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https://www.readbyqxmd.com/read/28717645/whole-genome-amplification-of-day-3-or-day-5-human-embryos-biopsies-provides-a-suitable-dna-template-for-pcr-based-techniques-for-genotyping-a-complement-of-preimplantation-genetic-testing
#1
Elizabeth Schaeffer, Bruno López-Bayghen, Adina Neumann, Leonardo M Porchia, Rafael Camacho, Efraín Garrido, Rocío Gómez, Felipe Camargo, Esther López-Bayghen
Our objective was to determine if whole genome amplification (WGA) provides suitable DNA for qPCR-based genotyping for human embryos. Single blastomeres (Day 3) or trophoblastic cells (Day 5) were isolated from 342 embryos for WGA. Comparative Genomic Hybridization determined embryo sex as well as Trisomy 18 or Trisomy 21. To determine the embryo's sex, qPCR melting curve analysis for SRY and DYS14 was used. Logistic regression indicated a 4.4%, 57.1%, or 98.8% probability of a male embryo when neither gene, SRY only, or both genes were detected, respectively (accuracy = 94...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28701744/massively-parallel-whole-genome-amplification-for-single-cell-sequencing-using-droplet-microfluidics
#2
Masahito Hosokawa, Yohei Nishikawa, Masato Kogawa, Haruko Takeyama
Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28693732/wheat-germ-agglutinin-and-lens-culinaris-agglutinin-sensitized-anisotropic-silver-nanoparticles-in-detection-of-bacteria-a-simple-photometric-assay
#3
Mariam V Mikaelyan, Gayane G Poghosyan, Olga D Hendrickson, Boris B Dzantiev, Vardan K Gasparyan
Efficacy of anisotropic silver nanoparticles sensitized with wheat germ agglutinin (WGA) and Lens culinaris agglutinin (LCA) was studied for detection of Staphylococcus aureus and Escherichia coli. It was demonstrated that interaction of these nanoparticles with bacteria stabilizes them and prevents their aggregation upon addition of sodium chloride; such stabilization depends on bacteria concentration. High concentration of bacteria results in higher stabilization whereas low concentration leads to aggregation of nanoparticles...
August 15, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28686627/wga-based-lectin-affinity-gel-electrophoresis-a-novel-method-for-the-detection-of-o-glcnac-modified-proteins
#4
Yuji Kubota, Ko Fujioka, Mutsuhiro Takekawa
Post-translational modification with O-linked β-N-acetylglucosamine (O-GlcNAc) occurs selectively on serine and/or threonine residues of cytoplasmic and nuclear proteins, and dynamically regulates their molecular functions. Since conventional strategies to evaluate the O-GlcNAcylation level of a specific protein require time-consuming steps, the development of a rapid and easy method for the detection and quantification of an O-GlcNAcylated protein has been a challenging issue. Here, we describe a novel method in which O-GlcNAcylated and non-O-GlcNAcylated forms of proteins are separated by lectin affinity gel electrophoresis using wheat germ agglutinin (WGA), which primarily binds to N-acetylglucosamine residues...
2017: PloS One
https://www.readbyqxmd.com/read/28666423/precision-oncology-using-a-limited-number-of-cells-optimization-of-whole-genome-amplification-products-for-sequencing-applications
#5
Shonan Sho, Colin M Court, Paul Winograd, Sangjun Lee, Shuang Hou, Thomas G Graeber, Hsian-Rong Tseng, James S Tomlinson
BACKGROUND: Sequencing analysis of circulating tumor cells (CTCs) enables "liquid biopsy" to guide precision oncology strategies. However, this requires low-template whole genome amplification (WGA) that is prone to errors and biases from uneven amplifications. Currently, quality control (QC) methods for WGA products, as well as the number of CTCs needed for reliable downstream sequencing, remain poorly defined. We sought to define strategies for selecting and generating optimal WGA products from low-template input as it relates to their potential applications in precision oncology strategies...
July 1, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28648723/a-protocol-for-the-simultaneous-identification-of-chitin-containing-particles-and-their-associated-bacteria
#6
Florencia Biancalana, Germán A Kopprio, Rubén J Lara, Cecilia Alonso
Chitin is the second most abundant polymer on Earth, playing a crucial role in the biogeochemical cycles. A core issue for studying its processing in aquatic systems is the identification and enumeration of chitin-containing particles and organisms, ideally in a manner that can be directly linked to bulk chitin quantification. The aim of this study was the development of such a technique. We successfully combined the methodology of bulk chitin determination using wheat germ agglutinin (FITC-WGA) for staining chitin-containing particles and organisms along with CARD-FISH staining of either chitin-containing eukaryotic cells or bacteria associated with them...
June 7, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28642587/systematic-comparison-of-two-whole-genome-amplification-methods-for-targeted-next-generation-sequencing-using-frozen-and-ffpe-normal-and-cancer-tissues
#7
Pedro Mendez, Li Tai Fang, David M Jablons, Il-Jin Kim
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28639357/cerebellar-projections-to-the-ventral-lateral-geniculate-nucleus-and-the-thalamic-reticular-nucleus-in-the-cat
#8
Hiroyuki Nakamura
The ventral lateral geniculate nucleus (LGNv) is a retinorecipient part of the ventral thalamus and in cats, it consists of medial (M), medial intermediate (IM), lateral intermediate (IL), lateral (L), and dorsal (D) subdivisions. These subdivisions can be differentiated not only by their cytoarchitecture, but also by their connectivity and putative functions. The LGNv may play a role in visuomotor gating, in that there is evidence of cerebellar afferent projections to the intermediate subdivisions. The cerebellar posterior interpositus (IP) and lateral (LC) nuclei are known to project to IM and IL, but the specifics of these projections are unclear...
June 22, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/28633287/genetic-diseases-and-aneuploidies-can-be-detected-with-a-single-blastocyst-biopsy-a-successful-clinical-approach
#9
Maria Giulia Minasi, Francesco Fiorentino, Alessandra Ruberti, Anil Biricik, Elisabetta Cursio, Ettore Cotroneo, Maria Teresa Varricchio, Matteo Surdo, Francesca Spinella, Ermanno Greco
STUDY QUESTION: Can simultaneous detection of aneuploidies and genetic diseases or chromosomal aberrations in blastocysts reduce the chance of transferring embryos with low implantation potential, guaranteeing good clinical outcomes? SUMMARY ANSWER: The screening for chromosomal aneuploidies revealed that 50.6% of blastocysts diagnosed free of genetic disease or balanced, were aneuploid, therefore avoiding the transfer of blastocysts potentially resulting in implantation failures, miscarriages, or in some cases, in health affected live births...
June 12, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28611458/performance-of-four-modern-whole-genome-amplification-methods-for-copy-number-variant-detection-in-single-cells
#10
Lieselot Deleye, Laurentijn Tilleman, Ann-Sophie Vander Plaetsen, Senne Cornelis, Dieter Deforce, Filip Van Nieuwerburgh
Whole genome amplification (WGA) has become an invaluable tool to perform copy number variation (CNV) detection in single, or a limited number of cells. Unfortunately, current WGA methods introduce representation bias that limits the detection of small CNVs. New WGA methods have been introduced that might have the potential to reduce this bias. We compared the performance of PicoPLEX DNA-Seq (Picoseq), DOPlify, REPLI-g and Ampli-1 WGA for aneuploidy screening and copy number analysis using shallow whole genome massively parallel sequencing (MPS), starting from single or a limited number of cells...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28586236/inspecting-targeted-deep-sequencing-of-whole-genome-amplified-dna-versus-fresh-dna-for-somatic-mutation-detection-a-genetic-study-in-myelodysplastic-syndrome-patients
#11
Laura Palomo, Francisco Fuster-Tormo, Daniel Alvira, Vera Ademà, María Pilar Armengol, Paula Gómez-Marzo, Nuri de Haro, Mar Mallo, Blanca Xicoy, Lurdes Zamora, Francesc Solé
Whole genome amplification (WGA) has become an invaluable method for preserving limited samples of precious stock material and has been used during the past years as an alternative tool to increase the amount of DNA before library preparation for next-generation sequencing. Myelodysplastic syndromes (MDS) are a group of clonal hematopoietic stem cell disorders characterized by presenting somatic mutations in several myeloid-related genes. In this work, targeted deep sequencing has been performed on four paired fresh DNA and WGA DNA samples from bone marrow of MDS patients, to assess the feasibility of using WGA DNA for detecting somatic mutations...
June 6, 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28586046/enhanced-effect-of-nuclear-localization-signal-peptide-during-ultrasound%C3%A2-targeted-microbubble-destruction%C3%A2-mediated-gene-transfection
#12
Sheng Cao, Qing Zhou, Jin-Ling Chen, Nan Jiang, Yi-Jia Wang, Qing Deng, Bo Hu, Rui-Qiang Guo
Ultrasound‑targeted microbubble destruction (UTMD) can promote the entry of plasmid DNA (pDNA) into the cell cytoplasm, by increasing the permeability of the cell membrane. But the transfection efficiency remains low due to inability of the pDNA to enter the nucleus. Various methods have been explored to improve the UTMD transfection efficiency, but with little success. In cells, the classic nuclear localization signal (cNLS) peptide is an amino acid sequence that signals proteins that are due for nuclear transport...
July 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28572171/the-comparison-of-the-performance-of-four-whole-genome-amplification-kits-on-ion-proton-platform-in-copy-number-variation-detection
#13
Xinyi Zhang, Bo Liang, Xiaoyan Xu, Feifei Zhou, Lingyin Kong, Jingjing Shen, Yingying Xia, Liming Xuan, Yan Mao, Yongfeng Xue, Jichun Tan
With the development and clinical application of genomics, more and more concern is focused on single-cell sequencing. In the process of single-cell sequencing, whole genome amplification is a key step to enrich sample DNA. Previous studies have compared the performance of different WGA strategies on Illumina sequencing platforms, but there is no related research aimed at Ion Proton platform, which is also a popular next-generation sequencing platform. Here by amplifying cells from six cell lines with different karyotypes, we estimated the data features of four common commercial WGA kits (PicoPLEX WGA Kit, GenomePlex Single Cell Whole Genome Amplification Kit, MALBAC Single Cell Whole Genome Amplification Kit, and REPLI-g Single Cell Kit), including median absolute pairwise difference, uniformity, reproducibility, and fidelity, and examined their performance of copy number variation detection...
June 1, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28556796/sugar-binding-profiles-of-chitin-binding-lectins-from-the-hevein-family-a-comprehensive-study
#14
Yoko Itakura, Sachiko Nakamura-Tsuruta, Junko Kominami, Hiroaki Tateno, Jun Hirabayashi
Chitin-binding lectins form the hevein family in plants, which are defined by the presence of single or multiple structurally conserved GlcNAc (N-acetylglucosamine)-binding domains. Although they have been used as probes for chito-oligosaccharides, their detailed specificities remain to be investigated. In this study, we analyzed six chitin-binding lectins, DSA, LEL, PWM, STL, UDA, and WGA, by quantitative frontal affinity chromatography. Some novel features were evident: WGA showed almost comparable affinity for pyridylaminated chitotriose and chitotetraose, while LEL and UDA showed much weaker affinity, and DSA, PWM, and STL had no substantial affinity for the former...
May 30, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28548214/the-performance-of-malbac-and-mda-methods-in-the-identification-of-concurrent-mutations-and-aneuploidy-screening-to-diagnose-beta-thalassaemia-disorders-at-the-single-and-multiple-cell-levels
#15
WeiQiang Liu, HuiMin Zhang, Dan Hu, SiJia Lu, XiaoFang Sun
AIM: To select an optimal whole-genome amplification (WGA) method to improve the efficiency of the preimplantation genetic diagnosis and screening (PGD/PGS) of beta-thalassaemia disorders. METHODS: Fifty-seven fibroblast samples with defined beta-thalassaemia variations and forty-eight single-blastomere samples were amplified from single-, two-, and five-cell samples by multiple annealing and looping-based amplification cycles (MALBAC) and the multiple displacement amplification (MDA) method...
May 26, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28546995/the-cost-and-cost-trajectory-of-whole-genome-analysis-guiding-treatment-of-patients-with-advanced-cancers
#16
Deirdre Weymann, Janessa Laskin, Robyn Roscoe, Kasmintan A Schrader, Stephen Chia, Stephen Yip, Winson Y Cheung, Karen A Gelmon, Aly Karsan, Daniel J Renouf, Marco Marra, Dean A Regier
BACKGROUND: Limited data exist on the real-world costs of applying whole-genome analysis (WGA) in a clinical setting. We estimated the costs of applying WGA to guide treatments for patients with advanced cancers and characterized how costs evolve over time. METHODS: The setting is the British Columbia Cancer Agency Personalized OncoGenomics (POG) program in British Columbia, Canada. Cost data were obtained for patients who enrolled in the program from 2012 to 2015...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28540705/crename-a-molecular-microbiology-method-enabling-multiparametric-assessment-of-potable-drinking-water
#17
Luc Bissonnette, Andrée F Maheux, Michel G Bergeron
The microbial assessment of potable/drinking water is done to ensure that the resource is free of fecal contamination indicators or waterborne pathogens. Culture-based methods for verifying the microbial safety are limited in the sense that a standard volume of water is generally tested for only one indicator (family) or pathogen.In this work, we describe a membrane filtration-based molecular microbiology method, CRENAME (Concentration Recovery Extraction of Nucleic Acids and Molecular Enrichment), exploiting molecular enrichment by whole genome amplification (WGA) to yield, in less than 4 h, a nucleic acid preparation which can be repetitively tested by real-time PCR for example, to provide multiparametric presence/absence tests (1 colony forming unit or microbial particle per standard volume of 100-1000 mL) for bacterial or protozoan parasite cells or particles susceptible to contaminate potable/drinking water...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28539275/mucosal-transfer-of-wheat-germ-agglutinin-modified-lipid-polymer-hybrid-nanoparticles-for-oral-delivery-of-oridonin
#18
Ying Liu, Jinguang Liu, Jun Liang, Meiying Zhang, Zhe Li, Zhi Wang, Beilei Dang, Nianping Feng
Wheat germ agglutinin-modified lipid-polymer hybrid nanoparticles (WGA-LPNs) promote cellular uptake after oral delivery via receptor-mediated endocytosis and bioadhesion. Understanding the mucosal transport of WGA-LPNs would help to improve bioavailability and ensure therapeutic efficacy. In this study, WGA-LPNs interacted with mucin, forming larger agglomerates with intact core-shell structure. The interaction of WGA-LPNs with mucin improved enterocyte endocytosis in Caco-2 cells. An in situ intestinal diffusion study in mice confirmed that WGA-LPNs reached enterocytes and underwent endocytosis, despite interference from mucin...
May 21, 2017: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/28521959/cancer-cell-death-induced-by-nanomagnetolectin
#19
Dina M M AlSadek, Haitham A Badr, Tamer A Al-Shafie, Sabry M El-Bahr, Motawa E El-Houseini, Leyla B Djansugurova, Chen-Zhong Li, Hafiz Ahmed
Magnetic nanoparticles represent a new paradigm for molecular targeting therapy in cancer. However, the transformative targeting potential of magnetic nanoparticles has been stymied by a key obstacle-safe delivery to specified target cells in vivo. As cancer cells grow under nutrient deprivation and hypoxic conditions and decorate cell surface with excessive sialoglycans, sialic acid binding lectins might be suitable for targeting cancer cells in vivo. Here we explore the potential of magnetic nanoparticles functionalized with wheat germ lectin (WGA) conjugate, so-called nanomagnetolectin, as apoptotic targetable agents for prostate cancer...
May 10, 2017: European Journal of Cell Biology
https://www.readbyqxmd.com/read/28497359/the-pattern-of-thalamocortical-and-brain-stem-projections-to-the-vibrissae-related-sensory-and-motor-cortices-in-de-whiskered-congenital-hypothyroid-rats
#20
Mohammad Reza Afarinesh, Gila Behzadi
The present study is designed to investigate the plastic organization of the thalamo-cortical (TC) and brain stem afferents of whisker primary sensory (wS1) and motor (wM1) cortical areas in congenital hypothyroid (CH) pups following whisker deprivation (WD) from neonatal to adolescence period. Maternal hypothyroidism was induced by adding propylthiouracil (PTU) to the drinking water from early embryonic day 16 to postnatal day (PND) 60. Pregnant rats were divided into intact and CH groups (n = 8). In each group, the total whiskers of pups (4 of 8) were trimmed continuously from PND 1 to PND 60...
August 2017: Metabolic Brain Disease
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