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https://www.readbyqxmd.com/read/28088763/scater-pre-processing-quality-control-normalization-and-visualization-of-single-cell-rna-seq-data-in-r
#1
Davis J McCarthy, Kieran R Campbell, Aaron T L Lun, Quin F Wills
MOTIVATION: Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization. RESULTS: We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data...
January 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28088761/amplification-of-unscheduled-dna-synthesis-signal-enables-fluorescence-based-single-cell-quantification-of-transcription-coupled-nucleotide-excision-repair
#2
Franziska Wienholz, Wim Vermeulen, Jurgen A Marteijn
Nucleotide excision repair (NER) comprises two damage recognition pathways: global genome NER (GG-NER) and transcription-coupled NER (TC-NER), which remove a wide variety of helix-distorting lesions including UV-induced damage. During NER, a short stretch of single-stranded DNA containing damage is excised and the resulting gap is filled by DNA synthesis in a process called unscheduled DNA synthesis (UDS). UDS is measured by quantifying the incorporation of nucleotide analogues into repair patches to provide a measure of NER activity...
January 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28088752/microfluidic-approaches-for-isolation-detection-and-characterization-of-extracellular-vesicles-current-status-and-future-directions
#3
REVIEW
Shima Gholizadeh, Mohamed Shehata Draz, Maryam Zarghooni, Amir Sanati-Nezhad, Saeid Ghavami, Hadi Shafiee, Mohsen Akbari
Extracellular vesicles (EVs) are cell-derived vesicles present in body fluids that play an essential role in various cellular processes, such as intercellular communication, inflammation, cellular homeostasis, survival, transport, and regeneration. Their isolation and analysis from body fluids have a great clinical potential to provide information on a variety of disease states such as cancer, cardiovascular complications and inflammatory disorders. Despite increasing scientific and clinical interest in this field, there are still no standardized procedures available for the purification, detection, and characterization of EVs...
December 30, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28088722/in-situ-denitrification-and-dnra-rates-in-groundwater-beneath-an-integrated-constructed-wetland
#4
M M R Jahangir, O Fenton, C Müller, R Harrington, P Johnston, K G Richards
Evaluation of the environmental benefits of constructed wetlands (CWs) requires an understanding of their impacts on the groundwater quality under the wetlands. Empirical mass-balance (nitrogen in/nitrogen out) approaches for estimating nitrogen (N) removal in CWs do not characterise the final fate of N; where nitrate (NO3(-)-N) could be reduced to either ammonium (NH4(+)-N) or N2 with the potential for significant production of N2O. Herein, in situ denitrification and DNRA (dissimilatory nitrate reduction to ammonium) rates were measured in groundwater beneath cells of an earthen lined integrated constructed wetland (ICW, used to remove the nutrients from municipal wastewater) using the (15)N-enriched NO3(-)-N push-pull method...
January 7, 2017: Water Research
https://www.readbyqxmd.com/read/28088698/metformin-enhancing-the-antitumor-efficacy-of-carboplatin-against-ehrlich-solid-carcinoma-grown-in-diabetic-mice-effect-on-igf-1-and-tumoral-expression-of-igf-1-receptors
#5
Dina M Abo-Elmatty, Eman A Ahmed, Mona K Tawfik, Seham A Helmy
Diabetes has been listed as a risk factor for various types of cancer. Cancer cell development can be promoted by increased levels of IGF-1 and hyperinsulinemia that are associated with diabetes type II. Metformin is an anti-diabetic agent and its potential antitumor impact has become the objective of numerous studies. In this vein, we hypothesize that using metformin in diabetes type II mice may synergistic with carboplatin for reducing the risk of cancer. Therefore, the study aimed to evaluate the in vivo antitumor activity of metformin against solid EAC tumor growth in female diabetic mice and its potential pro-apoptotic and anti-proliferative effects with clarification of its inconclusive biological mechanisms...
January 12, 2017: International Immunopharmacology
https://www.readbyqxmd.com/read/28088670/fibrin-hydrogels-induce-mixed-dorsal-ventral-spinal-neuron-identities-during-differentiation-of-human-induced-pluripotent-stem-cells
#6
John M Edgar, Meghan Robinson, Stephanie M Willerth
: We hypothesized that generating spinal motor neurons (sMNs) from human induced pluripotent stem cell (hiPSC)-derived neural aggregates (NAs) using a chemically-defined differentiation protocol would be more effective inside of 3D fibrin hydrogels compared to 2D poly-L-ornithine(PLO)/laminin-coated tissue culture plastic surfaces. We performed targeted RNA-Seq using next generation sequencing to determine the substrate-specific differences in gene expression that regulate cell phenotype...
January 11, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28088645/towards-solving-the-hard-problem-of-consciousness-the-varieties-of-brain-resonances-and-the-conscious-experiences-that-they-support
#7
Stephen Grossberg
The hard problem of consciousness is the problem of explaining how we experience qualia or phenomenal experiences, such as seeing, hearing, and feeling, and knowing what they are. To solve this problem, a theory of consciousness needs to link brain to mind by modeling how emergent properties of several brain mechanisms interacting together embody detailed properties of individual conscious psychological experiences. This article summarizes evidence that Adaptive Resonance Theory, or ART, accomplishes this goal...
December 6, 2016: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28088643/molecular-mechanisms-of-bio-catalysis-of-heme-extraction-from-hemoglobin
#8
Serzhan Sakipov, Olga Rafikova, Maria G Kurnikova, Ruslan Rafikov
Red blood cell hemolysis in sickle cell disease (SCD) releases free hemoglobin. Extracellular hemoglobin and its degradation products, free heme and iron, are highly toxic due to oxidative stress induction and decrease in nitric oxide availability. We propose an approach that helps to eliminate extracellular hemoglobin toxicity in SCD by employing a bacterial protein system that evolved to extract heme from extracellular hemoglobin. NEAr heme Transporter (NEAT) domains from iron-regulated surface determinant proteins from Staphylococcus aureus specifically bind free heme as well as facilitate its extraction from hemoglobin...
January 7, 2017: Redox Biology
https://www.readbyqxmd.com/read/28088634/chitosan-g-poly-n-isopropylacrylamide-copolymers-as-delivery-carriers-for-intracameral-pilocarpine-administration
#9
Jui-Yang Lai, Li-Jyuan Luo
This study reports, for the first time, the development of a chitosan-g-poly(N-isopropylacrylamide) (Chi-PN) biodegradable in situ gelling delivery system for ocular pilocarpine administration through intracameral injection. The number of thermo-responsive polymer segments grafted onto the chitosan via carbodiimide-mediated formation of amide linkages was greatly affected by varying the feeding amount of carboxyl-terminated poly(N-isopropylacrylamide) in the synthesis, thereby determining the phase transition temperature and enzymatic degradability of Chi-PN materials...
January 11, 2017: European Journal of Pharmaceutics and Biopharmaceutics
https://www.readbyqxmd.com/read/28088622/reactive-oxygen-species-and-cancer-paradox-to-promote-or-to-suppress
#10
REVIEW
Sehamuddin Galadari, Anees Rahman, Siraj Pallichankandy, Faisal Thayyullathil
Reactive oxygen species (ROS), a group of highly reactive ions and molecules, are increasingly being appreciated as powerful signaling molecules involved in the regulation of a variety of biological processes. Indeed, their role is continuously being delineated in a variety of pathophysiological conditions. For instance, cancer cells are shown to have increased ROS levels in comparison to their normal counterparts. This is partly due to an enhanced metabolism and mitochondrial dysfunction in cancer cells. The escalated ROS generation in cancer cells contributes to the biochemical and molecular changes necessary for the tumor initiation, promotion and progression, as well as, tumor resistance to chemotherapy...
January 11, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28088615/cloning-heterologous-expression-and-biochemical-characterization-of-a-non-specific-endoglucanase-family-12-from-aspergillus-terreus-nih2624
#11
Fernando Segato, Bruno Dias, Gabriela L Berto, Dyoni M de Oliveira, Flávio H M De Souza, Matheus Augusto R N da Silva, Ana Paula Citadini, Mario T Murakami, André R L Damásio, Fábio Márcio Squina, Igor Polikarpov
The cellulases from Glycoside Hydrolyses family 12 (GH12) play an important role in cellulose degradation and plant cell wall deconstruction being widely used in a number of bioindustrial processes. Aiming to contribute toward better comprehension of these class of the enzymes, here we describe a high-yield secretion of a endoglucanase GH12 from Aspegillus terreus (AtGH12), which was cloned and expressed in Aspergillus nidulans strain A773. The purified protein was used for complete biochemical and functional characterization...
January 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28088584/proton-pump-inhibition-and-cancer-therapeutics-a-specific-tumor-targeting-or-it-is-a-phenomenon-secondary-to-a-systemic-buffering
#12
REVIEW
Enrico Spugnini, Stefano Fais
One of the unsolved mysteries in oncology includes the strategies that cancer cells adopt to cope with an adverse microenvironment. However, we knew, from the Warburg's discovery that through their metabolism based on sugar fermentation, cancer cells acidify their microenvironment and this progressive acidification induces a selective pressure, leading to the development of very malignant cells entirely armed to survive in the hostile microenvironment generated by their own metabolism. In the last decades a primordial role for proton exchangers has been supported as a key tumor advantage in facing off the acidic milieu...
January 11, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28088583/environmental-carcinogenesis-and-ph-homeostasis-not-only-a-matter-of-dysregulated-metabolism
#13
REVIEW
Kévin Hardonniere, Laurence Huc, Odile Sergent, Jørn A Holme, Dominique Lagadic-Gossmann
According to the World Health Organization, around 20% of all cancers would be due to environmental factors. Among these factors, several chemicals are indeed well recognized carcinogens. The widespread contaminant benzo[a]pyrene (B[a]P), an often used model carcinogen of the polycyclic aromatic hydrocarbons' family, has been suggested to target most, if not all, cancer hallmarks described by Hanahan and Weinberg. It is classified as a group I carcinogen by the International Agency for Research on Cancer; however, the precise intracellular mechanisms underlying its carcinogenic properties remain yet to be thoroughly defined...
January 11, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28088549/redistribution-of-elements-between-wastes-and-organic-bearing-material-in-the-dispersion-train-of-gold-bearing-sulfide-tailings-part-i-geochemistry-and-mineralogy
#14
B Yu Saryg-Ool, I N Myagkaya, I S Kirichenko, M A Gustaytis, O V Shuvaeva, S M Zhmodik, E V Lazareva
Migration and redistribution of elements during prolonged interaction of cyanide wastes with the underlying natural organic-bearing material have been studied in two ~40cm deep cores that sample primary ores and their weathering profile (wastes I and II, respectively) in the dispersion train of gold-bearing sulfide tailings in Siberia. Analytical results of SR-XRF, whole-rock XRF, AAS, CHNS, and SEM measurements of core samples show high K, Sr, Ti, and Fe enrichments and correlation of P2O5 and Mn with LOI and Corg...
January 11, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28088541/secretory-pathway-optimization-of-cho-producer-cells-by-co-engineering-of-the-mitosrna-1978-target-genes-cers2-and-tbc1d20
#15
Lisa A Pieper, Michaela Strotbek, Till Wenger, Martin Gamer, Monilola A Olayioye, Angelika Hausser
Chinese Hamster Ovary (CHO) cells are the most commonly used host for the production of biopharmaceuticals. Although transcription and translation engineering strategies have been employed to generate high-producer cell clones, the secretory pathway still remains a bottleneck in cellular productivity. In this study we show that ectopic expression of a human mitochondrial genome-encoded small RNA (mitosRNA-1978) in an IgG expressing CHO cell line strongly improved specific productivity by functioning in a microRNA-like fashion...
January 11, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28088524/possible-roles-of-the-transcription-factor-nrf1-nfe2l1-in-neural-homeostasis-by-regulating-the-gene-expression-of-deubiquitinating-enzymes
#16
Hiroaki Taniguchi, Shota Okamuro, Misaki Kohji, Tsuyoshi Waku, Kaori Kubo, Atsushi Hatanaka, Yimeng Sun, A M Masudul Azad Chowdhury, Akiyoshi Fukamizu, Akira Kobayashi
The transcription factor Nrf1 (NFE2L1) maintains protein homeostasis (proteostasis) by regulating the gene expression of proteasome subunits in response to proteasome inhibition. The deletion of the Nrf1 gene in neural stem/progenitor cells causes severe neurodegeneration due to the accumulation of ubiquitinated proteins in Purkinje cells and motor neurons (Nrf1 NKO mice). However, the molecular mechanisms governing this neurodegenerative process remain unclear. We demonstrate herein that the loss of Nrf1 leads to the reduced gene expression of the deubiquitinating enzymes (DUBs) but not proteasome subunits in Nrf1 NKO mice between P7 and P18...
January 11, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28088513/an-immunogram-for-the-cancer-immunity-cycle-towards-personalized-immunotherapy-of-lung-cancer
#17
Takahiro Karasaki, Kazuhiro Nagayama, Hideki Kuwano, Jun-Ichi Nitadori, Masaaki Sato, Masaki Anraku, Akihiro Hosoi, Hirokazu Matsushita, Yasuyuki Morishita, Kosuke Kashiwabara, Masaki Takazawa, Osamu Ohara, Kazuhiro Kakimi, Jun Nakajima
INTRODUCTION: The interaction of immune cells and cancer cells shapes the immunosuppressive tumor microenvironment. For successful cancer immunotherapy, comprehensive knowledge of anti-tumor immunity as a dynamic spacio-temporal process is required for each individual patient. To this end, we developed an immunogram for the cancer-immunity cycle using next-generation sequencing. METHODS: Whole-exome sequencing and RNA-Seq was performed in 20 non-small cell lung cancer patients (12 adenocarcinoma, 7 squamous cell carcinoma, and 1 large cell neuroendocrine carcinoma)...
January 11, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28088503/evidence-for-splice-transcript-variants-of-tmem165-a-gene-involved-in-cdg
#18
Marie-Ange Krzewinski-Recchi, Sven Potelle, Anne Marie-Mir, Dorothée Vicogne, Eudoxie Dulary, Sandrine Duvet, Willy Morelle, Geoffroy de Bettignies, François Foulquier
BACKGROUND: Defects in TMEM165 gene cause a type-II Congenital Disorder of Glycosylation affecting Golgi glycosylation processes. TMEM165 patients exhibit psychomotor retardation, important osteoporosis, scoliosis, irregular epiphyses and thin bone cortex. Human TMEM165 protein is highly conserved in evolution and belongs to the family of UPF0016 membrane proteins which could be an unique group of Ca(2+)/H(+) antiporters regulating Ca(2+) and pH homeostasis and mainly localized in the Golgi apparatus...
January 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28088490/microwave-based-treatments-of-wheat-kernels-do-not-abolish-gluten-epitopes-implicated-in-celiac-disease
#19
Carmen Gianfrani, Gianfranco Mamone, Barbara la Gatta, Alessandra Camarca, Luigia Di Stasio, Francesco Maurano, Stefania Picascia, Vito Capozzi, Giuseppe Perna, Gianluca Picariello, Aldo Di Luccia
Microwave based treatment (MWT) of wet wheat kernels induced a striking reduction of gluten, up to <20 ppm as determined by R5-antibodybased ELISA, so that wheat could be labeled as gluten-free. In contrast, analysis of gluten peptides by G12 antibody-based ELISA, mass spectrometry-based proteomics and in vitro assay with T cells of celiac subjects, indicated no difference of antigenicity before and after MWT. SDS-PAGE analysis and Raman spectroscopy demonstrated that MWT simply induced conformational modifications, reducing alcohol solubility of gliadins and altering the access of R5-antibody to the gluten epitopes...
January 11, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28088469/estrogen-induced-expression-of-tissue-factor-pathway-inhibitor-2-in-mcf7-cells-involves-lysine-specific-demethylase-1
#20
Marianne S Andresen, Huda Omar Ali, Christiane Filion Myklebust, Per Morten Sandset, Benedicte Stavik, Nina Iversen, Grethe Skretting
Hormone-sensitive cancers can be influenced by estrogens, a process usually mediated through the estrogen receptor (ER). Tissue factor pathway inhibitor type 2 (TFPI-2) is a Kunitz-type serine protease inhibitor involved in regulating the extracellular matrix. The present study demonstrates that the expression of TFPI-2 can be induced by estrogens. Breast cancer data from GOBO displayed increased levels of TFPI-2 and increased survival in patients with ERα+ tumors. Treatment of MCF7 cells (ERα+) with 17β-estradiol (E2) or 17α-ethinyl estradiol (EE2) increased TFPI-2 mRNA and protein levels...
January 11, 2017: Molecular and Cellular Endocrinology
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