scholarly journals δ13C and δD Values of n-Alkanes from In-Reservoir Biodegraded Oils: Implications for Understanding the Mechanisms of Biodegradation and for Petroleum Exploration

Geosciences ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 365
Author(s):  
Nikolai Pedentchouk ◽  
Barry Bennett ◽  
Steve Larter
Keyword(s):  
Organic Compounds ◽  
Source Rock ◽  
Petroleum Exploration ◽  
Type Ii ◽  
Site Specific ◽  
Specific Process ◽  
Biodegraded Oils ◽  
Biodegradation Process ◽  
Oil Source ◽  
A Site

This study investigates the magnitude and direction of stable C and H isotope shifts of n-C15–30 alkanes from biodegraded oils sourced from Type II (Oil suite S) and Type II/III (Oil suite H) kerogens. Compound-specific isotope data show a 2.0‰ 13C-enrichment and no D-enrichment of n-alkanes in the most biodegraded oil from sample suite S. Similarly, there is a 1.5–2.5‰ 13C-enrichment and no D-enrichment in Oil suite H. Overall, there is a <2.5‰ δ13C and <20‰ δD variability among individual n-alkanes in the whole sequence of biodegradation. N-alkanes from the least biodegraded Oil H samples are 2–4‰ 13C-enriched in comparison with the least biodegraded Oil S. However, there are no differences in the δD values of n-alkanes in these samples. Our indirect isotopic evidence suggests (1) a site-specific biodegradation process, most likely at position C-2 and/or C-3 or another site-specific process, and (2) a significant D/H exchange between organic compounds in the source rock and isotopically similar marine formation waters. We conclude that, unlike δD methodology, investigation of δ13C composition of n-alkanes has strong potential as a supplementary tool for oil–oil and oil–source-rock correlation even in biodegraded oils when n-alkanes are present.

scholarly journals V(D)J recombination: signal and coding joint resolution are uncoupled and depend on parallel synapsis of the sites.

1993 ◽  
Vol 13 (3) ◽  
pp. 1363-1370 ◽  
Author(s):  
K M Sheehan ◽  
M R Lieber
Keyword(s):  
Genome Stability ◽  
Lymphoid Cells ◽  
Chromosomal Translocations ◽  
Synaptic Inhibition ◽  
Site Specific ◽  
Coding Sequences ◽  
Specific Process ◽  
A Site ◽  
Joint Resolution

V(D)J recombination in lymphoid cells is a site-specific process in which the activity of the recombinase enzyme is targeted to signal sequences flanking the coding elements of antigen receptor genes. The order of the steps in this reaction and their mechanistic interdependence are important to the understanding of how the reaction fails and thereby contributes to genomic instability in lymphoid cells. The products of the normal reaction are recombinant joints linking the coding sequences of the receptor genes and, reciprocally, the signal ends. Extrachromosomal substrate molecules were modified to inhibit the physical synapsis of the recombination signals. In this way, it has been possible to assess how inhibiting the formation of one joint affects the resolution efficiency of the other. Our results indicate that signal joint and coding joint formation are resolved independently in that they can be uncoupled from each other. We also find that signal synapsis is critical for the generation of recombinant products, which greatly restricts the degree of potential single-site cutting that might otherwise occur in the genome. Finally, inversion substrates manifest synaptic inhibition at much longer distances than do deletion substrates, suggesting that a parallel rather than an antiparallel alignment of the signals is required during synapsis. These observations are important for understanding the interaction of V(D)J signals with the recombinase. Moreover, the role of signal synapsis in regulating recombinase activity has significant implications for genome stability regarding the frequency of recombinase-mediated chromosomal translocations.

scholarly journals A Site-Specific Genetic Modification for Induction of Pluripotency and Subsequent Isolation of Derived Lung Alveolar Epithelial Type II Cells

Stem Cells ◽  
2014 ◽  
Vol 32 (2) ◽  
pp. 402-413 ◽  
Author(s):  
Qing Yan ◽  
Yuan Quan ◽  
Huanhuan Sun ◽  
Xinmiao Peng ◽  
Zhengyun Zou ◽  
...  
Keyword(s):  
Genetic Modification ◽  
Type Ii Cells ◽  
Type Ii ◽  
Site Specific ◽  
Alveolar Epithelial ◽  
A Site

A Site-Specific Approach for the Development of Soil Cleanup Guidelines for Trace Organic Compounds

2021 ◽  
pp. 321-342
Author(s):  
B. G. Ibbotson ◽  
D. M. Gorber ◽  
D. W. Reades ◽  
D. Smyth ◽  
I. Munro ◽  
...  
Keyword(s):  
Organic Compounds ◽  
Trace Organic Compounds ◽  
Site Specific ◽  
Specific Approach ◽  
Soil Cleanup ◽  
A Site ◽  
Trace Organic

scholarly journals Oil chemometrics and geochemical correlation in the Weixinan Sag, Beibuwan Basin, South China Sea

2020 ◽  
Vol 38 (6) ◽  
pp. 2695-2710
Author(s):  
Yao-Ping Wang ◽  
Xin Zhan ◽  
Tao Luo ◽  
Yuan Gao ◽  
Jia Xia ◽  
...  
Keyword(s):  
Source Rock ◽  
Principal Component ◽  
Sedimentary Basins ◽  
Oil Field ◽  
Source Rocks ◽  
Petroleum Exploration ◽  
Crude Oils ◽  
Geochemical Parameters ◽  
Group I ◽  
Oil Source

The oil–oil and oil–source rock correlations, also termed as geochemical correlations, play an essential role in the construction of petroleum systems, guidance of petroleum exploration, and definition of reservoir compartments. In this study, the problems arising from oil–oil and oil–source rock correlations were investigated using chemometric methods on oil and source rock samples from the WZ12 oil field in the Weixinan sag in the Beibuwan Basin. Crude oil from the WZ12 oil field can be classified into two genetic families: group A and B, using multidimensional scaling and principal component analysis. Similarly, source rocks of the Liushagang Formation, including its first, second, and third members, can be classified into group I and II, corresponding to group B and A crude oils, respectively. The principle geochemical parameters in the geochemical correlation for the characterisation and classification of crude oils and source rocks were 4MSI, C27Dia/C27S, and C24 Tet/C26 TT. This study provides insights into the selection of appropriate geochemical parameters for oil–oil and oil–source rock correlations, which can also be applied to other sedimentary basins.

Site-specific control of silica mineralization on DNA using a designed peptide

2016 ◽  
Vol 52 (21) ◽  
pp. 4010-4013 ◽  
Author(s):  
Makoto Ozaki ◽  
Kazuma Nagai ◽  
Hiroto Nishiyama ◽  
Takaaki Tsuruoka ◽  
Satoshi Fujii ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Organic Compounds ◽  
Peptide Nucleic Acids ◽  
Inorganic Compounds ◽  
Specific Method ◽  
Site Specific ◽  
A Site ◽  
Specific Control

We developed a site-specific method for precipitating inorganic compounds using organic compounds, DNA, and designed peptides with peptide nucleic acids (PNAs).

scholarly journals Selection on the Genes of Euplotes crassus Tec1 and Tec2 Transposons: Evolutionary Appearance of a Programmed Frameshift in a Tec2 Gene Encoding a Tyrosine Family Site-Specific Recombinase

2003 ◽  
Vol 2 (1) ◽  
pp. 95-102 ◽  
Author(s):  
Thomas G. Doak ◽  
David J. Witherspoon ◽  
Carolyn L. Jahn ◽  
Glenn Herrick
Keyword(s):  
Purifying Selection ◽  
Ciliated Protozoa ◽  
Type Ii ◽  
Gene Encoding ◽  
Site Specific ◽  
Euplotes Crassus ◽  
Type Site ◽  
Selection For ◽  
A Site

ABSTRACT The Tec1 and Tec2 transposons of the ciliate Euplotes crassus carry a gene for a tyrosine-type site-specific recombinase. The expression of the Tec2 gene apparently uses a programmed +1 frameshift. To test this hypothesis, we first examined whether this gene has evolved under purifying selection in Tec1 and Tec2. Each element carries three genes, and each has evolved under purifying selection for the function of its encoded protein, as evidenced by a dearth of nonsynonymous changes. This distortion of divergence is apparent in codons both 5′ and 3′ of the frameshift site. Thus, Tec2 transposons have diverged from each other while using a programmed +1 frameshift to produce recombinase, the function of which is under purifying selection. What might this function be? Tyrosine-type site-specific recombinases are extremely rare in eukaryotes, and Tec elements are the first known eukaryotic type II transposons to encode a site-specific recombinase. Tec elements also encode a widespread transposase. The Tec recombinase might function in transposition, resolve products of transposition (bacterial replicative transposons use recombinase or resolvase to separate joined replicons), or provide a function that benefits the ciliate host. Transposons in ciliated protozoa are removed from the macronucleus, and it has been proposed that the transposons provide this “excisase” activity.

V(D)J recombination: signal and coding joint resolution are uncoupled and depend on parallel synapsis of the sites

1993 ◽  
Vol 13 (3) ◽  
pp. 1363-1370
Author(s):  
K M Sheehan ◽  
M R Lieber
Keyword(s):  
Genome Stability ◽  
Lymphoid Cells ◽  
Chromosomal Translocations ◽  
Synaptic Inhibition ◽  
Site Specific ◽  
Coding Sequences ◽  
Specific Process ◽  
A Site ◽  
Joint Resolution

V(D)J recombination in lymphoid cells is a site-specific process in which the activity of the recombinase enzyme is targeted to signal sequences flanking the coding elements of antigen receptor genes. The order of the steps in this reaction and their mechanistic interdependence are important to the understanding of how the reaction fails and thereby contributes to genomic instability in lymphoid cells. The products of the normal reaction are recombinant joints linking the coding sequences of the receptor genes and, reciprocally, the signal ends. Extrachromosomal substrate molecules were modified to inhibit the physical synapsis of the recombination signals. In this way, it has been possible to assess how inhibiting the formation of one joint affects the resolution efficiency of the other. Our results indicate that signal joint and coding joint formation are resolved independently in that they can be uncoupled from each other. We also find that signal synapsis is critical for the generation of recombinant products, which greatly restricts the degree of potential single-site cutting that might otherwise occur in the genome. Finally, inversion substrates manifest synaptic inhibition at much longer distances than do deletion substrates, suggesting that a parallel rather than an antiparallel alignment of the signals is required during synapsis. These observations are important for understanding the interaction of V(D)J signals with the recombinase. Moreover, the role of signal synapsis in regulating recombinase activity has significant implications for genome stability regarding the frequency of recombinase-mediated chromosomal translocations.

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