been variable, and species adaptation, mediated by climate oscillations, has resulted in the formation of local populations.

Environmental impact of nutrients from nordic fish farming

1995 ◽  
Vol 31 (10) ◽  
pp. 61-71 ◽  
Author(s):  
M. Enell
Keyword(s):  
Major Part ◽  
Fish Farming ◽  
Fish Farms ◽  
Feed Composition ◽  
The North ◽  
Comprehensive Development ◽  
The Baltic ◽  
Inland Water Bodies ◽  
The Impact ◽  
Feed Coefficient

During the last 20 years there has been an interesting development of the Nordic fish farming, with regard to the feeding and farming technology and to the increase in production quantities. During the period 1974-1994 the production increased from 15,800 to about 250,000 tonnes/year. In 1974 the major part of the production was in Denmark, and in 1994 the major part was in Norway. The nutrient impact of fish farming on surrounding sea areas is mainly a function of the feed coefficient, the feed composition and metabolic processes in the fish. The comprehensive development of the feed composition and the feeding technology has resulted in reduced load of unmetabolized nutrients from fish farms, calculated per tonne fish produced. In 1974 the mean Nordic feed coefficient was 2.08 and in 1994 the coefficient was 1.25. Feed coefficients of 1.0-1.1 are now reported for Danish and Norwegian freshwater and marine fish farms. The nitrogen (N) and phosphorus (P) content of the feed has decreased, in addition the quality of the nutrient substances in the feed has changed, especially for N. The N content has decreased from 7.8 to 6.8% during the period 1974-1994 and the content of P has decreased from 1.7 to 0.7% during the same period. This development of the feed coefficient and the feed composition has resulted in a present load from a typical Nordic fish farm of 55 kg N and 4.8 kg P/t fish produced. The figures for 1974 were 132 kg N and 31 kg P/t fish produced. The Nordic fish farming production in 1994 resulted in a load of about 13,750 t N and about 1,200 t P on the actual recipients. The load from the Swedish, Finnish and Danish fish farming operations, with the Baltic Sea and the Skagerrak as the recipients, is negligible in comparison with other pollution sources. The quantities of N and P from the fish farming are equal to 0.5% of the atmospheric deposition on the sea surface and 3% of the atmospheric P load. Norwegian, Icelandic and the Faroe Islands fish farming operations are using the North Sea and the Norwegian Sea as the recipients. However, the nutrient load from single fish farms in certain coastal and inland water bodies can be significant and must be considered in the impact assessment together with other sources.

scholarly journals Treadmill Running Changes Endothelial Lipase Expression: Insights from Gene and Protein Analysis in Various Striated Muscle Tissues and Serum

Biomolecules ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 906
Author(s):  
Agnieszka Mikłosz ◽  
Bartłomiej Łukaszuk ◽  
Adrian Chabowski ◽  
Jan Górski
Keyword(s):  
Protein Expression ◽  
Density Lipoprotein ◽  
Treadmill Running ◽  
Endothelial Lipase ◽  
Type I ◽  
Fiber Types ◽  
Gene And Protein Expression ◽  
Single Bout ◽  
The Impact ◽  
White Gastrocnemius

Endothelial lipase (EL) is an enzyme capable of HDL phospholipids hydrolysis. Its action leads to a reduction in the serum high-density lipoprotein concentration, and thus, it exerts a pro-atherogenic effect. This study examines the impact of a single bout exercise on the gene and protein expression of the EL in skeletal muscles composed of different fiber types (the soleus—mainly type I, the red gastrocnemius—mostly IIA, and the white gastrocnemius—predominantly IIX fibers), as well as the diaphragm, and the heart. Wistar rats were subjected to a treadmill run: 1) t = 30 [min], V = 18 [m/min]; 2) t = 30 [min], V = 28 [m/min]; 3) t = 120 [min], V = 18 [m/min] (designated: M30, F30, and M120, respectively). We established EL expression in the total muscle homogenates in sedentary animals. Resting values could be ordered with the decreasing EL protein expression as follows: endothelium of left ventricle > diaphragm > red gastrocnemius > right ventricle > soleus > white gastrocnemius. Furthermore, we observed that even a single bout of exercise was capable of inducing changes in the mRNA and protein level of EL, with a clearer pattern observed for the former. After 30 min of running at either exercise intensity, the expression of EL transcript in all the cardiovascular components of muscles tested, except the soleus, was reduced in comparison to the respective sedentary control. The protein content of EL varied with the intensity and/or duration of the run in the studied whole tissue homogenates. The observed differences between EL expression in vascular beds of muscles may indicate the muscle-specific role of the lipase.

scholarly journals Morphological Variations of Wild Populations of Brycon dentex (Characidae, Teleostei) in the Guayas Hydrographic Basin (Ecuador). The Impact of Fishing Policies and Environmental Conditions

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1901
Author(s):  
Ana Gonzalez-Martinez ◽  
Carmen De-Pablos-Heredero ◽  
Martin González ◽  
Jorge Rodriguez ◽  
Cecilio Barba ◽  
...  
Keyword(s):  
Discriminant Analysis ◽  
Environmental Conditions ◽  
Anthropogenic Activity ◽  
Freshwater Species ◽  
Fishing Pressure ◽  
Wild Populations ◽  
Morphometric Variation ◽  
Morphological Variations ◽  
Body Development ◽  
The Impact

The Guayas, located in Ecuador, is the largest basin in the Pacific Ocean and has an inventory of 123 native freshwater species. Most of these are endemic species that are threatened or at-risk due to anthropogenic activity and the modification, fragmentation, and destruction of habitats. The aim of this study was to determine the morphometric variation in three wild populations of Brycon dentex in the Guayas basin rivers and their connections to fishing management and environmental conditions. A total of 200 mature fish were captured, and 26 morphometric parameters were measured. The fishing policies (Hypothesis 1) and environmental conditions (Hypothesis 2) were considered fixed factors and were validated by t-tests. The morphological variation among the three populations (Hypothesis 3) was validated through a discriminant analysis. Fishing policies and resource management were found to generate morphological differences associated with body development. In addition, the environmental conditions were found to influence the size and structure of Brycon dentex populations. The analyzed populations were discriminated by the generated morphometric models, which differentiated Cluster 1 (Quevedo and Mocache rivers) with high fishing pressure from Cluster 2 (Pintado river) with medium–low fishing pressure. Morphometric differentiation by discriminant analysis is a direct and economic methodology that can be applied as an indicator of diversity maintenance.

scholarly journals 16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Gene Diversity ◽  
Salinity Gradient ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ice Shelf ◽  
The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

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