keyword
https://read.qxmd.com/read/38534246/a-point-of-care-nucleic-acid-quantification-method-by-counting-light-spots-formed-by-lamp-amplicons-on-a-paper-membrane
#1
JOURNAL ARTICLE
Yanju Chen, Yuanyuan Zhu, Cheng Peng, Xiaofu Wang, Jian Wu, Huan Chen, Junfeng Xu
Nucleic acid quantification, allowing us to accurately know the copy number of target nucleic acids, is significant for diagnosis, food safety, agricultural production, and environmental protection. However, current digital quantification methods require expensive instruments or complicated microfluidic chips, making it difficult to popularize in the point-of-care detection. Paper is an inexpensive and readily available material. In this study, we propose a simple and cost-effective paper membrane-based digital loop-mediated isothermal amplification (LAMP) method for nucleic acid quantification...
March 10, 2024: Biosensors
https://read.qxmd.com/read/38534243/a-careful-insight-into-ddi-type-receptor-layers-on-the-way-to-improvement-of-click-biology-based-immunosensors
#2
JOURNAL ARTICLE
Sylwia Karoń, Marcin Drozd, Elżbieta Malinowska
Protein-based microarrays are important tools for high-throughput medical diagnostics, offering versatile platforms for multiplex immunodetection. However, challenges arise in protein microarrays due to the heterogeneous nature of proteins and, thus, differences in their immobilization conditions. This article advocates DNA-directed immobilization (DDI) as a solution, emphasizing its rapid and cost-effective fabrication of biosensing platforms. Thiolated single-stranded DNA and its analogues, such as ZNA® and PNA probes, were used to immobilize model proteins ( anti -CRP antibodies and SARS-CoV nucleoprotein)...
March 6, 2024: Biosensors
https://read.qxmd.com/read/38531652/structural-and-functional-effects-of-inosine-modification-in-mrna
#3
JOURNAL ARTICLE
Herra G Mendoza, Peter A Beal
Inosine (I), resulting from the deamination of adenosine (A), is a prominent modification in the human transcriptome. The enzymes responsible for the conversion of adenosine to inosine in human mRNAs are the ADARs (adenosine deaminases acting on RNA). Inosine modification introduces a layer of complexity to mRNA processing and function, as it can impact various aspects of RNA biology, including mRNA stability, splicing, translation, and protein binding. The relevance of this process is emphasized in the growing number of human disorders associated with dysregulated A-to-I editing pathways...
March 26, 2024: RNA
https://read.qxmd.com/read/38530903/sequence-dependence-in-nucleosome-dynamics
#4
JOURNAL ARTICLE
Prabir Khatua, Phu K Tang, Abhik Ghosh Moulick, Rutika Patel, Anjela Manandhar, Sharon M Loverde
The basic packaging unit of eukaryotic chromatin is the nucleosome that contains 145-147 base pair duplex DNA wrapped around an octameric histone protein. While the DNA sequence plays a crucial role in controlling the positioning of the nucleosome, the molecular details behind the interplay between DNA sequence and nucleosome dynamics remain relatively unexplored. This study analyzes this interplay in detail by performing all-atom molecular dynamics simulations of nucleosomes, comparing the human α-satellite palindromic (ASP) and the strong positioning "Widom-601" DNA sequence at time scales of 12 μs...
March 26, 2024: Journal of Physical Chemistry. B
https://read.qxmd.com/read/38530284/structure-and-internal-dynamics-of-short-rna-duplexes-determined-by-a-combination-of-pulsed-epr-methods-and-md-simulations
#5
JOURNAL ARTICLE
Maximilian Gauger, Marcel Heinz, Anna-Lena J Halbritter, Lukas S Stelzl, Nicole Erlenbach, Gerhard Hummer, Snorri Th Sigurdsson, Thomas Prisner
We used EPR spectroscopy to characterize the structure of RNA duplexes and their internal twist, stretch and bending motions. We prepared eight 20 base-pair long RNA duplexes containing the rigid spin-label Çm, a cytidine analogue, at two positions and acquired orientation-selective PELDOR/DEER data. By using different frequency bands (X-, Q-, G-band), detailed information about the distance and orientation of the labels was obtained and provided insights into the global conformational dynamics of the RNA duplex...
March 26, 2024: Angewandte Chemie
https://read.qxmd.com/read/38530020/intra-operative-duplex-ultrasound-scanning-in-renal-transplantation-protocol-and-service-requirements
#6
Linda Thebridge, Charles Fisher, Vikram Puttaswamy, Carol Pollock, Jillian Clarke
Intra-operative duplex ultrasound in renal transplantation was first described in 1998 and whilst reported in problematic cases, there are few reports of its routine use and no current published protocols. Since 2013, we have used intra-operative ultrasound in all renal transplants. The formal protocol used since August 2020 is presented as a reference document for other transplant centres. A Canon Aplio 800 ultrasound system with an i22LH8 hockey-stick transducer is used to image the renal cortex and major vessels, and an i8CX1 matrix transducer to image the graft during and after fascial closure...
March 26, 2024: Journal of Medical Radiation Sciences
https://read.qxmd.com/read/38529806/selective-duplex-formation-in-mixed-sequence-libraries-of-synthetic-polymers
#7
JOURNAL ARTICLE
Mohit Dhiman, Ronan Cons, Oliver N Evans, Joseph T Smith, Cecilia J Anderson, Rafel Cabot, Daniil O Soloviev, Christopher A Hunter
Recognition-encoded melamine oligomers (REMO) are synthetic polymers that feature an alternating 1,3,5-triazine-piperazine backbone and side-chains equipped with either a phenol or phosphine oxide recognition unit. An automated method for the solid-phase synthesis (SPS) of REMO of any specified sequence has been developed starting from dichlorotriazine monomer building blocks. Complementary homo-oligomers with either six phenols or six phosphine oxides were synthesized and shown to form a stable duplex in nonpolar solvents by NMR denaturation experiments...
March 26, 2024: Journal of the American Chemical Society
https://read.qxmd.com/read/38529488/gapless-assembly-of-complete-human-and-plant-chromosomes-using-only-nanopore-sequencing
#8
Sergey Koren, Zhigui Bao, Andrea Guarracino, Shujun Ou, Sara Goodwin, Katharine M Jenike, Julian Lucas, Brandy McNulty, Jimin Park, Mikko Rautianinen, Arang Rhie, Dick Roelofs, Harrie Schneiders, Ilse Vrijenhoek, Koen Nijbroek, Doreen Ware, Michael C Schatz, Erik Garrison, Sanwen Huang, William Richard McCombie, Karen H Miga, Alexander H J Wittenberg, Adam M Phillippy
The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, this approach for complete, "telomere-to-telomere" genome assembly relies on multiple sequencing platforms, limiting its accessibility. ONT "Duplex" sequencing reads, where both strands of the DNA are read to improve quality, promise high per-base accuracy. To evaluate this new data type, we generated ONT Duplex data for three widely-studied genomes: human HG002, Solanum lycopersicum Heinz 1706 (tomato), and Zea mays B73 (maize)...
March 19, 2024: bioRxiv
https://read.qxmd.com/read/38528369/r2d-ligase-unveiling-a-novel-dna-ligase-with-surprising-dna-to-rna-ligation-activity
#9
JOURNAL ARTICLE
Sigurd Eidem Gundesø, Ulli Rothweiler, Elise Heimland, Yvonne Piotrowski, Inger Kristine Rødum, Jenny Johansson Söderberg, Ildikó Moustaka Gábor, Terese Solstad, Adele Williamson, Olav Lanes, Bernd Ketelsen Striberny
DNA ligases catalyze bond formation in the backbone of nucleic acids via the formation of a phosphodiester bond between adjacent 5' phosphates and 3' hydroxyl groups on one strand of the duplex. While DNA ligases preferentially ligate single breaks in double-stranded DNA (dsDNA), they are capable of ligating a multitude of other nucleic acid substrates like blunt-ended dsDNA, TA overhangs, short overhangs and various DNA-RNA hybrids. Here we report a novel DNA ligase from Cronobacter phage CR 9 (R2D Ligase) with an unexpected DNA-to-RNA ligation activity...
March 2024: Biotechnology Journal
https://read.qxmd.com/read/38526107/ultrafast-spectroscopy-study-of-dna-photophysics-after-proflavine-intercalation
#10
JOURNAL ARTICLE
Jie Zhou, Xueli Wang, Menghui Jia, Xiaoxiao He, Haifeng Pan, Jinquan Chen
Proflavine (PF), an acridine DNA intercalating agent, has been widespread applied as an anti-microbial and topical antiseptic agent due to its ability to suppress DNA replication. On the other hand, various studies show that PF intercalation to DNA can increase photogenotoxicity and has potential chances to induce carcinomas of skin appendages. However, the effects of PF intercalation on the photophysical and photochemical properties of DNA have not been sufficiently explored. In this study, the excited state dynamics of the PF intercalated d(GC)9 • d(GC)9 and d(AT)9 • d(AT)9 DNA duplex are investigated in an aqueous buffer solution...
March 28, 2024: Journal of Chemical Physics
https://read.qxmd.com/read/38521581/purification-and-biochemical-characterization-of-the-g4-resolvase-and-dna-helicase-fancj
#11
JOURNAL ARTICLE
Tomasz Kulikowicz, Joshua A Sommers, Kathleen F Fuchs, Yuliang Wu, Robert M Brosh
G-quadruplex (G4) DNA or RNA poses a unique nucleic acid structure in genomic transactions. Because of the unique topology presented by G4, cells have exquisite mechanisms and pathways to metabolize G4 that arise in guanine-rich regions of the genome such as telomeres, promoter regions, ribosomal DNA, and other chromosomal elements. G4 resolvases are often represented by a class of molecular motors known as helicases that disrupt the Hoogsteen hydrogen bonds in G4 by harnessing the chemical energy of nucleoside triphosphate hydrolysis...
2024: Methods in Enzymology
https://read.qxmd.com/read/38521316/an-optimized-microrna-detection-platform-based-on-pam-formation-regulated-crispr-cas12a-activation
#12
JOURNAL ARTICLE
Dawei Li, Pengda Liang, Shen Ling, Yapeng Wu, Bei Lv
MicroRNAs (miRNAs) have emerged as biomarkers for the diagnosis and prognosis of various diseases, such as cancer. Recent advancements in CRISPR/Cas12a-based biosensors in combination with hybridization chain reaction (HCR) make it a promising approach for miRNA detection. To increase the compatibility of HCR and CRISPR/Cas12a, we compared two design strategies of hairpin DNA in HCR. The results showed that different arrangements of the protospacer sequence and protospacer adjacent motif (PAM) in the hairpin DNA could affect the sensing performance...
March 21, 2024: International Journal of Biological Macromolecules
https://read.qxmd.com/read/38520301/relationship-between-vitamin-d-receptors-gene-polymorphism-and-arteriogenic-erectile-dysfunction
#13
JOURNAL ARTICLE
Ahmed Rashad Elshahid, Amr Mohamed Zaky, Yasser Mamdouh Hasanein Goda, Nabil Fathy Ismail
BACKGROUND: Over the past few decades, a number of studies have linked vitamin-D deficiency with ED (Erectile dysfunction) risk factors. There is a clear correlation between VD (vitamin-D) levels and ED, according to observational and interventional researches that have been reported in the literature. This crucial information encouraged scientists to investigate the impact of VD on erectile function in greater detail. The fact that vitamin D is a component of a healthy penis that begins in early life has just come to light, however there haven't been many research looking at the connection between vitamin D receptor gene polymorphism and erectile dysfunction...
March 23, 2024: Urologia
https://read.qxmd.com/read/38518558/a-handheld-isothermal-fluorescence-detector-for-duplex-visualization-of-aquatic-pathogens-via-enhanced-one-pot-lamp-pfago-assay
#14
JOURNAL ARTICLE
Feibiao Pang, Tao Zhang, Fengyi Dai, Kaizheng Wang, Tianjiao Jiao, Zuoying Zhang, Liyi Zhang, Mingli Liu, Peng Hu, Jinzhao Song
The expansion of large-scale aquaculture has exacerbated the challenge of aquatic diseases, resulting in substantial economic losses annually. Currently, traditional laboratory-based diagnostic methods are time-consuming and costly, hindering on-site testing for individual farmers. We address this issue by developing a state-of-the-art handheld isothermal nucleic acid amplification device (WeD-1) capable of fluorescence tracking of reactions and integrating it with an enhanced one-pot Prokaryotic Argonaute based nucleic acid detection method, enabling duplex visual detection of aquatic pathogens...
March 8, 2024: Biosensors & Bioelectronics
https://read.qxmd.com/read/38516978/silver-induced-chirality-controlled-spin-filtration-observed-in-ss-dna-functionalized-with-mos2
#15
JOURNAL ARTICLE
Abhinandan Kumar, Subrata Majumder
Chiral molecules can exhibit strong spin-orbit coupling, which can result in a large spin polarization. This is due to the fact that the energy levels of the electrons in a chiral molecule are strongly influenced by the chiral structure of the molecule, which can result in the separation of the energy levels for electrons with different spin orientations. We report a controlled spin-selective transmission of electrons through 20 base-paired poly-cytosine molecules functionalized with MoS2 flakes on ITO glass via the quantum mechanical tunneling effect...
March 28, 2024: Journal of Chemical Physics
https://read.qxmd.com/read/38516589/unusual-ni%C3%A2-ni-interaction-in-ni-ii-complexes-as-potential-inhibitors-for-the-development-of-new-anti-sars-cov-2-omicron-drugs
#16
JOURNAL ARTICLE
Simranjeet Singh, Mukesh Choudhary
Two nickel(ii) coordination complexes [Ni(L)]2 (1) and [Ni(L)] n (2) of a tetradentate Schiff base ligand ( H 2 L ) derived from 2-hydroxy-1-naphthaldehyde with ethylenediamine were synthesized, designed, and characterized via spectroscopic and single crystal XRD analyses. Both nickel(ii) complexes exhibited unusual Ni⋯Ni interactions and were fully characterized via single-crystal X-ray crystallography. Nickel(ii) complexes [Ni(L)]2 (1) and [Ni(L)] n (2) crystallize in monoclinic and triclinic crystal systems with P 21 / c and P 1̄ space groups, respectively, and revealed square planar geometry around each Ni(ii) ion...
March 20, 2024: RSC medicinal chemistry
https://read.qxmd.com/read/38514059/rapid-and-reliable-hla-b-59-01-genotyping-to-prevent-carbonic-anhydrase-inhibitor-induced-severe-cutaneous-adverse-reactions
#17
JOURNAL ARTICLE
Ji Young Huh, Yong Ju Song, Geon Park
OBJECTIVE: Carbonic anhydrase inhibitors (CAIs) are intraocular pressure-reducing medications used in ophthalmology. Human leukocyte antigen- B*59:01 ( HLA-B*59:01 ) is strongly associated with CAI-induced severe cutaneous adverse reactions (SCARs). This study aimed to develop and validate a rapid and economical screening method for HLA-B*59:01 to prevent carbonic anhydrase inhibitor-induced SCARs. METHODS: Duplex allele-specific polymerase chain reaction (PCR) with an internal control was performed for HLA-B*59:01 genotyping...
January 2024: Annals of Clinical and Laboratory Science
https://read.qxmd.com/read/38505329/understanding-and-managing-a-case-of-the-omphalocele-exstrophy-imperforate-anus-spinal-defect-complex
#18
Khulud Mahmood Nurani, Waleed Abdalla, Khalid Mohamed Ayub
The omphalocele-exstrophy-imperforate anus-spinal defects (OEIS) complex is a rare birth disorder involving a combination of gastrointestinal, musculoskeletal, renal, neural, and genitourinary system defects. We present a case report of a neonate with OEIS born by vertex spontaneous delivery to non-consanguineous parents. The major presenting defect was exstrophy of the cecum lying between two exstrophied halves of the bladder, an imperforate anus and spina bifida myelomeningocele. Explorative laparotomy revealed a duplex kidney system, attachment of the terminal ileum and cecum to the exstrophy, and a sausage-like atretic large bowel...
March 2024: Journal of Surgical Case Reports
https://read.qxmd.com/read/38504497/gene-doping-control-analysis-of-human-erythropoietin-transgene-in-equine-plasma-by-pcr-liquid-chromatography-high-resolution-tandem-mass-spectrometry
#19
JOURNAL ARTICLE
Bruce Pui-Nam Yuen, Kin-Sing Wong, Yat-Ming So, Wai Him Kwok, Hiu Wing Cheung, Terence See Ming Wan, Emmie Ngai-Man Ho, Wing-Tak Wong
Gene doping involves the misuse of genetic materials to alter an athlete's performance, which is banned at all times in both human and equine sports. Quantitative polymerase chain reaction (qPCR) assays have been used to control the misuse of transgenes in equine sports. Our laboratory recently developed and implemented duplex as well as multiplex qPCR assays for transgenes detection. To further advance gene doping control, we have developed for the first time a sensitive and definitive PCR-liquid chromatography high-resolution tandem mass spectrometry (PCR-LC-HRMS/MS) method for transgene detection with an estimated limit of detection of below 100 copies/mL for the human erythropoietin (hEPO) transgene in equine plasma...
March 19, 2024: Analytical Chemistry
https://read.qxmd.com/read/38501975/origins-of-second-malignancies-in-children-and-mutational-footprint-of-chemotherapy-in-normal-tissues
#20
JOURNAL ARTICLE
Mònica Sánchez-Guixé, Ferran Muiños, Morena Pinheiro-Santin, Víctor González-Huici, Carlos J Rodriguez-Hernandez, Alexandra Avgustinova, Cinzia Lavarino, Abel González-Pérez, Jaume Mora, Núria López-Bigas
UNLABELLED: Pediatric cancers are rare diseases, and children without known germline predisposing conditions who develop a second malignancy during developmental ages are extremely rare. We present four such clinical cases and, through whole-genome and error-correcting ultra-deep duplex sequencing of tumor and normal samples, we explored the origin of the second malignancy in four children, uncovering different routes of development. The exposure to cytotoxic therapies was linked to the emergence of a secondary acute myeloid leukemia...
March 19, 2024: Cancer Discovery
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