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Genes to Cells: Devoted to Molecular & Cellular Mechanisms

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https://www.readbyqxmd.com/read/28205312/essential-roles-of-tbx3-in-embryonic-skin-development-during-epidermal-stratification
#1
Ryo Ichijo, Yui Iizuka, Hirokazu Kubo, Fumiko Toyoshima
Stepwise differentiation of epidermal cells is essential for development of stratified epithelium, but the underlying mechanisms remain unclear. Here, we show that Tbx3, a member of the T-box family of transcription factors, plays a pivotal role in this mechanism. Tbx3 is expressed in both basal and suprabasal cells in the interfollicular epidermis of mouse embryos. Epidermis-specific Tbx3 conditional knockout (cKO) embryos are small in size and display a thinner epidermis with an impaired barrier function...
February 16, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28185378/ric-8a-an-activator-protein-of-g%C3%AE-i-controls-mammalian-epithelial-cell-polarity-for-tight-junction-assembly-and-cystogenesis
#2
Kanako Chishiki, Sachiko Kamakura, Junya Hayase, Hideki Sumimoto
Correct cyst morphogenesis of epithelial cells requires apical-basal polarization, which is partly regulated by mitotic spindle orientation, a process dependent on the heterotrimeric G protein subunit Gαi and its binding protein LGN. Here, we show that in three-dimensional culture of mammalian epithelial Madin-Darby canine kidney (MDCK) cells, the Gαi-activating protein Ric-8A is crucial for orientation of the mitotic spindle and formation of normal cysts that comprise a single layer of polarized cells with their apical surfaces lining an inner lumen...
February 10, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28185367/codon-degeneracy-and-amino-acid-abundance-influence-the-measures-of-codon-usage-bias-improved-nc-n%C3%AC-c-and-encprime-n%C3%AC-c-measures
#3
Siddhartha Sankar Satapathy, Ajit Kumar Sahoo, Suvendra Kumar Ray, Tapash Chandra Ghosh
Effective number of codons (N^c) and its variant N^'c (effective number of codons prime) are the two widely used methods for measuring unequal usage of synonymous codons in coding sequences, known as the codon usage bias (CUB). The mathematical formula used in calculating N^c and N^'c values is giving inappropriate measures of CUB in case of low abundance of amino acids. In addition, the magnitude of error also varies according to codon degeneracy. In this study, a modified formula for N^c and N^'c has been developed to measure the CUB more accurately...
February 10, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28151579/mediator-cyclin-dependent-kinases-upregulate-transcription-of-inflammatory-genes-in-cooperation-with-nf-%C3%AE%C2%BAb-and-c-ebp%C3%AE-on-stimulation-of-toll-like-receptor-9
#4
Seiji Yamamoto, Tomoko Hagihara, Yoshiyuki Horiuchi, Akira Okui, Shotaro Wani, Tokuyuki Yoshida, Takao Inoue, Aki Tanaka, Takashi Ito, Yutaka Hirose, Yoshiaki Ohkuma
In eukaryotes, the Mediator complex has important roles in regulation of transcription by RNA polymerase II. Mediator is a large complex with more than 20 subunits that form head, middle, tail and CDK/cyclin modules. Among them, CDK8 and/or CDK19 (CDK8/19), and their counterpart cyclin C, form the CDK/cyclin module together with Mediator subunits MED12 and MED13. Despite evidences of both activation and repression, the precise functional roles of CDK8/19 in transcription are still elusive. Our previous results indicate that CDK8/19 recruits epigenetic regulators to repress immunoresponse genes...
February 2, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28124402/knock-in-strategy-at-3-end-of-crx-gene-by-crispr-cas9-system-shows-the-gene-expression-profiles-during-human-photoreceptor-differentiation
#5
Kohei Homma, Sumiko Usui, Makoto Kaneda
Fluorescent reporter gene knock-in induced pluripotent stem cell (iPSC) lines have been used to evaluate the efficiency of differentiation into specific cell lineages. Here, we report a knock-in strategy for the generation of human iPSC reporter lines in which a 2A peptide sequence and a red fluorescent protein (E2-Crimson) gene were inserted at the termination codon of the cone-rod homeobox (Crx) gene, a photoreceptor-specific transcriptional factor gene. The knock-in iPSC lines were differentiated into fluorescence-expressing cells in 3D retinal differentiation culture, and the fluorescent cells also expressed Crx specifically in the nucleus...
January 26, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28111885/severe-damage-to-the-placental-fetal-capillary-network-causes-mid-to-late-fetal-lethality-and-reduction-in-placental-size-in-peg11-rtl1-ko-mice
#6
Moe Kitazawa, Masaru Tamura, Tomoko Kaneko-Ishino, Fumitoshi Ishino
Paternally expressed 11/Retrotransposon-like 1 (Peg11/Rtl1) knockout (KO) mice show mid- to late fetal lethality or late fetal growth retardation associated with frequent neonatal lethality. The lethal phenotype is largely dependent on genetic background and becomes more severe with each succeeding generation in the course of backcross experiments to C57BL/6 (B6). We previously suggested that these lethal and growth phenotypes in the fetal stages were due to severe defects in placental fetal capillaries in the labyrinth layer...
January 23, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28105749/octopamine-enhances-oxidative-stress-resistance-through-the-fasting-responsive-transcription-factor-daf-16-foxo-in%C3%A2-c-%C3%A2-elegans
#7
Haruka Hoshikawa, Masaharu Uno, Sakiko Honjoh, Eisuke Nishida
Dietary restriction regimens lead to enhanced stress resistance and extended life span in many species through the regulation of fasting and/or diet-responsive mechanisms. The fasting stimulus is perceived by sensory neurons and causes behavioral and metabolic adaptations. Octopamine (OA), one of the Caenorhabditis elegans neurotransmitters, is involved in behavioral adaptations, and its levels are increased under fasting conditions. However, it remains largely unknown how OA contributes to the fasting responses...
January 20, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28105742/yeasts-for-global-happiness-report-of-the-14th-international-congress-on-yeasts-icy14-held-in-awaji-island
#8
Daisuke Watanabe, Hiroshi Takagi
The 14th International Congress on Yeasts (ICY14) was held at Awaji Yumebutai International Conference Center (Awaji, Hyogo) in Japan from 11 to 15 September 2016. The main slogan of ICY14 was 'Yeasts for Global Happiness', which enabled us to acknowledge the high-potential usefulness of yeasts contributing to the global happiness in terms of food/beverage, health/medicine and energy/environment industries, as well as to basic biosciences. In addition, two more concepts were introduced: 'from Japan to the world' and 'from senior to junior'...
January 20, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28102564/pkn2-is-essential-for-mouse-embryonic-development-and-proliferation-of-mouse-fibroblasts
#9
Sally Danno, Koji Kubouchi, Mona Mehruba, Manabu Abe, Rie Natsume, Kenji Sakimura, Satoshi Eguchi, Masahiro Oka, Masanori Hirashima, Hiroki Yasuda, Hideyuki Mukai
PKN2, a member of the protein kinase N (PKN) family, has been suggested by in vitro culture cell experiments to bind to Rho/Rac GTPases and contributes to cell-cell contact and cell migration. To unravel the in vivo physiological function of PKN2, we targeted the PKN2 gene. Constitutive disruption of the mouse PKN2 gene resulted in growth retardation and lethality before embryonic day (E) 10.5. PKN2(-/-) embryo did not undergo axial turning and showed insufficient closure of the neural tube. Mouse embryonic fibroblasts (MEFs) derived from PKN2(-/-) embryos at E9...
January 19, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28097777/activin-a-in-combination-with-erk1-2-mapk-pathway-inhibition-sustains-propagation-of-mouse-embryonic-stem-cells
#10
Yuhei Ashida, May Nakajima-Koyama, Akira Hirota, Takuya Yamamoto, Eisuke Nishida
The Activin/Nodal/TGF-β signaling pathway plays a major role in maintaining mouse epiblast stem cells (EpiSCs). The EpiSC-maintaining medium, which contains Activin A and bFGF, induces differentiation of mouse embryonic stem cells (ESCs) to EpiSCs. Here, we show that Activin A also has an ability to efficiently propagate ESCs without differentiation to EpiSCs when combined with a MEK inhibitor PD0325901. ESCs cultured in Activin+PD retained high-level expression of naive pluripotency-related transcription factors...
January 18, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28097745/immature-core-protein-of-hepatitis-c-virus-induces-an-unfolded-protein-response-through-inhibition-of-erad-l-in-a-yeast-model-system
#11
Shota Takahashi, Naoko Sato, Junichi Kikuchi, Hideaki Kakinuma, Jun Okawa, Yukiko Masuyama, Singo Iwasa, Hayato Irokawa, Gi-Wook Hwang, Akira Naganuma, Michinori Kohara, Shusuke Kuge
The structural protein Core of hepatitis C virus (HCV), a cytosolic protein, induces endoplasmic reticulum (ER) stress and unfolded protein response (UPR) in hepatocytes, and is responsible for the pathogenesis of persistent HCV infection. Using yeast as a model system, we evaluated mechanisms underlying Core-induced interference of ER homeostasis and UPR, and found that UPR is induced by the immature Core (aa 1-191, Core191) but not by the mature Core (aa 1-177, Core177). Interestingly, Core191 inhibits both ERAD-L, a degradation system responsible for misfolded/unfolded proteins in the ER lumen, and ERAD-M, a degradation system responsible for proteins carrying a misfolded/unfolded region in the ER membrane...
January 18, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28097744/in-situ-electrical-monitoring-of-cancer-cells-invading-vascular-endothelial-cells-with-semiconductor-based-biosensor
#12
Toshiya Sakata, Yusuke Matsuse
Cellular dynamics is very closely related to ionic behaviors, most of which have been hardly monitored in real time, whereas semiconductor-based biosensors have the unique advantage of direct detection of ionic charges in a real-time and noninvasive manner. In this study, we monitored the invasion process of cancer cells into the vascular endothelial layer in real time by a label-free method using a field-effect transistor (FET) biosensor. Endothelial cells were cultured on the sensing surface of the FET gate, to form a basement membrane between the endothelial cells and the sensing surface...
January 18, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28084684/secretome-analysis-to-elucidate-metalloprotease-dependent-ectodomain-shedding-of-glycoproteins-during-neuronal-differentiation
#13
Kazuya Tsumagari, Kyoko Shirakabe, Mayu Ogura, Fuminori Sato, Yasushi Ishihama, Atsuko Sehara-Fujisawa
Many membrane proteins are subjected to limited proteolyses at their juxtamembrane regions, processes referred to as ectodomain shedding. Shedding ectodomains of membrane-bound ligands results in activation of downstream signaling pathways, whereas shedding those of cell adhesion molecules causes loss of cell-cell contacts. Secreted proteomics (secretomics) using high-resolution mass spectrometry would be strong tools for both comprehensive identification and quantitative measurement of membrane proteins that undergo ectodomain shedding...
January 13, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28084671/functional-mutations-in-spike-glycoprotein-of-zaire-ebolavirus-associated-with-an-increase-in-infection-efficiency
#14
Mahoko Takahashi Ueda, Yohei Kurosaki, Taisuke Izumi, Yusuke Nakano, Olamide K Oloniniyi, Jiro Yasuda, Yoshio Koyanagi, Kei Sato, So Nakagawa
Ebola virus (EBOV) is extremely virulent, and its glycoprotein is necessary for viral entry. EBOV may adapt to its new host humans during outbreaks by acquiring mutations especially in glycoprotein, which allows EBOV to spread more efficiently. To identify these evolutionary selected mutations and examine their effects on viral infectivity, we used experimental-phylogenetic-structural interdisciplinary approaches. In evolutionary analysis of all available Zaire ebolavirus glycoprotein sequences, we detected two codon sites under positive selection, which are located near/within the region critical for the host-viral membrane fusion, namely alanine-to-valine and threonine-to-isoleucine mutations at 82 (A82V) and 544 (T544I), respectively...
January 13, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28084665/novel-trna-function-in-amino-acid-sensing-of-yeast-tor-complex1
#15
Yoshiaki Kamada
TOR complex1 (TORC1), a master regulator of cell growth, is regulated by amino acids. Amino acids are fundamental nutrients, and 20 species of amino acids building proteins are not interchangeable with each other. Therefore, TORC1 should sense each amino acid individually. Mammalian mTORC1 is controlled by Rag GTPases and their regulators. However, Rag factors are dispensable for amino acid sensing by TORC1 in the budding yeast, suggesting an alternative mechanism of TORC1 regulation. Here, genetic investigation discovered the involvement of (aminoacyl-)tRNA ((aa-)tRNA) in TORC1 regulation...
January 13, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28078824/corrigendum
#16
(no author information available yet)
No abstract text is available yet for this article.
January 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28078823/hippo-vs-crab-tissue-specific-functions-of-the-mammalian-hippo-pathway
#17
REVIEW
Miki Nishio, Tomohiko Maehama, Hiroki Goto, Keisuke Nakatani, Wakako Kato, Hirofumi Omori, Yosuke Miyachi, Hideru Togashi, Yohei Shimono, Akira Suzuki
The Hippo signaling pathway is a vital suppressor of tumorigenesis that is often inactivated in human cancers. In normal cells, the Hippo pathway is triggered by external forces such as cell crowding, or changes to the extracellular matrix or cell polarity. Once activated, Hippo signaling down-regulates transcription supported by the paralogous cofactors YAP1 and TAZ. The Hippo pathway's functions in normal and cancer biology have been dissected by studies of mutant mice with null or conditional tissue-specific mutations of Hippo signaling elements...
January 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/27976495/detection-of-dna-double-strand-breaks-by-pulsed-field-gel-electrophoresis
#18
Yuri Kawashima, Nahomi Yamaguchi, Rie Teshima, Hisashi Narahara, Yoshio Yamaoka, Hirofumi Anai, Yoshihiro Nishida, Katsuhiro Hanada
A DNA double-strand break (DSB) is one of the most cytotoxic DNA lesions because unrepaired DSBs cause chromosomal aberrations and cell death. Although many physiological DSBs occur at DNA replication sites, the molecular mechanisms underlying this remain poorly understood. There was therefore a need to develop a highly specific method to detect DSB fragments containing DNA replication sites. Here we investigated whether pulsed-field gel electrophoresis (PFGE) combined with visualization of DNA replication sites by immunoblotting using halogenized deoxyuridines, such as BrdU and IdU, was sufficient for this detection...
January 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/27976481/irradiation-with-uv-c-inhibits-tnf-%C3%AE-dependent-activation-of-the-nf-%C3%AE%C2%BAb-pathway-in-a-mechanism-potentially-mediated-by-reactive-oxygen-species
#19
Katarzyna Szoltysek, Anna Walaszczyk, Patryk Janus, Marek Kimmel, Piotr Widlak
Pathways depending on the NF-κB transcription factor are essential components of cellular response to stress. Plethora of stimuli modulating NF-κB includes inflammatory signals, ultraviolet radiation (UV) and reactive oxygen species (ROS), yet interference between different factors affecting NF-κB remains relatively understudied. Here, we aim to characterize the influence of UV radiation on TNF-α-induced activity of the NF-κB pathway. We document inhibition of TNF-α-induced activation of NF-κB and subsequent suppression of NF-κB-regulated genes in cells exposed to UV-C several hours before TNF-α stimulation...
January 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/27935189/epigenetic-regulation-of-the-glucose-transporter-gene-slc2a1-by-%C3%AE-hydroxybutyrate-underlies-preferential-glucose-supply-to-the-brain-of-fasted-mice
#20
Kosuke Tanegashima, Yukiko Sato-Miyata, Masabumi Funakoshi, Yasumasa Nishito, Toshiro Aigaki, Takahiko Hara
We carried out liquid chromatography-tandem mass spectrometry analysis of metabolites in mice. Those metabolome data showed that hepatic glucose content is reduced, but that brain glucose content is unaffected, during fasting, consistent with the priority given to brain glucose consumption during fasting. The molecular mechanisms for this preferential glucose supply to the brain are not fully understood. We also showed that the fasting-induced production of the ketone body β-hydroxybutyrate (β-OHB) enhances expression of the glucose transporter gene Slc2a1 (Glut1) via histone modification...
January 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
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