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https://www.readbyqxmd.com/read/28091601/massively-parallel-digital-transcriptional-profiling-of-single-cells
#1
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu, Mark T Gregory, Joe Shuga, Luz Montesclaros, Jason G Underwood, Donald A Masquelier, Stefanie Y Nishimura, Michael Schnall-Levin, Paul W Wyatt, Christopher M Hindson, Rajiv Bharadwaj, Alexander Wong, Kevin D Ness, Lan W Beppu, H Joachim Deeg, Christopher McFarland, Keith R Loeb, William J Valente, Nolan G Ericson, Emily A Stevens, Jerald P Radich, Tarjei S Mikkelsen, Benjamin J Hindson, Jason H Bielas
Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3' mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs...
January 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28067040/large-pore-3-d-cubic-mesoporous-kit-6-hybrid-bearing-hard-soft-donor-combined-ligand-for-enhancing-u-vi-capture-an-experimental-and-theoretical-investigation
#2
Li-Yong Yuan, Lin Zhu, Chengliang Xiao, Qun-Yan Wu, Nan Zhang, Ji-Pan Yu, Zhifang Chai, Wei-Qun Shi
The preorganized tetradentate phenanthrolineamide (DAPhen) ligand with hard-soft donors combined in the same molecule has been found to possess high extraction ability towards actinides over lanthanides from acidic aqueous solution in our previous work. Herein, we grafted phenanthrolineamide groups onto a large pore three-dimensional (3-D) cubic silica support by the reaction of DAPhen siloxane with KIT-6 substrate to prepare a novel uranium-selective sorbent, KIT-6-DAPhen. The as-synthesized sorbent was well characterized by SEM, HRTEM, N2 adsorption/desorption, XRD, FT-IR, 13C CP/MAS NMR, and TGA techniques, which confirmed the consummation of the functionalization...
January 9, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28065599/homology-requirements-and-competition-between-gene-conversion-and-break-induced-replication-during-double-strand-break-repair
#3
Anuja Mehta, Annette Beach, James E Haber
Saccharomyces cerevisiae mating-type switching is initiated by a double-strand break (DSB) at MATa, leaving one cut end perfectly homologous to the HMLα donor, while the second end must be processed to remove a non-homologous tail before completing repair by gene conversion (GC). When homology at the matched end is ≤150 bp, efficient repair depends on the recombination enhancer, which tethers HMLα near the DSB. Thus, homology shorter than an apparent minimum efficient processing segment can be rescued by tethering the donor near the break...
December 22, 2016: Molecular Cell
https://www.readbyqxmd.com/read/28063388/nanostructured-biosensor-for-detecting-glucose-in-tear-by-applying-fluorescence-resonance-energy-transfer-quenching-mechanism
#4
Longyi Chen, Wai Hei Tse, Yi Chen, Matthew W McDonald, James Melling, Jin Zhang
In this paper, a nanostructured biosensor is developed to detect glucose in tear by using fluorescence resonance energy transfer (FRET) quenching mechanism. The designed FRET pair, including the donor, CdSe/ZnS quantum dots (QDs), and the acceptor, dextran-binding malachite green (MG-dextran), was conjugated to concanavalin A (Con A), an enzyme with specific affinity to glucose. In the presence of glucose, the quenched emission of QDs through the FRET mechanism is restored by displacing the dextran from Con A...
December 23, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28057026/advances-in-rare-cell-isolation-an-optimization-and-evaluation-study
#5
Stefan Schreier, Piamsiri Sawaisorn, Rachanee Udomsangpetch, Wannapong Triampo
BACKGROUND: Rare nucleated CD45 negative cells in peripheral blood may be malignant such as circulating tumor cells. Untouched isolation thereof by depletion of normal is favored yet still technological challenging. We optimized and evaluated a novel magnetic bead-based negative selection approach for enhanced enrichment of rare peripheral blood nucleated CD45 negative cells and investigated the problem of rare cell contamination during phlebotomy. METHODS: Firstly, the performance of the magnetic cell separation system was assessed using leukocytes and cultivated fibroblast cells in regard to depletion efficiency and the loss of cells of interest...
January 5, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28045905/human-leukocytes-kill-brugia-malayi-microfilariae-independently-of-dna-based-extracellular-trap-release
#6
Ciaran J McCoy, Barbara J Reaves, Steeve Giguère, Ruby Coates, Balázs Rada, Adrian J Wolstenholme
BACKGROUND: Wuchereria bancrofti, Brugia malayi and Brugia timori infect over 100 million people worldwide and are the causative agents of lymphatic filariasis. Some parasite carriers are amicrofilaremic whilst others facilitate mosquito-based disease transmission through blood-circulating microfilariae (Mf). Recent findings, obtained largely from animal model systems, suggest that polymorphonuclear leukocytes (PMNs) contribute to parasitic nematode-directed type 2 immune responses. When exposed to certain pathogens PMNs release extracellular traps (NETs) in the form of chromatin loaded with various antimicrobial molecules and proteases...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28034960/elevated-dna-oxidation-and-dna-repair-enzyme-expression-in-brain-white-matter-in-major-depressive-disorder
#7
Attila Szebeni, Katalin Szebeni, Timothy P DiPeri, Luke A Johnson, Craig A Stockmeier, Jessica D Crawford, Michelle J Chandley, Liza J Hernandez, Katherine C Burgess, Russell W Brown, Gregory A Ordway
BACKGROUND: Pathology of white matter in brains of patients with major depressive disorder (MDD) is well-documented, but the cellular and molecular basis of this pathology are poorly understood. METHODS: Levels of DNA oxidation and gene expression of DNA damage repair enzymes were measured in Brodmann area 10 (BA10) and/or amygdala (uncinate fasciculus) white matter tissue from brains of MDD (n=10) and psychiatrically normal control donors (n=13). DNA oxidation was also measured in BA10 white matter of schizophrenia donors (n=10) and in prefrontal cortical white matter from control rats (n=8) and rats with repeated stress-induced anhedonia (n=8)...
December 29, 2016: International Journal of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28003942/clinical-usage-and-economic-effectiveness-of-a-recently-developed-epidermal-autograft-harvesting-system-in-13-chronic-wound-patients-in-a-university-based-wound-center
#8
Angela Hulsey, Paul Linneman, Jeff Litt
INTRODUCTION:  Chronic wounds are a significant healthcare problem in the United States. Their costs approach 25 billion dollars in the United States. Current wound-care treatments of local wound care, moist dressings, and source control, while necessary for wound healing, are frequently not enough to ensure complete wound closure. The current surgical technique of split-thickness skin grafting is an operative procedure, painful, time-consuming, and leaves significant donor site wounds...
November 14, 2016: Curēus
https://www.readbyqxmd.com/read/28003547/detection-of-prions-in-the-plasma-of-presymptomatic-and-symptomatic-patients-with-variant-creutzfeldt-jakob-disease
#9
Daisy Bougard, Jean-Philippe Brandel, Maxime Bélondrade, Vincent Béringue, Christiane Segarra, Hervé Fleury, Jean-Louis Laplanche, Charly Mayran, Simon Nicot, Alison Green, Arlette Welaratne, David Narbey, Chantal Fournier-Wirth, Richard Knight, Robert Will, Pierre Tiberghien, Stéphane Haïk, Joliette Coste
Variant Creutzfeldt-Jakob disease (vCJD) is a human prion disease resulting from the consumption of meat products contaminated by the agent causing bovine spongiform encephalopathy. Evidence supporting the presence of a population of silent carriers that can potentially transmit the disease through blood transfusion is increasing. The development of a blood-screening assay for both symptomatic vCJD patients and asymptomatic carriers is urgently required. We show that a diagnostic assay combining plasminogen-bead capture and protein misfolding cyclic amplification (PMCA) technologies consistently detected minute amounts of abnormal prion protein from French and British vCJD cases in the required femtomolar range...
December 21, 2016: Science Translational Medicine
https://www.readbyqxmd.com/read/28002483/physical-characteristics-of-a-citrullinated-pro-filaggrin-epitope-recognized-by-anti-citrullinated-protein-antibodies-in-rheumatoid-arthritis-sera
#10
Nicole Hartwig Trier, Bettina Eide Holm, Ole Slot, Henning Locht, Hanne Lindegaard, Anders Svendsen, Gunnar Houen
Rheumatoid arthritis (RA) is an autoimmune disease of complex etiology. A characteristic feature of a subset of RA is the presence of anti-citrullinated protein antibodies (ACPA), which correlate with a progressive disease course. In this study, we employed streptavidin capture enzyme-linked immunosorbent assay to analyze ACPA reactivity. Using the pro-filaggrin peptide HQCHQEST-Cit-GRSRGRCGRSGS, as template, we analyzed the reactivity of RA sera and healthy donor sera to various peptides in order to determine the physical characteristics of the citrullinated pro-filaggrin epitope and to examine whether biotin labelling influence antibody recognition...
2016: PloS One
https://www.readbyqxmd.com/read/27993881/flow-cytometric-panel-reactive-antibody-results-and-the-ability-to-find-transfusion-compatible-platelets-after-antibody-desensitization-for-allogeneic-bone-marrow-transplant
#11
Eric R Rosenbaum, Soumya Pandey, Terry O Harville, Gina A Drobena, Michele Cottler-Fox
BACKGROUND: Panel reactive antibody (PRA) reduction protocols are used to decrease anti-HLA antibodies with concomitant PRA monitoring as a measure of successful treatment prior to organ and haploidentical blood and marrow transplant (BMT). We hypothesized that the more sensitive flow cytometry (FC) based assays for PRA [FlowPRA(®) and Luminex(®) based Single Antigen Bead (SAB)] would also correlate with the ability to find compatible platelets for allosensitized recipients. METHODS: A female patient with myelodysplastic syndrome and a high HLA class I PRA [>90% PRA and cPRA by complement-dependent cytotoxicity (CDC) assay and Flow PRA] required allogeneic BMT...
December 2016: Annals of Clinical and Laboratory Science
https://www.readbyqxmd.com/read/27990211/automated-electrorotation-shows-electrokinetic-separation-of-pancreatic-cancer-cells-is-robust-to-acquired-chemotherapy-resistance-serum-starvation-and-emt
#12
Timothy Lannin, Wey-Wey Su, Conor Gruber, Ian Cardle, Chao Huang, Fredrik Thege, Brian Kirby
We used automated electrorotation to measure the cytoplasmic permittivity, cytoplasmic conductivity, and specific membrane capacitance of pancreatic cancer cells under environmental perturbation to evaluate the effects of serum starvation, epithelial-to-mesenchymal transition, and evolution of chemotherapy resistance which may be associated with the development and dissemination of cancer. First, we compared gemcitabine-resistant BxPC3 subclones with gemcitabine-naive parental cells. Second, we serum-starved BxPC3 and PANC-1 cells and compared them to untreated counterparts...
November 2016: Biomicrofluidics
https://www.readbyqxmd.com/read/27984510/factors-that-influence-the-quality-of-rna-from-the-pancreas-of-organ-donors
#13
Tiffany Philips, Irina Kusmartseva, Ivan C Gerling, Martha Campbell-Thompson, Clive Wasserfall, Alberto Pugliese, Jeffrey A Longmate, Desmond A Schatz, Mark A Atkinson, John S Kaddis
OBJECTIVES: Attaining high-quality RNA from the tissues or organs of deceased donors used for research can be challenging due to physiological and logistical considerations. In this investigation, METHODS: RNA Integrity Number (RIN) was determined in pancreatic samples from 236 organ donors and used to define high (≥6.5) and low (≤4.5) quality RNAs. Logistic regression was used to evaluate the potential effects of novel or established organ and donor factors on RIN. RESULTS: Univariate analysis revealed donor cause of death (odds ratio [OR], 0...
February 2017: Pancreas
https://www.readbyqxmd.com/read/27973864/tracking-co-i-intermediate-in-operando-in-photocatalytic-hydrogen-evolution-by-x-ray-transient-absorption-spectroscopy-and-dft-calculation
#14
Zhi-Jun Li, Fei Zhan, Hongyan Xiao, Xiaoyi Zhang, Qing-Yu Kong, Xiang-Bing Fan, Wen-Qiang Liu, Mao-Yong Huang, Cheng Huang, Yu-Ji Gao, Xu-Bing Li, Qing-Yuan Meng, Ke Feng, Bin Chen, Chen-Ho Tung, Hai-Feng Zhao, Ye Tao, Li-Zhu Wu
X-ray transient absorption spectroscopy (XTA) and optical transient spectroscopy (OTA) were used to probe the Co(I) intermediate generated in situ from an aqueous photocatalytic hydrogen evolution system, with [Ru(II)(bpy)3]Cl2·6H2O as the photosensitizer, ascorbic acid/ascorbate as the electron donor, and the Co-polypyridyl complex ([Co(II)(DPA-Bpy)Cl]Cl) as the precatalyst. Upon exposure to light, the XTA measured at Co K-edge visualizes the grow and decay of the Co(I) intermediate, and reveals its Co-N bond contraction of 0...
December 15, 2016: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/27973583/structure-and-mechanism-of-staphylococcus-aureus-tars-the-wall-teichoic-acid-%C3%AE-glycosyltransferase-involved-in-methicillin-resistance
#15
Solmaz Sobhanifar, Liam J Worrall, Dustin T King, Gregory A Wasney, Lars Baumann, Robert T Gale, Michael Nosella, Eric D Brown, Stephen G Withers, Natalie C J Strynadka
In recent years, there has been a growing interest in teichoic acids as targets for antibiotic drug design against major clinical pathogens such as Staphylococcus aureus, reflecting the disquieting increase in antibiotic resistance and the historical success of bacterial cell wall components as drug targets. It is now becoming clear that β-O-GlcNAcylation of S. aureus wall teichoic acids plays a major role in both pathogenicity and antibiotic resistance. Here we present the first structure of S. aureus TarS, the enzyme responsible for polyribitol phosphate β-O-GlcNAcylation...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27960171/are-basophils-and-mast-cells-masters-in-hiv-infection
#16
Gianni Marone, Gilda Varricchi, Stefania Loffredo, Maria Rosaria Galdiero, Felice Rivellese, Amato de Paulis
The World Health Organization AIDS epidemic update estimates that more than 37 million people are living with HIV infection. Despite the unprecedented success of antiretroviral treatments, significant challenges remain in the fight against HIV. In particular, how uninfected cells capture HIV and transmit virions to target cells remains an unanswered question. Tissue mast cells and peripheral blood basophils can be exposed to virions or HIV products during infection. Several HIV proteins (i.e., envelope glycoproteins gp120 and gp41, Tat, and Nef) can interact with distinct surface receptors expressed by human basophils and mast cells and modulate their functional responses at different levels...
2016: International Archives of Allergy and Immunology
https://www.readbyqxmd.com/read/27956810/hepatitis-e-virus-western-cape-south-africa
#17
Richie G Madden, Sebastian Wallace, Mark Sonderup, Stephen Korsman, Tawanda Chivese, Bronwyn Gavine, Aniefiok Edem, Roxy Govender, Nathan English, Christy Kaiyamo, Odelia Lutchman, Annemiek A van der Eijk, Suzan D Pas, Glynn W Webb, Joanne Palmer, Elizabeth Goddard, Sean Wasserman, Harry R Dalton, C Wendy Spearman
AIM: To conduct a prospective assessment of anti-hepatitis E virus (HEV) IgG seroprevalence in the Western Cape Province of South Africa in conjunction with evaluating risk factors for exposure. METHODS: Consenting participants attending clinics and wards of Groote Schuur, Red Cross Children's Hospital and their affiliated teaching hospitals in Cape Town, South Africa, were sampled. Healthy adults attending blood donor clinics were also recruited. Patients with known liver disease were excluded and all major ethnic/race groups were included to broadly represent local demographics...
November 28, 2016: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/27935872/feasibility-of-a-novel-one-stop-iset-device-to-capture-ctcs-and-its-clinical-application
#18
Fangfang Chen, Shuyi Wang, Yuan Fang, Liang Zheng, Xuan Zhi, Boran Cheng, Yuanyuan Chen, Chunxiao Zhang, Dongdong Shi, Haibin Song, Congli Cai, Pengfei Zhou, Bin Xiong
INTRODUCTION: Circulating tumor cells (CTCs) play a crucial role in cancer metastasis. In this study, we introduced a novel isolation method by size of epithelial tumor cells (ISET) device with automatic isolation and staining procedure, named one-stop ISET (osISET) and validated its feasibility to capture CTCs from cancer patients. Moreover, we aim to investigate the correlation between clinicopathologic features and CTCs in colorectal cancer (CRC) in order to explore its clinical application...
December 8, 2016: Oncotarget
https://www.readbyqxmd.com/read/27931516/expansion-of-hair-follicle-stem-cells-sticking-to-isolated-sebaceous-glands-to-generate-in-vivo-epidermal-structures
#19
Huishan Zhang, Huashan Zhao, Jingqiao Qiao, Shoubing Zhang, Shuang Liu, Na Li, Xiaohua Lei, Lina Ning, Yujing Cao, Enkui Duan
Hair follicle stem cells (HFSCs) are considered one of the useful donor cell types for skin regenerative medicine owing to their robust proliferative capacity and multipotency. However, methods for easily and effectively obtaining HFSCs from a limited skin biopsy are still lacking. Here we report a novel approach for obtaining a subpopulation of HFSCs from a small skin sample from the rat tail, which uses the sebaceous glands (SGs) to capture the adjacent HFSCs. By means of organ culture, keratinocytes were expanded from the detached SGs, which also included adherent HFSCs from the hair follicle that could be passaged at the single-cell level...
November 2016: Cell Transplantation
https://www.readbyqxmd.com/read/27930330/simultaneous-dimension-reduction-and-adjustment-for-confounding-variation
#20
Zhixiang Lin, Can Yang, Ying Zhu, John Duchi, Yao Fu, Yong Wang, Bai Jiang, Mahdi Zamanighomi, Xuming Xu, Mingfeng Li, Nenad Sestan, Hongyu Zhao, Wing Hung Wong
Dimension reduction methods are commonly applied to high-throughput biological datasets. However, the results can be hindered by confounding factors, either biological or technical in origin. In this study, we extend principal component analysis (PCA) to propose AC-PCA for simultaneous dimension reduction and adjustment for confounding (AC) variation. We show that AC-PCA can adjust for (i) variations across individual donors present in a human brain exon array dataset and (ii) variations of different species in a model organism ENCODE RNA sequencing dataset...
December 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
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