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Conditional knock-out

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https://www.readbyqxmd.com/read/28651420/-effects-of-hypoxia-inducible-factor-1%C3%AE-on-p311-and-its-influence-on-the-migration-of-murine-epidermal-stem-cells
#1
Z D Xu, H S Li, S Wang, W F He, J Wu, G X Luo
Objective: To explore the effects of hypoxia inducible factor-1α (HIF-1α) on P311 and its influence on the migration of murine epidermal stem cells (ESCs) under hypoxia in vitro. Methods: Two kinds of murine ESCs were isolated and obtained from 15 neonatal wild-type C57BL/6J mice and 5 congeneric source P311 gene knock-out mice, respectively. The first passage of cells were used in the following experiments after morphologic observation and detection of expression of cell surface markers CD71 and CD49f with flow cytometer...
May 20, 2017: Zhonghua Shao Shang za Zhi, Zhonghua Shaoshang Zazhi, Chinese Journal of Burns
https://www.readbyqxmd.com/read/28629365/evaluation-and-improvement-of-the-regulatory-inference-for-large-co-expression-networks-with-limited-sample-size
#2
Wenbin Guo, Cristiane P G Calixto, Nikoleta Tzioutziou, Ping Lin, Robbie Waugh, John W S Brown, Runxuan Zhang
BACKGROUND: Co-expression has been widely used to identify novel regulatory relationships using high throughput measurements, such as microarray and RNA-seq data. Evaluation studies on co-expression network analysis methods mostly focus on networks of small or medium size of up to a few hundred nodes. For large networks, simulated expression data usually consist of hundreds or thousands of profiles with different perturbations or knock-outs, which is uncommon in real experiments due to their cost and the amount of work required...
June 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28628130/lipid-production-in-nannochloropsis-gaditana-is-doubled-by-decreasing-expression-of-a-single-transcriptional-regulator
#3
Imad Ajjawi, John Verruto, Moena Aqui, Leah B Soriaga, Jennifer Coppersmith, Kathleen Kwok, Luke Peach, Elizabeth Orchard, Ryan Kalb, Weidong Xu, Tom J Carlson, Kristie Francis, Katie Konigsfeld, Judit Bartalis, Andrew Schultz, William Lambert, Ariel S Schwartz, Robert Brown, Eric R Moellering
Lipid production in the industrial microalga Nannochloropsis gaditana exceeds that of model algal species and can be maximized by nutrient starvation in batch culture. However, starvation halts growth, thereby decreasing productivity. Efforts to engineer N. gaditana strains that can accumulate biomass and overproduce lipids have previously met with little success. We identified 20 transcription factors as putative negative regulators of lipid production by using RNA-seq analysis of N. gaditana during nitrogen deprivation...
June 19, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28620460/a-putative-antiviral-role-of-plant-cytidine-deaminases
#4
Susana Martín, José M Cuevas, Ana Grande-Pérez, Santiago F Elena
BACKGROUND: A mechanism of innate antiviral immunity operating against viruses infecting mammalian cells has been described during the last decade.  Host cytidine deaminases ( e.g., APOBEC3 proteins) edit viral genomes, giving rise to hypermutated nonfunctional viruses; consequently, viral fitness is reduced through lethal mutagenesis.  By contrast, sub-lethal hypermutagenesis may contribute to virus evolvability by increasing population diversity.  To prevent genome editing, some viruses have evolved proteins that mediate APOBEC3 degradation...
2017: F1000Research
https://www.readbyqxmd.com/read/28620030/functions-of-protein-phosphatase-6-in-nf-%C3%AE%C2%BAb-signaling-and-in-lymphocytes
#5
REVIEW
Magdalena A Ziembik, Timothy P Bender, James M Larner, David L Brautigan
Protein phosphatase-6 (PP6) is a member of the PPP family of Ser/Thr phosphatases involved in intracellular signaling. PP6 is conserved among all eukaryotes, and genetics in model organisms indicates it has non-redundant functions relative to other PPP phosphatases. PP6 functions in association with conserved SAPS subunits and, in vertebrate species, forms heterotrimers with Ankrd subunits. Multiple studies have demonstrated how PP6 exerts negative control at different steps of nuclear factor kappaB signaling...
June 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28615693/the-ccr4-not-complex-contributes-to-repression-of-major-histocompatibility-complex-class-ii-transcription
#6
Alfonso Rodríguez-Gil, Olesja Ritter, Vera V Saul, Jochen Wilhelm, Chen-Yuan Yang, Rudolf Grosschedl, Yumiko Imai, Keiji Kuba, Michael Kracht, M Lienhard Schmitz
The multi-subunit CCR4 (carbon catabolite repressor 4)-NOT (Negative on TATA) complex serves as a central coordinator of all different steps of eukaryotic gene expression. Here we performed a systematic and comparative analysis of cells where the CCR4-NOT subunits CNOT1, CNOT2 or CNOT3 were individually downregulated using doxycycline-inducible shRNAs. Microarray experiments showed that downregulation of either CNOT subunit resulted in elevated expression of major histocompatibility complex class II (MHC II) genes which are found in a gene cluster on chromosome 6...
June 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28607399/rim1-2-in-retinal-ganglion-cells-are-required-for-the-refinement-of-ipsilateral-axons-and-eye-specific-segregation
#7
Ahlem Assali, Corentin Le Magueresse, Mohamed Bennis, Xavier Nicol, Patricia Gaspar, Alexandra Rebsam
Neural activity is crucial for the refinement of neuronal connections during development, but the contribution of synaptic release mechanisms is not known. In the mammalian retina, spontaneous neural activity controls the refinement of retinal projections to the dorsal lateral geniculate nucleus (dLGN) and the superior colliculus (SC) to form appropriate topographic and eye-specific maps. To evaluate the role of synaptic release, the rab-interacting molecules (RIMs), a family of active zone proteins that play a central role in calcium-triggered release, were conditionally ablated in a subset of retinal ganglion cells (RGCs)...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28603486/comparison-of-sirtuin-3-levels-in-als-and-huntington-s-disease-differential-effects-in-human-tissue-samples-vs-transgenic-mouse-models
#8
Eva Buck, Hanna Bayer, Katrin S Lindenberg, Johannes Hanselmann, Noemi Pasquarelli, Albert C Ludolph, Patrick Weydt, Anke Witting
Neurodegenerative diseases are characterized by distinct patterns of neuronal loss. In amyotrophic lateral sclerosis (ALS) upper and lower motoneurons degenerate whereas in Huntington's disease (HD) medium spiny neurons in the striatum are preferentially affected. Despite these differences the pathophysiological mechanisms and risk factors are remarkably similar. In addition, non-neuronal features, such as weight loss implicate a dysregulation in energy metabolism. Mammalian sirtuins, especially the mitochondrial NAD+ dependent sirtuin 3 (SIRT3), regulate mitochondrial function and aging processes...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28595911/manganese-exposure-exacerbates-progressive-motor-deficits-and-neurodegeneration-in-the-mitopark-mouse-model-of-parkinson-s-disease-relevance-to-gene-and-environment-interactions-in-metal-neurotoxicity
#9
Langley Monica R, Ghaisas Shivani, Ay Muhammet, Luo Jie, Palanisamy Bharathi N, Jin Huajun, Anantharam Vellareddy, Arthi Kanthasamy, Anumantha G Kanthasamy
Parkinson's disease (PD) is now recognized as a neurodegenerative condition caused by a complex interplay of genetic and environmental influences. Chronic manganese (Mn) exposure has been implicated in the development of PD. Since mitochondrial dysfunction is associated with PD pathology as well as Mn neurotoxicity, we investigated whether Mn exposure augments mitochondrial dysfunction and neurodegeneration in the nigrostriatal dopaminergic system using a newly available mitochondrially defective transgenic mouse model of PD, the MitoPark mouse...
June 5, 2017: Neurotoxicology
https://www.readbyqxmd.com/read/28557002/mtorc1-signaling-is-essential-for-germinal-center-reaction
#10
Bingshou Li, Zhirong Li, Pengcheng Wang, Qizhao Huang, Lifan Xu, Ran He, Lilin Ye, Qiang Bai
The mammalian target of rapamycin (mTOR) is a serine-threonine kinase that has been shown to be essential for the differentiation and function of various immune cells. Earlier in vitro studies showed that mTOR signaling regulates B cell biology by supporting their activation and proliferation. However, how mTOR signaling temporally regulates in vivo germinal center B (GCB) cell development and differentiation into short-lived plasma cells, long-lived plasma cells and memory cells is still not well understood...
May 30, 2017: Immunology
https://www.readbyqxmd.com/read/28538158/glnk-facilitates-the-dynamic-regulation-of-bacterial-nitrogen-assimilation
#11
Adam Gosztolai, Jörg Schumacher, Volker Behrends, Jacob G Bundy, Franziska Heydenreich, Mark H Bennett, Martin Buck, Mauricio Barahona
Ammonium assimilation in Escherichia coli is regulated by two paralogous proteins (GlnB and GlnK), which orchestrate interactions with regulators of gene expression, transport proteins, and metabolic pathways. Yet how they conjointly modulate the activity of glutamine synthetase, the key enzyme for nitrogen assimilation, is poorly understood. We combine experiments and theory to study the dynamic roles of GlnB and GlnK during nitrogen starvation and upshift. We measure time-resolved in vivo concentrations of metabolites, total and posttranslationally modified proteins, and develop a concise biochemical model of GlnB and GlnK that incorporates competition for active and allosteric sites, as well as functional sequestration of GlnK...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28518103/structure-function-studies-in-mouse-embryonic-stem-cells-using-recombinase-mediated-cassette-exchange
#12
Tim Pieters, Lieven Haenebalcke, Kenneth Bruneel, Niels Vandamme, Tino Hochepied, Jolanda van Hengel, Dagmar Wirth, Geert Berx, Jody J Haigh, Frans van Roy, Steven Goossens
Gene engineering in mouse embryos or embryonic stem cells (mESCs) allows for the study of the function of a given protein. Proteins are the workhorses of the cell and often consist of multiple functional domains, which can be influenced by posttranslational modifications. The depletion of the entire protein in conditional or constitutive knock-out (KO) mice does not take into account this functional diversity and regulation. An mESC line and a derived mouse model, in which a docking site for FLPe recombination-mediated cassette exchange (RMCE) was inserted within the ROSA26 (R26) locus, was previously reported...
April 27, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28497532/arabidopsis-thaliana-epoxide-hydrolase1-ateh1-is-a-cytosolic-epoxide-hydrolase-involved-in-the-synthesis-of-poly-hydroxylated-cutin-monomers
#13
Emmanuelle Pineau, Lin Xu, Hugues Renault, Adrien Trolet, Nicolas Navrot, Pascaline Ullmann, Bertrand Légeret, Gaëtan Verdier, Fred Beisson, Franck Pinot
Epoxide hydrolases (EHs) are present in all living organisms. They have been extensively characterized in mammals; however, their biological functions in plants have not been demonstrated. Based on in silico analysis, we identified AtEH1 (At3g05600), a putative Arabidopsis thaliana epoxide hydrolase possibly involved in cutin monomer synthesis. We expressed AtEH1 in yeast and studied its localization in vivo. We also analyzed the composition of cutin from A. thaliana lines in which this gene was knocked out...
May 12, 2017: New Phytologist
https://www.readbyqxmd.com/read/28497232/tamoxifen-for-induction-of-cre-recombination-may-confound-fibrosis-studies-in-female-mice
#14
Lucas L Falke, Roel Broekhuizen, Alwin Huitema, Erik Maarseveen, Tri Q Nguyen, Roel Goldschmeding
A variety of conditional knock-out mice relying on Tamoxifen-driven ERT2/Cre -mediated recombination are available and have been used to study involvement of specific genes in kidney disease. However, recent data suggest that Tamoxifen itself might attenuate fibrosis when administered during experimental models of kidney disease. It has remained unclear whether this still applies also if kidney damage is initiated after a wash-out period has been implemented. Here we report that the commonly applied regimen of administration of 4 alternate day doses of 1mg Tamoxifen per mouse until 14 days prior to start of the actual experiment, in this case the induction of obstructive nephropathy by Unilateral Ureteral Obstruction (UUO), still attenuated fibrosis in female obstructed mouse kidneys, whereas this effect was not seen in male obstructed kidneys...
June 2017: Journal of Cell Communication and Signaling
https://www.readbyqxmd.com/read/28488216/knock-out-serum-replacement-and-melatonin-effects-on-germ-cell-differentiation-in-murine-testicular-explant-cultures
#15
Ahmed Reda, Halima Albalushi, Sheyla Cisneros Montalvo, Mirja Nurmio, Zeliha Sahin, Mi Hou, Niels Geijsen, Jorma Toppari, Olle Söder, Jan-Bernd Stukenborg
Finding robust culture conditions for in vitro maturation (IVM) of male germ cells is still a challenge. Recently, a testis organ culture method, using Knockout Serum Replacement (KSR), was suggested as a promising approach. However, the efficiency of that model is still not optimal. Hence, we have tried to establish the culture conditions in two laboratories, and to improve the reliability of the culture system to generate mature germ cells. Male mice at three days of age were sacrificed. Testes were cut into small pieces which were cultured atop agarose stands, using Minimum Essential Medium alpha supplemented with different supplements; melatonin, Glutamax, and different concentrations of KSR...
May 9, 2017: Annals of Biomedical Engineering
https://www.readbyqxmd.com/read/28481957/deletion-of-shp2-in-bronchial-epithelial-cells-impairs-il-25-production-in-vitro-but-has-minor-influence-on-asthmatic-inflammation-in-vivo
#16
Zhangwei Qiu, Jiesen Zhou, Fang Liu, Xuejun Qin, Yuanrong Dai, Yuehai Ke, Zhihua Chen, Wen Li, Songmin Ying, Huahao Shen
Shp2 played an important role in cigarette-smoke-mediated inflammation, surfactant homeostasis and asthmatic airway remodeling. However, whether shp2 plays a key role in epithelium-associated allergic reaction is still unknown. In this study, LPS and OVA were observed to induce the production of IL-25 in bronchial epithelial cells in vitro via the activation of MAPK p38 and JNK. Furthermore, blockage of Shp2 by its specific inhibitor PHPS1 or by siRNA-mediated depletion was found to reduce the production of IL-25 in epithelial cells as well as the up-regulated LPS-triggered activation of JNK but not p38...
2017: PloS One
https://www.readbyqxmd.com/read/28437187/synergy-between-choroid-plexus-epithelial-cell-conditioned-medium-and-knockout-serum-replacement-converts-human-adipose-derived-stem-cells-to-dopamine-secreting-neurons
#17
Mahdi Eskandarian Boroujeni, Mossa Gardaneh, Mehrnoosh Hasan Shahriari, Abbas Aliaghaei, Sanaz Hasani
Human adipose-derived stem cells (hADSCs) have great capacity to differentiate into mesodermal origins as well as nonmesodermal lineages, including neural cells. This valuable feature paves the way for the therapeutic application of hADSCs for neurodegenerative maladies such as Parkinson's disease (PD). We tested the capacity of choroid plexus epithelial cell-conditioned medium (CPEC-CM) alone or cocktailed with knockout serum (KS) to induce dopaminergic (DAergic) differentiation of hADSCs. To this end, hADSCs from lipoaspirate were phenotypically characterized and shown to maintain mesodermal multipotency so that selected media easily differentiated them into osteoblasts, chondrocytes, and adipocytes...
April 27, 2017: Rejuvenation Research
https://www.readbyqxmd.com/read/28432097/diazotrophy-overcomes-the-deleterious-growth-phenotype-of-glne-deletion-in-azotobacter-vinelandii
#18
Florence Mus, Alex Tseng, Ray Dixon, John W Peters
Overcoming the inhibitory effects of excess environmental ammonium on nitrogenase synthesis or activity, or preventing ammonium assimilation, have both been considered as strategies to increase the amount of fixed nitrogen transferred from bacterial to plant partners in associative or symbiotic plant-diazotroph relationships. The GlnE adenylyltransferase/adenylyl-removing enzyme catalyzes reversible adenylylation of glutamine synthetase (GS), thereby affecting the post translational regulation of ammonium assimilation critical for appropriate coordination of carbon and nitrogen assimilation...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28429761/a-specific-nanobody-prevents-amyloidogenesis-of-d76n-%C3%AE-2-microglobulin-in-vitro-and-modifies-its-tissue-distribution-in-vivo
#19
Sara Raimondi, Riccardo Porcari, P Patrizia Mangione, Guglielmo Verona, Julien Marcoux, Sofia Giorgetti, Graham W Taylor, Stephan Ellmerich, Maurizio Ballico, Stefano Zanini, Els Pardon, Raya Al-Shawi, J Paul Simons, Alessandra Corazza, Federico Fogolari, Manuela Leri, Massimo Stefani, Monica Bucciantini, Julian D Gillmore, Philip N Hawkins, Maurizia Valli, Monica Stoppini, Carol V Robinson, Jan Steyaert, Gennaro Esposito, Vittorio Bellotti
Systemic amyloidosis is caused by misfolding and aggregation of globular proteins in vivo for which effective treatments are urgently needed. Inhibition of protein self-aggregation represents an attractive therapeutic strategy. Studies on the amyloidogenic variant of β2-microglobulin, D76N, causing hereditary systemic amyloidosis, have become particularly relevant since fibrils are formed in vitro in physiologically relevant conditions. Here we compare the potency of two previously described inhibitors of wild type β2-microglobulin fibrillogenesis, doxycycline and single domain antibodies (nanobodies)...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28417080/applying-a-systems-approach-to-thyroid-physiology-looking-at-the-whole-with-a-mitochondrial-perspective-instead-of-judging-single-tsh-values-or-why-we-should-know-more-about-mitochondria-to-understand-metabolism
#20
REVIEW
Roy Moncayo, Helga Moncayo
Classical thinking in endocrine physiology squeezes our diagnostic handling into a simple negative feedback mechanism with a controller and a controlled variable. In the case of the thyroid this is reduced to TSH and fT3 and fT4, respectively. The setting of this tight notion has no free space for any additions. In this paper we want to challenge this model of limited application by proposing a construct based on a systems approach departing from two basic considerations. In first place since the majority of cases of thyroid disease develop and appear during life it has to be considered as an acquired condition...
June 2017: BBA Clinical
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