scholarly journals Rainfall Alters Permafrost Soil Redox Conditions, but Meta-Omics Show Divergent Microbial Community Responses by Tundra Type in the Arctic

Soil Systems ◽  
2021 ◽  
Vol 5 (1) ◽  
pp. 17
Author(s):  
Karl J. Romanowicz ◽  
Byron C. Crump ◽  
George W. Kling
Keyword(s):  
Gene Expression ◽  
Anaerobic Metabolism ◽  
Cellular Growth ◽  
The Arctic ◽  
Soil Conditions ◽  
Tundra Soils ◽  
Ch4 Production ◽  
Soil Mesocosms ◽  
Tussock Tundra ◽  
O2 Concentration

Soil anoxia is common in the annually thawed surface (‘active’) layer of permafrost soils, particularly when soils are saturated, and supports anaerobic microbial metabolism and methane (CH4) production. Rainfall contributes to soil saturation, but can also introduce oxygen, causing soil oxidation and altering anoxic conditions. We simulated a rainfall event in soil mesocosms from two dominant tundra types, tussock tundra and wet sedge tundra, to test the impacts of rainfall-induced soil oxidation on microbial communities and their metabolic capacity for anaerobic CH4 production and aerobic respiration following soil oxidation. In both types, rainfall increased total soil O2 concentration, but in tussock tundra there was a 2.5-fold greater increase in soil O2 compared to wet sedge tundra due to differences in soil drainage. Metagenomic and metatranscriptomic analyses found divergent microbial responses to rainfall between tundra types. Active microbial taxa in the tussock tundra community, including bacteria and fungi, responded to rainfall with a decline in gene expression for anaerobic metabolism and a concurrent increase in gene expression for cellular growth. In contrast, the wet sedge tundra community showed no significant changes in microbial gene expression from anaerobic metabolism, fermentation, or methanogenesis following rainfall, despite an initial increase in soil O2 concentration. These results suggest that rainfall induces soil oxidation and enhances aerobic microbial respiration in tussock tundra communities but may not accumulate or remain in wet sedge tundra soils long enough to induce a community-wide shift from anaerobic metabolism. Thus, rainfall may serve only to maintain saturated soil conditions that promote CH4 production in low-lying wet sedge tundra soils across the Arctic.

scholarly journals Temporal, Spatial, and Temperature Controls on Organic Carbon Mineralization and Methanogenesis in Arctic High-Centered Polygon Soils

2021 ◽  
Vol 11 ◽  
Author(s):  
Taniya Roy Chowdhury ◽  
Erin C. Berns ◽  
Ji-Won Moon ◽  
Baohua Gu ◽  
Liyuan Liang ◽  
...  
Keyword(s):  
Water Content ◽  
Active Layer ◽  
Temporal Dynamics ◽  
The Arctic ◽  
Soil Conditions ◽  
Organic Soils ◽  
Tundra Soils ◽  
Organic C ◽  
Arctic Soils ◽  
Mineral Soils

Warming temperatures in continuous permafrost zones of the Arctic will alter both hydrological and geochemical soil conditions, which are strongly linked with heterotrophic microbial carbon (C) cycling. Heterogeneous permafrost landscapes are often dominated by polygonal features formed by expanding ice wedges: water accumulates in low centered polygons (LCPs), and water drains outward to surrounding troughs in high centered polygons (HCPs). These geospatial differences in hydrology cause gradients in biogeochemistry, soil C storage potential, and thermal properties. Presently, data quantifying carbon dioxide (CO2) and methane (CH4) release from HCP soils are needed to support modeling and evaluation of warming-induced CO2 and CH4 fluxes from tundra soils. This study quantifies the distribution of microbial CO2 and CH4 release in HCPs over a range of temperatures and draws comparisons to previous LCP studies. Arctic tundra soils were initially characterized for geochemical and hydraulic properties. Laboratory incubations at −2, +4, and +8°C were used to quantify temporal trends in CO2 and CH4 production from homogenized active layer organic and mineral soils in HCP centers and troughs, and methanogen abundance was estimated from mcrA gene measurements. Results showed that soil water availability, organic C, and redox conditions influence temporal dynamics and magnitude of gas production from HCP active layer soils during warming. At early incubation times (2–9 days), higher CO2 emissions were observed from HCP trough soils than from HCP center soils, but increased CO2 production occurred in center soils at later times (>20 days). HCP center soils did not support methanogenesis, but CH4-producing trough soils did indicate methanogen presence. Consistent with previous LCP studies, HCP organic soils showed increased CO2 and CH4 production with elevated water content, but HCP trough mineral soils produced more CH4 than LCP mineral soils. HCP mineral soils also released substantial CO2 but did not show a strong trend in CO2 and CH4 release with water content. Knowledge of temporal and spatial variability in microbial C mineralization rates of Arctic soils in response to warming are key to constraining uncertainties in predictive climate models.

CARP Plays a Key Role in Cellular Growth Under Hypertrophic Stimuli in Neonatal Rat Ventricular Myocytes

2013 ◽  
Vol 9 ◽  
Author(s):  
Tara A Shrout
Keyword(s):  
Gene Expression ◽  
Ventricular Myocytes ◽  
Cellular Growth ◽  
Neonatal Rat ◽  
Transcriptional Level ◽  
Dual Nature ◽  
Hypertrophic Growth ◽  
Rat Ventricular Myocytes ◽  
Neonatal Rat Ventricular Myocytes ◽  
Over Time

Cardiac hypertrophy is a growth process that occurs in response to stress stimuli or injury, and leads to the induction of several pathways to alter gene expression. Under hypertrophic stimuli, sarcomeric structure is disrupted, both as a consequence of gene expression and local changes in sarcomeric proteins. Cardiac-restricted ankyrin repeat protein (CARP) is one such protein that function both in cardiac sarcomeres and at the transcriptional level. We postulate that due to this dual nature, CARP plays a key role in maintaining the cardiac sarcomere. GATA4 is another protein detected in cardiomyocytes as important in hypertrophy, as it is activated by hypertrophic stimuli, and directly binds to DNA to alter gene expression. Results of GATA4 activation over time were inconclusive; however, the role of CARP in mediating hypertrophic growth in cardiomyocytes was clearly demonstrated. In this study, Neonatal Rat Ventricular Myocytes were used as a model to detect changes over time in CARP and GATA4 under hypertrophic stimulation by phenylephrine and high serum media. Results were detected by analysis of immunoblotting. The specific role that CARP plays in mediating cellular growth under hypertrophic stimuli was studied through immunofluorescence, which demonstrated that cardiomyocyte growth with hypertrophic stimulation was significantly blunted when NRVMs were co-treated with CARP siRNA. These data suggest that CARP plays an important role in the hypertrophic response in cardiomyocytes.

scholarly journals Commuting to Work: Nucleolar Long Non-Coding RNA Control Ribosome Biogenesis from Near and Far

2021 ◽  
Vol 7 (3) ◽  
pp. 42
Author(s):  
Victoria Mamontova ◽  
Barbara Trifault ◽  
Lea Boten ◽  
Kaspar Burger
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Ribosome Biogenesis ◽  
Intergenic Spacer ◽  
Cellular Growth ◽  
Rrna Synthesis ◽  
Protein Coding ◽  
Non Coding Rna ◽  
And Function ◽  
In Cis

Gene expression is an essential process for cellular growth, proliferation, and differentiation. The transcription of protein-coding genes and non-coding loci depends on RNA polymerases. Interestingly, numerous loci encode long non-coding (lnc)RNA transcripts that are transcribed by RNA polymerase II (RNAPII) and fine-tune the RNA metabolism. The nucleolus is a prime example of how different lncRNA species concomitantly regulate gene expression by facilitating the production and processing of ribosomal (r)RNA for ribosome biogenesis. Here, we summarise the current findings on how RNAPII influences nucleolar structure and function. We describe how RNAPII-dependent lncRNA can both promote nucleolar integrity and inhibit ribosomal (r)RNA synthesis by modulating the availability of rRNA synthesis factors in trans. Surprisingly, some lncRNA transcripts can directly originate from nucleolar loci and function in cis. The nucleolar intergenic spacer (IGS), for example, encodes nucleolar transcripts that counteract spurious rRNA synthesis in unperturbed cells. In response to DNA damage, RNAPII-dependent lncRNA originates directly at broken ribosomal (r)DNA loci and is processed into small ncRNA, possibly to modulate DNA repair. Thus, lncRNA-mediated regulation of nucleolar biology occurs by several modes of action and is more direct than anticipated, pointing to an intimate crosstalk of RNA metabolic events.

scholarly journals Comparison of the Essential Cellular Functions of the Two murA Genes of Bacillus anthracis

2008 ◽  
Vol 52 (6) ◽  
pp. 2009-2013 ◽  
Author(s):  
G. C. Kedar ◽  
Vickie Brown-Driver ◽  
Daniel R. Reyes ◽  
Mark T. Hilgers ◽  
Mark A. Stidham ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacillus Anthracis ◽  
High Resistance ◽  
Gene Replacement ◽  
Cellular Growth ◽  
Cellular Functions

ABSTRACT Targeted antisense and gene replacement mutagenesis experiments demonstrate that only the murA1 gene and not the murA2 gene is required for the normal cellular growth of Bacillus anthracis. Antisense-based modulation of murA1 gene expression hypersensitizes cells to the MurA-specific antibiotic fosfomycin despite the normally high resistance of B. anthracis to this drug.

scholarly journals Designing problems of oil fields infrustructre in the Arctic under the climate change

2021 ◽  
Vol 6 (3) ◽  
pp. 130-135
Author(s):  
Elena A. Poskonina ◽  
Anna N. Kurchatova
Keyword(s):  
Climate Change ◽  
Oil And Gas ◽  
Thermal Stabilization ◽  
Oil Fields ◽  
The Arctic ◽  
Soil Conditions ◽  
Industrial Facilities ◽  
Oil And Gas Fields ◽  
Gas Fields ◽  
Forecast Modeling

Background. Designing problems of oil fields infrastructure in the Arctic under climate change, namely, applying of temperature coefficient when calculating bearing capacity, heaving of lightly loaded foundations, optimization of thermal stabilization solutions are presented in the article. Aim. To change the strategy for designing foundations on permafrost by choosing the worst soil conditions to the implementation of an invariant matrix for designing and construction of soil bases and foundations considering specifics of industrial facilities of oil and gas fields based on unified numerical calculations (regulations). Materials and methods. An overview of the current regulatory requirements to the design of foundations on permafrost is made. The analysis of forecast modeling of the temperature of soil bases of typical industrial facilities of oil and gas fields to justify design solutions and also the use of thermal stabilization systems is done. Results. It is proposed to develop a regional directory of weather stations with long observation period based on updated climate data to decrease the volume of designing work and the amount of mistakes in applying of thermal stabilization systems. It is necessary to create regional dynamic models of permafrost geosystems, implement forecast modeling of seasonal thawing potential depth and frozen ground temperature in natural landscapes on the base of geotechnical monitoring data and select adaptation methods to existing or expecting climate change trends. Conclusions. Regulations on designing and construction of soil bases and foundations on permafrost considering specifics of industrial facilities of oil and gas fields is an effective solution. It allows moving on the strategy implementation of uniform approaches to oil fields development on permafrost: from designing for every structure on the base of typical solutions and results of engineering surveys to invariant matrix of project solutions.

scholarly journals Cadmium-associated differential methylation throughout the placental genome: epigenome-wide association study of two US birth cohorts

2017 ◽  
Author(s):  
Todd M. Everson ◽  
Tracy Punshon ◽  
Brian P. Jackson ◽  
Ke Hao ◽  
Luca Lambertini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Fetal Development ◽  
Meta Analysis ◽  
Reproductive Toxicity ◽  
Differential Methylation ◽  
Cellular Growth ◽  
Birth Cohorts ◽  
Inflammatory Signaling ◽  
P Values

AbstractBackgroundCadmium (Cd) is a ubiquitous toxicant that during pregnancy can impair fetal development. Cd sequesters in the placenta where it can impair placental function, impacting fetal development. We aimed to investigate Cd-associated variations in placental DNA methylation (DNAM), associations with gene expression, and identify novel pathways involved in Cd-associated reproductive toxicity.MethodsUsing placental DNAM and Cd concentrations in the New Hampshire Birth Cohort Study (NHBCS, n=343) and the Rhode Island Child Health Study (RICHS, n=141), we performed an EWAS between Cd and DNAM, adjusting for tissue heterogeneity using a reference-free method. Cohort-specific results were aggregated via inverse variance weighted fixed effects meta-analysis, and variably methylated CpGs were associated with gene expression. We then performed functional enrichment analysis and tests for associations between gene expression and birth metrics.ResultsWe identified 17 Cd-associated differentially methylated CpG sites with meta-analysis p-values < 1e-05, two of which were within a 5% false discovery rate (FDR). Methylation levels at 9 of the 17 loci were associated with increased expression of 6 genes (5% FDR): TNFAIP2, EXOC3L4, GAS7, SREBF1, ACOT7, and RORA. Higher placental expression of TNFAIP2 and ACOT7, and lower expression of RORA, were associated with lower birth weight z-scores (p-values < 0.05).ConclusionCd associated differential DNAM and corresponding DNAM-expression associations at these loci are involved in inflammatory signaling and cell growth. The expression levels of genes involved in inflammatory signaling (TNFAIP2, ACOT7, and RORA), were also associated with birth metrics, suggesting a role for inflammatory processes in Cd-associated reproductive toxicity.SignificanceCadmium is a toxic environmental pollutant that can impair fetal development. The mechanisms underlying this toxicity are unclear, though disrupted placental functions could play an important role. In this study we examined associations between cadmium concentrations and DNA methylation throughout the placental genome, across two US birth cohorts. We observed cadmium-associated differential methylation, and corresponding methylation-expression associations at genes involved in cellular growth processes and/or immune and inflammatory signaling. This study provides supporting evidence that disrupted placental epigenetic regulation of cellular growth and immune/inflammatory signaling could play a role in cadmium associated reproductive toxicity in human pregnancies.

scholarly journals Is geographical variation driving the transcriptomic responses to multiple stressors in the kelp Saccharina latissima?

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Cátia Marina Machado Monteiro ◽  
Huiru Li ◽  
Kai Bischof ◽  
Inka Bartsch ◽  
Klaus Ulrich Valentin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Multiple Stressors ◽  
The Arctic ◽  
Saccharina Latissima ◽  
Salinity Treatment ◽  
Pigment Synthesis ◽  
Ecotypic Differentiation ◽  
Low Salinity ◽  
Transcriptomic Responses

Abstract Background Kelps (Laminariales, Phaeophyceae) are brown macroalgae of utmost ecological, and increasingly economic, importance on temperate to polar rocky shores. Omics approaches in brown algae are still scarce and knowledge of their acclimation mechanisms to the changing conditions experienced in coastal environments can benefit from the application of RNA-sequencing. Despite evidence of ecotypic differentiation, transcriptomic responses from distinct geographical locations have, to our knowledge, never been studied in the sugar kelp Saccharina latissima so far. Results In this study we investigated gene expression responses using RNA-sequencing of S. latissima from environments with contrasting temperature and salinity conditions – Roscoff, in temperate eastern Atlantic, and Spitsbergen in the Arctic. Juvenile sporophytes derived from uniparental stock cultures from both locations were pre-cultivated at 8 °C and SA 30. Sporophytes acclimated to 0 °C, 8 °C and 15 °C were exposed to a low salinity treatment (SA 20) for 24 h. Hyposalinity had a greater impact at the transcriptomic level than the temperature alone, and its effects were modulated by temperature. Namely, photosynthesis and pigment synthesis were extensively repressed by low salinity at low temperatures. Although some responses were shared among sporophytes from the different sites, marked differences were revealed by principal component analysis, differential expression and GO enrichment. The interaction between low temperature and low salinity drove the largest changes in gene expression in sporophytes from Roscoff while specimens from Spitsbergen required more metabolic adjustment at higher temperatures. Moreover, genes related to cell wall adjustment were differentially expressed between Spitsbergen and Roscoff control samples. Conclusions Our study reveals interactive effects of temperature and salinity on transcriptomic profiles in S. latissima. Moreover, our data suggest that under identical culture conditions sporophytes from different locations diverge in their transcriptomic responses. This is probably connected to variations in temperature and salinity in their respective environment of origin. The current transcriptomic results support the plastic response pattern in sugar kelp which is a species with several reported ecotypes. Our data provide the baseline for a better understanding of the underlying processes of physiological plasticity and may help in the future to identify strains adapted to specific environments and its genetic control.

130. MICROARRAY ANALYSIS OF FOETAL MOUSE BRAIN FOLLOWING INDUCTION OF MITOCHONDRIAL DYSFUNCTION DURING PRE-IMPLANTATION EMBRYO DEVELOPMENT

2009 ◽  
Vol 21 (9) ◽  
pp. 49
Author(s):  
T. Fullston ◽  
M. Mitchell ◽  
S. Wakefield ◽  
A. Filby ◽  
M. Lane
Keyword(s):  
Gene Expression ◽  
Cell Death ◽  
Mitochondrial Dysfunction ◽  
Embryo Development ◽  
Epigenetic Modification ◽  
Gene Array ◽  
Early Embryo ◽  
Cellular Growth ◽  
Early Embryo Development ◽  
Foetal Brain

Environmental stress can disrupt mitochondrial function in the pre-implantation embryo, subsequently hindering embryo viability. Brain tissue is also sensitive to developmental perturbations, and we have previously discovered genes involved in neurological function and epigenetic modification are differentially expressed in blastocysts following mitochondrial dysfunction by amino-oxyacetate (AOA). In this study CBAxC57Bl6 2 cell stage mouse embryos were cultured in 5μM-AOA without pyruvate for 72h to induce mitochondrial dysfunction. Blastocyst stage embryos were then transferred to pseudopregnant recipients and the expression profile of day 18 foetal brains was interrogated using microarray. mRNA from mouse whole brain (4 per treatment) was extracted and analysed using an Affymetrix gene array. Ingenuity Pathway Analysis software identified persistent alterations in gene expression pathways in foetal brain after AOA treatment during embryo culture, that were subsequently confirmed by qPCR. Expression was significantly increased by both array and qPCR (>1.5 fold, p<0.05) for; 1) Eomes (1.9, 2.9 fold respectively), a T-box transcription factor involved in differentiation, cell death and development, 2) Nr4a3 (1.8, 2.2 fold respectively), a steroid hormone receptor and putative transcriptional activator and 3) Nola3 (1.7, 1.9 fold respectively), a small nucleolar ribonucleoprotein involved in rRNA processing. Neurological disease, behavioural disorders, carbohydrate metabolism, cellular growth and proliferation, cell death, DNA replication, recombination and repair pathways also showed altered gene expression (>1.25 fold). qPCR was performed on 28 genes exhibiting the greatest change in expression. 24/28 genes confirmed the array data, and of the 4 genes that did not; two had expression not detected by qPCR (Snhg1, Speer6-ps1), and two contradicted array results (Atp1b3 p=0.05, Stk38l p=0.06). This study links mitochondrial dysfunction during early embryo development and persistent molecular changes in the developing foetal brain. This indicates that insults incurred during early embryo development can cause permanent changes that we predict results from aberrant epigenetic modification.

scholarly journals Potential Arctic tundra vegetation shifts in response to changing temperature, precipitation and permafrost thaw

2016 ◽  
Vol 13 (22) ◽  
pp. 6229-6245 ◽  
Author(s):  
Henk-Jan van der Kolk ◽  
Monique M. P. D. Heijmans ◽  
Jacobus van Huissteden ◽  
Jeroen W. M. Pullens ◽  
Frank Berendse
Keyword(s):  
Climate Change ◽  
The Arctic ◽  
Soil Conditions ◽  
Climate Change Scenarios ◽  
Vegetation Shifts ◽  
Permafrost Thaw ◽  
Temperature And Precipitation ◽  
Tundra Vegetation ◽  
Tundra Ecosystem ◽  
Wide Range

Abstract. Over the past decades, vegetation and climate have changed significantly in the Arctic. Deciduous shrub cover is often assumed to expand in tundra landscapes, but more frequent abrupt permafrost thaw resulting in formation of thaw ponds could lead to vegetation shifts towards graminoid-dominated wetland. Which factors drive vegetation changes in the tundra ecosystem are still not sufficiently clear. In this study, the dynamic tundra vegetation model, NUCOM-tundra (NUtrient and COMpetition), was used to evaluate the consequences of climate change scenarios of warming and increasing precipitation for future tundra vegetation change. The model includes three plant functional types (moss, graminoids and shrubs), carbon and nitrogen cycling, water and permafrost dynamics and a simple thaw pond module. Climate scenario simulations were performed for 16 combinations of temperature and precipitation increases in five vegetation types representing a gradient from dry shrub-dominated to moist mixed and wet graminoid-dominated sites. Vegetation composition dynamics in currently mixed vegetation sites were dependent on both temperature and precipitation changes, with warming favouring shrub dominance and increased precipitation favouring graminoid abundance. Climate change simulations based on greenhouse gas emission scenarios in which temperature and precipitation increases were combined showed increases in biomass of both graminoids and shrubs, with graminoids increasing in abundance. The simulations suggest that shrub growth can be limited by very wet soil conditions and low nutrient supply, whereas graminoids have the advantage of being able to grow in a wide range of soil moisture conditions and have access to nutrients in deeper soil layers. Abrupt permafrost thaw initiating thaw pond formation led to complete domination of graminoids. However, due to increased drainage, shrubs could profit from such changes in adjacent areas. Both climate and thaw pond formation simulations suggest that a wetter tundra can be responsible for local shrub decline instead of shrub expansion.

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