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https://www.readbyqxmd.com/read/28337907/a-single-cell-based-platform-for-copy-number-variation-profiling-through-digital-counting-of-amplified-genomic-dna-fragments
#1
Chunmei Li, Zhilong Yu, Yusi Fu, Yuhong Pang, Yanyi Huang
We develop a novel single-cell-based platform through digital counting of amplified genomic DNA fragments, named multi-fraction amplification (mfA), to detect the copy number variations (CNVs) in a single cell. Amplification is required to acquire genomic information from a single cell, while introducing unavoidable bias. Unlike prevalent methods that directly infers CNV profiles from the pattern of sequencing depth, our mfA platform denatures and separates the DNA molecules from a single cell into multiple fractions of reaction mix before amplification...
March 24, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28326203/esthetic-rehabilitation-of-anterior-teeth-with-copy-milled-restorations-a-report-of-two-cases
#2
Sapna Rani, Jyoti Devi, Chandan Jain, Parul Mutneja, Mahesh Verma
Digitalization has become part and parcel of contemporary prosthodontics with the probability of most of the procedures being based on the digital techniques in the near future. This digital revolution started in the latter half of the 20th century by converting analog objects/signals into digital bits and bytes. Recent developments in all-ceramic materials and systems of computer-aided designing and computer-aided manufacturing (CAD/CAM), copy milling, and so forth offer excellent esthetics and superb biocompatibility...
2017: Case Reports in Dentistry
https://www.readbyqxmd.com/read/28322802/simple-quantitative-pcr-analysis-for-allelic-pten-loss-in-tumor-progression
#3
Xingping Wu, Ailin Zhu, Xiaowu Pang, Guiqin Xie, Xinbin Gu
We describe a simple method to accurately detect and quantify both Pten mutation and allele-specific loss using allele-specific PCR analysis. Our approach used a heterozygous genomic DNA with one wild-type and one mutant Pten allele as a reference at a single concentration to calculate the percent ratio of the wild-type Pten gene for the detection of allele-specific gene loss. With a standard curve, ratios from PCR data were used to quantitate the wild-type Pten allele copy number loss in tumor specimens. We demonstrate the utility of our approach to calculate allele-specific Pten loss during tumor progression and show that our approach generates quantitative data that are comparable to those obtained from digital droplet PCR...
March 18, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28322208/prevalence-and-pathogen-load-estimates-for-the-fungus-batrachochytrium-dendrobatidis-are-impacted-by-its-dna-copy-number-variation
#4
Eria A Rebollar, Douglas C Woodhams, Brandon LaBumbard, Jos Kielgast, Reid N Harris
The ribosomal gene complex is a multi-copy region that is widely used for phylogenetic analyses of organisms from all 3 domains of life. In fungi, the copy number of the internal transcribed spacer (ITS) is used to detect abundance of pathogens causing diseases such as chytridiomycosis in amphibians and white nose syndrome in bats. Chytridiomycosis is caused by the fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), and is responsible for declines and extinctions of amphibians worldwide...
March 21, 2017: Diseases of Aquatic Organisms
https://www.readbyqxmd.com/read/28319152/a-digital-pcr-method-for-identifying-and-quantifying-adulteration-of-meat-species-in-raw-and-processed-food
#5
Junan Ren, Tingting Deng, Wensheng Huang, Ying Chen, Yiqiang Ge
Meat adulteration is a worldwide concern. In this paper, a new droplet digital PCR (ddPCR) method was developed for the quantitative determination of the presence of chicken in sheep and goat meat products. Meanwhile, a constant (multiplication factor) was introduced to transform the ratio of copy numbers to the proportion of meats. The presented ddPCR method was also proved to be more accurate (showing bias of less than 9% in the range from 5% to 80%) than real-time PCR, which has been widely used in this determination...
2017: PloS One
https://www.readbyqxmd.com/read/28303130/new-approaches-on-quantification-of-campylobacter-jejuni-in-poultry-samples-the-use-of-digital-pcr-and-real-time-pcr-against-the-iso-standard-plate-count-method
#6
Bojan Papić, Mateja Pate, Urška Henigman, Urška Zajc, Igor Gruntar, Majda Biasizzo, Matjaž Ocepek, Darja Kušar
Campylobacteriosis is the most frequently reported bacterial food-borne illness in the European Union and contaminated broiler meat is considered the most important source of infection in humans. The aim of the present study was to evaluate real-time PCR (qPCR) and digital PCR (dPCR) for quantification of Campylobacter jejuni in 75 broiler neck-skin samples collected from a poultry slaughterhouse, and to compare them with the ISO 10272-2 standard plate count method. For qPCR standard curve, C. jejuni-negative neck-skin samples were spiked with C...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28294696/cerebrospinal-fluid-mtdna-concentration-is-elevated-in-multiple-sclerosis-disease-and-responds-to-treatment
#7
Cyra E Leurs, Petar Podlesniy, Ramon Trullas, Lisanne Balk, Martijn D Steenwijk, Arjan Malekzadeh, Fredrik Piehl, Bernard Mj Uitdehaag, Joep Killestein, Jack van Horssen, C E Teunissen
BACKGROUND: Mitochondrial dysfunction is increasingly recognized as an important feature of multiple sclerosis (MS) pathology and may be relevant for clinical disease progression. However, it is unknown whether mitochondrial DNA (mtDNA) levels in the cerebrospinal fluid (CSF) associate with disease progression and therapeutic response. OBJECTIVES: To evaluate whether CSF concentrations of mtDNA in MS patients can serve as a marker of ongoing neuropathology and may be helpful to differentiate between MS disease subtypes...
March 1, 2017: Multiple Sclerosis: Clinical and Laboratory Research
https://www.readbyqxmd.com/read/28291853/an-in-vitro-evaluation-of-the-loosening-of-different-interchangeable-abutments-in-internal-connection-type-implants
#8
Ji-Man Park, Chang-Hyun Baek, Seong-Joo Heo, Seong-Kyun Kim, Jai-Young Koak, Shin-Koo Kim, Urs C Belser
PURPOSE: The aim of this study was to compare the loosening of interchangeable one-piece abutments connected to internal-connection-type implants after cyclic loading. MATERIALS AND METHODS: Four implant abutment groups (n = 7 in each group) with Straumann tissue-level implants were assessed: Straumann solid abutment (group S), Southern Implants solid abutment (group SI), Implant Direct straight abutment (group ID), and Blue Sky Bio regular platform abutment (group BSB)...
March 2017: International Journal of Oral & Maxillofacial Implants
https://www.readbyqxmd.com/read/28284873/establishing-a-reference-dataset-for-the-authentication-of-spinal-muscular-atrophy-cell-lines-using-str-profiling-and-digital-pcr
#9
Deborah L Stabley, Jennifer Holbrook, Ashlee W Harris, Kathryn J Swoboda, Thomas O Crawford, Katia Sol-Church, Matthew E R Butchbach
Fibroblasts and lymphoblastoid cell lines (LCLs) derived from individuals with spinal muscular atrophy (SMA) have been and continue to be essential for translational SMA research. Authentication of cell lines helps ensure reproducibility and rigor in biomedical research. This quality control measure identifies mislabeling or cross-contamination of cell lines and prevents misinterpretation of data. Unfortunately, authentication of SMA cell lines used in various studies has not been possible because of a lack of a reference...
February 6, 2017: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/28281732/utilisation-of-three-dimensional-printed-heart-models-for-operative-planning-of-complex-congenital-heart-defects
#10
Peter Olejník, Matej Nosal, Tomas Havran, Adriana Furdova, Maros Cizmar, Michal Slabej, Andrej Thurzo, Pavol Vitovic, Martin Klvac, Tibor Acel, Jozef Masura
BACKGROUND: To evaluate the accuracy of the three-dimensional printing of cardiovascular structures.To explore whether utilization of three-dimensional printed heart replicas can improve surgical and catheter interventional planning in patients with complex congenital heart defects. METHODS: Between December 2014 and November 2015, we fabricated n=8 cardiovascular models based on computed tomography data in patients with complex spatial anatomical relationships of cardiovascular structures...
March 10, 2017: Kardiologia Polska
https://www.readbyqxmd.com/read/28274670/detection-of-copy-number-variations-in-melanocytic-lesions-utilising-array-based-comparative-genomic-hybridisation
#11
Nima Mesbah Ardakani, Carla Thomas, Cleo Robinson, Kym Mina, Nathan Tobias Harvey, Benhur Amanuel, Benjamin Andrew Wood
Distinction between melanocytic naevi and melanoma occasionally poses a diagnostic challenge in ambiguous cases showing overlapping histological features. Melanomas are characterised by the presence of multiple genomic copy number variants (CNVs), while this is not a feature of naevi. We assessed the feasibility and utility of array-based comparative genomic hybridisation (aCGH) to assess CNVs in melanocytic lesions. DNA was extracted from formalin fixed, paraffin embedded (FFPE) sections of unambiguous naevi (n=19) and melanomas (n=19)...
March 5, 2017: Pathology
https://www.readbyqxmd.com/read/28274280/a-novel-duplex-ddpcr-assay-for-the-diagnosis-of-schistosomiasis-japonica-proof-of-concept-in-an-experimental-mouse-model
#12
Kosala G Weerakoon, Catherine A Gordon, Pengfei Cai, Geoffrey N Gobert, Mary Duke, Gail M Williams, Donald P McManus
The current World Health Organization strategic plan targets the elimination of schistosomiasis as a public health problem by 2025 and accurate diagnostics will play a pivotal role in achieving this goal. DNA-based detection methods provide a viable alternative to some of the commonly used tests, notably microscopy and serology, for the diagnosis of schistosomiasis. The detection of parasite cell-free DNA in different clinical samples is a recent valuable advance, which provides significant benefits for accurate disease diagnosis...
March 9, 2017: Parasitology
https://www.readbyqxmd.com/read/28264649/segmental-duplications-and-evolutionary-acquisition-of-uv-damage-response-in-the-spata31-gene-family-of-primates-and-humans
#13
Cemalettin Bekpen, Sven Künzel, Chen Xie, Muthukrishnan Eaaswarkhanth, Yen-Lung Lin, Omer Gokcumen, Cezmi A Akdis, Diethard Tautz
BACKGROUND: Segmental duplications are an abundant source for novel gene functions and evolutionary adaptations. This mechanism of generating novelty was very active during the evolution of primates particularly in the human lineage. Here, we characterize the evolution and function of the SPATA31 gene family (former designation FAM75A), which was previously shown to be among the gene families with the strongest signal of positive selection in hominoids. The mouse homologue for this gene family is a single copy gene expressed during spermatogenesis...
March 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28259698/glycemia-but-not-the-metabolic-syndrome-is-associated-with-cognitive-decline-findings-from-the-european-male-ageing-study
#14
Margot J Overman, Neil Pendleton, Terence W O'Neill, Gyorgy Bartfai, Felipe F Casanueva, Gianni Forti, Giulia Rastrelli, Aleksander Giwercman, Thang S Han, Ilpo T Huhtaniemi, Krzysztof Kula, Michael E J Lean, Margus Punab, David M Lee, Elon S Correa, Tomas Ahern, Michaël R Laurent, Sabine M P Verschueren, Leen Antonio, Evelien Gielen, Martin K Rutter, Dirk Vanderschueren, Frederick C W Wu, Jos Tournoy
OBJECTIVE: Previous research has indicated that components of the metabolic syndrome (MetS), such as hyperglycemia and hypertension, are negatively associated with cognition. However, evidence that MetS itself is related to cognitive performance has been inconsistent. This longitudinal study investigates whether MetS or its components affect cognitive decline in aging men and whether any interaction with inflammation exists. METHODS: Over a mean of 4.4 years (SD ± 0...
February 7, 2017: American Journal of Geriatric Psychiatry
https://www.readbyqxmd.com/read/28251648/two-stage-keypoint-detection-scheme-for-region-duplication-forgery-detection-in-digital-images
#15
Mahmoud Emam, Qi Han, Hongli Zhang
In digital image forensics, copy-move or region duplication forgery detection became a vital research topic recently. Most of the existing keypoint-based forgery detection methods fail to detect the forgery in the smooth regions, rather than its sensitivity to geometric changes. To solve these problems and detect points which cover all the regions, we proposed two steps for keypoint detection. First, we employed the scale-invariant feature operator to detect the spatially distributed keypoints from the textured regions...
March 2, 2017: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/28231382/accurate-measurement-of-transgene-copy-number-in-crop-plants-using-droplet-digital-pcr
#16
Ray Collier, Kasturi Dasgupta, Yan-Ping Xing, Bryan Tarape Hernandez, Min Shao, Dominica Rohozinski, Emma Kovak, Jeanie Lin, Maria Luiza P de Oliveira, Ed Stover, Kent F McCue, Frank G Harmon, Ann Blechl, James G Thomson, Roger Thilmony
Genetic transformation is a powerful means for the improvement of crop plants, but requires labor and resource intensive methods. An efficient method for identifying single copy transgene insertion events from a population of independent transgenic lines is desirable. Currently transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes...
February 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28228143/relationship-between-salivary-pancreatic-amylase-and-body-mass-index-a-systems-biology-approach
#17
Amélie Bonnefond, Loïc Yengo, Aurélie Dechaume, Mickaël Canouil, Maxime Castelain, Estelle Roger, Frédéric Allegaert, Robert Caiazzo, Violeta Raverdy, Marie Pigeyre, Abdelilah Arredouani, Jean-Michel Borys, Claire Lévy-Marchal, Jacques Weill, Ronan Roussel, Beverley Balkau, Michel Marre, François Pattou, Thierry Brousseau, Philippe Froguel
BACKGROUND: Salivary (AMY1) and pancreatic (AMY2) amylases hydrolyze starch. Copy number of AMY1A (encoding AMY1) was reported to be higher in populations with a high-starch diet and reduced in obese people. These results based on quantitative PCR have been challenged recently. We aimed to re-assess the relationship between amylase and adiposity using a systems biology approach. METHODS: We assessed the association between plasma enzymatic activity of AMY1 or AMY2, and several metabolic traits in almost 4000 French individuals from D...
February 23, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28213308/simultaneous-estimation-of-detection-sensitivity-and-absolute-copy-number-from-digital-pcr-serial-dilution
#18
Xutao Deng, Brian S Custer, Michael P Busch, Sonia Bakkour, Tzong-Hae Lee
Digital polymerase chain reaction (dPCR) is a refinement of the conventional PCR approach to nucleic acid detection and absolute quantification. Digital PCR works by partitioning a sample of DNA or cDNA into many individual, parallel PCR reactions. Current quantification methods rely on the assumption that the PCR reactions are always able to detect single target molecules. When the assumption does not hold, the copy numbers will be severely underestimated. We developed a novel dPCR quantification method which determines whether the single copy assumption is violated or not by simultaneously estimating the assay sensitivity and the copy numbers using serial dilution data sets...
February 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28211674/monte-carlo-modeling-based-digital-loop-mediated-isothermal-amplification-on-a-spiral-chip-for-absolute-quantification-of-nucleic-acids
#19
Yun Xia, Shuangqian Yan, Xian Zhang, Peng Ma, Wei Du, Xiaojun Feng, Bi-Feng Liu
Digital loop-mediated isothermal amplification (dLAMP) is an attractive approach for absolute quantification of nucleic acids with high sensitivity and selectivity. Theoretical and numerical analysis of dLAMP provides necessary guidance for the design and analysis of dLAMP devices. In this work, a mathematical model was proposed on the basis of the Monte Carlo method and the theories of Poisson statistics and chemometrics. To examine the established model, we fabricated a spiral chip with 1200 uniform and discrete reaction chambers (9...
March 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193077/partition-volume-variability-in-digital-polymerase-chain-reaction-methods-polydispersity-causes-bias-but-can-improve-precision
#20
Joel Tellinghuisen
The role of partition volume variability, or polydispersity, in digital polymerase chain reaction methods is examined through formal considerations and Monte Carlo simulations. Contrary to intuition, polydispersity causes little precision loss for low average copy number per partition μ and can actually improve precision when μ exceeds ∼4. It does this by negatively biasing the estimates of μ, thus increasing the number of negative (null) partitions N0. In keeping with binomial statistics, this increases the relative precision of N0 and hence of the biased estimate m of μ...
December 20, 2016: Analytical Chemistry
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