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Journal of Obstetrics and Gynaecology :... Aug 2022This study aimed to investigate the association between deoxyribonucleic acid (DNA) integrity parameters and advanced maternal age (AMA)-related infertility. The...
This study aimed to investigate the association between deoxyribonucleic acid (DNA) integrity parameters and advanced maternal age (AMA)-related infertility. The granulosa cells and the lymphocytes obtained from 119 infertile women were recruited. Patients were divided into two groups: the AMA group (≥35 years, = 26) and the non-AMA group (<35 years, = 93). The tail length, tail moment and tail DNA percentage were evaluated as the DNA integrity parameters using comet assay. Infertility duration (=.001), luteinising hormone (=.01) and progesterone levels (<.0001) were higher and smoking was more prevalent in the AMA group (=.001). AMA group was stimulated with higher gonadotropin doses (=.04) and had decreased anti-mullerian hormone levels (<.0001). All of DNA integrity parameters were distributed homogenously between the groups; however, the tail length of lymphocytes was higher (=.02) in the AMA group. Fertilisation was lower (=.02), oocyte quality was tended to be poor (=.03) and blastocyst transfer was lower in the AMA group (=.03). Embryo quality was distributed homogenously between the groups. Implantation, clinical pregnancy and live birth rates were similar between the groups. Impact Statement Advanced maternal age (AMA)-related infertility is associated with diminished ovarian reserve and alteration in follicular environment resulting in poor oocyte quality; however, the exact pathophysiologic mechanism is not clear. Tail length, tail deoxyribonucleic acid (DNA) percentage, tail moment of granulosa cells were nonsignificantly higher in the AMA group compared to younger patients. All of the DNA integrity parameters of lymphocytes were nonsignificantly higher; however, only tail length of lymphocytes was statistically higher in the AMA group than the non-AMA group. A positive correlation was observed between DNA integrity parameters of lymphocytes and body mass index. There were no correlations between DNA integrity parameters of granulosa cells and lymphocyte and infertility duration, gonadotropin dose, duration of ovarian stimulation, oocyte score, embryo score, basal hormone levels and anti-mullerian hormone levels. Our findings offer new insight for further understanding the role of granulosa cells in mediating the poor reproductive outcome of ageing patients. Understanding the mechanisms of ovarian ageing and poor oocyte quality in women with AMA may help to identify specific targets for improving oocyte quality with ageing.
Topics: Anti-Mullerian Hormone; DNA; Female; Fertilization in Vitro; Gonadotropins; Granulosa Cells; Humans; Infertility, Female; Luteinizing Hormone; Lymphocytes; Ovulation Induction; Pregnancy; Pregnancy Rate; Progesterone
PubMed: 35611871
DOI: 10.1080/01443615.2022.2054689 -
Sub-cellular Biochemistry 2022Nucleic acid methylation is a fundamental epigenetic mechanism that impinges upon several cellular attributes, including metabolism and energy production. The... (Review)
Review
Nucleic acid methylation is a fundamental epigenetic mechanism that impinges upon several cellular attributes, including metabolism and energy production. The dysregulation of deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) methylation can lead to metabolic rewiring in the cell, which in turn facilitates tumor development. Here, we review the current knowledge on the interplay between DNA/RNA methylation and metabolic programs in cancer cells. We also discuss the mechanistic role of these pathways in tumor development and progression.
Topics: Humans; RNA; DNA Methylation; Neoplasms; DNA; Homeostasis
PubMed: 36301496
DOI: 10.1007/978-3-031-07634-3_7 -
Biosensors & Bioelectronics Oct 2023Deoxyribonucleic acid (DNA) is a carrier of genetic information. DNA hybridization is characterized by predictability, diversity, and specificity owing to the strict... (Review)
Review
Deoxyribonucleic acid (DNA) is a carrier of genetic information. DNA hybridization is characterized by predictability, diversity, and specificity owing to the strict complementary base-pairing assembly mode, which stimulates the use of DNA to build a variety of nanomachines, including DNA tweezers, motors, walkers, and robots. DNA nanomachines have become prevalent for signal amplification and transformation in the field of biosensing, providing a new method for constructing highly sensitive sensing analysis strategies. DNA tweezers have exhibited unique advantages in biosensing applications owing to their simple structures and fast responses. The two-state conformation of DNA tweezers, the open and closed states, enable them to open and close autonomously after stimulation, thus facilitating the quick detection of corresponding signal changes of different targets. This review discusses the recent progress in the application of DNA nanotweezers in the field of biosensing, and the trends in their development for application in the field of biosensing are summarized.
Topics: DNA; Biosensing Techniques; Nucleic Acid Hybridization; Nucleic Acid Conformation
PubMed: 37421799
DOI: 10.1016/j.bios.2023.115445 -
Analytica Chimica Acta Apr 2020Due to its unique programmability, nanosized structure, and biocompatible properties, deoxyribonucleic acid (DNA) has attracted increasing attention for the construction... (Review)
Review
Due to its unique programmability, nanosized structure, and biocompatible properties, deoxyribonucleic acid (DNA) has attracted increasing attention for the construction of versatile nanostructures and nanomaterials. This review summarizes the recent developments in DNA-templated fluorescent nanomaterials, including DNA-stabilized quantum dots (QDs) and DNA-templated metal nanoclusters (NCs), as well as their applications in bioanalysis. These fluorescent nanomaterials not only have good fluorescence properties but also exhibit excellent performance in DNA recognition, which greatly expands the range of their bioanalytical applications. Finally, we discuss some current challenges and future work in this field, with the goal of further promoting the potential applications and developments of DNA-templated fluorescent nanomaterials in biochemical analysis.
Topics: Biosensing Techniques; DNA; Fluorescent Dyes; Ions; Nanostructures; Particle Size; Proteins; Spectrometry, Fluorescence; Surface Properties
PubMed: 32138908
DOI: 10.1016/j.aca.2020.01.023 -
ACS Biomaterials Science & Engineering Nov 2022Deoxyribonucleic acid (DNA) evolved as a tool for storing and transmitting genetic information within cells, but outside the cell, DNA can also serve as "construction...
Deoxyribonucleic acid (DNA) evolved as a tool for storing and transmitting genetic information within cells, but outside the cell, DNA can also serve as "construction material" present in microbial biofilms or various body fluids, such as cystic fibrosis, sputum, and pus. In the present work, we investigate the mechanics of biofilms formed from Xen 5, Xen 30, and 1408 using oscillatory shear rheometry at different levels of compression and recreate these mechanics in systems of entangled DNA and cells. The results show that the compression-stiffening and shear-softening effects observed in biofilms can be reproduced in DNA networks with the addition of an appropriate number of microbial cells. Additionally, we observe that these effects are cell-type dependent. We also identify other mechanisms that may significantly impact the viscoelastic behavior of biofilms, such as the compression-stiffening effect of DNA cross-linking by bivalent cations (Mg, Ca, and Cu) and the stiffness-increasing interactions of Xen 5 biofilm with Pf1 bacteriophage produced by . This work extends the knowledge of biofilm mechanobiology and demonstrates the possibility of modifying biopolymers toward obtaining the desired biophysical properties.
Topics: Biofilms; Pseudomonas aeruginosa; Staphylococcus aureus; DNA
PubMed: 36301743
DOI: 10.1021/acsbiomaterials.2c00777 -
Turk Kardiyoloji Dernegi Arsivi : Turk... Mar 2023Mitochondria are cell organelles that play an important role in various cellular processes, especially in aerobic respiration and energy production. Although it has its... (Review)
Review
Mitochondria are cell organelles that play an important role in various cellular processes, especially in aerobic respiration and energy production. Although it has its own genome, the mitochondrial genome does not encode all of the proteins necessary for the mitochondria to function. Nuclear genome is needed for increased mitochondrial number, metabolic activities associated with mitochondria, and replication of mitochondrial deoxyribonucleic acid. As a result of mitochondria dysfunction in cells, oxidative stress occurs with the formation of reactive oxygen species, a product of oxidative metabolism, and the oxidant/antioxidant imbalance. Reactive oxygen species damage cellular molecules such as proteins, ribonucleic acid, deoxyribonucleic acid, and mitochondrial deoxyribonucleic acid under the conditions of oxidative stress. Molecular changes as a result of the reactive oxygen species cause the loss of mitochondria function, resulting in an increased number of dysfunctional mitochondria. Thus, the loss of function of mitochondria and defects in oxidative metabolism increase the formation of reactive oxygen species and cause an increase in mutations in mitochondrial deoxyribonucleic acid. These results also affect mitochondrial biogenesis and accelerate the formation of multifactorial diseases as a result of the decrease in the number of functional mitochondria. In addition, microribonucleic acids, one of the epigenetic regulators, regulate nuclear and mitochondrial genes that control mitochondrial functions. Mitochondrial deoxyribonucleic acid mutated with reactive oxygen species, altered nuclear genome regulators and micro-ribonucleic acids, have been associated with various diseases mediated by mitochondrial dysfunction, including aging and coronary artery disease.
Topics: Humans; Reactive Oxygen Species; Coronary Artery Disease; Mitochondria; Oxidative Stress; DNA, Mitochondrial
PubMed: 36916804
DOI: 10.5543/tkda.2022.39448 -
BMC Nephrology Oct 2019Cell-free deoxyribonucleic acid DNA (cf-DNA) in urine is promising due to the advantage of urine as an easily obtained and non-invasive sample source over tissue and...
INTRODUCTION
Cell-free deoxyribonucleic acid DNA (cf-DNA) in urine is promising due to the advantage of urine as an easily obtained and non-invasive sample source over tissue and blood. In clinical practice, it is important to identify non-invasive biomarkers of chronic kidney disease (CKD) in monitoring and surveillance of disease progression. Information is limited, however, regarding the relationship between urine and plasma cf-DNA and the renal outcome in CKD patients.
METHODS
One hundred and thirty-one CKD patients were enrolled between January 2016 and September 2018. Baseline urine and plasma cell-free mitochondrial DNA (cf-mtDNA) and cell-free nuclear DNA (cf-nDNA) were isolated using quantitative real-time PCR. Estimated glomerular filtration rate (eGFR) measurement was performed at baseline and 6-month follow-up. Favorable renal outcome was defined as eGFR at 6 months minus baseline eGFR> = 0. Receiver operator characteristics (ROC) curve analysis was performed to assess different samples of cf-DNA to predict favorable renal outcomes at 6 months. A multivariate linear regression model was used to evaluate independent associations between possible predictors and different samples of cf-DNA.
RESULTS
Patients with an advanced stage of CKD has significantly low plasma cf-nDNA and high plasma neutrophil gelatinase-associated lipocalin (NGAL) levels. Low urine cf-mtDNA, cf-nDNA levels and low plasma NGAL were significantly correlated with favorable renal outcomes at 6 months. The urine albumin-creatinine ratio (ACR) or urine protein-creatinine ratio (PCR) level is a robust predictor of cf-mtDNA and cf-nDNA in CKD patients. Baseline urine levels of cf-mtDNA and cf-nDNA could predict renal outcomes at 6 months.
CONCLUSIONS
Urinary cf-mtDNA and cf-nDNA may provide novel prognostic biomarkers for renal outcome in CKD patients. The levels of plasma cf-nDNA and plasma NGAL are significantly correlated with the severity of CKD.
Topics: Adult; Aged; Albuminuria; Area Under Curve; Biomarkers; Cell-Free Nucleic Acids; Creatinine; DNA, Mitochondrial; Disease Progression; Female; Glomerular Filtration Rate; Humans; Lipocalin-2; Male; Middle Aged; Predictive Value of Tests; Prognosis; ROC Curve; Renal Insufficiency, Chronic
PubMed: 31660901
DOI: 10.1186/s12882-019-1549-x -
Bio Systems Mar 2023The necessity to record and store biological data is increasing in due course of time. However, it is quite difficult to understand biological mechanisms and keep a... (Review)
Review
The necessity to record and store biological data is increasing in due course of time. However, it is quite difficult to understand biological mechanisms and keep a track of these events in some storage mediums. DNA (deoxyribonucleic acid) is the best candidate for the storage of cellular events in the biological system. It is energy efficient as well as stable at the same time. DNA-based writers and memory devices are continually evolving and finding new avenues in terms of their wide range of applications. Among all the DNA-based storage devices that employ enzymes like recombinases, nucleases, integrases, and polymerases, one of the most popular tools used for these devices is the emerging and versatile CRISPR Cas technology. CRISPR Cas is a prokaryotic immune system that keeps a memory of viral attacks and protects prokaryotes from potential future infections. The main aim of this short review is to study such molecular recorders and writers that employ CRISPR Cas technologies and obtain an in-depth overview of the mechanisms involved and the applications of these molecular devices.
Topics: CRISPR-Cas Systems; Prokaryotic Cells; DNA
PubMed: 36842456
DOI: 10.1016/j.biosystems.2023.104870 -
Astrobiology Aug 2022Life detection on Mars is an important topic that includes a direct search for biomarkers. This requires instruments for biomarker detection that are compact,...
Life detection on Mars is an important topic that includes a direct search for biomarkers. This requires instruments for biomarker detection that are compact, lightweight, and able to withstand operations in space. Solid-state nanopores are excellent candidates that allow fast single-molecule detection. They can withstand high temperatures and be sterilized to minimize planetary contamination. The instruments are portable with low-power requirements. We demonstrate a few key results in advancing the use of nanopores for in-space applications. First, we developed modified deoxyribonucleic acid (DNA) extraction protocols to extract DNA from Mars analog soils. Second, we used silicon nitride nanopores to demonstrate the detection of extracted DNA and corresponding current characteristics. The yields and properties of extracted DNA (, estimated diameters) varied somewhat by soil types, extraction methods, and nanopores used. The yields varied from a minimum of 0.9 ng DNA/g soil for a magnesium carbonate sample from Lake Salda to a maximum of 210 ng DNA/g soil for a calcium carbonate sample from Trona Pinnacles. For a given soil type, yields from different methods varied by a factor of up to 50. These observations motivate future studies with a broader range of Mars-like soils and improved instruments to increase signal-to-noise-ratio at higher measurement bandwidths.
Topics: DNA; Mars; Nanopores; Soil
PubMed: 35731031
DOI: 10.1089/ast.2021.0051 -
International Journal of Molecular... Oct 2022Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous group of diseases that are one of the leading causes of vision loss in young and aged... (Review)
Review
Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous group of diseases that are one of the leading causes of vision loss in young and aged individuals. IRDs are mainly caused by a loss of the post-mitotic photoreceptor neurons of the retina, or by the degeneration of the retinal pigment epithelium. Unfortunately, once these cells are damaged, it is irreversible and leads to permanent vision impairment. Thought to be previously incurable, gene therapy has been rapidly evolving to be a potential treatment to prevent further degeneration of the retina and preserve visual function. The development of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) base and prime editors have increased the capabilities of the genome editing toolbox in recent years. Both base and prime editors evade the creation of double-stranded breaks in deoxyribonucleic acid (DNA) and the requirement of donor template of DNA for repair, which make them advantageous methods in developing clinical therapies. In addition, establishing a permanent edit within the genome could be better suited for patients with progressive degeneration. In this review, we will summarize published uses of successful base and prime editing in treating IRDs.
Topics: Humans; Aged; CRISPR-Cas Systems; CRISPR-Associated Protein 9; Gene Editing; Retina; Retinal Diseases; DNA
PubMed: 36293232
DOI: 10.3390/ijms232012375