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Journal articles on the topic 'DNA-compatible reactions'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Shi, Ying, Yan-ran Wu, Jian-qiang Yu, Wan-nian Zhang, and Chun-lin Zhuang. "DNA-encoded libraries (DELs): a review of on-DNA chemistries and their output." RSC Advances 11, no. 4 (2021): 2359–76. http://dx.doi.org/10.1039/d0ra09889b.

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We summarize a series of novel DNA-compatible chemistry reactions for DNA-encoded chemical library (DEL) building blocks and analyse the druggability of screened hit molecules via DELs in the past five years.

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2

Fan, Zhoulong, Shuai Zhao, Tao Liu, et al. "Merging C(sp3)–H activation with DNA-encoding." Chemical Science 11, no. 45 (2020): 12282–88. http://dx.doi.org/10.1039/d0sc03935g.

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Tran-Hoang, Nam, та Thomas Kodadek. "Solid-Phase Synthesis of β-Amino Ketones Via DNA-Compatible Organocatalytic Mannich Reactions". ACS Combinatorial Science 20, № 2 (2018): 55–60. http://dx.doi.org/10.1021/acscombsci.7b00151.

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Shu, Keitou, та Thomas Kodadek. "Solid-Phase Synthesis of β-Hydroxy Ketones Via DNA-Compatible Organocatalytic Aldol Reactions". ACS Combinatorial Science 20, № 5 (2018): 277–81. http://dx.doi.org/10.1021/acscombsci.8b00001.

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Favalli, Nicholas, Gabriele Bassi, Tania Zanetti, Jörg Scheuermann, and Dario Neri. "Screening of Three Transition Metal‐Mediated Reactions Compatible with DNA‐Encoded Chemical Libraries." Helvetica Chimica Acta 102, no. 4 (2019): e1900033. http://dx.doi.org/10.1002/hlca.201900033.

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6

Liu, Wentao, Wei Huang, Qian Lin, et al. "Development of DNA-compatible hydroxycarbonylation reactions using chloroform as a source of carbon monoxide." Bioorganic & Medicinal Chemistry 38 (May 2021): 116118. http://dx.doi.org/10.1016/j.bmc.2021.116118.

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7

Wang, Jie, Helena Lundberg, Shota Asai, et al. "Kinetically guided radical-based synthesis of C(sp3)−C(sp3) linkages on DNA." Proceedings of the National Academy of Sciences 115, no. 28 (2018): E6404—E6410. http://dx.doi.org/10.1073/pnas.1806900115.

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DNA-encoded libraries (DEL)-based discovery platforms have recently been widely adopted in the pharmaceutical industry, mainly due to their powerful diversity and incredible number of molecules. In the two decades since their disclosure, great strides have been made to expand the toolbox of reaction modes that are compatible with the idiosyncratic aqueous, dilute, and DNA-sensitive parameters of this system. However, construction of highly important C(sp3)−C(sp3) linkages on DNA through cross-coupling remains unexplored. In this article, we describe a systematic approach to translating standar

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Kundu, Nandini, Brian E. Young, and Jonathan T. Sczepanski. "Kinetics of heterochiral strand displacement from PNA–DNA heteroduplexes." Nucleic Acids Research 49, no. 11 (2021): 6114–27. http://dx.doi.org/10.1093/nar/gkab499.

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Abstract Dynamic DNA nanodevices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation remains challenging due to nuclease degradation and other cellular factors. Use of l-DNA, the nuclease resistant enantiomer of native d-DNA, provides a promising solution. On this basis, we recently developed a strand displacement methodology, referred to as ‘heterochiral’ strand displacement, that enables robust l-DNA nanodevices to be sequence-specifically interfaced with endogenous d-nucleic acids. However, the underlying reaction – strand displacement

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Qu, Yi, Huanan Wen, Rui Ge, et al. "Copper-Mediated DNA-Compatible One-Pot Click Reactions of Alkynes with Aryl Borates and TMS-N3." Organic Letters 22, no. 11 (2020): 4146–50. http://dx.doi.org/10.1021/acs.orglett.0c01219.

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10

Whang, I., J. Lee, and M. Jayaram. "Active-site assembly and mode of DNA cleavage by Flp recombinase during full-site recombination." Molecular and Cellular Biology 14, no. 11 (1994): 7492–98. http://dx.doi.org/10.1128/mcb.14.11.7492.

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A combination of half-site substrates and step arrest mutants of Flp, a site-specific recombinase of the integrase family, had earlier revealed the following features of the half-site recombination reaction. (i) The Flp active site is assembled by sharing of catalytic residues from at least two monomers of the protein. (ii) A Flp monomer does not cleave the half site to which it is bound (DNA cleavage in cis); rather, it cleaves a half site bound by a second Flp monomer (DNA cleavage in trans). For the lambda integrase (Int protein), the prototype member of the Int family, catalytic complement

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Whang, I., J. Lee, and M. Jayaram. "Active-site assembly and mode of DNA cleavage by Flp recombinase during full-site recombination." Molecular and Cellular Biology 14, no. 11 (1994): 7492–98. http://dx.doi.org/10.1128/mcb.14.11.7492-7498.1994.

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A combination of half-site substrates and step arrest mutants of Flp, a site-specific recombinase of the integrase family, had earlier revealed the following features of the half-site recombination reaction. (i) The Flp active site is assembled by sharing of catalytic residues from at least two monomers of the protein. (ii) A Flp monomer does not cleave the half site to which it is bound (DNA cleavage in cis); rather, it cleaves a half site bound by a second Flp monomer (DNA cleavage in trans). For the lambda integrase (Int protein), the prototype member of the Int family, catalytic complement

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12

Favalli, Nicholas, Gabriele Bassi, Davide Bianchi, Jörg Scheuermann, and Dario Neri. "Large screening of DNA-compatible reaction conditions for Suzuki and Sonogashira cross-coupling reactions and for reverse amide bond formation." Bioorganic & Medicinal Chemistry 41 (July 2021): 116206. http://dx.doi.org/10.1016/j.bmc.2021.116206.

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13

Haegi, Anita, Valentina Catalano, Laura Luongo, et al. "A Newly Developed Real-Time PCR Assay for Detection and Quantification of Fusarium oxysporum and Its Use in Compatible and Incompatible Interactions with Grafted Melon Genotypes." Phytopathology® 103, no. 8 (2013): 802–10. http://dx.doi.org/10.1094/phyto-11-12-0293-r.

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A reliable and species-specific real-time quantitative polymerase chain reaction (qPCR) assay was developed for detection of the complex soilborne anamorphic fungus Fusarium oxysporum. The new primer pair, designed on the translation elongation factor 1-α gene with an amplicon of 142 bp, was highly specific to F. oxysporum without cross reactions with other Fusarium spp. The protocol was applied to grafted melon plants for the detection and quantification of F. oxysporum f. sp. melonis, a devastating pathogen of this cucurbit. Grafting technologies are widely used in melon to confer resistance

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14

Dawadi, Surendra, Nicholas Simmons, Gabriella Miklossy, et al. "Discovery of potent thrombin inhibitors from a protease-focused DNA-encoded chemical library." Proceedings of the National Academy of Sciences 117, no. 29 (2020): 16782–89. http://dx.doi.org/10.1073/pnas.2005447117.

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DNA-encoded chemical libraries are collections of compounds individually coupled to unique DNA tags serving as amplifiable identification barcodes. By bridging split-and-pool combinatorial synthesis with the ligation of unique encoding DNA oligomers, million- to billion-member libraries can be synthesized for use in hundreds of healthcare target screens. Although structural diversity and desirable molecular property ranges generally guide DNA-encoded chemical library design, recent reports have highlighted the utility of focused DNA-encoded chemical libraries that are structurally biased for a

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Tsuji, Gakushi, Satoshi Fujii, Takeshi Sunami, and Tetsuya Yomo. "Sustainable proliferation of liposomes compatible with inner RNA replication." Proceedings of the National Academy of Sciences 113, no. 3 (2015): 590–95. http://dx.doi.org/10.1073/pnas.1516893113.

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Although challenging, the construction of a life-like compartment via a bottom–up approach can increase our understanding of life and protocells. The sustainable replication of genome information and the proliferation of phospholipid vesicles are requisites for reconstituting cell growth. However, although the replication of DNA or RNA has been developed in phospholipid vesicles, the sustainable proliferation of phospholipid vesicles has remained difficult to achieve. Here, we demonstrate the sustainable proliferation of liposomes that replicate RNA within them. Nutrients for RNA replication a

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Surrette, Christine, David Shoudy, Alex Corwin, et al. "Microfluidic Tissue Mesodissection in Molecular Cancer Diagnostics." SLAS TECHNOLOGY: Translating Life Sciences Innovation 22, no. 4 (2016): 425–30. http://dx.doi.org/10.1177/2211068216680208.

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We present a mesodissection platform that retains the advantages of laser-based dissection instrumentation with the speed and ease of manual dissection. Tissue dissection in clinical laboratories is often performed by manually scraping a physician-selected region from standard glass slide mounts. In this manner, costs associated with dissection remain low, but spatial resolution is compromised. In contrast, laser microdissection methods maintain spatial resolution that matches the requirements for analysis of important tissue heterogeneity but remains costly and labor intensive. We demonstrate

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Szymanski, Irma O., and Sharyn L. Orton. "Since the Process of Transfusion-Induced Alloimmunization Is Not Harmless, Can We Mitigate It?" Blood 124, no. 21 (2014): 5101. http://dx.doi.org/10.1182/blood.v124.21.5101.5101.

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Abstract Transfusion protocols have remained unchanged for decades. Accordingly, it is necessary to avoid transfusion reactions by giving patients ABO- and irregular antibody-compatible red blood cells (RBC). Prevention of immunization to the Rh antigen D is also required since anti-D may cause a serious hemolytic disease of fetus and newborn. Prevention of transfusion-induced immunization to other blood group antigens is neither required nor feasible for the general transfused population. We consider the process of alloimmunization to be harmful due to the following untoward effects: 1) Destr

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18

Rooney, Sean, Frederick W. Alt, David Lombard, et al. "Defective DNA Repair and Increased Genomic Instability in Artemis-deficient Murine Cells." Journal of Experimental Medicine 197, no. 5 (2003): 553–65. http://dx.doi.org/10.1084/jem.20021891.

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In developing lymphocytes, the recombination activating gene endonuclease cleaves DNA between V, D, or J coding and recombination signal (RS) sequences to form hairpin coding and blunt RS ends, which are fused to form coding and RS joins. Nonhomologous end joining (NHEJ) factors repair DNA double strand breaks including those induced during VDJ recombination. Human radiosensitive severe combined immunodeficiency results from lack of Artemis function, an NHEJ factor with in vitro endonuclease/exonuclease activities. We inactivated Artemis in murine embryonic stem (ES) cells by targeted mutation

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Parham, Nicholas J., François J. Picard, Régis Peytavi, et al. "Specific Magnetic Bead–Based Capture of Genomic DNA from Clinical Samples: Application to the Detection of Group B Streptococci in Vaginal/Anal Swabs." Clinical Chemistry 53, no. 9 (2007): 1570–76. http://dx.doi.org/10.1373/clinchem.2007.091389.

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Abstract Background: Group B streptococci (GBS) are a leading cause of sepsis and meningitis in newborns. We previously developed a rapid diagnostic system for GBS detection from vaginal/anal samples obtained from pregnant women during delivery. To facilitate the adaptation of this method for point-of-care testing, we have developed a specific and efficient GBS DNA capture method that is compatible with both PCR and nonamplification detection technologies. Methods: Superparamagnetic beads were functionalized with oligonucleotide capture probes of different lengths and used to capture GBS genom

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Matsumura, Ichiro. "Methylase-assisted subcloning for high throughput BioBrick assembly." PeerJ 8 (September 11, 2020): e9841. http://dx.doi.org/10.7717/peerj.9841.

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The BioBrick standard makes possible iterated pairwise assembly of cloned parts without any depletion of unique restriction sites. Every part that conforms to the standard is compatible with every other part, thereby fostering a worldwide user community. The assembly methods, however, are labor intensive or inefficient compared to some newer ones so the standard may be falling out of favor. An easier way to assemble BioBricks is described herein. Plasmids encoding BioBrick parts are purified from Escherichia coli cells that express a foreign site-specific DNA methyltransferase, so that each is

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21

Brenier-Pinchart, Marie-Pierre, Emmanuelle Varlet-Marie, Florence Robert-Gangneux, et al. "Impact of pre-analytic step duration on molecular diagnosis of toxoplasmosis for five types of biological samples." PLOS ONE 16, no. 2 (2021): e0246802. http://dx.doi.org/10.1371/journal.pone.0246802.

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Introduction Toxoplasma-PCR is essential to diagnose ocular, cerebral, disseminated and congenital toxoplasmosis. This multicenter study evaluated the impact of sample storage duration at +4°C on PCR assay performances in order to propose guidelines for the storage of samples during shipment or/and before PCR. Materials and methods Five matrices, amniotic (AF), cerebrospinal (CSF), and bronchoalveolar lavage fluids (BALF), whole blood (WB) and buffy coat (BC), were artificially spiked with different amounts of Toxoplasma gondii (20, 100, 500 tachyzoites per mL of sample) or with previously inf

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22

Mokany, Elisa, Yee Lee Tan, Simon M. Bone, Caroline J. Fuery, and Alison V. Todd. "MNAzyme qPCR with Superior Multiplexing Capacity." Clinical Chemistry 59, no. 2 (2013): 419–26. http://dx.doi.org/10.1373/clinchem.2012.192930.

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BACKGROUND MNAzymes (nucleic acid enzymes formed from multiple partial enzymes) can be linked to PCR to provide a highly specific method for target detection and quantification. We investigated the feasibility of multiplexing MNAzyme quantitative PCR (qPCR) methods. METHODS We combined MNAzyme components with PCR primers and standard qPCR reagents to perform MNAzyme qPCR and reverse-transcription qPCR (RT-qPCR) assays with a set of universal reporter probes. Assays were performed on single targets and in multiplex formats that combined up to 5 different targets in a single reaction. RESULTS A

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23

Kohn, L. M. "The clonal dynamic in wild and agricultural plant–pathogen populations." Canadian Journal of Botany 73, S1 (1995): 1231–40. http://dx.doi.org/10.1139/b95-383.

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The stability or change in clone frequencies during the disease cycle and from year to year is what I term the clonal dynamic. Among pathogenic fungi, the prevalence of efficient asexual reproduction affords the opportunity for invasive, epidemic, clonal colonization and spread. Clonality is probably most extreme in monoculture, although it could be expected to be important in wild plants and in transfers of adaptive pathogenic genotypes between wild and cultivated plants. The clonal dynamic was studied in Sclerotinia sclerotiorum in two experiments, one on four Canadian field populations of c

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24

Zheng, Zhi, Yuling Luo, and Gary McMaster. "Sensitive and Quantitative Measurement of Gene Expression Directly from Peripheral Whole Blood, without RNA Isolation and Target Amplification." Blood 106, no. 11 (2005): 4518. http://dx.doi.org/10.1182/blood.v106.11.4518.4518.

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Abstract Peripheral blood gene expression analysis is increasingly used for diagnosis and prognosis of hematological diseases, as well as for surrogate biomarker discovery in a wide range of non-hematological disorders. However, a critical issue concerning the potential clinical application of these research findings relates to the validity and reproducibility of the blood mRNA quantitation results. Current gene expression technologies often depend on multiple steps: 1) blood isolation; 2) RNA purification and 3) subsequent enzymatic reactions, which affect the accuracy and consistency of resu

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Riccio, Gennaro, Eduardo Sommella, Nadia Badolati та ін. "Annurca Apple Polyphenols Protect Murine Hair Follicles from Taxane Induced Dystrophy and Hijacks Polyunsaturated Fatty Acid Metabolism toward β-Oxidation". Nutrients 10, № 11 (2018): 1808. http://dx.doi.org/10.3390/nu10111808.

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Chemotherapy-induced alopecia (CIA) is a common side effect of conventional chemotherapy and represents a major problem in clinical oncology. Even months after the end of chemotherapy, many cancer patients complain of hair loss, a condition that is psychologically difficult to manage. CIA disturbs social and sexual interactions and causes anxiety and depression. Synthetic drugs protecting from CIA and endowed with hair growth stimulatory properties are prescribed with caution by oncologists. Hormones, growth factors, morphogens could unwontedly protect tumour cells or induce cancer cell prolif

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Spyridonidis, Alexandros, Philipp Faber, Loizos Petrikkos, and Jurgen Finke. "Alloanatigenic Reactions after Hematopoietic Cell Transplantation Induce Genomic Alterations in Epithelial Cells as Shown in Human Studies and in an In Vitro Model." Blood 108, no. 11 (2006): 3213. http://dx.doi.org/10.1182/blood.v108.11.3213.3213.

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Abstract Previous studies from our group demonstrated frequent genomic alterations measured by microsatellite instability (MSI) in non-neoplastic epithelial tissues of patients who underwent allogeneic hematopoietic cell transplantation (HCT) (Blood2006;107:3389–3396). These genomic alterations were found only after allogeneic but not after autologous HCT, and therefore we hypothesized that an “allogeneic” effect is substantially involved in the mutation process. We extended our previous analyses by examining 210 bucall swabs obtained from 70 patients between day (d+) 26 and d+3514 after allog

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Petersen, Jesper, Martin Dufva, and Henrik Birgens. "Inexpensive DNA Microarray Application for Screening of Beta-Globin Mutations in Low-Resource Settings." Blood 114, no. 22 (2009): 4067. http://dx.doi.org/10.1182/blood.v114.22.4067.4067.

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Abstract Abstract 4067 Poster Board III-1002 Development of public health related products are, in general, driven by clinical usefulness in combination with economic feasibility. Not surprisingly, a high throughput, automated robotic system is not an option in a low-resource setting as exists in the majority of countries with high prevalence of hemoglobinopathies. Diagnostics developed for resource rich areas may not be feasible in such areas but certain parts of these technologies can be transformed into low-cost diagnostics suitable for resource poor settings. Hemoglobinopathies are traditi

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Martinez, Aline Amorim, Alessandra Midori Kuniyoshi, Mihoko Yamamoto, et al. "Loss of red cell ABH Antigens and Hypermethylation of the ABO Gene Promoter region is frequent in Myeloid Malignancies." Blood 114, no. 22 (2009): 3151. http://dx.doi.org/10.1182/blood.v114.22.3151.3151.

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Abstract Abstract 3151 Poster Board III-88 Background Loss of red blood cell (RBC) antigens may occur in solid tumors and in hematological diseases; however the mechanisms involved in these changes are not fully understood. Aberrant DNA hypermethylation is thought to be involved in acute myeloid leukemia (AML) as well as in myelodysplastic syndromes (MDS), and the methylation of cytosines residues in the dinucleotide CpG may account for the expression patterns of the ABO genes. In this study we investigated loss of RBC ABH antigens and the possible role of DNA methylation in the ABO promoter g

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François, Celia, Celia Martinez, Clement Faye, et al. "The Utilization of Linear Polylysine Coupled with Mechanic Forces to Extract Microbial DNA from Different Matrices." Microorganisms 8, no. 12 (2020): 1901. http://dx.doi.org/10.3390/microorganisms8121901.

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Molecular approaches are powerful tools that are used for medical or environmental diagnoses. However, the main limitations of such a tools are that they extract low levels of DNA and they do not remove the inhibitors of polymerase chain reaction (PCR). Although the use of polycation to complex and purify DNA has been described in the literature, elution often requires a high ionic strength or pH levels not compatible with molecular analyses. In this paper, we described a new process that is based on the complexation of DNA with linear polylysine, followed by capturing the complex by a cation

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Barouqa, Mohammad, Kenji Ikemura, Henny Billett, et al. "Neutrophilic Extracellular Traps (NETs); A Subset of Smudge Cells Identifiable by Peripheral Smear Autoanalyzers in the Rising Era of Artificial Intelligence." American Journal of Clinical Pathology 154, Supplement_1 (2020): S10—S11. http://dx.doi.org/10.1093/ajcp/aqaa137.018.

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Abstract Background Digitized microscopy such as CellaVision® technology has revolutionized the laboratory. Smudge cells, also called basket cells, are usually seen in lymphoproliferative disorders representing remnants from degenerated lymphocytes (DLs). CellaVision® classifies DLs and web-like remnants as smudge cells. The morphology of the web-like remnants is compatible with Neutrophil Extracellular Traps (NETs) where extracellular decondensed DNA chromatin network is formed as one of several neutrophilic reactions to stress. Currently, we lack clinical tests that reliably identify and qua

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Woodhall, J. W., B. Lutomirska, J. C. Peters, and P. S. Wharton. "Rhizoctonia solani Anastomosis Group 3 is Predominant in Potato Tubers in Poland." Plant Disease 97, no. 9 (2013): 1245. http://dx.doi.org/10.1094/pdis-05-12-0482-pdn.

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Rhizoctonia solani is a species complex of 13 related but genetically distinct anastomosis groups (AGs). In potato, R. solani can infect the stems, stolons, and roots, resulting in quantitative losses. It can also cause qualitative losses through blemishes occurring on progeny tubers, such as black scurf and elephant hide (corky cracking). Knowledge of the AG in local populations is important because they differ in host range, fungicide sensitivity, and disease severity (2). To determine the AGs present in Poland, 54 tuber samples displaying typical R. solani symptoms were taken from six diffe

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Shtenberg, Giorgi, Naama Massad-Ivanir, Oren Moscovitz, et al. "Biosensor based on DNA directed immobilization of enzymes onto optically sensitive porous Si." MRS Proceedings 1569 (2013): 195–200. http://dx.doi.org/10.1557/opl.2013.806.

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ABSTRACTOptical biosensor for monitoring proteolytic activity is constructed by DNA-directed immobilization of enzymes onto porous Silicon nanostructures. This sensor configuration allows both protease recycling and easy surface regeneration for subsequent biosensing analysis by means of mild dehybridization conditions. We demonstrate real-time analysis of minute quantities of proteases paving the way for substrate profiling and the identification of cleavage sites. The biosensor is compatible with common proteomic methods and allows for a successful downstream mass spectrometry analysis of th

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Hu, Hezhi, Jingmeng Cheng, Chunyang Wei, et al. "Pre-Degassed Microfluidic Chamber-Based Digital PCR Device for Meat Authentication Applications." Micromachines 12, no. 6 (2021): 694. http://dx.doi.org/10.3390/mi12060694.

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Droplet digital polymerase chain reaction (ddPCR) suffers from the need for specific equipment and skilled personnel; thus, we here present a chamber-based digital PCR microfluidic device that is compatible with fluorescence image read-out systems and removes bubbles by a pre-degassed microfluidic device that consists of a pilot channel and micro chamber arrays. Digitalized PCR reagents are introduced into micro chambers, and thermocycles are taken to perform a DNA amplification process. Then, fluorescence images of a micro chamber array are read out and analyzed to obtain the total number of

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Yang, Kun, Giovanni Stracquadanio, Jingchuan Luo, Jef D. Boeke, and Joel S. Bader. "BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts." Bioinformatics 32, no. 6 (2015): 937–39. http://dx.doi.org/10.1093/bioinformatics/btv664.

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Abstract Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with a

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Schroeder, Max R., and Vladimir Loparev. "Rapid Inactivation of Non-Endospore-Forming Bacterial Pathogens by Heat Stabilization is Compatible with Downstream Next-Generation Sequencing." Applied Biosafety 24, no. 3 (2019): 129–33. http://dx.doi.org/10.1177/1535676019861261.

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Introduction: Heat stabilization treatment preserves the in vivo state of biological samples by rapidly inactivating enzymes that cause degradation of proteins and nucleic acids. Historically, proteomics studies used this technique as an alternative to chemical fixation. More recently, microbiologists discovered that heat stabilization treatment rapidly inactivates pathogens present in tissue samples and preserves deoxyribonucleic acid (DNA) in the tissue. However, these recent studies did not investigate the inactivation of high-density bacterial suspensions and the quality of bacterial DNA.

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Habu, Tsuyoshi, Fumio Kishida, Miki Morikita, Akira Kitajima, Toshiaki Yamada, and Ryutaro Tao. "A Simple and Rapid Procedure for the Detection of Self-Compatible Individuals in Japanese Apricot (Prunus mume Sieb. et Zucc.) Using the Loop-Mediated Isothermal Amplification (LAMP) Method." HortScience 41, no. 5 (2006): 1156–58. http://dx.doi.org/10.21273/hortsci.41.5.1156.

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Japanese apricot (Prunus mume Sieb. et Zucc.) exhibits S-RNase-based gametophytic self-incompatibility as do other Prunus species. Both self-incompatible and self-compatible Japanese apricot cultivars are grown commercially in Japan. These self-compatible cultivars are shown to have a common S-haplotype called Sf that contains Sf-RNase and SFBf (S-haplotype-specific F-box protein). This study describes a simple and rapid detection of SFBf, in Japanese apricot, based on loop-mediated isothermal amplification (LAMP) method. A set of 4 primers, F3, B3, FIP, and BIP primer, were designed from the

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Delaney, M. A., K. A. Terio, K. M. Colegrove, M. B. Briggs, and M. J. Kinsel. "Occlusive Fungal Tracheitis in 4 Captive Bottlenose Dolphins (Tursiops truncatus)." Veterinary Pathology 50, no. 1 (2012): 172–76. http://dx.doi.org/10.1177/0300985812446153.

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Respiratory disease is common in dolphins, primarily affecting pulmonary parenchyma and sparing large airways. Over a 10-year period, 4 captive adult bottlenose dolphins succumbed to chronic, progressive respiratory disease with atypical recurrent upper respiratory signs. All dolphins had severe, segmental to circumferential fibrosing tracheitis that decreased luminal diameter. Histologically, tracheal cartilage, submucosa, and mucosa were distorted and replaced by extensive fibrosis and pyogranulomatous inflammation centered on fungal hyphae. In 3 of 4 cases, hyphae were morphologically compa

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Oliveira, Luiz Carlos Marques de, Priscilla Dias Silva Abrahão, and Sergio Borges de Amorim. "Detection of hepatitis B virus DNA in sera from 18 alcoholic carriers of "anti-HBc alone" and response to a single dose of hepatitis B vaccine." Arquivos de Gastroenterologia 45, no. 3 (2008): 252–54. http://dx.doi.org/10.1590/s0004-28032008000300017.

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To evaluate the possibility of occult hepatitis B virus (HBV) infection in alcoholics carriers of "anti-HBc alone", and to verify the behavior of this serological pattern after a single dose of hepatitis B vaccine, 18 alcoholics who had this serological profile were evaluated by the polymerase chain reaction method, and 17 of them were vaccined. All were negative for HBV DNA. Nine (52.9%) of those vaccined had anamnestic response, mainly those with positive anti-HBe (8/10; 80%). "Anti-HBc alone" was compatible with low levels of anti-HBs in half of the patients, and probably with false positiv

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Li, Qingbo, and Edward S. Yeung. "Simple Two-Color Base-Calling Schemes for DNA Sequencing Based on Standard Four-Label Sanger Chemistry." Applied Spectroscopy 49, no. 10 (1995): 1528–33. http://dx.doi.org/10.1366/0003702953965470.

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Two base-calling schemes for DNA sequencing are evaluated. Both are based on data collected from two broad-band emission channels derived from either one- or two-excitation channels. Standard four-dye Sanger reaction products are used in conjunction with capillary electrophoretic separation in a polymer matrix. Data acquisition is compatible with high light-throughput imaging and minimal data storage. In one scheme, commercial chromatographic software provides peak recognition and peak heights. The peak-height ratios from the two channels provide base-calling accuracies of 99.3% and 97.1% thro

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Andrade, Rosilene Viana de, Cesare Massone, Meline Nogueira Barbosa de Lucena, et al. "The use of polymerase chain reaction to confirm diagnosis in skin biopsies consistent with american tegumentary leishmaniasis at histopathology: a study of 90 cases." Anais Brasileiros de Dermatologia 86, no. 5 (2011): 892–96. http://dx.doi.org/10.1590/s0365-05962011000500005.

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BACKGROUND: Cutaneous leishmaniasis is a chronic, infectious disease caused by protozoa of the genus leishmania. The incidence of this disease is high in Brazil, with 19,746 new cases having been detected in 2008. The presence of amastigotes in the cytoplasm of histiocytes constitutes diagnosis of the disease; however, their presence is rarely found in late lesions, making histological diagnosis difficult. Polymerase chain reaction has been shown to represent a highly sensitive and specific technique for the diagnosis of cutaneous leishmaniasis. OBJECTIVES: To use polymerase chain reaction to

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Dreaden, Tyler J., John M. Davis, Carrie L. Harmon, et al. "Development of Multilocus PCR Assays for Raffaelea lauricola, Causal Agent of Laurel Wilt Disease." Plant Disease 98, no. 3 (2014): 379–83. http://dx.doi.org/10.1094/pdis-07-13-0772-re.

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Laurel wilt, caused by the fungus Raffaelea lauricola, is an exotic disease that affects members of the Lauraceae plant family in the southeastern United States. The disease is spreading rapidly in native forests and is now found in commercial avocado groves in south Florida, where an accurate diagnostic method would improve disease management. A polymerase chain reaction (PCR) method based on amplifying the ribosomal small-subunit DNA, with a detection limit of 0.0001 ng, was found to be suitable for some quantitative PCR applications; however, it was not taxon specific. Genomic sequencing of

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Behrmann, Ole, Matthias Hügle, Franz Eckardt, et al. "3D Printed Monolithic Microreactors for Real-Time Detection of Klebsiella pneumoniae and the Resistance Gene blaNDM-1 by Recombinase Polymerase Amplification." Micromachines 11, no. 6 (2020): 595. http://dx.doi.org/10.3390/mi11060595.

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We investigate the compatibility of three 3D printing materials towards real-time recombinase polymerase amplification (rtRPA). Both the general ability of the rtRPA reaction to occur while in contact with the cured 3D printing materials as well as the residual autofluorescence and fluorescence drift in dependence on post curing of the materials is characterized. We 3D printed monolithic rtRPA microreactors and subjected the devices to different post curing protocols. Residual autofluorescence and drift, as well as rtRPA kinetics, were then measured in a custom-made mobile temperature-controll

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GUL, Sheraz, Richard BROWN, Earl MAY, et al. "Staphylococcus aureus DNA ligase: characterization of its kinetics of catalysis and development of a high-throughput screening compatible chemiluminescent hybridization protection assay." Biochemical Journal 383, no. 3 (2004): 551–59. http://dx.doi.org/10.1042/bj20040054.

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DNA ligases are key enzymes involved in the repair and replication of DNA. Prokaryotic DNA ligases uniquely use NAD+ as the adenylate donor during catalysis, whereas eukaryotic enzymes use ATP. This difference in substrate specificity makes the bacterial enzymes potential targets for therapeutic intervention. We have developed a homogeneous chemiluminescence-based hybridization protection assay for Staphylococcus aureus DNA ligase that uses novel acridinium ester technology and demonstrate that it is an alternative to the commonly used radiometric assays for ligases. The assay has been used to

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Angeline, T., H. R. Krithiga, W. Isabel, A. J. Asirvatham, and A. Poornima. "Endothelial Nitric Oxide Synthase Gene Polymorphism (G894T) and Diabetes Mellitus (Type II) among South Indians." Oxidative Medicine and Cellular Longevity 2011 (2011): 1–4. http://dx.doi.org/10.1155/2011/462607.

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The objective of the study is to find out whether the endothelial nitric oxide synthase (eNOS) G894T single-nucleotide polymorphism is associated with type 2 diabetes mellitus in South Indian (Tamil) population. A total number of 260 subjects comprising 100 type 2 diabetic mellitus patients and 160 healthy individuals with no documented history of diabetes were included for the study. DNA was isolated, and eNOS G894T genotyping was performed using the polymerase chain reaction followed by restriction enzyme analysis usingBan II. The genotype distribution in patients and controls were compatibl

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Fenton, James A. L., Jan-Willem Vaandrager, Wilhelmina M. Aarts, et al. "Follicular lymphoma with a novel t(14;18) breakpoint involving the immunoglobulin heavy chain switch mu region indicates an origin from germinal center B cells." Blood 99, no. 2 (2002): 716–18. http://dx.doi.org/10.1182/blood.v99.2.716.

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Abstract With the use of DNA-fiber fluorescent in situ hybridization, a BCL2 protein positive follicular lymphoma with a novel BCL2 breakpoint involving the immunoglobulin heavy chain (IGH) switch mu (Sμ) region instead of the JH orDH gene segments was identified. Sequence analysis showed that the genomic breakpoint is localized between the Sμ region of the IGH complex and the first intron of BCL2. Reverse-transcriptase polymerase chain reaction showed expression of a unique hybrid IGH-BCL2 transcript involving the transcription initiation site Iμ. Sequence analysis of the VH region of the fun

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Abdelbaky, Ahmed S., Ivan A. Prokhorov, Igor P. Smirnov, Kristina M. Koroleva, Vitaliy I. Shvets та Yulia G. Kirillova. "Synthesis of α-(R)-/γ-(S)-Dimethyl Substituted Peptide Nucleic Acid Submonomer Using Mitsunobu Reaction". Letters in Organic Chemistry 16, № 5 (2019): 437–46. http://dx.doi.org/10.2174/1570178616666190118155031.

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One of the major challenges facing modern biochemical and biomedical technologies are finding molecular tools for diagnosis and detection of genetic diseases. In this connection, several classes of oligonucleotides have been developed that can recognize and bind to DNA and RNA with high affinity and sequence selectivity and withstand enzymatic degradation by proteases and nucleases; however, few can traverse the cell membrane on their own. One such promising class of nucleic acid mimics developed in the last two decades which showed good results in vitro, are the peptide nucleic acids (PNAs).

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Davitkov, Darko, Milos Vucicevic, Jevrosima Stevanovic, et al. "Clinical babesiosis and molecular identification of Babesia canis and Babesia gibsoni infections in dogs from Serbia." Acta Veterinaria Hungarica 63, no. 2 (2015): 199–208. http://dx.doi.org/10.1556/avet.2015.017.

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Canine babesiosis is a frequent and clinically significant tick-borne disease. Sixty symptomatic dogs with clinical findings compatible with babesiosis were included in this study conducted in Serbia. After clinical examination, blood samples were taken for microscopic examination, complete blood count (CBC), Canine SNAP 4Dx Test, DNA analyses and sequencing. The main clinical signs included apathy, anorexia, fever, brown/red discoloration of urine, pale mucous membranes, icterus, splenomegaly, and vomiting. The main clinicopathological findings in Babesia infections were a slight to severe th

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Lipej, Z., J. Segalés, I. Toplak, et al. "Postweaning multisystemic wasting syndrome (pmws) in pigs in Croatia: Detection and characterisation of porcine circovirus type 2 (pcv2)." Acta Veterinaria Hungarica 53, no. 3 (2005): 385–96. http://dx.doi.org/10.1556/avet.53.2005.3.11.

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The objective of this study was to characterise porcine circovirus type 2 (PCV2) from pigs with naturally occurring postweaning multisystemic wasting syndrome (PMWS) in Croatia, and to determine the epizootiological, clinical and pathomorphological features of the disease. During a systematic health monitoring programme conducted in the period from January 2002 to June 2003, PMWS was suspected on eight different pig-producing farms in Croatia. The diagnosis of PMWS met all three key criteria: the presence of compatible clinical signs, the presence of the characteristic microscopic lymphoid les

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Schlegel, PG, R. Aharoni, DE Smilek, et al. "Prevention of graft-versus-host disease by peptides binding to class II major histocompatibility complex molecules." Blood 84, no. 8 (1994): 2802–10. http://dx.doi.org/10.1182/blood.v84.8.2802.2802.

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Abstract Graft-versus-host disease across minor histocompatibility barriers was induced in two different models by transplanting allogeneic bone marrow and spleen cells into irradiated H-2-compatible recipient mice. In this report, we show that administration of peptides with high binding affinity for the respective class II major histocompatibility complex molecules after transplantation is capable of preventing the development of graft-versus-host disease in two different murine models. The peptides used were myelin basic protein residues 1 through 11 with alanine at position 4 (Ac 1–11[4A])

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Schlegel, PG, R. Aharoni, DE Smilek, et al. "Prevention of graft-versus-host disease by peptides binding to class II major histocompatibility complex molecules." Blood 84, no. 8 (1994): 2802–10. http://dx.doi.org/10.1182/blood.v84.8.2802.bloodjournal8482802.

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Graft-versus-host disease across minor histocompatibility barriers was induced in two different models by transplanting allogeneic bone marrow and spleen cells into irradiated H-2-compatible recipient mice. In this report, we show that administration of peptides with high binding affinity for the respective class II major histocompatibility complex molecules after transplantation is capable of preventing the development of graft-versus-host disease in two different murine models. The peptides used were myelin basic protein residues 1 through 11 with alanine at position 4 (Ac 1–11[4A]) for I-Au

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