Seasonal comparison of potential denitrification rates and nitrogen functional genes with sediment depths in the wetland, Korea

Wetlands provide not only habitats for a wide range of organisms but also ecological functions of degrading and removing pollutants from water body through a variety of physical, chemical and biological processes. Seasonal variation including recent increases in the frequency of floods and droughts have affected the hydrological environment of wetlands. Furthermore, these effects may result in changes in redox conditions in the nitrogen biogeochemical process in wetland sediments. Therefore, in this study, the potential denitrification rate and denitrification-related gene quantitative analysis was performed to investigate seasonal nitrogen dynamics of wetland sediments associated with surface and groundwater interactions in Baekseok reservoir wetlands (Gunsan-si, Jeollabuk Province, Korea). Sediment from two different sites (i.e., PA and PB) in wetland were collected with different depths in June and December 2019 to investigate seasonal effects on denitrification with sediment depths. Potential denitrification rate experiments were performed using the acetylene inhibition technique, and denitrification-related gene quantification was performed by qPCR analysis. As a result of potential denitrification rate, PA sites ranged from 2.67&#8211;3.27 ng N2O/g/hr and 3.13&#8211;15.13 ng N2O/g/hr in June and December, respectively. PB sites ranged from 2.43-6.30 ng N2O/g/hr and 5.47-6.30 ng N2O/g/hr. Overall, higher levels were observed at 0&#8211;10 cm, with higher denitrification rates in December than in June. The qPCR analysis showed that the narG, nirS and nosZ gene copy number ranges for the PA site in June showed 1.82 x 106 &#8211; 6.15 x 107 copies/g, and in December 7.71 x 105 &#8211; 5.97 x 108 copies/g. The narG, nirS and nosZ gene copy number ranges for the PB site in June showed 3.53 x 105 &#8211; 3.86 x 108 copies/g, and in December, 1.24 x 106 &#8211; 3.47 x 108 copies/g. Overall, both sites had higher copy numbers in December than in June, corresponding to an increase in potential denitrification rate in December.

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Screening and Absolute Quantification of a β-lactamase Resistance Gene NDM-1 in Lake Sediment

10.21203/rs.3.rs-608035/v1 ◽

2021 ◽

Author(s):

Rajeev Ranjan ◽

Shashidhar Thatikonda

Keyword(s):

Lake Sediment ◽

Copy Number ◽

Quantitative Polymerase Chain Reaction ◽

Horizontal Transmission ◽

Gene Copy Number ◽

Absolute Quantification ◽

Gene Copy ◽

Qpcr Analysis ◽

Wide Range ◽

Template Dna

Abstract The extensive usage of antibiotics in humans and veterinary medicine and their discharge into the aquatic environment hasten the growth, selection, and horizontal transmission of ARGs in a given bacterial community. New Delhi Metallo-β-lactamase-1(NDM-1) is an enzyme that hydrolyzes a wide range of β-lactams antibiotics, including carbapenems. The rapid distribution of NDM-1 harboring bacteria accounts for a significant public health menace worldwide. The presence of the NDM-1 inhibited the potential of β–lactam antibiotics for treating infections caused by bacterial strains carrying such resistances, leaving minimal treatment options available. NDM-1 harboring bacteria have been detected in clinical specimens and environmental compartments where bacterial infections are ubiquitous. In this study, identification and absolute quantification of NDM-1 in sixteen lake sediment samples collected in and around Hyderabad, India, was carried out using a real-time quantitative polymerase chain reaction (qPCR) and results were expressed in gene copy number/ng (nanogram) of template DNA. 13 samples (out of 16) shown a positive signal for NDM-1 during qPCR analysis. Durgamcheru lake, Kandi lake, and Singur dam showed a negative signal for the NDM-1 during qPCR analysis among the tested samples. The remaining sampling locations tested positive with the highest gene copy number/ng of template DNA observed in the Amberpet STP (71.8). Hierarchical clustering analysis was performed to categorize the sampling location into different clusters based on pollution sources and observed results expressed in the form of a dendrogram.

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The Role of Cell Growth-Related Gene Copy Number Variation in Autoimmune Thyroid Disease

Biological Trace Element Research ◽

10.1007/s12011-019-01880-7 ◽

2019 ◽

Vol 195 (2) ◽

pp. 409-416 ◽

Cited By ~ 2

Author(s):

Yunfeng Guan ◽

Lixiang Liu ◽

Qingzhen Jia ◽

Xing Jin ◽

Yi Pang ◽

...

Keyword(s):

Cell Growth ◽

Copy Number ◽

Autoimmune Thyroid Disease ◽

Gene Copy Number ◽

Gene Copy ◽

Related Gene ◽

Autoimmune Thyroid ◽

Gene Copy Number Variation ◽

Number Variation

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Effect of 51p1-related gene copy number (V1-69 locus) on production of hepatitis C-associated cryoglobulins

Clinical & Experimental Immunology ◽

10.1046/j.1365-2249.2001.01406.x ◽

2001 ◽

Vol 123 (1) ◽

pp. 88-93 ◽

Cited By ~ 9

Author(s):

E. H. Sasso ◽

P. Ghillani ◽

L. Musset ◽

J. C. Piette ◽

P. Cacoub

Keyword(s):

Hepatitis C ◽

Copy Number ◽

Gene Copy Number ◽

Gene Copy ◽

Related Gene

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Assessment of HER-2/neu, с-MYC and CCNE1 gene copy number variations and protein expression in endometrial carcinomas

Experimental Oncology ◽

10.32471/exp-oncology.2312-8852.vol-41-no-2.12973 ◽

2019 ◽

Vol 41 (2) ◽

Author(s):

L.G. Buchynska ◽

◽

O.V. Brieieva* ◽

N.P. Iurchenko ◽

◽

...

Keyword(s):

Protein Expression ◽

Copy Number ◽

Gene Copy Number ◽

Copy Number Variations ◽

Gene Copy ◽

Her 2 ◽

Endometrial Carcinomas

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Faculty Opinions recommendation of Diet and the evolution of human amylase gene copy number variation.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1092307.546722 ◽

2007 ◽

Author(s):

Magnus Ingelman-Sundberg

Keyword(s):

Copy Number Variation ◽

Copy Number ◽

Gene Copy Number ◽

Gene Copy ◽

Amylase Gene ◽

Gene Copy Number Variation ◽

Number Variation

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Faculty Opinions recommendation of RNA polymerase I activators count and adjust ribosomal RNA gene copy number.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.734776122.793556076 ◽

2019 ◽

Author(s):

Angela Taddei

Keyword(s):

Rna Polymerase ◽

Ribosomal Rna ◽

Copy Number ◽

Gene Copy Number ◽

Rna Polymerase I ◽

Gene Copy ◽

Ribosomal Rna Gene ◽

Polymerase I

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Estimating Copy-Number Proportions: The Comeback of Sanger Sequencing

Genes ◽

10.3390/genes12020283 ◽

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.

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

Scientific Reports ◽

10.1038/s41598-021-86120-6 ◽

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.

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