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https://www.readbyqxmd.com/read/28934494/derivatives-of-bst-like-gss-polymerase-with-improved-processivity-and-inhibitor-tolerance
#1
Igor P Oscorbin, Ekaterina A Belousova, Ulyana A Boyarskikh, Aleksandr I Zakabunin, Evgeny A Khrapov, Maksim L Filipenko
At the moment, one of the actual trends in medical diagnostics is a development of methods for practical applications such as point-of-care testing, POCT or research tools, for example, whole genome amplification, WGA. All the techniques are based on using of specific DNA polymerases having strand displacement activity, high synthetic processivity, fidelity and, most significantly, tolerance to contaminants, appearing from analysed biological samples or collected under purification procedures. Here, we have designed a set of fusion enzymes based on catalytic domain of DNA polymerase I from Geobacillus sp...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28919755/synthetic-high-density-lipoprotein-nanodisks-for-targeted-withalongolide-delivery-to-adrenocortical-carcinoma
#2
Rui Kuai, Chitra Subramanian, Peter T White, Barbara N Timmermann, James J Moon, Mark S Cohen, Anna Schwendeman
Adrenocortical carcinoma (ACC) is a rare endocrine malignancy and has a 5-year survival rate of <35%. ACC cells require cholesterol for steroid hormone production, and this requirement is met via expression on the cell surface of a high level of SRB1, responsible for the uptake of high-density lipoproteins (HDLs), which carry and transport cholesterol in vivo. Here, we describe how this natural lipid carrier function of SRB1 can be utilized to improve the tumor-targeted delivery of a novel natural product derivative - withalongolide A 4,19,27-triacetate (WGA-TA) - which has shown potent antitumor efficacy, but poor aqueous solubility...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28916708/architectural-delineation-and-molecular-identification-of-extracellular-matrix-in-ascidian-embryos-and-larvae
#3
Jiankai Wei, Guilin Wang, Xiang Li, Ping Ren, Haiyan Yu, Bo Dong
The extracellular matrix (ECM) not only provides essential physical scaffolding for cellular constituents but also initiates crucial biochemical and biomechanical cues that are required for tissue morphogenesis. In this study, we utilized wheat germ agglutinin (WGA) staining to characterize the ECM architecture in ascidian embryos and larvae. The results showed three distinct populations of ECM presenting in Ciona embryogenesis: the outer layer localized at the surface of embryo, an inner layer of notochord sheath and the apical ECM secreted by the notochord...
September 15, 2017: Biology Open
https://www.readbyqxmd.com/read/28915574/comparative-study-of-whole-genome-amplification-and-next-generation-sequencing-performance-of-single-cancer-cells
#4
Anna Babayan, Malik Alawi, Michael Gormley, Volkmar Müller, Harriet Wikman, Ryan P McMullin, Denis A Smirnov, Weimin Li, Maria Geffken, Klaus Pantel, Simon A Joosse
BACKGROUND: Whole genome amplification (WGA) is required for single cell genotyping. Effectiveness of currently available WGA technologies in combination with next generation sequencing (NGS) and material preservation is still elusive. RESULTS: In respect to the accuracy of SNP/mutation, indel, and copy number aberrations (CNA) calling, the HiSeq2000 platform outperformed IonProton in all aspects. Furthermore, more accurate SNP/mutation and indel calling was demonstrated using single tumor cells obtained from EDTA-collected blood in respect to CellSave-preserved blood, whereas CNA analysis in our study was not detectably affected by fixation...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28910311/hearing-impairment-in-premature-newborns-analysis-based-on-the-national-hearing-screening-database-in-poland
#5
Katarzyna Wroblewska-Seniuk, Grazyna Greczka, Piotr Dabrowski, Joanna Szyfter-Harris, Jan Mazela
OBJECTIVES: The incidence of sensorineural hearing loss is between 1 and 3 per 1000 in healthy neonates and 2-4 per 100 in high-risk infants. The national universal neonatal hearing screening carried out in Poland since 2002 enables selection of infants with suspicion and/or risk factors of hearing loss. In this study, we assessed the incidence and risk factors of hearing impairment in infants ≤33 weeks' gestational age (wga). METHODS: We analyzed the database of the Polish Universal Newborns Hearing Screening Program from 2010 to 2013...
2017: PloS One
https://www.readbyqxmd.com/read/28906588/surface-glycan-pattern-of-canine-equine-and-ovine-bone-marrow-derived-mesenchymal-stem-cells
#6
Salvatore Desantis, Gianluca Accogli, Antonio Crovace, Edda G Francioso, Alberto Maria Crovace
The use of bone marrow-derived mesenchymal stem cells (MSCs) for clinical and experimental studies is increasing, but full characterization of MSCs in veterinary species is hindered by the variability in species-specific cell surface marker expression and antibody cross reactivity. Recent studies demonstrated that the glycans in the glycocalyx of MSCs are promising candidates as cell biomarkers. In the present study, we analyzed the glycocalyx of canine MSCs (cMSCs), ovine MSCs (oMSCs), and equine MSCs (eMSCs) using a cell microarray procedure in which MSCs were spotted on microarray slides and incubated with a panel of 14 biotinylated lectins and Cy3-conjugated streptavidin...
September 14, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28903902/single-cell-gene-variation-analysis-method-for-single-gland
#7
Yan Zhou, Chao-Jie Wang, Chun-Chao Zhu, Jiang-Rong Chen, Ming Cheng, Yu-Liang Deng, Yan Guo
Single-cell analysis of heterogeneity has become the cutting-edge technology for profound understandings of relationships between cell populations. At present, common methods used in single cellular genomic research are mainly microfluidic technologies (Fluidigm) or based on microwells, both requiring a uniform size of cells at the entrance. However, the size of cells in specific tissues can vary from type to type. To address this issue, we need to establish a method to identify genomic features of individual cells of different sizes...
August 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28892497/improved-dop-pcr-idop-pcr-a-robust-and-simple-wga-method-for-efficient-amplification-of-low-copy-number-genomic-dna
#8
Konstantin A Blagodatskikh, Vladimir M Kramarov, Ekaterina V Barsova, Alexey V Garkovenko, Dmitriy S Shcherbo, Andrew A Shelenkov, Vera V Ustinova, Maria R Tokarenko, Simon C Baker, Tatiana V Kramarova, Konstantin B Ignatov
Whole-genome amplification (WGA) techniques are used for non-specific amplification of low-copy number DNA, and especially for single-cell genome and transcriptome amplification. There are a number of WGA methods that have been developed over the years. One example is degenerate oligonucleotide-primed PCR (DOP-PCR), which is a very simple, fast and inexpensive WGA technique. Although DOP-PCR has been regarded as one of the pioneering methods for WGA, it only provides low genome coverage and a high allele dropout rate when compared to more modern techniques...
2017: PloS One
https://www.readbyqxmd.com/read/28881392/on-the-road-to-replacing-invasive-testing-with-cell-based-nipt-five-clinical-cases-with-aneuploidies-microduplication-unbalanced-structural-rearrangement-or-mosaicism
#9
Else Marie Vestergaard, Ripudaman Singh, Palle Schelde, Lotte Hatt, Katarina Ravn, Rikke Christensen, Dorte Launholt Lildballe, Olav Bjørn Petersen, Niels Uldbjerg, Ida Vogel
OBJECTIVE: Trophoblastic fetal cells harvested from maternal blood have the capacity to be used for copy number analyses in a non-invasive prenatal test (cbNIPT). Potentially this will result in increased resolution for detection of subchromosomal aberrations due to high quality DNA not intermixed with maternal DNA. We present five selected clinical cases from first trimester pregnancies where cbNIPT was used to demonstrate a wide range of clinically relevant aberrations. METHOD: Blood samples were collected from high risk pregnancies in gestational week 12+1 to 12+5...
September 7, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28871230/comparative-analysis-for-glycopatterns-and-complex-type-n-glycans-of-glycoprotein-in-sera-from-chronic-hepatitis-b-and-c-infected-patients
#10
Xinmin Qin, Yonghong Guo, Haoqi Du, Yaogang Zhong, Jiaxu Zhang, Xuetian Li, Hanjie Yu, Zhiwei Zhang, Zhansheng Jia, Zheng Li
Background: Chronic infection with HBV (CHB) or HCV (CHC) is the most common chronic viral hepatitis that can lead to cirrhosis and hepatocellular carcinoma in humans, their infections have distinct pathogenic processes, however, little is known about the difference of glycoprotein glycopatterns in serum between hepatitis B virus (HBV)- and hepatitis C virus (HCV)-infected patients. Methods: A method combining the lectin microarrays, letin-mediated affinity capture glycoproteins, and MALDI-TOF/TOF-MS was employed to analyze serum protein glycopatterns and identify the glycan structures from patients with CHB (n = 54) or CHC(n = 47), and healthy volunteers (HV, n = 35)...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28853542/1d-reactor-decentralized-mda-for-uniform-and-accurate-whole-genome-amplification
#11
Junji Li, Na Lu, Xulian Shi, Yi Qiao, Liang Chen, Mengqin Duan, Yong Hou, Qinyu Ge, Yuhan Tao, Jing Tu, Zuhong Lu
Multiple displacement amplification (MDA), a most popular isothermal whole genome amplification (WGA) method, suffers the major hurdle of highly uneven amplification, thus, leading to many problems in approaching biological applications related to copy-number assessment. In addition to the optimization of reagents and conditions, complete physical separation of the entire reaction system into numerous tiny chambers or droplets using microfluidic devices, has been proven efficient to mitigate this amplifying bias in recent works...
September 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28846733/paracoccin-distribution-supports-its-role-in-paracoccidioides-brasiliensis-growth-and-dimorphic-transformation
#12
Aline Ferreira Oliveira, Fabricio Freitas Fernandes, Vânia Sammartino Mariano, Fausto Almeida, Luciana Pereira Ruas, Leandro Licursi Oliveira, Constance Oliver, Maria Celia Jamur, Maria Cristina Roque-Barreira
Paracoccidioides brasiliensis yeast was reported to express paracoccin, a GlcNAc-binding protein that displays N-acetyl-β-d-glucosaminidase (NAGase) activity. Highly specific anti-paracoccin antibodies have been previously used to examine the localization of paracoccin in yeast and inhibit its growth in vitro. In the present study, anti-paracoccin antibodies were used to characterize, by scanning confocal microscopy, the distribution of paracoccin in P. brasiliensis hyphae, transition forms from hyphae to yeast, and mature yeast...
2017: PloS One
https://www.readbyqxmd.com/read/28823068/stress-affects-surface-glycoconjugates-of-the-rat-endometrium-at-the-time-of-implantation
#13
Elham Aliabadi, Zohreh Makoolati, Tahereh Talaei-Khozani, Fakhreddin Mesbah Ardekani
One of the treatments to infertility is In Vitro Fertilization (IVF). In the course of IVF, fertilization rate can be improved through stress reduction. Probably one of the causes of low outcome of IVF is changes in uterine glycoconjugates that are first site of contact between blastocyst and uterus, due to stress, e.g., stress of injection. Thus, the study of the injectional stress effects on implantation period is very important to improve the outcome of IVF. Sixteen mature female rats were divided to experimental and control groups...
August 19, 2017: Glycoconjugate Journal
https://www.readbyqxmd.com/read/28812241/plasma-glycoproteomic-study-of-therapeutic-hypothermia-reveals-novel-markers-predicting-neurologic-outcome-post-cardiac-arrest
#14
Wenjun Deng, Jing Cao, Lei Chen, David McMullin, James L Januzzi, Ferdinando S Buonanno, Eng H Lo, MingMing Ning
Therapeutic hypothermia (TH) is a neuroprotective treatment post-cardiac arrest but is grossly underutilized. After TH induction, traditional biomarkers and parameters can no long predict clinical outcome due to a lack of understanding of hypothermic response. Innovative approaches to better understand the clinical effect of TH will help to prognosticate outcome and expand beneficial population. Protein glycosylation is an important extracellular post-translational modification, regulating various extracellular signaling pathways...
August 15, 2017: Translational Stroke Research
https://www.readbyqxmd.com/read/28811027/design-of-carbohydrate-electron-transfer-peptides-for-human-histocytic-lymphoma-cell-sensing
#15
Kazuharu Sugawara, Toshihiko Kadoya, Hideki Kuramitz, Yoshihiro Mihara
A carbohydrate/electro-transfer peptide probe was fabricated to perform cell sensing. The probe consisted of a cello-oligosaccharide that was created by the conjugation of an electron-transfer peptide (Y5C) and a carbohydrate via a Schiff base. An oxidation wave due to a phenolic hydroxyl group was obtained by scanning with a glassy carbon electrode. This cell-sensing system was based on a competitive reaction between carbohydrates on a cell surface and the probe as each reacted to a protein that recognized the carbohydrate...
August 29, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28782554/endocytosis-in-primary-mesenchyme-cells-during-sea-urchin-larval-skeletogenesis
#16
Christopher E Killian, Fred H Wilt
The sea urchin larval embryo elaborates two calcitic endoskeletal elements called spicules. Spicules are synthesized by the primary mesenchyme cells (PMCs) and begin to form at early gastrula stage. It is known that the calcium comprising the spicules comes from the seawater and we wish to further consider the mode of calcium transport from the extracellular seawater to the PMCs and then onto the forming spicules. We used PMC in vitro cultures, calcein, fluorescently labeled dextran, and fluorescently labeled Wheat Germ Agglutinin (WGA) to track calcium transport from the seawater into PMCs and spicules and to determine how molecules from the surface of PMCs interact with the incoming calcium...
August 3, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28756875/glycopattern-analysis-of-acidic-secretion-in-the-intestine-of-the-red-eared-slender-turtle-trachemys-scripta-elegans-testudines-emydidae
#17
Giovanni Scillitani, Donatella Mentino, Maria Mastrodonato
The secretion of the goblet cells in the intestine of Trachemys scripta elegans was studied in situ by histochemical methods to analyze the diversity of sugar chains, with particular regard to the acidic glycans. Conventional histochemical stains (Periodic acid-Schiff, Alcian Blue pH 2.5, High Iron Diamine) and binding with ten FITC-labelled lectins combined with chemical and enzymatic pre-treatments were used to characterize the oligosaccharidic chains. The intestine can be divided into three regions, i.e...
July 23, 2017: Tissue & Cell
https://www.readbyqxmd.com/read/28741788/molecular-analysis-of-single-circulating-tumour-cells-following-long-term-storage-of-clinical-samples
#18
Barbara Mesquita, Dominic G Rothwell, Deborah J Burt, Francesca Chemi, Fabiola Fernandez-Gutierrez, Daniel Slane-Tan, Jenny Antonello, Mathew Carter, Louise Carter, Marina Parry, Lynsey Franklin, Richard Marais, Fiona Blackhall, Caroline Dive, Ged Brady
The CellSearch® semi-automated CTC enrichment and staining system has been established as the "gold standard" for CTC enumeration with CellSearch® CTC counts recognized by the FDA as prognostic for a number of cancers. We and others have gone on to show that molecular analysis of CellSearch® CTCs isolated shortly after CellSearch® enrichment provides another valuable layer of information that has potential clinical utility including predicting response to treatment. Although CellSearch® CTCs can be readily isolated after enrichment, the process of analysing a single CellSearch® patient sample, which may contain many CTCs, is both time consuming and costly...
July 25, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28740869/comparing-sequencing-assays-and-human-machine-analyses-in-actionable-genomics-for-glioblastoma
#19
Kazimierz O Wrzeszczynski, Mayu O Frank, Takahiko Koyama, Kahn Rhrissorrakrai, Nicolas Robine, Filippo Utro, Anne-Katrin Emde, Bo-Juen Chen, Kanika Arora, Minita Shah, Vladimir Vacic, Raquel Norel, Erhan Bilal, Ewa A Bergmann, Julia L Moore Vogel, Jeffrey N Bruce, Andrew B Lassman, Peter Canoll, Christian Grommes, Steve Harvey, Laxmi Parida, Vanessa V Michelini, Michael C Zody, Vaidehi Jobanputra, Ajay K Royyuru, Robert B Darnell
OBJECTIVE: To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each. METHODS: Tumor DNA was analyzed by a commercial targeted panel. In addition, tumor-normal DNA was analyzed by whole-genome sequencing (WGS) and tumor RNA was analyzed by RNA sequencing (RNA-seq). The WGS and RNA-seq data were analyzed by a team of bioinformaticians and cancer oncologists, and separately by IBM Watson Genomic Analytics (WGA), an automated system for prioritizing somatic variants and identifying drugs...
August 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28729688/improved-genome-recovery-and-integrated-cell-size-analyses-of-individual-uncultured-microbial-cells-and-viral-particles
#20
Ramunas Stepanauskas, Elizabeth A Fergusson, Joseph Brown, Nicole J Poulton, Ben Tupper, Jessica M Labonté, Eric D Becraft, Julia M Brown, Maria G Pachiadaki, Tadas Povilaitis, Brian P Thompson, Corianna J Mascena, Wendy K Bellows, Arvydas Lubys
Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils...
July 20, 2017: Nature Communications
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