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Genes to Cells: Devoted to Molecular & Cellular Mechanisms

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https://www.readbyqxmd.com/read/28791781/many-transcription-factors-contribute-to-c-%C3%A2-elegans-growth-and-fat-storage
#1
Akihiro Mori, Amy D Holdorf, Albertha J M Walhout
Reverse genetic screens by RNA interference (RNAi) in model organisms such as the nematode Caenorhabditis elegans have provided numerous insights into gene function, thereby connecting genotype to phenotype. However, genes that contribute only subtly are often missed because relatively large numbers of measurements and reliable quantification are required to overcome experimental and biological noise that may mask subtle phenotypic effects. Here, we address this challenge by focusing on two phenotypes in C...
August 8, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28791779/crystal-structure-of-the-xpo1p-nuclear-export-complex-bound-to-the-sxfg-pxfg-repeats-of-the-nucleoporin-nup42p
#2
Masako Koyama, Hidemi Hirano, Natsuki Shirai, Yoshiyuki Matsuura
Xpo1p (yeast CRM1) is the major nuclear export receptor that carries a plethora of proteins and ribonucleoproteins from the nucleus to cytoplasm. The passage of the Xpo1p nuclear export complex through nuclear pore complexes (NPCs) is facilitated by interactions with nucleoporins (Nups) containing extensive repeats of phenylalanine-glycine (so-called FG repeats), although the precise role of each Nup in the nuclear export reaction remains incompletely understood. Here we report structural and biochemical characterization of the interactions between the Xpo1p nuclear export complex and the FG repeats of Nup42p, a nucleoporin localized at the cytoplasmic face of yeast NPCs and has characteristic SxFG/PxFG sequence repeat motif...
August 8, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28776905/expression-of-cytokine-and-extracellular-matrix-mrnas-in-fetal-hepatic-stellate-cells
#3
Keai Sinn Tan, Kasem Kulkeaw, Yoichi Nakanishi, Daisuke Sugiyama
In mouse fetal liver, hepatoblasts, sinusoidal endothelial cells and macrophages (or erythroblastic islands) promote differentiation and proliferation of hematopoietic cells through cell-cell interactions and secretion of cytokines and extracellular matrix factors. Until now, we have had little knowledge of the hematopoietic cytokines or extracellular matrix mRNAs expressed in hepatic stellate cells. Using p75 neurotrophin receptor (p75NTR) to mark this cell population, we sorted 12.5, 14.5 and 16.5 dpc hepatic stellate cells and analyzed expression of cytokines and extracellular matrix mRNAs...
August 4, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28776895/characterization-of-sarcocystis-fayeri-s-actin-depolymerizing-factor-as-a-toxin-that-causes-diarrhea
#4
Daisuke Irikura, Morihiro Saito, Yoshiko Sugita-Konishi, Takahiro Ohnishi, Kei-Ichi Sugiyama, Maiko Watanabe, Akiko Yamazaki, Shinji Izumiyama, Hirotaka Sato, Yusuke Kimura, Rie Doi, Yoichi Kamata
Raw horsemeat has the potential to induce food poisoning which often presents with diarrheal symptoms. A sample of horsemeat was found to be infected with Sarcocystis fayeri, and a 15-kDa protein isolated from the cysts of S. fayeri was found to clearly show its diarrhea-inducing activity. A nested polymerase chain reaction was used to clone the cDNA of the 15-kDa protein. The deduced amino acid sequence showed homology to actin-depolymerizing factor (ADF). A recombinant 15-kDa protein depolymerized prepolymerized actins in a test tube...
August 4, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28776863/artificial-acceleration-of-mammalian-cell-reprogramming-by-bacterial-proteins
#5
Takashi Ikeda, Ikuo Uchiyama, Mio Iwasaki, Tetsuhiko Sasaki, Masato Nakagawa, Keisuke Okita, Shinji Masui
The molecular mechanisms of cell reprogramming and differentiation involve various signaling factors. Small molecule compounds have been identified to artificially influence these factors through interacting cellular proteins. Although such small molecule compounds are useful to enhance reprogramming and differentiation and to show the mechanisms that underlie these events, the screening usually requires a large number of compounds to identify only a very small number of hits (e.g., one hit among several tens of thousands of compounds)...
August 4, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28771906/cdk1-interacting-protein-cip1-is-regulated-by-the-s%C3%A2-phase-checkpoint-in-response-to-genotoxic-stress
#6
Ze Zhang, Ping Ren, Ajay A Vashisht, James A Wohlschlegel, David G Quintana, Fanli Zeng
In eukaryotic cells, a surveillance mechanism, the S phase checkpoint, detects and responds to insults that challenge chromosomal replication, arresting cell cycle progression and triggering appropriate events to prevent genomic instability. In the budding yeast Saccharomyces cerevisiae, Mec1/ATM/ATR, and its downstream kinase, Rad53/Chk2, mediate the response to genotoxic stress. In this study, we place Cip1, a recently identified Cdk1 inhibitor (CKI), under the regulation of Mec1 and Rad53 in response to genotoxic stress...
August 3, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28752912/functional-analysis-of-the-cyclophilin-ppib-role-in-bacterial-cell-division
#7
Aggeliki Skagia, Chrysoula Zografou, Anastasia Venieraki, Costas Fasseas, Panagiotis Katinakis, Maria Dimou
Escherichia coli PpiB is a peptidyl-prolyl cis/trans isomerase (PPIase, EC: 5.2.1.8) with chaperone activity. Here, we show that the ΔppiB deletion strain and the PpiB over-expression wild-type strain are both characterized by defects in cell division involving milder or severe cell filamentation, respectively. Using various PpiB mutants, we show that the PPIase activity of PpiB is necessary for the observed cell filamentation, whereas other structural features apart from the active site are also important for this phenotype...
July 28, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28745000/sycp3-regulates-strand-invasion-activities-of-rad51-and-dmc1
#8
Wataru Kobayashi, Noriko Hosoya, Shinichi Machida, Kiyoshi Miyagawa, Hitoshi Kurumizaka
The synaptonemal complex is a higher-ordered proteinaceous architecture formed between homologous chromosomes. SYCP3 is a major component of the lateral/axial elements in the synaptonemal complex and is essential for meiotic recombination. Previous genetic studies showed that SYCP3 functions in meiotic homologous recombination biased to interhomologous chromosomes, by regulating the strand invasion activities of the RAD51 and DMC1 recombinases. However, the mechanism by which SYCP3 regulates RAD51- and DMC1-mediated strand invasion remains elusive...
July 26, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28707405/generation-of-biallelic-f0-mutants-in-medaka-using-the-crispr-cas9-system
#9
Rie Sawamura, Natsumi Osafune, Takahiro Murakami, Fumiya Furukawa, Takeshi Kitano
Several animal models generated by genome editing methods develop somatic mosaic mutations including wild-type genome sequence in F0 generation because it is difficult to use editing tools at the one-cell stage. Producing complete knockout animals quickly is a great advantage in determining the function of target genes. This study investigated the generation of F0 knockout medaka using the CRISPR/Cas9 system. To determine whether this editing system induced mutations in the medaka genome at the one-cell stage, recombinant Cas9 protein, tracrRNA and crRNA for dead end (dnd), which is essential for germ cell development, were injected into one-cell stage embryos of olvas-DsRedExpress transgenic medaka...
July 14, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28695676/matrin3-binds-directly-to-intronic-pyrimidine-rich-sequences-and-controls-alternative-splicing
#10
Yuri Uemura, Takuya Oshima, Munetaka Yamamoto, Charles Jourdan Reyes, Pedro Henrique Costa Cruz, Toshiharu Shibuya, Yukio Kawahara
Matrin3 is an RNA-binding protein that is localized in the nuclear matrix. Although various roles in RNA metabolism have been reported for Matrin3, in vivo target RNAs to which Matrin3 binds directly have not been investigated comprehensively so far. Here, we show that Matrin3 binds predominantly to intronic regions of pre-mRNAs. Photoactivatable Ribonucleoside-Enhanced Cross-linking and Immunoprecipitation (PAR-CLIP) analysis using human neuronal cells showed that Matrin3 recognized pyrimidine-rich sequences as binding motifs, including the polypyrimidine tract, a splicing regulatory element...
July 11, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28695613/ngl-3-induced-presynaptic-differentiation-of-hippocampal-neurons-in-an-afadin-dependent-nectin-1-independent-manner
#11
Tomohiko Maruo, Kenji Mandai, Muneaki Miyata, Shotaro Sakakibara, Shujie Wang, Kousyoku Sai, Yu Itoh, Aika Kaito, Takeshi Fujiwara, Akira Mizoguchi, Yoshimi Takai
A hippocampal mossy fiber synapse, which is implicated in learning and memory, has a complex structure. We have previously shown using afadin-deficient mice that afadin plays multiple roles in the structural and functional differentiations of this synapse. We investigated here using a co-culture system with cultured hippocampal neurons and non-neuronal COS-7 cells expressing synaptogenic cell adhesion molecules (CAMs) whether afadin is involved in the presynaptic differentiation of hippocampal synapses. Postsynaptic CAMs NGL-3 (alias, a Lrrc4b gene product) and neuroligin induced presynaptic differentiation by trans-interacting with their respective presynaptic binding CAMs LAR (alias, a Ptprf gene product) and neurexin...
July 11, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28639742/two-zinc-finger-proteins-from-mycobacterium-smegmatis-dna-binding-and-activation-of-transcription
#12
Subho Ghosh, Dipankar Chatterji
Single zinc finger domain containing proteins are very few in number. Of numerous zinc finger proteins in eukaryotes, only three of them like GAGA, Superman and DNA binding by one finger (Dof) have single zinc finger domain. Although few zinc finger proteins have been described in eubacteria, no protein with single C4 zinc finger has been described in details in anyone of them. In this article, we are describing two novel C-terminal C4 zinc finger proteins-Msmeg_0118 and Msmeg_3613 from Mycobacterium smegmatis...
June 22, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28639422/medaka-and-zebrafish-contactin1-mutants-as-a-model-for-understanding-neural-circuits-for-motor-coordination
#13
Miki Takeuchi, Chikako Inoue, Akiko Goshima, Yusuke Nagao, Koichi Shimizu, Hiroki Miyamoto, Takashi Shimizu, Hisashi Hashimoto, Shigenobu Yonemura, Atsuo Kawahara, Yutaka Hirata, Masayuki Yoshida, Masahiko Hibi
A spontaneous medaka ro mutant shows abnormal wobbling and rolling swimming behaviors. By positional cloning, we mapped the ro locus to a region containing the gene encoding Contactin1b (Cntn1b), which is an immunoglobulin (Ig)-superfamily domain-containing membrane-anchored protein. The ro mutant had a deletion in the cntn1b gene that introduced a premature stop codon. Furthermore, cntn1b mutants generated by the CRISPR/Cas9 system and trans-heterozygotes of the CRISPR mutant allele and ro had abnormal swimming behavior, indicating that the cntn1b gene was responsible for the ro-mutant phenotype...
June 22, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28631873/roles-of-afadin-in-functional-differentiations-of-hippocampal-mossy-fiber-synapse
#14
Xiaoqi Geng, Tomohiko Maruo, Kenji Mandai, Irwan Supriyanto, Muneaki Miyata, Shotaro Sakakibara, Akira Mizoguchi, Yoshimi Takai, Masahiro Mori
A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse...
June 20, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28597544/endoplasmic-reticulum-proteins-sdf2-and-sdf2l1-act-as-components-of-the-bip-chaperone-cycle-to-prevent-protein-aggregation
#15
Tsutomu Fujimori, Ryoji Suno, Shun-Ichiro Iemura, Tohru Natsume, Ikuo Wada, Nobuko Hosokawa
The folding of newly synthesized proteins in the endoplasmic reticulum (ER) is assisted by ER-resident chaperone proteins. BiP (immunoglobulin heavy-chain-binding protein), a member of the HSP70 family, plays a central role in protein quality control. The chaperone function of BiP is regulated by its intrinsic ATPase activity, which is stimulated by ER-resident proteins of the HSP40/DnaJ family, including ERdj3. Here, we report that two closely related proteins, SDF2 and SDF2L1, regulate the BiP chaperone cycle...
June 9, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28557347/in-vitro-site-specific-recombination-mediated-by-the-tyrosine-recombinase-xera-of-thermoplasma-acidophilum
#16
Minji Jo, Yasuto Murayama, Yasuhiro Tsutsui, Hiroshi Iwasaki
In organisms with circular chromosomes, such as bacteria and archaea, an odd number of homologous recombination events can generate a chromosome dimer. Such chromosome dimers cannot be segregated unless they are converted to monomers before cell division. In Escherichia coli, dimer-to-monomer conversion is mediated by the paralogous XerC and XerD recombinases at a specific dif site in the replication termination region. Dimer resolution requires the highly conserved cell division protein/chromosome translocase FtsK, and this site-specific chromosome resolution system is present or predicted in most bacteria...
May 30, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28557307/pervasive-yet-nonuniform-contributions-of-dcp2-and-cnot7-to-maternal-mrna-clearance-in-zebrafish
#17
Yuichiro Mishima, Yukihide Tomari
mRNA degradation is a fundamental biological process that erases transcribed genetic information from cells. During maternal-to-zygotic transition of animal development, thousands of maternal mRNAs are degraded by multiple mechanisms including microRNAs and codon-mediated decay. Enzymatic requirements for maternal mRNA clearance, however, are not fully understood. Here, we analyzed a contribution of the decapping enzyme Dcp2 to maternal mRNA clearance in zebrafish by over-expressing catalytically inactive Dcp2 and performing RNA-seq analysis...
May 30, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28608430/erratum
#18
(no author information available yet)
No abstract text is available yet for this article.
June 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28544195/long-and-branched-polyamines-are-required-for-maintenance-of-the-ribosome-trna-his-and-trna-tyr-in-thermus-thermophilus-cells-at-high-temperatures
#19
Misa Nakashima, Ryota Yamagami, Chie Tomikawa, Yuki Ochi, Toshiyuki Moriya, Haruichi Asahara, Dominique Fourmy, Satoko Yoshizawa, Tairo Oshima, Hiroyuki Hori
Thermus thermophilus is an extremely thermophilic eubacterium that produces various polyamines. Aminopropylagmatine ureohydrolase (SpeB) and SAM decarboxylase-like protein 1 (SpeD1) are involved in the biosynthesis of spermidine from arginine. Because long and branched polyamines in T. thermophilus are synthesized from spermidine, the speB and speD1 gene-deleted strains (ΔspeB and ΔspeD1, respectively) cannot synthesize long and branched polyamines. Although neither strain grew at high temperatures (>75°C) in minimal medium, both strains survived at 80°C when they were cultured at 70°C until the mid-log phase and then shifted to 80°C...
May 24, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28544270/localization-and-domain-characterization-of-the-sfla-regulator-of-flagellar-formation-in-vibrio-alginolyticus
#20
Satoshi Inaba, Takehiko Nishigaki, Norihiro Takekawa, Seiji Kojima, Michio Homma
Many swimming bacteria use flagella as locomotive organelles. The spatial and numerical regulation of flagellar biosynthesis differs by bacterial species. The marine bacteria Vibrio alginolyticus use a single polar flagellum whose number is regulated positively by FlhF and negatively by FlhG. Cells lacking FlhF and FlhG have no flagellum. The motility defect in an flhFG deletion was suppressed by a mutation in the sflA gene that resulted in the production of multiple, peritrichous flagella. SflA is a Vibrio-specific protein...
May 22, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
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