scholarly journals Microbial Diversity and Ecosystem Functioning in Deadwood of Black Pine of a Temperate Forest

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1418
Author(s):  
Roberta Pastorelli ◽  
Alessandro Paletto ◽  
Alessandro Elio Agnelli ◽  
Alessandra Lagomarsino ◽  
Isabella De Meo
Keyword(s):  
Gene Copy Number ◽  
Chemical Properties ◽  
Environmental Parameters ◽  
Methanogenic Archaea ◽  
Total Carbon ◽  
Co2 Production ◽  
Gene Copy ◽  
Black Pine ◽  
Decay Class ◽  
Fungal Abundance

The present study provides a deeper insight on variations of microbial abundance and community composition concerning specific environmental parameters related to deadwood decay, focusing on a mesocosm experiment conducted with deadwood samples from black pine of different decay classes. The chemical properties and microbial communities of deadwood changed over time. The total carbon percentage remained constant in the first stage of decomposition, showing a significant increase in the last decay class. The percentage of total nitrogen and the abundances of nifH harbouring bacteria significantly increased as decomposition advanced, suggesting N wood-enrichment by microbial N immobilization and/or N2-fixation. The pH slightly decreased during decomposition and significantly correlated with fungal abundance. CO2 production was higher in the last decay class 5 and positively correlated with bacterial abundance. Production of CH4 was registered in one sample of decay class 3, which correlates with the highest abundance of methanogenic archaea that probably belonged to Methanobrevibacter genus. N2O consumption increased along decomposition progress, indicating a complete reduction of nitrate compounds to N2 via denitrification, as proved by the highest nosZ gene copy number in decay class 5. Conversely, our results highlighted a low involvement of nitrifying communities in deadwood decomposition.

scholarly journals Methane and Nitrous Oxide Flux after Biochar Application in Subtropical Acidic Paddy Soils under Tobacco-Rice Rotation

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yibin Huang ◽  
Chengji Wang ◽  
Cheng Lin ◽  
Yushu Zhang ◽  
Xi Chen ◽  
...  
Keyword(s):  
Nitrous Oxide ◽  
Copy Number ◽  
Gene Copy Number ◽  
Methanogenic Archaea ◽  
Soil Bulk Density ◽  
Gene Copy ◽  
Closed Chamber ◽  
Cropping Season ◽  
Water Saturated ◽  
Biochar Amendment

AbstractBiochar amendment is a good means of mitigating methane (CH4) and nitrous oxide (N2O) emissions. However, the effects of biochar amendment on N2O and CH4 reduction in soil under rotation with different soil moisture contents is not well understood. To understand CH4 and N2O flux from soil with biochar amendment under water-unsaturated and water-saturated conditions, a field experiment was conducted in a tobacco-rice rotation field in subtropical China to investigate N2O and CH4 emissions following soil amendment with tobacco straw biochar at rates of 0, 10, 40 and 80 t·ha−1 (B0, B10, B40 and B80, respectively). N2O and CH4 emissions were monitored by a closed-chamber method in the water-unsaturated tobacco (UT) and water-saturated rice (SR) seasons during the 2015 planting season. The soil pH increased from 5.4 in the control to 6.1 in the soil amended with biochar at 80 t·ha−1 in the UT season. During both the UT and SR seasons, with biochar amendment at 40 and 80 t·ha−1, the soil bulk density (BD) decreased, while the soil organic matter (SOM) and available potassium (Av. K) contents increased. N2O flux was significantly greater in UT than in SR in the controls but decreased with the application of biochar during both the UT and SR seasons. The cumulative CH4 emission decreased with the rate of biochar application and the methanotroph pmoA gene copy number in soils and increased with the methanogenic archaea 16Sr DNA gene copy number in soils during the rice-cropping season. These results indicated that biochar amendment could decrease methanogenic archaea and increase of methanotroph pmoA gene, which are the mechanistic origin for CH4 reduction.

scholarly journals The establishment of apple orchards as temperate forest garden systems and their impact on indigenous bacterial and fungal population abundance in Southern Ontario, Canada

2016 ◽  
Vol 32 (2) ◽  
pp. 157-168 ◽  
Author(s):  
P.C. Wartman ◽  
K.E. Dunfield ◽  
K. Khosla ◽  
C. Loucks ◽  
R.C. Van Acker ◽  
...  
Keyword(s):  
Apple Tree ◽  
Chemical Properties ◽  
Am Fungi ◽  
Gene Copy ◽  
Future Research ◽  
Chain Reactions ◽  
Soil Microbial ◽  
Fungal Abundance ◽  
Forest Garden ◽  
Plant Plant

AbstractThis research investigated soil microbial abundances affected by different ground management systems in establishing apple (Malus domestica cv. Idared, M9) orchards in Ontario, Canada. Four treatments, including forest garden systems with and without compost (FGSC and FGS), and grass understory systems with and without compost (GC and G), were assessed over two establishment years for gene copy abundance of soil arbuscular mycorrhizal (AM) fungi, total fungi and total bacteria using quantitative real-time polymerase chain reactions. Time had a greater effect on all three soil microbial abundances, with total bacterial and AM fungi decreasing and total fungal abundance increasing from spring 2013 to fall 2014. The changes were greatest between the sampling dates of fall 2013 and spring 2014, which is 1 yr after the establishment of the experimental apple plots. There were no significant differences in soil microbial abundances between treatments at any specific sampling date. Apple tree trunk circumference was greatest for FGSC and FGS after 2 yr, but no significant differences in GC and G treatments. In the last sampling period, fall 2014, FGSC plots had significantly greater trunk circumferences compared with G plots. Soil chemical properties neither changed over the 2 yr, nor did they differ between treatments at any one sampling time. We conclude that the apple-based FGS treatments can benefit apple tree growth and there is a basis for future research to explore specific plant–plant, plant–microbe and microbe–microbe relations in FGSs.

Impact of Dursban and Abate on Microbial Numbers and Some Chemical Properties of Standing Ponds

1975 ◽  
Vol 10 (1) ◽  
pp. 33-41 ◽  
Author(s):  
J. Butcher ◽  
M. Boyer ◽  
CD. Fowle
Keyword(s):  
Carbon Dioxide ◽  
Active Ingredient ◽  
Algal Blooms ◽  
Chemical Properties ◽  
Total Carbon ◽  
Dissolved Carbon ◽  
Photosynthetic Productivity ◽  
Dissolved Carbon Dioxide ◽  
Microbial Numbers

Abstract Eleven small ponds, lined with polyethylene, were used to assess the consequences of applications of *DursbanR at 0.004, 0.030, 0.100 and 1.000 ppm and AbateR at 0.025 and 0.100 ppm active ingredient. The treated ponds showed a more pronounced long-term increase in pH and dissolved oxygen and decreasing total and dissolved carbon dioxide in comparison with untreated ponds. Algal blooms were of longer duration in treated ponds than in controls. Total photosynthetic productivity was higher in treated ponds but bacterial numbers did not change significantly. Photosynthetic productivity was estimated by following the changes in total carbon dioxide.

scholarly journals Estimating Copy-Number Proportions: The Comeback of Sanger Sequencing

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 283
Author(s):  
Eyal Seroussi
Keyword(s):  
Copy Number ◽  
Sanger Sequencing ◽  
Cytosine Methylation ◽  
Direct Sequencing ◽  
Information Source ◽  
Gene Copy Number ◽  
Cost Effective ◽  
Gene Copy ◽  
Base Editing ◽  
Recent Developments

Determination of the relative copy numbers of mixed molecular species in nucleic acid samples is often the objective of biological experiments, including Single-Nucleotide Polymorphism (SNP), indel and gene copy-number characterization, and quantification of CRISPR-Cas9 base editing, cytosine methylation, and RNA editing. Standard dye-terminator chromatograms are a widely accessible, cost-effective information source from which copy-number proportions can be inferred. However, the rate of incorporation of dye terminators is dependent on the dye type, the adjacent sequence string, and the secondary structure of the sequenced strand. These variable rates complicate inferences and have driven scientists to resort to complex and costly quantification methods. Because these complex methods introduce their own biases, researchers are rethinking whether rectifying distortions in sequencing trace files and using direct sequencing for quantification will enable comparable accurate assessment. Indeed, recent developments in software tools (e.g., TIDE, ICE, EditR, BEEP and BEAT) indicate that quantification based on direct Sanger sequencing is gaining in scientific acceptance. This commentary reviews the common obstacles in quantification and the latest insights and developments relevant to estimating copy-number proportions based on direct Sanger sequencing, concluding that bidirectional sequencing and sophisticated base calling are the keys to identifying and avoiding sequence distortions.

scholarly journals Nongenotoxic ABCB1 activator tetraphenylphosphonium can contribute to doxorubicin resistance in MX-1 breast cancer cell line

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Raimonda Kubiliute ◽  
Indre Januskeviciene ◽  
Ruta Urbanaviciute ◽  
Kristina Daniunaite ◽  
Monika Drobniene ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cell Line ◽  
Protein Level ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Common Mechanism ◽  
Dna Hypomethylation ◽  
Mesenchymal Transition ◽  
Molecular Features

AbstractHyperactivation of ABC transporter ABCB1 and induction of epithelial–mesenchymal transition (EMT) are the most common mechanism of acquired cancer chemoresistance. This study describes possible mechanisms, that might contribute to upregulation of ABCB1 and synergistically boost the acquisition of doxorubicin (DOX) resistance in breast cancer MX-1 cell line. DOX resistance in MX-1 cell line was induced by a stepwise increase of drug concentration or by pretreatment of cells with an ABCB1 transporter activator tetraphenylphosphonium (TPP+) followed by DOX exposure. Transcriptome analysis of derived cells was performed by human gene expression microarrays and by quantitative PCR. Genetic and epigenetic mechanisms of ABCB1 regulation were evaluated by pyrosequencing and gene copy number variation analysis. Gradual activation of canonical EMT transcription factors with later activation of ABCB1 at the transcript level was observed in DOX-only treated cells, while TPP+ exposure induced considerable activation of ABCB1 at both, mRNA and protein level. The changes in ABCB1 mRNA and protein level were related to the promoter DNA hypomethylation and the increase in gene copy number. ABCB1-active cells were highly resistant to DOX and showed morphological and molecular features of EMT. The study suggests that nongenotoxic ABCB1 inducer can possibly accelerate development of DOX resistance.

scholarly journals Chromosome X aneusomy and androgen receptor gene copy number aberrations in apocrine carcinoma of the breast

2021 ◽  
Author(s):  
Anna Cremonini ◽  
Luca Saragoni ◽  
Luca Morandi ◽  
Angelo G. Corradini ◽  
Caterina Ravaioli ◽  
...  
Keyword(s):  
Androgen Receptor ◽  
Receptor Gene ◽  
Gene Copy Number ◽  
Androgen Receptor Gene ◽  
Gene Copy ◽  
Immunohistochemical Expression ◽  
Neoplastic Cells ◽  
Genetic Changes ◽  
Rare Tumours ◽  
Regulator Genes

AbstractCarcinomas with apocrine differentiation (CAD) of the breast are rare tumours typically presenting high immunohistochemical expression of androgen receptor (AR) which is a target molecule for personalised therapy. To date, no studies have evaluated the genetic changes that are associated with AR immunohistochemical expression in CADs. The present work aims to characterise AR status in CADs. Twenty CAD tumours were studied with immunohistochemistry, in situ fluorescence hybridization and DNA methylation analysis, to evaluate AR expression and its regulator status. All tumours demonstrated high AR immunohistochemical expression, with over 95% of the neoplastic cells showing AR positivity in 19/20 cases. CADs showed AR gene copy loss in a percentage of neoplastic cells ranging from 5 to 84% (mean 48.93%). AR regulator genes, including the MAGE family, UXT and FLNA, presented variable methylation levels, but were mainly hypomethylated and therefore all transcriptionally active. The results of this study indicate that CADs present AR monosomy, paralleled by higher transcriptional activity of the gene with potential to influence response to AR deprivation therapy.

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