DNA Isolation from Achieved Formalin-Fixed Paraffin-Embedded Tissues in a Series of 212 Thyroid Carcinoma Cases: The Influence of Preanalytical Factors on DNA Quantity and Purity

Nechifor-Boilă, Adela; Bănescu, Claudia; Zahan, Ancuța Elena; Moldovan, Valeriu; Szász, Emőke Andrea; Borda, Angela

doi:10.1136/jim-2019-001134

Cited by 3 publications

(2 citation statements)

References 27 publications

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“…RNA quality was assessed by RNase free agarose gel electrophoresis, Agilent 2100 Bioanalyzer, and NanoPhotometer spectrophotometer. Nine cDNA libraries were constructed, and the library quality was checked by the NanoPhotometer spectrophotometer (Nechifor-Boila et al, 2020), Qubit2.0 Fluorometer (Nechifor-Boila et al, 2020) and Agilent 2100 bioanalyzer (Panaro et al, 2000). The cDNA libraries were sequenced on an Illumina sequencing platform (Illumina HiSeq TM 4000) by Gene Denovo Biotechnology Co. (Guangzhou, China).…”

Section: Ofp Gene Expression Analysismentioning

confidence: 99%

Genome-wide identification and characterization of the OFP gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Wang

TaiLi²,

Sun³

et al. 2021

PeerJ

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Ovate family proteins (OFPs) are a class of proteins with a conserved OVATE domain that contains approximately 70 amino acid residues. OFP proteins are plant-specific transcription factors that participate in regulating plant growth and development and are widely distributed in many plants. Little is known about OFPs in Brassica rapa to date. We identified 29 OFP genes in Brassica rapa and found that they were unevenly distributed on 10 chromosomes. Intron gain events may have occurred during the structural evolution of BraOFP paralogues. Syntenic analysis verified Brassica genome triplication, and whole genome duplication likely contributed to the expansion of the OFP gene family. All BraOFP genes had light responsive- and phytohormone-related cis-acting elements. Expression analysis from RNA-Seq data indicated that there were obvious changes in the expression levels of six OFP genes in the Brassica rapa hybrid, which may contribute to the formation of heterosis. Finally, we found that the paralogous genes had different expression patterns among the hybrid and its parents. These results provide the theoretical basis for the further analysis of the biological functions of OFP genes across the Brassica species.

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Section: Ofp Gene Expression Analysismentioning

confidence: 99%

Genome-wide identification and characterization of the OFP gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Wang

TaiLi²,

Sun³

et al. 2021

PeerJ

View full text Add to dashboard Cite

show abstract

“…RNA quality was assessed by RNase free agarose gel electrophoresis, Agilent 2100 Bioanalyzer, and NanoPhotometer spectrophotometer. Nine cDNA libraries were constructed, and the library quality was checked by the NanoPhotometer spectrophotometer (Nechifor-Boila et al, 2020), Qubit2.0 Fluorometer (Nechifor-Boila et al, 2020 and Agilent 2100 bioanalyzer (Panaro et al, 2000). The cDNA libraries were sequenced on an Illumina sequencing platform (Illumina HiSeq™4000) by Gene Denovo Biotechnology Co. (Guangzhou, China).…”

Section: Ofp Gene Expression Analysismentioning

confidence: 99%

Peer Review #2 of "Genome-wide identification and characterization of the OFP gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis) (v0.1)"

2021

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Ovate Family Proteins (OFPs) are a class of proteins with a conserved OVATE domain that contains approximately 70 amino acid residues. OFP proteins are plant-specific transcription factors that participate in regulating plant growth and development and are widely distributed in many plants. Little is known about OFPs in Brassica rapa to date. We identified 29 OFP genes in Brassica rapa and found that they were unevenly distributed on 10 chromosomes. Intron gain events may have occurred during the structural evolution of BraOFP paralogues. Syntenic analysis verified Brassica genome triplication, and whole genome duplication likely contributed to the expansion of the OFP gene family. All BraOFP genes had light responsive-and phytohormone-related cis-acting elements. Expression analysis from RNA-Seq data indicated that there were obvious changes in the expression levels of six OFP genes in the Brassica rapa hybrid, which may contribute to the formation of heterosis. Finally, we found that the paralogous genes had different expression patterns among the hybrid and its parents. These results provide the theoretical basis for the further analysis of the biological functions of OFP genes across the Brassica species.

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HPV Detection in Breast Tumors and Associated Risk Factors in Northeastern Brazil

Nascimento,

São Marcos,

Fontes

et al. 2024

Cells

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Breast cancer risk factors include lifestyle, genetic–hormonal influences, and viral infections. Human papillomavirus (HPV), known primarily as the etiological agent of cervical cancer, also appears active in breast carcinogenesis, as evidenced in our study of 56 patients from northeastern Brazil. We assessed the clinical and sociodemographic characteristics, correlating them with various breast cancer tumor types. HPV detection involved amplifying the L1 region, with viral load measured using the E2/E6 ratio and viral activity indicated by E5 oncogene expression. Predominantly, patients over 56 years of age with healthy lifestyles showed a high incidence of invasive ductal carcinoma and triple-negative breast cancer. HPV was detected in 35.7% of cases, mostly HPV16, which is associated with high viral loads (80 copies per cell) and significant E5 expression. These results hint at a possible link between HPV and breast carcinogenesis, necessitating further studies to explore this association and the underlying viral mechanisms.

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DNA Isolation from Achieved Formalin-Fixed Paraffin-Embedded Tissues in a Series of 212 Thyroid Carcinoma Cases: The Influence of Preanalytical Factors on DNA Quantity and Purity

Cited by 3 publications

References 27 publications

Genome-wide identification and characterization of the OFP gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Genome-wide identification and characterization of the OFP gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Peer Review #2 of "Genome-wide identification and characterization of the OFP gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis) (v0.1)"

HPV Detection in Breast Tumors and Associated Risk Factors in Northeastern Brazil

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