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Conditional knock-out

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https://www.readbyqxmd.com/read/27919444/mechanistic-genomic-and-proteomic-study-on-the-effects-of-bisgma-derived-biodegradation-product-on-cariogenic-bacteria
#1
Lida Sadeghinejad, Dennis G Cvitkovitch, Walter L Siqueira, Justin Merritt, J Paul Santerre, Yoav Finer
OBJECTIVES: Investigate the effects of a Bis-phenyl-glycidyl-dimethacrylate (BisGMA) biodegradation product, bishydroxypropoxyphenyl-propane (BisHPPP), on gene expression and protein synthesis of cariogenic bacteria. METHODS: Quantitative real-time polymerase chain reaction was used to investigate the effects of BisHPPP on the expression of specific virulence-associated genes, i.e. gtfB, gtfC, gbpB, comC, comD, comE and atpH in Streptococcus mutans UA159. Possible mechanisms for bacterial response to BisHPPP were explored using gene knock-out and associated complemented strains of the signal peptide encoding gene, comC...
December 2, 2016: Dental Materials: Official Publication of the Academy of Dental Materials
https://www.readbyqxmd.com/read/27917181/nitric-oxide-responsive-heavy-metal-associated-gene-athmad1-contributes-to-development-and-disease-resistance-in-arabidopsis-thaliana
#2
Q Muhammad Imran, Noreen Falak, Adil Hussain, Bong-Gyu Mun, Arti Sharma, Sang-Uk Lee, Kyung-Min Kim, Byung-Wook Yun
Exposure of plants to different biotic and abiotic stress condition instigates significant change in the cellular redox status; resulting in the elevation of reactive nitrogen species that play signaling role in mediating defense responses. Heavy metal associated (HMA) domain containing genes are required for spatio-temporal transportation of metal ions that bind with various enzymes and co-factors within the cell. To uncover the underlying mechanisms mediated by AtHMA genes, we identified 14 Arabidopsis HMA genes that were differentially expressed in response to nitrosative stress through RNA-seq analysis...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27903723/cerebellar-shank2-regulates-excitatory-synapse-density-motor-coordination-and-specific-repetitive-and-anxiety-like-behaviors
#3
Seungmin Ha, Dongwon Lee, Yi Sul Cho, Changuk Chung, Ye-Eun Yoo, Jihye Kim, Jiseok Lee, Woohyun Kim, Hyosang Kim, Yong Chul Bae, Keiko Tanaka-Yamamoto, Eunjoon Kim
: Shank2 is a multidomain scaffolding protein implicated in the structural and functional coordination of multiprotein complexes at excitatory postsynaptic sites as well as in psychiatric disorders, including autism spectrum disorders. While Shank2 is strongly expressed in the cerebellum, whether Shank2 regulates cerebellar excitatory synapses, or contributes to the behavioral abnormalities observed in Shank2(-/-) mice, remains unexplored. Here we show that Shank2(-/-) mice show reduced excitatory synapse density in cerebellar Purkinje cells in association with reduced levels of excitatory postsynaptic proteins, including GluD2 and PSD-93, and impaired motor coordination in the Erasmus test...
November 30, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27903722/adenosine-kinase-deficiency-in-the-brain-results-in-maladaptive-synaptic-plasticity
#4
Ursula S Sandau, Mariana Colino-Oliveira, Abbie Jones, Bounmy Saleumvong, Shayla Q Coffman, Long Liu, Catarina Miranda-Lourenço, Cátia Palminha, Vânia L Batalha, Yiming Xu, Yuqing Huo, Maria J Diógenes, Ana M Sebastião, Detlev Boison
: Adenosine kinase (ADK) deficiency in human patients (OMIM:614300) disrupts the methionine cycle and triggers hypermethioninemia, hepatic encephalopathy, cognitive impairment, and seizures. To identify whether this neurological phenotype is intrinsically based on ADK deficiency in the brain or if it is secondary to liver dysfunction, we generated a mouse model with a brain-wide deletion of ADK by introducing a Nestin-Cre transgene into a line of conditional ADK deficient Adk(fl/fl) mice...
November 30, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27884048/microrna-142-is-a-multifaceted-regulator-in-organogenesis-homeostasis-and-disease
#5
REVIEW
A Shrestha, R T Mukhametshina, S Taghizadeh, E Vásquez-Pacheco, H Cabrera-Fuentes, A Rizvanov, B Mari, G Carraro, S Bellusci
Over the last decade, microRNA-142 (miR-142) is emerging as a major regulator of cell fate decision in the hematopoietic system. However, miR-142 is expressed in many other tissues and recent evidence suggest that it may play a more pleiotropic role during embryonic development. In addition, miR-142 has been shown to play important functions in disease. miR-142 displays a functional role in cancer, virus infection, inflammation and immune tolerance. Both a guide strand (miR-142-3p) and passenger strand (miR-142-5p) are generated from the miR-142 hairpin...
November 24, 2016: Developmental Dynamics: An Official Publication of the American Association of Anatomists
https://www.readbyqxmd.com/read/27864078/inappropriate-translation-inhibition-and-p-body-formation-cause-cold-sensitivity-in-tryptophan-auxotroph-yeast-mutants
#6
Lidia Ballester-Tomás, Jose A Prieto, Paula Alepuz, Asier González, Elena Garre, Francisca Randez-Gil
In response to different adverse conditions, most eukaryotic organisms, including Saccharomyces cerevisiae, downregulate protein synthesis through the phosphorylation of eIF2α (eukaryotic initiation factor 2α) by Gcn2, a highly conserved protein kinase. Gcn2 also controls the translation of Gcn4, a transcription factor involved in the induction of amino acid biosynthesis enzymes. Here, we have studied the functional role of Gcn2 and Gcn2-regulating proteins, in controlling translation during temperature downshifts of TRP1 and trp1 yeast cells...
November 15, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27852007/apc-conditional-knock-out-mouse-is-a-model-of-infantile-spasms-with-elevated-neuronal-%C3%AE-catenin-levels-neonatal-spasms-and-chronic-seizures
#7
Antonella Pirone, Jon Alexander, Lauren A Lau, David Hampton, Andrew Zayachkivsky, Amy Yee, Audrey Yee, Michele H Jacob, Chris G Dulla
Infantile spasms (IS) are a catastrophic childhood epilepsy syndrome characterized by flexion-extension spasms during infancy that progress to chronic seizures and cognitive deficits in later life. The molecular causes of IS are poorly defined. Genetic screens of individuals with IS have identified multiple risk genes, several of which are predicted to alter β-catenin pathways. However, evidence linking malfunction of β-catenin pathways and IS is lacking. Here, we show that conditional deletion in mice of the adenomatous polyposis coli gene (APC cKO), the major negative regulator of β-catenin, leads to excessive β-catenin levels and multiple salient features of human IS...
November 13, 2016: Neurobiology of Disease
https://www.readbyqxmd.com/read/27851790/functional-effect-of-the-mutations-similar-to-the-cleavage-during-platelet-activation-at-integrin-%C3%AE-3-cytoplasmic-tail-when-expressed-in-mouse-platelets
#8
Xiaofeng Shi, Jichun Yang, Xiongying Cui, Jiansong Huang, Zhangbiao Long, Yulan Zhou, Ping Liu, Lanlan Tao, Zheng Ruan, Bing Xiao, Wei Zhang, Dongya Li, Kesheng Dai, Jianhua Mao, Xiaodong Xi
Previous studies in Chinese hamster ovary cells showed that truncational mutations of β3 at sites of F754 and Y759 mimicking calpain cleavage regulate integrin signaling. The roles of the sequence from F754 to C-terminus and the conservative N756ITY759 motif in platelet function have yet to be elaborated. Mice expressing β3 with F754 and Y759 truncations, or NITY deletion (β3-ΔTNITYRGT, β3-ΔRGT, or β3-ΔNITY) were established through transplanting the homozygous β3-deficient mouse bone marrow cells infected by the GFP tagged MSCV MigR1 retroviral vector encoding different β3 mutants into lethally radiated wild-type mice...
2016: PloS One
https://www.readbyqxmd.com/read/27845164/enhanced-crispr-cas9-mediated-precise-genome-editing-by-improved-design-and-delivery-of-grna-cas9-nuclease-and-donor-dna
#9
Xiquan Liang, Jason Potter, Shantanu Kumar, Namritha Ravinder, Jonathan D Chesnut
While CRISPR-based gene knock out in mammalian cells has proven to be very efficient, precise insertion of genetic elements via the cellular homology directed repair (HDR) pathway remains a rate-limiting step to seamless genome editing. Under the conditions described here, we achieved up to 56% targeted integration efficiency with up to a six-nucleotide insertion in HEK293 cells. In induced pluripotent stem cells (iPSCs), we achieved precise genome editing rates of up to 45% by co-delivering the Cas9 RNP and donor DNA...
November 11, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27832146/ribozyme-mediated-grna-generation-for-in-vitro-and-in-vivo-crispr-cas9-mutagenesis
#10
Raymond Teck Ho Lee, Ashley Shu Mei Ng, Philip W Ingham
CRISPR/Cas9 is now regularly used for targeted mutagenesis in a wide variety of systems. Here we report the use of ribozymes for the generation of gRNAs both in vitro and in zebrafish embryos. We show that incorporation of ribozymes increases the types of promoters and number of target sites available for mutagenesis without compromising mutagenesis efficiency. We have tested this by comparing the efficiency of mutagenesis of gRNA constructs with and without ribozymes and also generated a transgenic zebrafish expressing gRNA using a heat shock promoter (RNA polymerase II-dependent promoter) that was able to induce mutagenesis of its target...
2016: PloS One
https://www.readbyqxmd.com/read/27826253/multiple-cranial-organ-defects-after-conditionally-knocking-out-fgf10-in-the-neural-crest
#11
Tathyane H N Teshima, Silvia V Lourenco, Abigail S Tucker
Fgf10 is necessary for the development of a number of organs that fail to develop or are reduced in size in the null mutant. Here we have knocked out Fgf10 specifically in the neural crest driven by Wnt1cre. The Wnt1creFgf10fl/fl mouse phenocopies many of the null mutant defects, including cleft palate, loss of salivary glands, and ocular glands, highlighting the neural crest origin of the Fgf10 expressing mesenchyme surrounding these organs. In contrast tissues such as the limbs and lungs, where Fgf10 is expressed by the surrounding mesoderm, were unaffected, as was the pituitary gland where Fgf10 is expressed by the neuroepithelium...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27821169/a-new-tool-for-the-chemical-genetic-investigation-of-the-plasmodium-falciparum-pfnek-2-nima-related-kinase
#12
Deborah F Mitcheson, Andrew R Bottrill, Katherine Carr, Christopher R Coxon, Celine Cano, Bernard T Golding, Roger J Griffin, Andrew M Fry, Christian Doerig, Richard Bayliss, Andrew B Tobin
BACKGROUND: Examining essential biochemical pathways in Plasmodium falciparum presents serious challenges, as standard molecular techniques such as siRNA cannot be employed in this organism, and generating gene knock-outs of essential proteins requires specialized conditional approaches. In the study of protein kinases, pharmacological inhibition presents a feasible alternative option. However, as in mammalian systems, inhibitors often lack the desired selectivity. Described here is a chemical genetic approach to selectively inhibit Pfnek-2 in P...
November 7, 2016: Malaria Journal
https://www.readbyqxmd.com/read/27812096/experimental-evolution-reveals-interplay-between-sch9-and-polyploid-stability-in-yeast
#13
Yi-Jin Lu, Krishna B S Swamy, Jun-Yi Leu
Polyploidization has crucial impacts on the evolution of different eukaryotic lineages including fungi, plants and animals. Recent genome data suggest that, for many polyploidization events, all duplicated chromosomes are maintained and genome reorganizations occur much later during evolution. However, newly-formed polyploid genomes are intrinsically unstable and often quickly degenerate into aneuploidy or diploidy. The transition between these two states remains enigmatic. In this study, laboratory evolution experiments were conducted to investigate this phenomenon...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27798140/conditional-deletion-of-the-l-type-calcium-channel-cav1-2-in-oligodendrocyte-progenitor-cells-affects-postnatal-myelination-in-mice
#14
Veronica T Cheli, Diara A Santiago González, Tenzing Namgyal Lama, Vilma Spreuer, Vance Handley, Geoffrey G Murphy, Pablo M Paez
: To determine whether L-type voltage-operated Ca(2+) channels (L-VOCCs) are required for oligodendrocyte progenitor cell (OPC) development, we generated an inducible conditional knock-out mouse in which the L-VOCC isoform Cav1.2 was postnatally deleted in NG2-positive OPCs. A significant hypomyelination was found in the brains of the Cav1.2 conditional knock-out (Cav1.2(KO)) mice specifically when the Cav1.2 deletion was induced in OPCs during the first 2 postnatal weeks. A decrease in myelin proteins expression was visible in several brain structures, including the corpus callosum, cortex, and striatum, and the corpus callosum of Cav1...
October 19, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27791392/impact-of-ataxin-2-knock-out-on-circadian-locomotor-behavior-and-per-immunoreaction-in-the-scn-of-mice
#15
Martina Pfeffer, Suzana Gispert, Georg Auburger, Helmut Wicht, Horst-Werner Korf
In Drosophila melanogaster, Ataxin-2 is a crucial activator of Period and is involved in the control of circadian rhythms. However, in mammals the function of Ataxin-2 is unknown despite its involvement in the inherited neurogenerative disease Spinocerebellar Ataxia type 2 in humans. Therefore, we analyzed locomotor behavior of Atxn2-deficient mice and their WT littermates under entrained- and free-running conditions as well as after experimental jet lag. Furthermore, we compared the PER1 and PER2 immunoreaction (IR) in the SCN...
October 28, 2016: Chronobiology International
https://www.readbyqxmd.com/read/27791022/flavodiiron-proteins-act-as-safety-valve-for-electrons-in-physcomitrella-patens
#16
Caterina Gerotto, Alessandro Alboresi, Andrea Meneghesso, Martina Jokel, Marjaana Suorsa, Eva-Mari Aro, Tomas Morosinotto
Photosynthetic organisms support cell metabolism by harvesting sunlight to fuel the photosynthetic electron transport. The flow of excitation energy and electrons in the photosynthetic apparatus needs to be continuously modulated to respond to dynamics of environmental conditions, and Flavodiiron (FLV) proteins are seminal components of this regulatory machinery in cyanobacteria. FLVs were lost during evolution by flowering plants, but are still present in nonvascular plants such as Physcomitrella patens We generated P...
October 25, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27779481/a-novel-non-opioid-binding-site-for-endomorphin-1
#17
I Lengyel, F Toth, D Biyashev, I Szatmari, K Monory, C Tomboly, G Toth, S Benyhe, A Borsodi
Endomorphins are natural amidated opioid tetrapeptides with the following structure: Tyr-Pro-Trp-Phe-NH2 (endomorphin-1), and Tyr-Pro-Phe-Phe-NH2 (endomorphin-2). Endomorphins interact selectively with the μ-opioid or MOP receptors and exhibit nanomolar or sub-nanomolar receptor binding affinities, therefore they suggested to be endogenous agonists for the μ-opioid receptors. Endomorphins mediate a number of characteristic opioid effects, such as antinociception, however there are several physiological functions in which endomorphins appear to act in a fashion that does not involve binding to and activation of the μ-opioid receptor...
August 2016: Journal of Physiology and Pharmacology: An Official Journal of the Polish Physiological Society
https://www.readbyqxmd.com/read/27776539/clip-gene-a-web-service-of-the-condition-specific-context-laid-integrative-analysis-for-gene-prioritization-in-mouse-tf-knockout-experiments
#18
Benjamin Hur, Sangsoo Lim, Heejoon Chae, Seokjun Seo, Sunwon Lee, Jaewoo Kang, Sun Kim
MOTIVATION: Transcriptome data from the gene knockout experiment in mouse is widely used to investigate functions of genes and relationship to phenotypes. When a gene is knocked out, it is important to identify which genes are affected by the knockout gene. Existing methods, including differentially expressed gene (DEG) methods, can be used for the analysis. However, existing methods require cutoff values to select candidate genes, which can produce either too many false positives or false negatives...
October 24, 2016: Biology Direct
https://www.readbyqxmd.com/read/27775873/generation-and-characterization-of-mice-bearing-null-alleles-of-nradd-nrh2
#19
Nicolas Unsain, Genevieve Dorval, Jae Hyung Sheen, Philip A Barker
The Neurotrophin receptor associated death domain gene (Nradd/Nrh2/Plaidd) is a type I transmembrane protein with a unique and short N-terminal extracellular domain and a transmembrane and intracellular domain that bears high similarity to the p75 neurotrophin receptor (p75NTR/Ngfr). Initial studies suggested that NRADD regulates neurotrophin signaling but very little is known about its physiological roles. We have generated and characterized NRADD conditional and germ-line null mouse lines. These mice are viable and fertile and dońt show evident abnormalities...
October 24, 2016: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/27761821/generation-of-tissue-specific-mouse-models-to-analyze-hdac-functions
#20
Astrid Hagelkruys, Mirjam A Moser, Christian Seiser
Histone deacetylases (HDACs) play crucial roles during mammalian development and for cellular homeostasis. In addition, these enzymes are promising targets for small molecule inhibitors in the treatment of cancer and neurological diseases. Conditional HDAC knock-out mice are excellent tools for defining the functions of individual HDACs in vivo and for identifying the molecular targets of HDAC inhibitors in disease. Here, we describe the generation of tissue-specific HDAC knock-out mice and delineate a strategy for the generation of conditional HDAC knock-in mice...
2017: Methods in Molecular Biology
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