154 results match your criteria repetitive oligo

A universal karyotypic system for hexaploid and diploid Avena species brings oat cytogenetics into the genomics era.

BMC Plant Biol 2021 May 12;21(1):213. Epub 2021 May 12.

Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, China.

Background: The identification of chromosomes among Avena species have been studied by C-banding and in situ hybridization. However, the complicated results from several cytogenetic nomenclatures for identifying oat chromosomes are often contradictory. A universal karyotyping nomenclature system for precise chromosome identification and comparative evolutionary studies would be essential for genus Avena based on the recently released genome sequences of hexaploid and diploid Avena species. Read More

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Chorus2: design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization.

Plant Biotechnol J 2021 May 7. Epub 2021 May 7.

Department of Plant Biology, Michigan State University, East Lansing, MI, USA.

Oligonucleotide (oligo)-fluorescence in situ hybridization (FISH) has rapidly becoming the new generation of FISH technique in plant molecular cytogenetics research. Genome-scale identification of single-copy oligos is the foundation of successful oligo-FISH experiments. Here, we introduce Chorus2, a software that is developed specifically for oligo selection. Read More

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Epitope Binning of Novel Monoclonal Anti F1 and Anti LcrV Antibodies and Their Application in a Simple, Short, HTRF Test for Clinical Plague Detection.

Pathogens 2021 Mar 2;10(3). Epub 2021 Mar 2.

The Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 7410001, Israel.

Mouse monoclonal antibodies were raised against plague disease biomarkers: the bacterial capsular protein fraction 1 (F1) and the low-calcium response-LcrV virulence factor (Vag). A novel tandem assay, employing BioLayer Interferometry (BLI), enabled the isolation of antibodies against four different epitopes on Vag. The tandem assay was carried out with hybridoma supernatants, circumventing the need for antibody purification. Read More

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Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes.

Nat Commun 2021 03 11;12(1):1576. Epub 2021 Mar 11.

Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel.

We apply an oligo-library and machine learning-approach to characterize the sequence and structural determinants of binding of the phage coat proteins (CPs) of bacteriophages MS2 (MCP), PP7 (PCP), and Qβ (QCP) to RNA. Using the oligo library, we generate thousands of candidate binding sites for each CP, and screen for binding using a high-throughput dose-response Sort-seq assay (iSort-seq). We then apply a neural network to expand this space of binding sites, which allowed us to identify the critical structural and sequence features for binding of each CP. Read More

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Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut.

BMC Plant Biol 2021 Feb 20;21(1):107. Epub 2021 Feb 20.

Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China.

Background: Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. Read More

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February 2021

Generation of Mouse Model (KI and CKO) via Easi-CRISPR.

Methods Mol Biol 2021 ;2224:1-27

Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, NY, USA.

Recent development of Easi-CRISPR (Efficient additions with ssDNA inserts-CRISPR) that utilizes long single-stranded DNA (lssDNA) of 0.2-2 kbases in length as donor templates to insert large segments of novel DNA sequences or to replace endogenous genes at precise locations in the genome has enabled CRISPR-assisted genome editing to make strides toward a more simple and rapid workflow. By leveraging the notion that short single-stranded DNA oligo (<200 bases) serves as efficient donor in mouse zygotes for facilitating HDR-mediated genome editing, Easi-CRISPR expands to use lssDNA as the donor which accelerates the timeline to as little as 2 months for creating most types of genetically engineered mouse models (F0). Read More

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Karyotyping chromosomes with multiple oligonucleotide probes reveals the genomic divergence in .

Genome 2021 Jan 29:1-12. Epub 2021 Jan 29.

Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu 611731, China.

The perennial species (genome V) contains many potentially valuable genes for the improvement of common wheat. Construction of a detailed karyotype of chromosomes will be useful for the detection of chromatin in wheat background. We established the standard karyotype of 1V-7V chromosomes through nondenaturing fluorescence in situ hybridization (ND-FISH) technique using 28 oligonucleotide probes from the wheat - partial amphiploid TDH-2 (AABBVV) and newly identified wheat - disomic translocation and addition lines D2138 (6VS. Read More

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January 2021

G4 Structures in Control of Replication and Transcription of rRNA Genes.

Front Plant Sci 2020 8;11:593692. Epub 2020 Oct 8.

Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia.

Genes encoding 45S ribosomal RNA (rDNA) are known for their abundance within eukaryotic genomes and for their unstable copy numbers in response to changes in various genetic and epigenetic factors. Commonly, we understand as epigenetic factors (affecting gene expression without a change in DNA sequence), namely DNA methylation, histone posttranslational modifications, histone variants, RNA interference, nucleosome remodeling and assembly, and chromosome position effect. All these were actually shown to affect activity and stability of rDNA. Read More

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October 2020

COMBinatorial Oligonucleotide FISH (COMBO-FISH) with Uniquely Binding Repetitive DNA Probes.

Methods Mol Biol 2020 ;2175:65-77

Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany.

During the last decade, genome sequence databases of many species have been more and more completed so that it has become possible to further develop a recently established technique of FISH (Fluorescence In Situ Hybridization) called COMBO-FISH (COMBinatorial Oligo FISH). In contrast to standard FISH techniques, COMBO-FISH makes use of a bioinformatic search in sequence databases for probe design, so that it can be done for any species so far sequenced. In the original approach, oligonucleotide stretches of typical lengths of 15-30 nucleotides were selected in such a way that they only co-localize at the given genome target. Read More

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An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells.

BMC Genomics 2020 Jun 29;21(1):448. Epub 2020 Jun 29.

Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75123, Uppsala, Sweden.

Background: Most diversity in the eukaryotic tree of life is represented by microbial eukaryotes, which is a polyphyletic group also referred to as protists. Among the protists, currently sequenced genomes and transcriptomes give a biased view of the actual diversity. This biased view is partly caused by the scientific community, which has prioritized certain microbes of biomedical and agricultural importance. Read More

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Fluorescent In Situ Hybridization Using Oligonucleotide-Based Probes.

Methods Mol Biol 2020 ;2148:71-83

Department of Plant Biology, Michigan State University, East Lansing, MI, USA.

Efficient and consistent chromosome identification is the foundation for successful cytogenetic studies. Fluorescent in situ hybridization (FISH) has been the most popular technique for chromosome identification in plants. Large insert genomic DNA clones, such as bacterial artificial chromosome (BAC) clones, and repetitive DNA sequences have been the most commonly used DNA probes for FISH. Read More

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Improving the Catalytic Performance of Pectate Lyase Through Pectate Lyase/Cu(PO) Hybrid Nanoflowers as an Immobilized Enzyme.

Front Bioeng Biotechnol 2020 3;8:280. Epub 2020 Apr 3.

State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, China.

Pectate lyases (Pels) can be used in the textile industrial process for cotton scouring and ramie degumming, and its hydrolyzed products oligo galacturonic acid, are high-value added agricultural and health products. In our previous studies, an alkaline pectate lyase PEL168 mutant, PEL3, was obtained with improved specific activity and thermostability. Here, a facile and rapid method for preparing an immobilized PEL3-inorganic hybrid nanoflower was developed, as it could improve its biocatalytic performance. Read More

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Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin.

PLoS Genet 2020 03 23;16(3):e1008673. Epub 2020 Mar 23.

Department of Molecular and Cell Biology, UC Berkeley and BSE Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.

Membraneless pericentromeric heterochromatin (PCH) domains play vital roles in chromosome dynamics and genome stability. However, our current understanding of 3D genome organization does not include PCH domains because of technical challenges associated with repetitive sequences enriched in PCH genomic regions. We investigated the 3D architecture of Drosophila melanogaster PCH domains and their spatial associations with the euchromatic genome by developing a novel analysis method that incorporates genome-wide Hi-C reads originating from PCH DNA. Read More

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Nanomolecular electronic devices based on AuNP molecule nanoelectrodes using molecular place-exchange process.

Nanotechnology 2020 May 17;31(22):225207. Epub 2020 Feb 17.

Applied Materials Science, Department of Engineering Sciences, Uppsala University, PO Box 534, Uppsala SE-75121, Sweden. Department of Electrical Engineering, Mirpur University of Science and Technology, Mirpur Azad Jammu and Kashmir 10250, Pakistan.

The implementation of electronics applications based on molecular electronics devices is hampered by the difficulty of placing a single or a few molecules with application-specific electronic properties in between metallic nanocontacts. Here, we present a novel method to fabricate 20 nm sized nanomolecular electronic devices (nanoMoED) using a molecular place-exchange process of nonconductive short alkyl thiolates with various short chain conductive oligomers. After the successful place-exchange with short-chain conjugated oligomers in the nanoMoED devices, a change in device resistance of up to four orders of magnitude for 4,4'-biphenyldithiol (BPDT), and up to three orders of magnitude for oligo phenylene-ethynylene (OPE), were observed. Read More

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Dynamic Behavior of Complex Coacervates with Internal Lipid Vesicles under Nonequilibrium Conditions.

Langmuir 2020 02 12;36(7):1709-1717. Epub 2020 Feb 12.

Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China.

During the evolution of life on earth, the emergence of lipid membrane-bounded compartments is one of the most enigmatic events. Endosymbiosis has been hypothesized as one of the solutions. In this work, using a coacervate droplet formed by single-stranded oligonucleotides (ss-oligo) and poly(l-lysine) (PLL) as the protocell model, we monitored the uptake of liposomes of different types and studied the dynamic behavior of the resulting composite droplet under the electric field. Read More

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February 2020

Molecular karyotyping of Siberian wild rye (Elymus sibiricus L.) with oligonucleotide fluorescence in situ hybridization (FISH) probes.

PLoS One 2020 17;15(1):e0227208. Epub 2020 Jan 17.

Key Laboratory of Crop Molecular Breeding, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.

Siberian wild rye (Elymus sibiricus L.), an allotetraploid species, is a potentially high-quality perennial forage crop native to temperate regions. We used fluorescently conjugated oligonucleotides, representing ten repetitive sequences, including 6 microsatellite repeats, two satellite repeats, and two ribosomal DNAs, to characterize E. Read More

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New ND-FISH-Positive Oligo Probes for Identifying Chromosomes in Wheat Backgrounds.

Int J Mol Sci 2019 Apr 25;20(8). Epub 2019 Apr 25.

Provincial Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China.

has been widely used to improve wheat ( L.) cultivars. Non-denaturing fluorescence in situ hybridization (ND-FISH) technology using oligonucleotides (oligo) as probes provides a convenient and efficient way to identify alien chromosomes in wheat backgrounds. Read More

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Fluorescence in situ hybridization in plants: recent developments and future applications.

Jiming Jiang

Chromosome Res 2019 09 9;27(3):153-165. Epub 2019 Mar 9.

Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.

Fluorescence in situ hybridization (FISH) was developed more than 30 years ago and has been the most paradigm-changing technique in cytogenetic research. FISH has been used to answer questions related to structure, mutation, and evolution of not only individual chromosomes but also entire genomes. FISH has served as an important tool for chromosome identification in many plant species. Read More

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September 2019

Extracorporeal membrane oxygenation support in a newborn with lower urinary tract obstruction and pulmonary hypoplasia: a case report.

J Med Case Rep 2018 Jul 17;12(1):210. Epub 2018 Jul 17.

Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Adenauerallee 119, 53113, Bonn, Germany.

Background: Survival of neonates with intrauterine renal insufficiency and oligo- or anhydramnios correlates with the severity of secondary pulmonary hypoplasia. Early prenatal diagnosis together with repetitive amnioinfusions and modern intensive care treatment have improved the prognosis of these neonates. Extracorporeal membrane oxygenation is an established treatment option, mainly applied to neonates with pulmonary hypoplasia caused by congenital diaphragmatic hernia. Read More

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Nucleosomes and DNA methylation shape meiotic DSB frequency in transposons and gene regulatory regions.

Genome Res 2018 04 12;28(4):532-546. Epub 2018 Mar 12.

Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.

Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced SPO11-1-oligonucleotides. Read More

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High-throughput construction of multiple cas9 gene variants via assembly of high-depth tiled and sequence-verified oligonucleotides.

Nucleic Acids Res 2018 05;46(9):e55

Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.

Selective retrieval of sequence-verified oligonucleotides (oligos) from next-generation sequencing (NGS) flow cells, termed megacloning, promises accurate and reliable gene synthesis. However, gene assembly requires a complete collection of overlapping sense and nonsense oligos, and megacloning does not typically guarantee the complete production of sequence-verified oligos. Therefore, missing oligos must be provided via repetitive rounds of megacloning, which introduces a bottleneck for scaled-up efforts at gene assembly. Read More

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Precise identification of wheat - Thinopyrum intermedium translocation chromosomes carrying resistance to wheat stripe rust in line Z4 and its derived progenies.

Genome 2018 Mar 22;61(3):177-185. Epub 2018 Feb 22.

a School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.

The wheat - Thinopyrum intermedium derived line Z4 has displayed novel and effective stripe rust resistance for over 40 years. This study aimed to precisely identify the chromosome constitution of line Z4 and determine the stripe rust resistance contribution using multicolor fluorescent in situ hybridization (FISH) and molecular marker analysis. The results indicated that the Z4 line (2n = 44) contained two pairs of non-Robertsonian translocations without the 3A chromosomes of wheat. Read More

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Oligonucleotides and ND-FISH Displaying Different Arrangements of Tandem Repeats and Identification of Dasypyrum villosum Chromosomes in Wheat Backgrounds.

Molecules 2017 Jun 14;22(6). Epub 2017 Jun 14.

Provincial Key Laboratory of Plant Breeding and Genetics, Sichuan Agriculture University, Chengdu 611130, China.

Oligonucleotide probes and the non-denaturing fluorescence in situ hybridization (ND-FISH) technique are widely used to analyze plant chromosomes because they are convenient tools. New oligonucleotide probes, Oligo-Ku, Oligo-3B117.1, Oligo-3B117. Read More

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Development of oligonucleotides and multiplex probes for quick and accurate identification of wheat and Thinopyrum bessarabicum chromosomes.

Genome 2017 Feb 14;60(2):93-103. Epub 2016 Sep 14.

a State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China.

In comparison with general FISH for preparing probes in terms of time and cost, synthesized oligonucleotide (oligo hereafter) probes for FISH have many advantages such as ease of design, synthesis, and labeling. Low cost and high sensitivity and resolution of oligo probes greatly simplify the FISH procedure as a simple, fast, and efficient method of chromosome identification. In this study, we developed new oligo and oligo multiplex probes to accurately and efficiently distinguish wheat (Triticum aestivum, 2n = 6x, AABBDD) and Thinopyrum bessarabicum (2n = 2x = 14, JJ) chromosomes. Read More

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February 2017

New Oligonucleotide Probes for ND-FISH Analysis to Identify Barley Chromosomes and to Investigate Polymorphisms of Wheat Chromosomes.

Genes (Basel) 2016 Dec 5;7(12). Epub 2016 Dec 5.

Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agriculture University, Wenjiang, Chengdu 611130, China.

Oligonucleotide probes that can be used for non-denaturing fluorescence in situ hybridization (ND-FISH) analysis are convenient tools for identifying chromosomes of wheat ( L.) and its relatives. New oligonucleotide probes, Oligo-HvT01, Oligo-pTa71-1, Oligo-s120. Read More

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December 2016

New molecular markers and cytogenetic probes enable chromosome identification of wheat-Thinopyrum intermedium introgression lines for improving protein and gluten contents.

Planta 2016 Oct 11;244(4):865-76. Epub 2016 Jun 11.

School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China.

Main Conclusion: New molecular markers were developed for targeting Thinopyrum intermedium 1St#2 chromosome, and novel FISH probe representing the terminal repeats was produced for identification of Thinopyrum chromosomes. Thinopyrum intermedium has been used as a valuable resource for improving the disease resistance and yield potential of wheat. A wheat-Th. Read More

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October 2016

Molecular cytogenetic characterization of Dasypyrum breviaristatum chromosomes in wheat background revealing the genomic divergence between Dasypyrum species.

Mol Cytogenet 2016 25;9. Epub 2016 Jan 25.

School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054 China.

Background: The uncultivated species Dasypyrum breviaristatum carries novel diseases resistance and agronomically important genes of potential use for wheat improvement. The development of new wheat-D. breviaristatum derivatives lines with disease resistance provides an opportunity for the identification and localization of resistance genes on specific Dasypyrum chromosomes. Read More

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January 2016

A Search for Blood Biomarkers for Autism: Peptoids.

Sci Rep 2016 Jan 14;6:19164. Epub 2016 Jan 14.

Department of Psychiatry, UT Southwestern Medical Center, Dallas TX.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impairments in social interaction and communication, and restricted, repetitive patterns of behavior. In order to identify individuals with ASD and initiate interventions at the earliest possible age, biomarkers for the disorder are desirable. Research findings have identified widespread changes in the immune system in children with autism, at both systemic and cellular levels. Read More

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January 2016

Detection of stably expressed piRNAs in human blood.

Int J Clin Exp Med 2015 15;8(8):13353-8. Epub 2015 Aug 15.

Department of Urology, The First Affiliated Hospital of Nanjing Medical University Nanjing 210029, China.

Background: Circulating microRNAs are potential markers for disease detection. A novel class of small non-coding RNAs called Piwi-interacting RNAs (piRNAs) has been recently reported to participate in the epigenetic regulation of cancers and other diseases. This study aims to discover blood-based piRNAs which can be used as markers for disease detection and monitoring. Read More

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November 2015

Up-Regulation of Oligodendrocyte Lineage Markers in the Cerebellum of Autistic Patients: Evidence from Network Analysis of Gene Expression.

Mol Neurobiol 2016 08 21;53(6):4019-4025. Epub 2015 Jul 21.

Faculty of Life Sciences, The University of Manchester, Manchester, UK.

Autism is a neurodevelopmental disorder manifested by impaired social interaction, deficits in communication skills, restricted interests, and repetitive behaviors. In neurodevelopmental, neurodegenerative, and psychiatric disorders, glial cells undergo morphological, biochemical, and functional rearrangements, which are critical for neuronal development, neurotransmission, and synaptic connectivity. Cerebellar function is not limited to motor coordination but also contributes to cognition and may be affected in autism. Read More

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