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Medical & Biological Engineering &... Mar 2024Glioblastoma multiforme (GBM) is one of the deadliest tumours. This study aimed to construct radiogenomic prognostic models of glioblastoma overall survival (OS) based...
Glioblastoma multiforme (GBM) is one of the deadliest tumours. This study aimed to construct radiogenomic prognostic models of glioblastoma overall survival (OS) based on magnetic resonance imaging (MRI) Gd-T1WI images and deoxyribonucleic acid (DNA) methylation-seq and to understand the related biological pathways. The ResNet3D-18 model was used to extract radiomic features, and Lasso-Cox regression analysis was utilized to establish the prognostic models. A nomogram was constructed by combining the radiogenomic features and clinicopathological variables. The DeLong test was performed to compare the area under the curve (AUC) of the models. We screened differentially expressed genes (DEGs) with original ribonucleic acid (RNA)-seq in risk stratification and used Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotations for functional enrichment analysis. For the 1-year OS models, the AUCs of the radiogenomic set, methylation set and deep learning set in the training cohort were 0.864, 0.804 and 0.787, and those in the validation cohort were 0.835, 0.768 and 0.651, respectively. The AUCs of the 0.5-, 1- and 2-year nomograms in the training cohort were 0.943, 0.861 and 0.871, and those in the validation cohort were 0.864, 0.885 and 0.805, respectively. A total of 245 DEGs were screened; functional enrichment analysis showed that these DEGs were associated with cell immunity. The survival risk-stratifying radiogenomic models for glioblastoma OS had high predictability and were associated with biological pathways related to cell immunity.
Topics: Humans; Glioblastoma; Brain Neoplasms; Prognosis; Magnetic Resonance Imaging; Methylation; Risk Assessment; DNA
PubMed: 38057447
DOI: 10.1007/s11517-023-02971-3 -
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 -
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 -
JNMA; Journal of the Nepal Medical... Aug 2023Cervical cancer is one of the leading causes of morbidity and mortality among women globally as well as in Nepal. It is attributable to persistent infection by high-risk...
Knowledge of Cervical Cancer Screening and Prevention by Human Papillomavirus Deoxyribonucleic Acid and Human Papillomavirus Vaccination among Women Attending a Tertiary Care Centre.
INTRODUCTION
Cervical cancer is one of the leading causes of morbidity and mortality among women globally as well as in Nepal. It is attributable to persistent infection by high-risk human papillomavirus, especially human papillomavirus-16 and human papillomavirus-18. The aim of this study was to find out the knowledge of cervical cancer screening and prevention by human papillomavirus deoxyribonucleic acid and human papillomavirus vaccination among women attending a tertiary care centre.
METHODS
A descriptive cross-sectional study was conducted in patients attending the outpatient Department of Gynaecology in a tertiary care centre from 18 March to 30 April 2023. After calculating sample size and taking a convenience sampling a survey questionnaire on knowledge of Cervical Cancer Screening and Prevention by Human Papillomavirus Deoxyribonucleic Acid and Human Papillomavirus Vaccination was collected. The point estimate was calculated at a 95% confidence interval.
RESULTS
Among 508 women, 42 (8.25%) (5.86-10.64, 95% Confidence Interval) had knowledge of cervical cancer screening and prevention by human papillomavirus deoxyribonucleic acid and human papillomavirus vaccination. According to the questionnaires with a total sample of 508, 164 (32.28%) know about cervical cancer, 15 (2.95%) know about HPV infection, 14 (2.76%) know about HPV infection causes cervical cancer, and 21 (4.13%) know about HPV transmitted through multiple sex partners.
CONCLUSIONS
The knowledge of cervical cancer screening and prevention by human papillomavirus deoxyribonucleic acid and human papillomavirus vaccination among women is very low. This study recommends having a health education and awareness programme on it to increase knowledge.
KEYWORDS
cervical cancer; human papillomavirus; pap smear; sexual intercourse; vaccination.
Topics: Female; Humans; Uterine Cervical Neoplasms; Papillomavirus Infections; Human Papillomavirus Viruses; Early Detection of Cancer; Cross-Sectional Studies; Tertiary Care Centers; Health Knowledge, Attitudes, Practice; Papillomaviridae; Papillomavirus Vaccines; Vaccination; DNA
PubMed: 38289809
DOI: 10.31729/jnma.8248 -
Journal of Biomolecular Structure &... 2022Here, we report the physicochemical interaction among iron oxide nanoparticles (MNPs) and essential biomolecules, namely, serum albumin (BSA, HSA), collagen and...
Here, we report the physicochemical interaction among iron oxide nanoparticles (MNPs) and essential biomolecules, namely, serum albumin (BSA, HSA), collagen and deoxyribonucleic acid (DNA) in the presence of various cationic, anionic and non-ionic surfactants. Iron oxide nanoparticles are synthesized by the wet chemical process and are characterized by X-ray powder diffraction analysis (XRD), Fourier transform infrared spectroscopic, UV-Vis spectroscopy, scanning electron microscopy and energy-dispersive X-ray spectroscopy mapping studies . The conjugation of MNPs protein was analyzed using UV-Vis spectroscopy, fluorescence spectroscopy, circular dichroism technique and gel electrophoresis. The spectroscopic investigation illustrates the surfactant-dependent binding between MNPs and protein. Gel electrophoresis in the absence and presence of MNPs-surfactant systems has been used to study the impact on DNA structure. It was found that Tween 80 imparts better stability as well as biocompatibility to the synthesized MNPs. The findings offer extensive information on the influence of various surfactant coatings on MNP surfaces and their influence on vital biomolecules, making it useful for designing MNPs for biological applications.Communicated by Ramaswamy H. Sarma.
Topics: Surface-Active Agents; Magnetite Nanoparticles; Serum Albumin; Chemical Phenomena; DNA; Spectroscopy, Fourier Transform Infrared
PubMed: 34542389
DOI: 10.1080/07391102.2021.1977701 -
ACS Nano Nov 2022With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 10 GB by 2025. Traditional storage methods have... (Review)
Review
With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 10 GB by 2025. Traditional storage methods have difficulties keeping pace given that current storage media have a maximum density of 10 GB/mm. As such, data production will far exceed the capacity of currently available storage methods. The costs of maintaining and transferring data, as well as the limited lifespans and significant data losses associated with current technologies also demand advanced solutions for information storage. Nature offers a powerful alternative through the storage of information that defines living organisms in unique orders of four bases (A, T, C, G) located in molecules called deoxyribonucleic acid (DNA). DNA molecules as information carriers have many advantages over traditional storage media. Their high storage density, potentially low maintenance cost, ease of synthesis, and chemical modification make them an ideal alternative for information storage. To this end, rapid progress has been made over the past decade by exploiting user-defined DNA materials to encode information. In this review, we discuss the most recent advances of DNA-based data storage with a major focus on the challenges that remain in this promising field, including the current intrinsic low speed in data writing and reading and the high cost per byte stored. Alternatively, data storage relying on DNA nanostructures (as opposed to DNA sequence) as well as on other combinations of nanomaterials and biomolecules are proposed with promising technological and economic advantages. In summarizing the advances that have been made and underlining the challenges that remain, we provide a roadmap for the ongoing research in this rapidly growing field, which will enable the development of technological solutions to the global demand for superior storage methodologies.
Topics: Sequence Analysis, DNA; DNA; Information Storage and Retrieval
PubMed: 36256971
DOI: 10.1021/acsnano.2c06748 -
Molecules (Basel, Switzerland) Mar 2021The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer... (Review)
Review
The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.
Topics: DNA; Nanostructures; Nanotechnology
PubMed: 33801952
DOI: 10.3390/molecules26061502 -
The Journal of Physical Chemistry... May 2023DNA alkylating agents are widely used in anticancer pharmacology. Although shown to induce cross-linking and/or methylation of DNA, how they affect the mechanical...
DNA alkylating agents are widely used in anticancer pharmacology. Although shown to induce cross-linking and/or methylation of DNA, how they affect the mechanical properties of DNA and activity of DNA enzymes remains to be elucidated. Here, we perform single-molecule optical tweezer experiments on DNA treated with alkylating agents, including melphalan, cisplatin, and dacarbazine. While all three drugs induce a significant increase of overstretching force and a reduction of hysteresis, suggesting stabilization of DNA against shearing forces, their effects on elasticity of DNA were quite different, with the largest change in persistence length induced by cisplatin. Furthermore, we find that these alkylating-agent-induced changes on DNA have different effects on processivity of DNA polymerase, with melphalan and cisplatin showing significantly reduced activity and dacarbazine showing little effect. Overall, our results provide new insights into the effects for these alkylating agents, which could potentially facilitate a better design of related drugs.
Topics: Alkylating Agents; Melphalan; Cisplatin; Antineoplastic Agents, Alkylating; Dacarbazine; DNA; Spectrum Analysis
PubMed: 37194946
DOI: 10.1021/acs.jpclett.3c00740 -
Biosensors Feb 2023This communication aims at discussing strategies based on developments from nanotechnology focused on the next generation of sequencing (NGS). In this regard, it should... (Review)
Review
This communication aims at discussing strategies based on developments from nanotechnology focused on the next generation of sequencing (NGS). In this regard, it should be noted that even in the advanced current situation of many techniques and methods accompanied with developments of technology, there are still existing challenges and needs focused on real samples and low concentrations of genomic materials. The approaches discussed/described adopt spectroscopical techniques and new optical setups. PCR bases are introduced to understand the role of non-covalent interactions by discussing about Nobel prizes related to genomic material detection. The review also discusses colorimetric methods, polymeric transducers, fluorescence detection methods, enhanced plasmonic techniques such as metal-enhanced fluorescence (MEF), semiconductors, and developments in metamaterials. In addition, nano-optics, challenges linked to signal transductions, and how the limitations reported in each technique could be overcome are considered in real samples. Accordingly, this study shows developments where optical active nanoplatforms generate signal detection and transduction with enhanced performances and, in many cases, enhanced signaling from single double-stranded deoxyribonucleic acid (DNA) interactions. Future perspectives on miniaturized instrumentation, chips, and devices aimed at detecting genomic material are analyzed. However, the main concept in this report derives from gained insights into nanochemistry and nano-optics. Such concepts could be incorporated into other higher-sized substrates and experimental and optical setups.
Topics: Nanotechnology; Optics and Photonics; Metals; High-Throughput Nucleotide Sequencing; DNA, Single-Stranded
PubMed: 36832027
DOI: 10.3390/bios13020260 -
Biomaterials Jan 2021Deoxyribonucleic acid (DNA) is a molecular carrier of genetic information that can be fabricated into functional nanomaterials in biochemistry and engineering fields.... (Review)
Review
Deoxyribonucleic acid (DNA) is a molecular carrier of genetic information that can be fabricated into functional nanomaterials in biochemistry and engineering fields. Those DNA nanostructures, synthesized via Watson-Crick base pairing, show a wide range of attributes along with excellent applicability, precise programmability, and extremely low cytotoxicity in vitro and in vivo. In this review, the applications of functionalized DNA nanostructures in bioimaging and tumor therapy are summarized. We focused on approaches involving DNA origami nanostructures due to their widespread use in previous and current reports. Non-DNA origami nanostructures such as DNA tetrahedrons are also covered. Finally, the remaining challenges and perspectives regarding DNA nanostructures in the biomedical arena are discussed.
Topics: DNA; Humans; Nanostructures; Nanotechnology; Neoplasms
PubMed: 33285441
DOI: 10.1016/j.biomaterials.2020.120560