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https://www.readbyqxmd.com/read/28324828/evaluation-of-dna-damage-and-physiological-responses-in-nile-tilapia-oreochromis-niloticus-linnaeus-1758-exposed-to-sub-lethal-diclofenac-dcf
#1
Pramod K Pandey, Malachy N O Ajima, Kundan Kumar, Nalini Poojary, Saurav Kumar
The frequent bioaccumulation of pharmaceuticals in the aquatic ecosystem has raised a concern about their possible ecotoxicological consequences. DNA damage, haematological changes and activities of oxidative stress enzymes in Nile tilapia, Oreochromis niloticus in response to diclofenac (DCF) exposure were investigated for up to 60 days at the concentrations of 0.17, 0.34 and 0.68mgL(-1) in the fish liver. Evaluation of genotoxic effects of the drug in the liver, using single-cell gel electrophoresis, showed DNA damage on exposure at the concentrations of 0...
March 8, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28324613/analysis-of-protein-kinetics-using-fluorescence-recovery-after-photobleaching-frap
#2
Nickolaos Nikiforos Giakoumakis, Maria Anna Rapsomaniki, Zoi Lygerou
Fluorescence recovery after photobleaching (FRAP) is a cutting-edge live-cell functional imaging technique that enables the exploration of protein dynamics in individual cells and thus permits the elucidation of protein mobility, function, and interactions at a single-cell level. During a typical FRAP experiment, fluorescent molecules in a defined region of interest within the cell are bleached by a short and powerful laser pulse, while the recovery of the fluorescence in the region is monitored over time by time-lapse microscopy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324494/analysis-of-average-telomere-length-in-human-telomeric-protein-knockout-cells-generated-by-crispr-cas9
#3
Jun Xu, Zhou Songyang, Dan Liu, Hyeung Kim
Telomeres play an important role in ensuring the integrity of the genome. Telomere shortening can lead to loss of genetic information and trigger DNA damage responses. Cultured mammalian cells have served as critical model systems for studying the function of telomere binding proteins and telomerase. Tremendous heterogeneity can be observed both between species and within a single cell population. Recent advances in genome editing (such as the development of the CRISPR/Cas9 platform) have further enabled researchers to carry out loss-of-function analysis of how disrupting key players in telomere maintenance affects telomere length regulation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28323970/obesity-modulates-inflammation-and-lipid-metabolism-oocyte-gene-expression-a-single-cell-transcriptome-perspective
#4
Meghan L Ruebel, Matthew Cotter, Clark R Sims, Dean M Moutos, Thomas M Badger, Mario A Cleves, Kartik Shankar, Aline Andres
Context: It is hypothesized that obesity adversely affects the ovarian environment which can disrupt oocyte maturation and may further impact embryonic development. Objective: This study aimed to compare oocyte gene expression profiles and follicular fluid (FF) content from overweight/obese (OW) women and normal weight (NW) women who were undergoing fertility treatments. Design: Using single cell transcriptomic analyses, we investigated oocyte gene expression using RNA-seq...
March 15, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28323941/the-diverse-metabolic-roles-of-peripheral-serotonin
#5
Alyce M Martin, Richard L Young, Lex Leong, Geraint B Rogers, Nick J Spencer, Claire F Jessup, Damien J Keating
Serotonin (5-hydroxytryptamine, 5-HT) is a multi-functional bioamine with important signaling roles in a range of physiological pathways. Almost all the 5-HT in our body is synthesized in specialized enteroendocrine cells within the gastrointestinal (GI) mucosa called enterochromaffin (EC) cells. These cells provide all our circulating 5-HT. While we have long appreciated the important roles of 5-HT within the gut including the modulation of GI motility, there is recently emerging evidence of the physiological and clinical significance of gut-derived 5-HT outside of the gut...
March 1, 2017: Endocrinology
https://www.readbyqxmd.com/read/28323615/stella-modulates-transcriptional-and-endogenous-retrovirus-programs-during-maternal-to-zygotic-transition
#6
Yun Huang, Jong Kyoung Kim, Dang Vinh Do, Caroline Lee, Christopher A Penfold, Jan J Zylicz, John C Marioni, Jamie A Hackett, M Azim Surani
The maternal-to-zygotic transition (MZT) marks the period when the embryonic genome is activated and acquires control of development. Maternally inherited factors play a key role in this critical developmental process, which occurs at the 2-cell stage in mice. We investigated the function of the maternally inherited factor STELLA (DPPA3) using single-cell/embryo approaches. We show that loss of maternal STELLA results in widespread transcriptional mis-regulation and a partial failure of MZT. Strikingly, activation of endogenous retroviruses (ERVs) is significantly impaired in Stella maternal/zygotic knockout embryos, which in turn leads to a failure to upregulate chimeric transcripts...
March 21, 2017: ELife
https://www.readbyqxmd.com/read/28323412/temporary-single-cell-coating-for-bioprocessing-via-a-cationic-polymer
#7
Ricardo Da Conceicao Ribeiro, Deepali Pal, David Jamieson, Kenneth Samora Rankin, Matthew Benning, Kenneth W Dalgarno, Ana Marina Ferreira
Temporary single cell coating is a useful tool for cell processing, allowing manipulation of cells to prevent cell attachment and agglomeration, before re-establishing normal cell function. In this paper, a speckled coating method using a known polycation (poly-L-lysine, PLL) is described to induce cell surface electrostatic charges on three different cell types - two bone cancer cell lines and fibroblasts. The morphology of the PLL speckled coating on the cell surface, internalization and metabolization of the polymer, and prevention of cellular aggregations are reported...
March 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28319730/deconstructing-the-germinal-center-one-cell-at-a-time
#8
REVIEW
Chad R Dufaud, Louise J McHeyzer-Williams, Michael G McHeyzer-Williams
Successful vaccination relies on driving the immune response towards high specificity, affinity and longevity. Germinal centers facilitate the evolution of antigen-specific B cells by iterative rounds of diversification, selection, and differentiation to memory and plasma cells. Experimental evidence points to B cell receptor affinity and amount of antigen presented to follicular helper T cells as main drivers of clonal evolution. Concurrent studies suggest that modifiers of cognate contact, temporal mechanisms, and stochastic factors can also shape diversity and influence differentiation to memory and plasma cells, but molecular pathways driving these selection decisions are unresolved...
March 17, 2017: Current Opinion in Immunology
https://www.readbyqxmd.com/read/28319669/cell-adhesion-on-dynamic-supramolecular-surfaces-probed-by-fluid-force-microscopy-based-single-cell-force-spectroscopy
#9
Shrikrishnan Sankaran, Leena Jaatinen, Jenny Brinkmann, Tomaso Zambelli, Janos Vörös, Pascal Jonkheijm
Biomimetic and stimuli-responsive cell-material interfaces are actively being developed to study and control various cell-dynamics phenomena. Since cells naturally reside in the highly dynamic and complex environment of the extracellular matrix, attempts are being made to replicate these conditions in synthetic biomaterials. Supramolecular chemistry, dealing with non-covalent interactions, has recently provided possibilities to incorporate such dynamicity and responsiveness in various types of architectures...
March 20, 2017: ACS Nano
https://www.readbyqxmd.com/read/28319112/accurate-identification-of-single-nucleotide-variants-in-whole-genome-amplified-single-cells
#10
Xiao Dong, Lei Zhang, Brandon Milholland, Moonsook Lee, Alexander Y Maslov, Tao Wang, Jan Vijg
Mutation analysis in single-cell genomes is prone to artifacts associated with cell lysis and whole-genome amplification. Here we addressed these issues by developing single-cell multiple displacement amplification (SCMDA) and a general-purpose single-cell-variant caller, SCcaller (https://github.com/biosinodx/SCcaller/). By comparing SCMDA-amplified single cells with unamplified clones from the same population, we validated the procedure as a firm foundation for standardized somatic-mutation analysis in single-cell genomics...
March 20, 2017: Nature Methods
https://www.readbyqxmd.com/read/28319093/human-haematopoietic-stem-cell-lineage-commitment-is-a-continuous-process
#11
Lars Velten, Simon F Haas, Simon Raffel, Sandra Blaszkiewicz, Saiful Islam, Bianca P Hennig, Christoph Hirche, Christoph Lutz, Eike C Buss, Daniel Nowak, Tobias Boch, Wolf-Karsten Hofmann, Anthony D Ho, Wolfgang Huber, Andreas Trumpp, Marieke A G Essers, Lars M Steinmetz
Blood formation is believed to occur through stepwise progression of haematopoietic stem cells (HSCs) following a tree-like hierarchy of oligo-, bi- and unipotent progenitors. However, this model is based on the analysis of predefined flow-sorted cell populations. Here we integrated flow cytometric, transcriptomic and functional data at single-cell resolution to quantitatively map early differentiation of human HSCs towards lineage commitment. During homeostasis, individual HSCs gradually acquire lineage biases along multiple directions without passing through discrete hierarchically organized progenitor populations...
March 20, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28319088/reference-component-analysis-of-single-cell-transcriptomes-elucidates-cellular-heterogeneity-in-human-colorectal-tumors
#12
Huipeng Li, Elise T Courtois, Debarka Sengupta, Yuliana Tan, Kok Hao Chen, Jolene Jie Lin Goh, Say Li Kong, Clarinda Chua, Lim Kiat Hon, Wah Siew Tan, Mark Wong, Paul Jongjoon Choi, Lawrence J K Wee, Axel M Hillmer, Iain Beehuat Tan, Paul Robson, Shyam Prabhakar
Intratumoral heterogeneity is a major obstacle to cancer treatment and a significant confounding factor in bulk-tumor profiling. We performed an unbiased analysis of transcriptional heterogeneity in colorectal tumors and their microenvironments using single-cell RNA-seq from 11 primary colorectal tumors and matched normal mucosa. To robustly cluster single-cell transcriptomes, we developed reference component analysis (RCA), an algorithm that substantially improves clustering accuracy. Using RCA, we identified two distinct subtypes of cancer-associated fibroblasts (CAFs)...
March 20, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28318058/nuclear-codon-reassignments-in-the-genomics-era-and-mechanisms-behind-their-evolution
#13
REVIEW
Martin Kollmar, Stefanie Mühlhausen
The canonical genetic code ubiquitously translates nucleotide into peptide sequence with several alterations known in viruses, bacteria, mitochondria, plastids, and single-celled eukaryotes. A new hypothesis to explain genetic code changes, termed tRNA loss driven codon reassignment, has been proposed recently when the polyphyly of the yeast codon reassignment events has been uncovered. According to this hypothesis, the driving force for genetic code changes are tRNA or translation termination factor loss-of-function mutations or loss-of-gene events...
March 20, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28317845/dna-damage-during-s-phase-mediates-the-proliferation-quiescence-decision-in-the-subsequent-g1-via-p21-expression
#14
Alexis R Barr, Samuel Cooper, Frank S Heldt, Francesca Butera, Henriette Stoy, Jörg Mansfeld, Béla Novák, Chris Bakal
Following DNA damage caused by exogenous sources, such as ionizing radiation, the tumour suppressor p53 mediates cell cycle arrest via expression of the CDK inhibitor, p21. However, the role of p21 in maintaining genomic stability in the absence of exogenous DNA-damaging agents is unclear. Here, using live single-cell measurements of p21 protein in proliferating cultures, we show that naturally occurring DNA damage incurred over S-phase causes p53-dependent accumulation of p21 during mother G2- and daughter G1-phases...
March 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28317836/microscale-symmetrical-electroporator-array-as-a-versatile-molecular-delivery-system
#15
Mengxing Ouyang, Winfield Hill, Jung Hyun Lee, Soojung Claire Hur
Successful developments of new therapeutic strategies often rely on the ability to deliver exogenous molecules into cytosol. We have developed a versatile on-chip vortex-assisted electroporation system, engineered to conduct sequential intracellular delivery of multiple molecules into various cell types at low voltage in a dosage-controlled manner. Micro-patterned planar electrodes permit substantial reduction in operational voltages and seamless integration with an existing microfluidic technology. Equipped with real-time process visualization functionality, the system enables on-chip optimization of electroporation parameters for cells with varying properties...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28317026/toxoplasma-gondii-ap2ix-4-regulates-gene-expression-during-bradyzoite-development
#16
Sherri Huang, Michael J Holmes, Joshua B Radke, Dong-Pyo Hong, Ting-Kai Liu, Michael W White, William J Sullivan
Toxoplasma gondii is a protozoan parasite of great importance to human and animal health. In the host, this obligate intracellular parasite persists as a tissue cyst that is imperceptible to the immune response and unaffected by current therapies. The tissue cysts facilitate transmission through predation and give rise to chronic cycles of toxoplasmosis in immunocompromised patients. Transcriptional changes accompany conversion of the rapidly replicating tachyzoites into the encysted bradyzoites, and yet the mechanisms underlying these alterations in gene expression are not well defined...
March 2017: MSphere
https://www.readbyqxmd.com/read/28317020/single-cell-reconstruction-of-oxytocinergic-neurons-reveals-separate-hypophysiotropic-and-encephalotropic-subtypes-in-larval-zebrafish
#17
Ulrich Herget, Jose Arturo Gutierrez-Triana, Oriana Salazar Thula, Boris Knerr, Soojin Ryu
Oxytocin regulates a diverse set of processes including stress, analgesia, metabolism, and social behavior. How such diverse functions are mediated by a single hormonal system is not well understood. Different functions of oxytocin could be mediated by distinct cell groups, yet it is currently unknown whether different oxytocinergic cell types exist that specifically mediate peripheral neuroendocrine or various central neuromodulatory processes via dedicated pathways. Using the Brainbow technique to map the morphology and projections of individual oxytocinergic cells in the larval zebrafish brain, we report here the existence of two main types of oxytocinergic cells: those that innervate the pituitary and those that innervate diverse brain regions...
January 2017: ENeuro
https://www.readbyqxmd.com/read/28315245/multidimensional-analysis-of-protease-substrates-and-their-cellular-origins-in-mixed-secretomes-from-multiple-cell-types
#18
Pascal Schlage, Ulrich Auf dem Keller
Although extracellular proteases are confronted with substrate proteins expressed by multiple cell types in vivo, in most protease substrate discovery approaches, the test protease is exposed to a test proteome (secretome) derived only from a single cell type. This limits the potential substrate space and prohibits the formation of protein complexes constituted of components derived from multiple cellular origins. Mixing of secretomes collected from multiple cell types addresses this issue, but information on the cellular origin of a substrate protein is lost...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28314726/global-distribution-patterns-and-pangenomic-diversity-of-the-candidate-phylum-latescibacteria-ws3
#19
Ibrahim F Farag, Noha H Youssef, Mostafa S Elshahed
We investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3) in 16S rRNA gene as well as metagenomic datasets. We document distinct distribution patterns for various "Latescibacteria" orders in 16S rRNA gene datasets, with prevalence of orders sediment_1 in terrestrial, PBSIII_9 in groundwater and temperate freshwater, and GN03 in pelagic marine, saline-hypersaline, and wastewater habitats. Using a fragment recruitment approach, we identified 68.9 Mb of "Latescibacteria"-affiliated contigs in publicly available metagenomic datasets comprising 73,079 proteins...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28314376/electrochemical-quantification-of-extracellular-local-h2o2-kinetics-originating-from-single-cells
#20
Monika Bozem, Phillip Knapp, Valentin Mirceski, Ewa Slowik, Ivan Bogeski, Reinhard Kappl, Christian Heinemann, Markus Hoth
AIMS: H2O2 is produced by all eukaryotic cells under physiological and pathological conditions. Due to its enormous relevance for cell signaling at low concentrations and anti-pathogenic function at high concentrations, precise quantification of extracellular local H2O2 concentrations ([H2O2]) originating from single cells is required. RESULTS: Using a scanning electrochemical microscope and bare platinum disk ultramicroelectrodes, we established sensitive long term measurements of extracellular [H2O2] kinetics originating from single primary human monocytes ex vivo...
March 17, 2017: Antioxidants & Redox Signaling
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