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https://www.readbyqxmd.com/read/28735485/genome-wide-analysis-of-dna-methylation-in-hematopoietic-cells-dna-methylation-analysis-by-wgbs
#1
Mira Jeong, Anna G Guzman, Margaret A Goodell
DNA methylation is a major epigenetic modification that regulates gene expression, genome imprinting, and development and has a role in diseases including cancer. There are various methods for whole-genome methylation profiling that differ in cost and resolution. Recent advances in high-throughput sequencing technologies coupled with bisulfite treatment enable absolute DNA methylation quantification and genome-wide single-nucleotide resolution analysis. In this chapter, we provide detailed protocols for whole-genome bisulfite sequencing (WGBS), which captures the complete methylome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735481/single-cell-mass-cytometry-of-acute-myeloid-leukemia-and-leukemia-stem-progenitor-cells
#2
Zhihong Zeng, Marina Konopleva, Michael Andreeff
Mass cytometry time-of-flight (CyTOF) empowers us to understand acute myeloid leukemia (AML) biology at the single-cell level. This technology, combined with advanced data-analysis methods, enables identification and characterization of the rare AML stem/progenitor cells that play key roles in drug resistance and AML relapse. Here we provide a protocol for AML sample preparation for CyTOF and keynotes emphasizing critical steps in and troubleshooting strategies for this procedure.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735458/the-efficacy-of-lapatinib-and-nilotinib-in-combination-with-radiation-therapy-in-a-model-of-nf2-associated-peripheral-schwannoma
#3
Iddo Paldor, Sara Abbadi, Nicolas Bonne, Xiaobu Ye, Fausto J Rodriguez, David Rowshanshad, MariaLisa Itzoe, Veronica Vigilar, Marco Giovannini, Henry Brem, Jaishri O Blakeley, Betty M Tyler
Neurofibromatosis type 2 (NF2), a neurogenetic condition manifest by peripheral nerve sheath tumors (PNST) throughout the neuroaxis for which there are no approved therapies. In vitro and in vivo studies presented here examine agents targeting signaling pathways, angiogenesis, and DNA repair mechanisms. In vitro dose response assays demonstrated potent activity of lapatinib and nilotinib against the mouse schwannoma SC4 (Nf2 (-/-)) cell line. We then examined the efficacy of everolimus, nilotinib, lapatinib, bevacizumab and radiation (RT) as mono- and combination therapies in flank and sciatic nerve in vivo NF2-PNST models...
July 22, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28735414/bone-mechanobiology-in-mice-toward-single-cell-in-vivo-mechanomics
#4
Ariane Scheuren, Esther Wehrle, Felicitas Flohr, Ralph Müller
Mechanically driven bone (re)modeling is a multiscale process mediated through complex interactions between multiple cell types and their microenvironments. However, the underlying mechanisms of how cells respond to mechanical signals are still unclear and are at the focus of the field of bone mechanobiology. Traditionally, this complex process has been addressed by reducing the system to single scales and cell types. It is only recently that more integrative approaches have been established to study bone mechanobiology across multiple scales in which mechanical load at the organ level is related to molecular responses at the cellular level...
July 22, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/28735392/mining-and-quantifying-in-vivo-molecular-interactions-in-abiotic-stress-acclimation
#5
Thorsten Seidel, Derya Kirasi
Stress acclimation is initialized by sensing the stressor, transducing the signal, and inducing the response. In particular, the signal transduction is driven by protein-protein interactions and the response might involve de novo complex formation, shifts in subcellular localization and, thus, transportation that is mediated by other proteins. The investigation of protein-protein interactions and their regulation upon abiotic stress is crucial for a deeper understanding of the underlying mechanisms. FRET measurements by sensitized emission allow for the analysis of protein-protein interactions in real time and have a high potential to provide new insights into the regulation of protein-protein interaction with respect to subcellular localization and time...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735351/multiple-correlation-analyses-revealed-complex-relationship-between-dna-methylation-and-mrna-expression-in-human-peripheral-blood-mononuclear-cells
#6
Fang-Fei Xie, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Hong Zhu, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Xiao-Wei Zhu, Wei Xia, Lan Wang, Pei He, Peng-Fei Bing, Xin Lu, Yong-Hong Zhang, Shu-Feng Lei
DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes...
July 22, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28735324/study-of-acid-phosphatase-in-solubilization-of-inorganic-phosphates-by-piriformospora-indica
#7
Swetha Seshagiri, Padmavathi Tallapragada
Phosphorus is an essential plant macronutrient present in the soil. Only a small portion of phosphorus in soil is taken up by plants and the rest of it becomes unavailable to plants as it is immobilized. Phosphate solubilizing microorganisms play a vital role in converting the insoluble form of phosphates to the soluble form. The present paper reports the solubilization of tricalcium phosphate, rock phosphate, single super phosphate, zinc phosphate and aluminum phosphate by Piriformospora indica with the production of organic acids as well as acid phosphatase...
January 2, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/28735186/development-of-a-robust-reporter-gene-assay-to-measure-the-bioactivity-of-anti-pd-1-anti-pd-l1-therapeutic-antibodies
#8
Lan Wang, Chuanfei Yu, Yalan Yang, Kai Gao, Junzhi Wang
Being regarded as the 'cancer panacea', the anti-PD-1/anti-PD-L1 monoclonal antibodies (mAbs) have become the R&D focus of biopharmaceutical industries. Several marketed such mAbs have been proved particularly effective in treating various cancers. However, the cell-based bioassay to measure the biological activities of the anti-PD-1/anti-PD-L1 mAbs as the lot release or stability test has been a great challenge to quality control laboratories due to the immunomodulating nature of the mAbs. Here, we describe the development and validation of a reporter gene assay consisting of two-cell systems to measure the bioactivity of the anti-PD-1/anti-PD-L1 mAbs...
May 8, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28735108/structural-biology-outside-the-box-inside-the-cell
#9
REVIEW
Jürgen M Plitzko, Benjamin Schuler, Philipp Selenko
Recent developments in cellular cryo-electron tomography, in-cell single-molecule Förster resonance energy transfer-spectroscopy, nuclear magnetic resonance-spectroscopy and electron paramagnetic resonance-spectroscopy delivered unprecedented insights into the inner workings of cells. Here, we review complementary aspects of these methods and provide an outlook toward joint applications in the future.
July 20, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28734992/endoscopic-muscle-biopsy-emb-of-the-duodenum-and-rectum-a-pilot-survival-study-in-a-porcine-model-to-detect-myenteric-neurons
#10
E Rajan, B Al-Bawardy, C J Gostout, L M Wong Kee Song, J L Deters, M A Knipschield, C E Bernard, G Farrugia
BACKGROUND AND AIMS: Small bowel and colorectal muscle biopsies require a surgical approach. Advancing our understanding of the pathophysiology of motility disorders, such as functional bowel disorders, intestinal pseudo-obstruction and slow transit constipation, is hindered by our inability to non-invasively obtain muscularis propria (MP) for evaluation of multiple cell types, including myenteric neurons. The aims of this study were to determine (1) technical feasibility, reproducibility and safety of performing duodenal endoscopic muscle biopsy (dEMB) and rectal endoscopic muscle biopsy (rEMB) using a clip-assist technique; and (2) presence of myenteric neurons in tissue samples...
July 19, 2017: Gastrointestinal Endoscopy
https://www.readbyqxmd.com/read/28734966/development-of-new-ganglioside-probes-and-unraveling-of-raft-domain-structure-by-single-molecule-imaging
#11
REVIEW
Kenichi G N Suzuki, Hiromune Ando, Naoko Komura, Takahiro Fujiwara, Makoto Kiso, Akihiro Kusumi
Gangliosides are involved in a variety of biological roles and are a component of lipid rafts found in cell plasma membranes (PMs). Gangliosides are especially abundant in neuronal PMs and are essential to their physiological functions. However, the dynamic behaviors of gangliosides have not been investigated in living cells due to a lack of fluorescent probes that behave like their parental molecules. We have recently developed, using an entirely chemical method, four new ganglioside probes (GM1, GM2, GM3, and GD1b) that act similarly to their parental molecules in terms of raft partitioning and binding affinity...
July 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28734931/piperlongumine-inhibits-tgf-%C3%AE-induced-epithelial-to-mesenchymal-transition-by-modulating-the-expression-of-e-cadherin-snail1-and-twist1
#12
Min-Ju Park, Da-Eun Lee, Man Kyu Shim, Eun Hyang Jang, Jong Kil Lee, Seo Young Jeong, Jong-Ho Kim
Cancer is a life-threatening disease, and the occurrence of metastasis, which increases the lethality of primary tumors, is increasing. The epithelial-to-mesenchymal transition (EMT) is a biological process by which epithelial cells lose cell-cell adhesion properties and acquire mesenchymal properties, including motility and invasiveness. EMT is considered an early stage of metastasis; therefore, inhibiting EMT may be an effective anticancer therapy. In the present study, the antimetastatic effect of piperlongumine (PL) was assessed in human cancer cells...
July 19, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/28734900/molecular-imaging-in-stem-cell-based-therapies-of-cardiac-diseases
#13
REVIEW
Xiang Li, Marcus Hacker
In the past 15years, despite regenerative medicine has shown great potential for cardiovascular diseases, the outcome and safety of stem cell transplantation has shown controversial results in the published literature. Medical imaging might be useful for monitoring and quantification transplanted cells within the heart and to serially characterize the effects of stem cell therapy of the myocardium. From the multiple available noninvasive imaging techniques, magnetic resonance imaging and nuclear imaging by positron (PET) or single photon emission computer tomography (SPECT) are the most used clinical approaches to follow the fate of transplanted stem cells in vivo...
July 19, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/28734876/t-cell-depletion-as-an-alternative-approach-for-patients-55-years-undergoing-allogeneic-stem-cell-transplantation-as-curative-therapy-for-hematologic-malignancies
#14
Ann A Jakubowski, Erica Petrlik, Molly Maloy, Patrick Hilden, Esperanza Papadopoulos, James W Young, Farid Boulad, Hugo Castro-Malaspina, Roni Tamari, Parastoo B Dahi, Jenna Goldberg, Guenther Koehne, Miguel-Angel Perales, Craig S Sauter, Richard J O'Reilly, Sergio Giralt
T cell depleted allogeneic hematopoietic stem cell transplantation (TCD HSCT) is curative treatment for hematologic malignancies in adults, shown to reduce graft vs. host disease (GVHD) without increased relapse. We retrospectively reviewed a single center, 11yr experience of 214 patients ≥55yrs to determine tolerability and efficacy in the older adult. The majority (70%) had myeloid diseases and most acute leukemias were in remission. Median age was 61 yrs with related and unrelated donors > 8/10 HLA matched...
July 19, 2017: Biology of Blood and Marrow Transplantation
https://www.readbyqxmd.com/read/28734865/single-factors-alone-can-induce-mesenchymal-like-morphology-but-not-promote-full-emt-in-breast-cancer-cell-lines-with-different-hormone-statuses
#15
Maria K Tveitarås, Inga Reigstad, Lina Leiss, Rolf K Reed, Linda Stuhr
BACKGROUND: Epithelial to mesenchymal transition (EMT) is considered to be important for cancer invasion and metastasis. Tumour hypoxia, in addition to Transforming Growth Factor-β (TGF-β) and Notch, amongst others, have been suggested to be involved in EMT. We therefore investigated if hypoxia, TGF-β1 and the Notch ligand Jagged-1 alone induced morphological changes with corresponding EMT signatures in different epithelial breast cancer cell lines in vitro. Furthermore, we also studied whether or not TGF-β1, or Jagged-1 in combination with hypoxia added any effect on EMT...
July 19, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28734802/co-transplantation-of-mesenchymal-and-neural-stem-cells-and-overexpressing-stromal-derived-factor-1-for-treating-spinal-cord-injury
#16
Andrew N Stewart, Griffin Kendziorski, Zachary M Deak, Dara J Brown, Matthew N Fini, Katherine L Copely, Julien Rossignol, Gary L Dunbar
Genetic engineering of mesenchymal stem cells (MSCs) and neuronal stem cells (NSCs) has been used to treat spinal cord injuries (SCI). As a mechanism of therapy, MSCs secrete high amounts of anti-inflammatory cytokines and trophic factors, while NSCs can differentiate into neuronal lineages and aid in tissue replacement. Additionally, the forced overexpression of secreted proteins can enhance the secretome of transplanted cells, which can increase therapeutic efficacy. This study utilized a combinational treatment consisting of MSCs, NSCs, and the forced overexpression of the chemokine stromal-derived factor-1 (SDF-1) from MSCs (SDF-1-MSCs), to treat a rat model of SCI...
July 19, 2017: Brain Research
https://www.readbyqxmd.com/read/28734796/clonal-composition-of-human-ovarian-cancer-based-on-copy-number-analysis-reveals-a-reciprocal-relation-with-oncogenic-mutation-status
#17
Kazuko Sakai, Masayo Ukita, Jeanette Schmidt, Longyang Wu, Marco De Velasco, Alan Roter, Luis Jevons, Kazuto Nishio, Masaki Mandai
Intratumoral heterogeneity of cancer cells remains largely unexplored. Here we investigated the composition of ovarian cancer and its biological relevance. A whole-genome single nucleotide polymorphism array was applied to detect the clonal composition of 24 formalin-fixed, paraffin-embedded samples of human ovarian cancer. Genome-wide segmentation data consisting of the log2 ratio (log2R) and B allele frequency (BAF) were used to calculate an estimate of the clonal composition number (CC number) for each tumor...
July 19, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28734795/monoclonal-antibodies-in-multiple-myeloma-a-new-wave-of-the-future
#18
REVIEW
Daniel W Sherbenou, Tomer M Mark, Peter Forsberg
In 2015, 2 monoclonal antibodies were approved for the treatment of relapsed or refractory multiple myeloma (RRMM), elotuzumab and daratumumab. Elotuzumab is a monoclonal IgG-κ antibody directed against SLAMF7 (signaling lymphocytic activation molecule F7), a cell surface receptor involved in natural killer cell activation. Daratumumab is a monoclonal IgG-κ antibody that binds to CD38, a transmembrane protein found on the surface of myeloma cells and responsible for cellular adhesion and ectoenzymatic activity...
June 27, 2017: Clinical Lymphoma, Myeloma & Leukemia
https://www.readbyqxmd.com/read/28734764/comparative-genomic-analysis-of-mycobacterium-tuberculosis-beijing-like-strains-revealed-specific-genetic-variations-associated-with-virulence-and-drug-resistance
#19
Juan Germán Rodríguez-Castillo, Camilo Pino, Luis Fernando Niño, Juan Carlos Rozo, Claudia Llerena-Polo, Carlos A Parra-López, Andreas Tauch, Martha Isabel Murcia-Aranguren
Isolates of the Mycobacterium tuberculosis lineage 2/East-Asian are considered one of the most successful strains due to their increased pathogenicity, hyper-virulence associated with drug resistance, and high transmission. Recent studies in Colombia have shown that the Beijing-like genotype is associated with multidrug-resistance and high prevalence in the southwest of the country, but the genetic basis of its success in dissemination is unknown. In contribution to this matter, we obtained the whole sequences of six genomes of clinical isolates assigned to the Beijing-like genotype...
July 19, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28734763/uncleaved-2a-peptide-of-foot-and-mouth-disease-virus-can-display-foreign-epitope-tag-at-the-virion-surface
#20
Jitendra K Biswal, Saravanan Subramaniam, Rajeev Ranjan, Bramhadev Pattnaik
Foot-and-mouth disease virus (FMDV) capsid precursor protein P1-2A is cleaved by viral-encoded 3C protease (3C(pro)) to generate VP0, VP3, VP1 and 2A proteins. It was reported earlier that substitution of a single amino acid residue within the 2A peptide sequence (L2P) blocked the 3C(pro) mediated VP1/2A cleavage and produced 'self-tagged' FMDV particles containing uncleaved 2A-peptide. To determine whether the uncleaved 2A-peptide can function as a target structure to harbour and display exogenous epitope on FMDV particles, a full-length FMDV cDNA clone containing a HA-tag within the uncleaved 2A-peptide sequence was constructed...
July 19, 2017: Infection, Genetics and Evolution
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