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Conditional knock-out

Christian Brigolin, Nathan McKenty, Kirit Pindolia, Barry Wolf
Biotinidase deficiency is an autosomal recessively inherited disorder characterized by neurological and cutaneous abnormalities. Untreated individuals with biotinidase deficiency cannot recycle biotin from biocytin (N-biotinyl-ϵ-lysine), the proteolytic digestion product of protein-bound biotin. Biotin therapy can markedly resolve symptoms, or can prevent the development of symptoms if initiated early. To understand better the pathogenesis of the neurological problems in the disorder in humans, we have compared gene transcription changes during the first week post-birth in the brains of biotinidase-deficient, transgenic, knock-out mice at days 1 and 8 and compared to changes in wildtype mice at the same times...
December 2016: Molecular Genetics and Metabolism Reports
Kamalakshi Deka, Archana Singh, Surajit Chakraborty, Rupak Mukhopadhyay, Sougata Saha
ATE1-mediated post-translational addition of arginine to a protein has been shown to regulate activity, interaction, and stability of the protein substrates. Arginylation has been linked to many different stress conditions, namely ER stress, cytosolic misfolded protein stress, and nitrosative stress. However, clear understanding about the effect of arginylation in cellular stress responses is yet to emerge. In this study, we investigated the role of arginylation in heat-stress response. Our findings suggest that Ate1 knock out (KO) cells are more susceptible to heat stress compared with its wild-type counterparts due to the induction of apoptosis in KO cells...
2016: Cell Death Discovery
Changhwan Ahn, Dongoh Lee, Jae-Hwan Lee, Hyun Yang, Beum-Soo An, Eui-Bae Jeung
It has been proposed that cellular Ca2+ signals activate hormone secretion. In pancreatic β cells, which produce insulin, Ca2+ signals have been known to contribute to insulin secretion. Prior to this study, we confirmed that insulin-secreting β cells express CaBP-9k, and assumed that CaBP-9k play a role in β cell insulin synthesis or secretion. Using CaBP-9k knock out (KO) mice, we demonstrated that ablation of CaBP-9k causes reducing insulin secretion and increasing serum glucose. To compare the role of CaBP-9k with pathophysiological conditions, we exposed wild-type and CaBP-9k KO mice to hypoxic conditions for 10 days...
2016: PloS One
Marthe H R Ludtmann, Plamena R Angelova, Natalia N Ninkina, Sonia Gandhi, Vladimir L Buchman, Andrey Y Abramov
: Misfolded α-synuclein is a key factor in the pathogenesis of Parkinson's disease (PD). However, knowledge about a physiological role for the native, unfolded α-synuclein is limited. Using brains of mice lacking α-, β-, and γ-synuclein, we report that extracellular monomeric α-synuclein enters neurons and localizes to mitochondria, interacts with ATP synthase subunit α, and modulates ATP synthase function. Using a combination of biochemical, live-cell imaging and mitochondrial respiration analysis, we found that brain mitochondria of α-, β-, and γ-synuclein knock-out mice are uncoupled, as characterized by increased mitochondrial respiration and reduced mitochondrial membrane potential...
October 12, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Marion Rauter, Jakub Kasprzak, Karin Becker, Jan Riechen, Sebastian Worch, Anja Hartmann, Martin Mascher, Uwe Scholz, Kim Baronian, Rüdiger Bode, Frieder Schauer, H Matthias Vorbrodt, Gotthard Kunze
BACKGROUND: The non-conventional yeast Arxula adeninivorans uses 1-butanol as a carbon source and has recently attracted attention as a promising organism for 1-butanol production. Alcohol dehydrogenases (adhp) are important catalysts in 1-butanol metabolism, but only Aadh1p from Arxula has been characterized. This enzyme is involved in ethanol synthesis but has a low impact on 1-butanol degradation. RESULTS: In this study, we identified and characterized a second adhp from A...
October 12, 2016: Microbial Cell Factories
Karolina Stefanowicz, Nausicaä Lannoo, Yafei Zhao, Lore Eggermont, Jonas Van Hove, Bassam Al Atalah, Els J M Van Damme
BACKGROUND: A small group of F-box proteins consisting of a conserved F-box domain linked to a domain homologous to the glycan-binding protein has been identified within the genome of Arabidopsis thaliana. Previously, the so-called F-box-Nictaba protein, encoded by the gene At2g02360, was shown to be a functional lectin which binds N-acetyllactosamine structures. Here, we present a detailed qRT-PCR expression analysis of F-box-Nictaba in Arabidopsis plants upon different stresses and hormone treatments...
October 4, 2016: BMC Plant Biology
Hans-Jörg Mai, Stéphanie Pateyron, Petra Bauer
BACKGROUND: FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is the central regulator of iron uptake in Arabidopsis thaliana roots. We performed transcriptome analyses of six day-old seedlings and roots of six week-old plants using wild type, a fit knock-out mutant and a FIT over-expression line grown under iron-sufficient or iron-deficient conditions. We compared genes regulated in a FIT-dependent manner depending on the developmental stage of the plants. We assembled a high likelihood dataset which we used to perform co-expression and functional analysis of the most stably iron deficiency-induced genes...
October 3, 2016: BMC Plant Biology
Shulin Shi, Tao Wang, Ziru Chen, Zhong Tang, Zhongchang Wu, David E Salt, Dai-Yin Chao, Fangjie Zhao
Rice is a major dietary source of the toxic metalloid arsenic. Reducing its accumulation in rice grain is of critical importance to food safety. Rice roots take up arsenate and arsenite depending on the prevailing soil conditions. The first step of arsenate detoxification is its reduction to arsenite, but the enzyme(s) catalyzing this reaction in rice remains unknown. Here, we identify OsHAC1;1 and OsHAC1;2 as arsenate reductases in rice. OsHAC1;1 and OsHAC1;2 are able to complement an Escherichia coli mutant lacking the endogenous arsenate reductase and to reduce arsenate to arsenite...
October 4, 2016: Plant Physiology
Bryan D Clifton, Pablo Librado, Shu-Dan Yeh, Edwin Solares, Daphne Real, Suvini Jayasekera, Wanting Zhang, Mijuan Shi, Ronni Park, Robert Magie, Hsiu-Ching Ma, Xiao-Qin Xia, Antonio Marco, Julio Rozas, José M Ranz
Gene clusters of recently duplicated genes are hotbeds for evolutionary change. However, our understanding of how mutational mechanisms and evolutionary forces shape the structural and functional evolution of these clusters is hindered by the high sequence identity among the copies, which typically results in their inaccurate representation in genome assemblies. The presumed testis-specific, chimeric gene Sdic originated and tandemly expanded in Drosophila melanogaster, contributing to increased male-male competition...
October 3, 2016: Molecular Biology and Evolution
Brian A Renda, Cindy Chan, Kristin N Parent, Jeffrey E Barrick
: Bacterial genomes commonly contain prophage sequences as a result of past infections with lysogenic phages. Many of these integrated viral sequences are believed to be cryptic, but prophage genes are sometimes co-opted by the host, and some prophages may be re-activated to form infectious particles when cells are stressed or mutate. We found that a previously uncharacterized filamentous phage emerged from the genome of Acinetobacter baylyi ADP1 during a laboratory evolution experiment...
September 19, 2016: Journal of Bacteriology
Rui Jin, Wei Zhou
Cancer cells devote the majority of their energy consumption to ribosome biogenesis, and pre-ribosomal RNA transcription accounts for 30-50% of all transcriptional activity. This aberrantly elevated biological activity is an attractive target for cancer therapeutic intervention if approaches can be developed to circumvent the development of side effects in normal cells. TIF-IA is a transcription factor that connects RNA polymerase I with the UBF/SL-1 complex to initiate the transcription of pre-ribosomal RNA...
September 15, 2016: Biochimica et Biophysica Acta
Avinash V Dharmadhikari, Jenny J Sun, Krzysztof Gogolewski, Brandi L Carofino, Vladimir Ustiyan, Misty Hill, Tadeusz Majewski, Przemyslaw Szafranski, Monica J Justice, Russell S Ray, Mary E Dickinson, Vladimir V Kalinichenko, Anna Gambin, Pawel Stankiewicz
FOXF1 heterozygous point mutations and genomic deletions have been reported in newborns with a neonatally lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACDMPV). However, no gain-of-function mutations in FOXF1 have been identified yet in human disease. To study the effects of FOXF1 overexpression in lung development, we generated a Foxf1 overexpression mouse model by knocking in a Cre-inducible Foxf1 allele into the ROSA26 (R26) locus. The mice were phenotyped using micro-computed tomography (micro-CT), head-out plethysmography, ChIP-seq and transcriptome analyses, immunohistochemistry, and lung histopathology...
September 16, 2016: Biology Open
Alexander Andreychenko, Morgan Magnin, Katsumi Inoue
Automated verification of living organism models allows us to gain previously unknown knowledge about underlying biological processes. In this paper we show how parametric time model checking can be applied to define the time behavior of biological oscillatory systems more precisely. In particular, we focus on the resilience properties of such systems. This notion was introduced to understand the behavior of biological systems (e.g. the mammalian circadian rhythm) that are reactive and adaptive enough to endorse major changes in their environment (e...
September 13, 2016: Bio Systems
Jennifer L Poitras, Diane Heiser, Li Li, Bao Nguyen, Kozo Nagai, Amy S Duffield, Christopher Gamper, Donald Small
Internal tandem duplications of the juxtamembrane domain of FLT3 (FLT3/ITD) are among the most common mutations in Acute Myeloid Leukemia (AML). Resulting in constitutive activation of the kinase, FLT3/ITD portends a particularly poor prognosis, with reduced overall survival and increased rates of relapse. We previously generated a knock-in mouse, harboring an internal tandem duplication at the endogenous Flt3 locus, which develops a fatal myeloproliferative neoplasm (MPN), but fails to develop acute leukemia, suggesting additional mutations are necessary for transformation...
September 12, 2016: Oncotarget
Erin F Spence, Daniel J Kanak, Benjamin R Carlson, Scott H Soderling
UNLABELLED: Dendritic filopodia are actin-rich structures that are thought to contribute to early spine synapse formation; however, the actin regulatory proteins important for early synaptogenesis are poorly defined. Using organotypic hippocampal slice cultures and primary neuron hippocampal cultures from Arp2/3 conditional knock-out mice, we analyze the roles of the Arp2/3 complex, an actin regulator that creates branched actin networks, and demonstrate it is essential for distinct stages of both structural and functional maturation of excitatory spine synapses...
September 14, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Isabella Ellinger
Active placental transport of maternal serum calcium (Ca(2+)) to the offspring is pivotal for proper development of the fetal skeleton as well as various organ systems. Moreover, extracellular Ca(2+) levels impact on distinct processes in mammalian reproduction. The calcium-sensing receptor (CaSR) translates changes in extracellular Ca(2+)-concentrations into cellular reactions. This review summarizes current knowledge on the expression of CaSR and its putative functions in reproductive organs. CaSR was detected in placental cells mediating materno-fetal Ca(2+)-transport such as the murine intraplacental yolk sac (IPYS) and the human syncytiotrophoblast...
2016: Frontiers in Physiology
Haisong Jiang, Sung-Ung Kang, Shuran Zhang, Senthilkumar Karuppagounder, Jinchong Xu, Yong-Kyu Lee, Bong-Gu Kang, Yunjong Lee, Jianmin Zhang, Olga Pletnikova, Juan C Troncoso, Shelia Pirooznia, Shaida A Andrabi, Valina L Dawson, Ted M Dawson
Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder. Recent studies have implicated a role for peroxisome proliferator-activated receptor γ coactivator protein-1α (PGC-1α) in PD and in animal or cellular models of PD. The role of PGC-1α in the function and survival of substantia nigra pars compacta (SNpc) dopamine neurons is not clear. Here we find that there are four different PGC-1α isoforms expressed in SH-SY5Y cells, and these four isoforms are expressed across subregions of mouse brain...
July 2016: ENeuro
Lisa M Broad, Adrian J Mogg, Elizabeth Eberle, Marcia Tolley, Dominic L Li, Kelly L Knopp
Transient receptor potential vanilloid 3 (TRPV3) is a member of the TRP (Transient Receptor Potential) super-family. It is a relatively underexplored member of the thermo-TRP sub-family (Figure 1), however, genetic mutations and use of gene knock-outs and selective pharmacological tools are helping to provide insights into its role and therapeutic potential. TRPV3 is highly expressed in skin, where it is implicated in skin physiology and pathophysiology, thermo-sensing and nociception. Gain of function TRPV3 mutations in rodent and man have enabled the role of TRPV3 in skin health and disease to be particularly well defined...
September 9, 2016: Pharmaceuticals
Nobuhiko Tachibana, Robert Cantrup, Rajiv Dixit, Yacine Touahri, Gaurav Kaushik, Dawn Zinyk, Narsis Daftarian, Jeff Biernaskie, Sarah McFarlane, Carol Schuurmans
UNLABELLED: All tissues are genetically programmed to acquire an optimal size that is defined by total cell number and individual cellular dimensions. The retina contains stereotyped proportions of one glial and six neuronal cell types that are generated in overlapping waves. How multipotent retinal progenitors know when to switch from making one cell type to the next so that appropriate numbers of each cell type are generated is poorly understood. Pten is a phosphatase that controls progenitor cell proliferation and differentiation in several lineages...
September 7, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Kenta Imai, Feike Hao, Naonobu Fujita, Yasuhiro Tsuji, Yukako Oe, Yasuhiro Araki, Maho Hamasaki, Takeshi Noda, Tamotsu Yoshimori
Autophagy is an intracellular degradation pathway conserved in eukaryotes. Among core autophagy-related (Atg) proteins, mammalian Atg9A is the sole multi-spanning transmembrane protein, and both of its N- and C-terminal domains are exposed to the cytoplasm. It is known that Atg9A travels through the trans-Golgi network (TGN) and the endosomal system under nutrient-rich conditions, and transiently localizes to the autophagosome upon autophagy induction. However, the significance of Atg9A trafficking for autophagosome formation remains elusive...
October 15, 2016: Journal of Cell Science
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