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International Journal of Molecular... May 2023Neutrophil Extracellular Traps (NETs) have been implicated in systemic lupus erythematosus (SLE) and antiphospholipid syndrome (APS) pathogenesis. The...
Neutrophil Extracellular Traps (NETs) have been implicated in systemic lupus erythematosus (SLE) and antiphospholipid syndrome (APS) pathogenesis. The myeloperoxidase-deoxyribonucleic acid (MPO-DNA) complex and nucleosomes are serum markers of NETosis. The aim of this study was to assess these NETosis parameters as markers for SLE and APS diagnosis and their association with clinical features and disease activity. A total of 138 people were included in the cross-sectional study: 30 with SLE without APS, 47 with SLE and APS, 41 patients with primary antiphospholipid syndrome (PAPS), and 20 seemingly healthy individuals. Serum MPO-DNA complex and nucleosome levels were determined via an enzyme-linked immunosorbent assay (ELISA). Informed consent was obtained from all subjects involved in the study. The Ethics Committee of the V.A. Nasonova Research Institute of Rheumatology (Protocol No. 25 dated 23 December 2021) approved the study. In patients with SLE without APS, the levels of the MPO-DNA complex were significantly higher compared to patients with SLE with APS, with PAPS, and healthy controls ( < 0.0001). Among patients with a reliable diagnosis of SLE, 30 had positive values of the MPO-DNA complex, of whom 18 had SLE without APS, and 12 had SLE with APS. Patients with SLE and positive MPO-DNA complex levels were significantly more likely to have high SLE activity (χ = 5.25, = 0.037), lupus glomerulonephritis (χ = 6.82, = 0.009), positive antibodies to dsDNA (χ = 4.82, = 0.036), and hypocomplementemia (χ = 6.72, = 0.01). Elevated MPO-DNA levels were observed in 22 patients with APS: 12 with SLE with APS and 10 with PAPS. There were no significant associations between positive levels of the MPO-DNA complex and clinical and laboratory manifestations of APS. The concentration of nucleosomes was significantly lower in the group of SLE patients (±APS) compared to controls and PAPS ( < 0.0001). In SLE patients, the frequency of low nucleosome levels was associated with high SLE activity (χ = 13.4, < 0.0001), lupus nephritis (χ = 4.1, = 0.043), and arthritis (χ = 3.89, = 0.048). An increase in the specific marker of NETosis, the MPO-DNA complex, was found in the blood serum of SLE patients without APS. Elevated levels of the MPO-DNA complex can be regarded as a promising biomarker of lupus nephritis, disease activity, and immunological disorders in SLE patients. Lower levels of nucleosomes were significantly associated with SLE (±APS). Low nucleosome levels were more common in patients with high SLE activity, lupus nephritis, and arthritis.
Topics: Humans; Antiphospholipid Syndrome; Nucleosomes; Lupus Nephritis; Cross-Sectional Studies; Lupus Erythematosus, Systemic; Arthritis; DNA; Biomarkers
PubMed: 37298160
DOI: 10.3390/ijms24119210 -
BioEssays : News and Reviews in... May 2022Phase separation underlies the formation of biomolecular condensates. We hypothesize the cellular processes that occur within condensates shape their structural...
Phase separation underlies the formation of biomolecular condensates. We hypothesize the cellular processes that occur within condensates shape their structural features. We use the example of transcription to discuss structure-function relationships in condensates. Various types of transcriptional condensates have been reported across the evolutionary spectrum in the cell nucleus as well as in mitochondrial and bacterial nucleoids. In vitro and in vivo observations suggest that transcriptional activity of condensates influences their supramolecular structure, which in turn affects their function. Condensate organization thus becomes driven by differences in miscibility among the DNA and proteins of the transcription machinery and the RNA transcripts they generate. These considerations are in line with the notion that cellular processes shape the structural properties of condensates, leading to a dynamic, mutual interplay between structure and function in the cell.
Topics: Biomolecular Condensates; DNA; Organelles; Proteins; RNA
PubMed: 35243657
DOI: 10.1002/bies.202200001 -
DNA Repair Apr 2020Covalent binding between proteins and a DNA strand produces DNA-protein crosslinks (DPC). DPC are one of the most deleterious types of DNA damage, leading to the... (Review)
Review
Covalent binding between proteins and a DNA strand produces DNA-protein crosslinks (DPC). DPC are one of the most deleterious types of DNA damage, leading to the blockage of DNA replication and transcription. Both DNA lesions and endogenous products with carbonyl functional groups can produce DPC in genomic DNA under normal physiological conditions. For example, formaldehyde, the most abundant endogenous human carcinogen, and apurinic/apyrimidinic (AP) sites, the most common type of endogenous DNA lesions, has been shown to crosslink proteins and/or DNA through their carbonyl functional groups. Unfortunately, compared to other types of DNA damage, DPC have been less studied and understood. However, a recent advancement has allowed researchers to determine accurate yields of various DNA lesions including formaldehyde-derived DPC with high sensitivity and specificity, paving the way for new developments in this field of research. Here, we review the current literature and remaining unanswered questions on DPC formation by endogenous formaldehyde and various aldehydic 2-deoxyribose lesions.
Topics: Aldehydes; Animals; DNA; DNA Damage; DNA-Binding Proteins; Humans
PubMed: 32070903
DOI: 10.1016/j.dnarep.2020.102806 -
Sensors (Basel, Switzerland) Jan 2023This systematic review describes and discusses three commercially available integrated systems for forensic DNA analysis, i.e., ParaDNA, RapidHIT, and ANDE. A variety of... (Review)
Review
This systematic review describes and discusses three commercially available integrated systems for forensic DNA analysis, i.e., ParaDNA, RapidHIT, and ANDE. A variety of aspects, such as performance, time-to-result, ease-of-use, portability, and costs (per analysis run) of these three (modified) rapid DNA analysis systems, are considered. Despite their advantages and developmental progress, major steps still have to be made before rapid systems can be broadly applied at crime scenes for full DNA profiling. Aspects in particular that need (further) improvement are portability, performance, the possibility to analyze a (wider) variety of (complex) forensic samples, and (cartridge) costs. Moreover, steps forward regarding ease-of-use and time-to-result will benefit the broader use of commercial rapid DNA systems. In fact, it would be a profit if rapid DNA systems could be used for full DNA profile generation as well as indicative analyses that can give direction to forensic investigators which will speed up investigations.
Topics: Forensic Genetics; Microsatellite Repeats; Polymerase Chain Reaction; DNA Fingerprinting; DNA
PubMed: 36772114
DOI: 10.3390/s23031075 -
Journal of Forensic NursingHistorically, evidence collection in sexual assault cases focused on obtaining foreign contributor bodily fluids through swab collection. With improvements in...
Historically, evidence collection in sexual assault cases focused on obtaining foreign contributor bodily fluids through swab collection. With improvements in deoxyribonucleic acid (DNA) analysis methods, DNA profiles can be developed from touch DNA and applied to sexual assault cases. Following a literature review on factors affecting touch DNA transfer, a groping case study with innovative evidence collection is presented to support the expansion of touch DNA evidence collection in sexual assault cases. The groping case led to the development of a statewide sexual assault touch DNA form to guide evidence collection. DNA findings from additional groping sexual assault cases are reported to further show and justify the importance of evidence collection in groping cases. Implications on multidisciplinary practices are summarized to promote evidence collection and analysis in groping sexual assault cases. As forensic nurses are educated to accurately collect DNA evidence and provide trauma-informed, patient-centered care, they are best suited to provide nursing care for patients who have experienced groping sexual assaults. Optimal DNA findings in groping and sexual assault cases are best achieved through development of strong multidisciplinary, collaborative relationships between forensic nurses and forensic scientists.
Topics: Chromosomes, Human, Y; DNA; DNA Contamination; DNA Fingerprinting; Female; Forensic Nursing; Humans; Male; Sex Offenses; Specimen Handling; Touch
PubMed: 33843809
DOI: 10.1097/JFN.0000000000000324 -
Biophysical Journal May 2022The gp16 ATPase is the constituent subunit of the pentameric dsDNA (double-stranded deoxyribonucleic acid) translocation motor of the Bacillus subtilis Φ29...
The gp16 ATPase is the constituent subunit of the pentameric dsDNA (double-stranded deoxyribonucleic acid) translocation motor of the Bacillus subtilis Φ29 bacteriophage. Although recent single-molecule studies have provided tantalizing clues about the activity of this motor, the mechanism by which the gp16 subunits couple the energy obtained from the binding and hydrolysis of ATP to the mechanical work of dsDNA translocation remains unknown. To address this need, we have characterized the binding of fluorophore-labeled ATP and ADP to monomeric gp16 using a stopped-flow fluorescence assay. These experiments show that the binding of ATP/ADP occurs through a single-step mechanism with corresponding affinities of 523.8 ± 247.3 nM for ATP and a lower limit of 30 μM for ADP. When analyzed through the lens of changes in free energy of the system, this difference in binding affinities is reasonable for a cyclical process of binding, hydrolysis, and product release. In addition to answering questions about the activity of monomeric gp16, these results are also a necessary step in constructing a model for intersubunit communication within the pentameric gp16 motor.
Topics: Adenosine Diphosphate; Adenosine Triphosphatases; Adenosine Triphosphate; Bacillus Phages; DNA, Viral; Hydrolysis; Kinetics
PubMed: 35421388
DOI: 10.1016/j.bpj.2022.04.013 -
Fa Yi Xue Za Zhi Oct 2023Skeleton and teeth are important biological samples. Due to their special structure and strong ability to resist degradation, they are ideal biological materials to... (Review)
Review
Skeleton and teeth are important biological samples. Due to their special structure and strong ability to resist degradation, they are ideal biological materials to retain DNA under natural condition. In many cases, such as historical figure identification, aged skeleton and teeth are usually the only biological samples. However, their DNA is in a state of trace, damage and degradation to different degrees, which requires special experimental treatment to achieve identification. This paper reviews the sample selection, DNA extraction, DNA enrichment and analysis approaches based on relevant research reports in recent years, aiming to promote the further development and improvement of the aged skeleton and teeth identification system.
Topics: Humans; Aged; Body Remains; DNA; Tooth; DNA Fingerprinting; Sequence Analysis, DNA
PubMed: 38006268
DOI: 10.12116/j.issn.1004-5619.2021.511209 -
Nature Communications Jan 2020DNA strand displacement reactions (SDRs) provide a set of intelligent toolboxes for developing molecular computation. Whereas SDR-based logic gate circuits have achieved...
DNA strand displacement reactions (SDRs) provide a set of intelligent toolboxes for developing molecular computation. Whereas SDR-based logic gate circuits have achieved a high level of complexity, the scale-up for practical achievable computational tasks remains a hurdle. Switching circuits that were originally proposed by Shannon in 1938 and nowadays widely used in telecommunication represent an alternative and efficient means to realize fast-speed and high-bandwidth communication. Here we develop SDR-based DNA switching circuits (DSCs) for implementing digital computing. Using a routing strategy on a programmable DNA switch canvas, we show that arbitrary Boolean functions can be represented by DSCs and implemented with molecular switches with high computing speed. We further demonstrate the implementation of full-adder and square-rooting functions using DSCs, which only uses down to 1/4 DNA strands as compared with a dual-rail logic expression-based design. We expect that DSCs provide a design paradigm for digital computation with biomolecules.
Topics: Algorithms; Computer Simulation; Computers; Computers, Molecular; DNA; Electricity
PubMed: 31913309
DOI: 10.1038/s41467-019-13980-y -
Medicine Apr 2023Endogenous fungal endophthalmitis is a challenging condition. There are no universally accepted diagnostic or management protocols. We share a case of endogenous fungal...
RATIONALE
Endogenous fungal endophthalmitis is a challenging condition. There are no universally accepted diagnostic or management protocols. We share a case of endogenous fungal endophthalmitis who was successfully treated, focusing on the diagnostic and treatment procedures.
PATIENT CONCERNS
A 31-year-old female with a history of fungal vaginitis and tinea corporis presented with progressive visual decrease in both eyes after having an induced abortion. Her best corrected visual acuity at presentation was 20/1000 in her right eye and 20/250 in her left eye. Upon slit lamp examination, mild inflammatory reaction in the anterior chamber was found. Dilated fundus examination revealed a hazy view of the optic disc and posterior retina, and there was a whitish mass with "string and pearls" just in front of the macular region in each eye.
DIAGNOSES
Bilateral fungal endogenous endophthalmitis was diagnosed empirically, which was confirmed later by deoxyribonucleic acid sequencing and culture of intraocular fluid.
INTERVENTIONS
Oral itraconazole and intravitreal voriconazole were administered to the patient at first. The intraocular inflammation was partially responsive to the medication, yet the visual acuity persisted to deteriorate and the vitreous whitish masses became more prominent. Then vitrectomy procedures were carried out and oral itraconazle was switched to intravenous fluconazole. The antifungal treatment lasted for 8 weeks.
OUTCOMES
The intraocular inflammation alleviated and visual acuity improved after vitrectomy. At the 9-month follow-up visit, the patient's best corrected visual acuity was 20/40 in the right eye and 20/30 in the left eye. There was no intraocular inflammatary reaction, and retinal scar was noticed in each eye.
LESSON
Early and correct diagnosis, coupled with prompt and aggressive treatment, is crucial for cases of fungal endogenous endophthalmitis. Deoxyribonucleic acid sequencing techniques can contribute to early diagnosis, while vitrectomy may be necessary when antifungal medication is insufficient in controlling the condition.
Topics: Humans; Pregnancy; Female; Adult; Antifungal Agents; Endophthalmitis; Voriconazole; Vitrectomy; Eye Infections, Fungal; Inflammation; DNA
PubMed: 37083776
DOI: 10.1097/MD.0000000000033585 -
International Journal of Urology :... May 2022Detection of genomic alterations in circulating tumor deoxyribonucleic acid of peripheral blood can guide the selection of systemic therapy in cancer patients. The...
OBJECTIVES
Detection of genomic alterations in circulating tumor deoxyribonucleic acid of peripheral blood can guide the selection of systemic therapy in cancer patients. The predictive significance of circulating tumor deoxyribonucleic acid in metastatic renal cell carcinoma remains unclear, especially for patients treated with immune checkpoint inhibitors.
METHODS
In this study, we collected plasma samples before and 1 month after commencing nivolumab monotherapy or nivolumab plus ipilimumab therapy from 14 metastatic renal cell carcinoma patients. We performed circulating tumor deoxyribonucleic acid genomic profiling in plasma cell-free deoxyribonucleic acid by next-generation sequencing using a commercially available pan-cancer panel (Guardant360 CDx). Additionally, we also performed whole exome sequencing of tumor tissues and compared the concordance of genomic profiles with circulating tumor deoxyribonucleic acid.
RESULTS
Nine patients had circulating tumor deoxyribonucleic acid in pretreatment plasma samples with a total of 20 mutations (15 single nucleotide variants, three insertions/deletions, and two copy number amplification). VHL (30.0%) was the most frequently mutated gene, followed by TP53 (20.0%), and 45.0% of circulating tumor deoxyribonucleic acid mutations were concordant with somatic mutations in tumor tissues. Patients with decreasing circulating tumor deoxyribonucleic acid mutant allele frequency had better progression free survival when compared to those with increasing mutant allele frequency (P = 0.0441).
CONCLUSIONS
Our findings revealed that early circulating tumor deoxyribonucleic acid dynamics can serve as a predictive biomarker for response to immune checkpoint inhibitors in metastatic renal cell carcinoma patients.
Topics: Biomarkers, Tumor; Carcinoma, Renal Cell; Circulating Tumor DNA; Female; Humans; Immune Checkpoint Inhibitors; Kidney Neoplasms; Male; Nivolumab
PubMed: 35184335
DOI: 10.1111/iju.14816