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Jieting Tang, Huarong Chen, Chi-Chun Wong, Dabin Liu, Tong Li, Xiaohong Wang, Jiafu Ji, Joseph Jy Sung, Jing-Yuan Fang, Jun Yu
Copy number alterations (CNAs) are crucial for colorectal cancer (CRC) development. In this study, DEAD box polypeptide 27 (DDX27) was identified to be highly amplified in both TCGA CRC (474/615) and primary CRC (47/103), which was positively correlated with its mRNA overexpression. High DDX27 mRNA (N = 199) and protein expression (N = 260) predicted poor survival in CRC patients. Ectopic expression of DDX27 increased CRC cells proliferation, migration and invasion, but suppressed apoptosis. Conversely, silencing of DDX27 exerted opposite effects in vitro and significantly inhibited murine xenograft tumor growth and lung metastasis in vivo...
March 14, 2018: Oncogene
Frank Curmi, Ruben J Cauchi
Gemin3, also known as DDX20 or DP103, is a DEAD-box RNA helicase which is involved in more than one cellular process. Though RNA unwinding has been determined in vitro , it is surprisingly not required for all of its activities in cellular metabolism. Gemin3 is an essential gene, present in Amoeba and Metazoa. The highly conserved N-terminus hosts the helicase core, formed of the helicase- and DEAD-domains, which, based on crystal structure determination, have key roles in RNA binding. The C-terminus of Gemin3 is highly divergent between species and serves as the interaction site for several accessory factors that could recruit Gemin3 to its target substrates and/or modulate its function...
March 9, 2018: Biochemical Society Transactions
Wenting Zhao, Zhen Wang, Zewei Sun, Yuxian He, Dongdong Jian, Xiaotong Hu, Wang Zhang, Liangrong Zheng
The DEAD box protein DDX5, an ATP-dependent RNA helicase, plays an important role in transcriptional regulation and is associated with solid tumors and leukemia. However, its role in oxLDL-induced lipid uptake in macrophages remains unclear. In this study, we detected the expression of DDX5 mRNA and protein in oxidized low-density lipoprotein (oxLDL)-treated human primary macrophages that were induced from monocytes isolated from human peripheral blood with or without several chemical inhibitors using quantitative real-time PCR (qRT-PCR) or Western blotting...
March 6, 2018: Experimental Cell Research
Mili Nailwal, Jenabhai B Chauhan
BACKGROUND: DEAD-box helicase 3, Y-linked (DBY) is a candidate gene of the AZF region which is involved in spermatogenesis process. Mutations in the DBY gene may disrupt the spermatogenesis and lead to infertility in men. Identification of functionally neutral mutation from the disease-causing mutation is the biggest challenge in human genetic variation analysis. Owing to the importance of DBY in male infertility, functional analysis was carried out to reveal the association between genetic mutation and phenotypic variation through various in silico approaches...
March 8, 2018: Interdisciplinary Sciences, Computational Life Sciences
Alexis H Bennett, Marie-Francoise O'Donohue, Stacey R Gundry, Aye T Chan, Jeffrey Widrick, Isabelle Draper, Anirban Chakraborty, Yi Zhou, Leonard I Zon, Pierre-Emmanuel Gleizes, Alan H Beggs, Vandana A Gupta
Gene expression in a tissue-specific context depends on the combined efforts of epigenetic, transcriptional and post-transcriptional processes that lead to the production of specific proteins that are important determinants of cellular identity. Ribosomes are a central component of the protein biosynthesis machinery in cells; however, their regulatory roles in the translational control of gene expression in skeletal muscle remain to be defined. In a genetic screen to identify critical regulators of myogenesis, we identified a DEAD-Box RNA helicase, DDX27, that is required for skeletal muscle growth and regeneration...
March 2018: PLoS Genetics
Meriem Bekliz, Said Azza, Hervé Seligmann, Philippe Decloquement, Didier Raoult, Bernard La Scola
Acanthamoeba polyphaga mimivirus is the first giant virus ever described, with a 1.2-Mb genome which encodes 979 proteins including central components of the translation apparatus. One of these proteins, R458, was predicted to initiate translation, although its specific role remains unknown.We silenced the R458 gene using siRNA and compared viral fitness and protein expression in silenced versus wild-type mimivirus. Silencing decreased growth rate but viral particle production at the end of the viral cycle was unaffected...
March 7, 2018: Journal of Virology
Tobias Brandmann, Hana Fakim, Zoya Padamsi, Ji-Young Youn, Anne-Claude Gingras, Marc R Fabian, Martin Jinek
The LSM domain-containing protein LSM14/Rap55 plays a role in mRNA decapping, translational repression, and RNA granule (P-body) assembly. How LSM14 interacts with the mRNA silencing machinery, including the eIF4E-binding protein 4E-T and the DEAD-box helicase DDX6, is poorly understood. Here we report the crystal structure of the LSM domain of LSM14 bound to a highly conserved C-terminal fragment of 4E-T. The 4E-T C-terminus forms a bi-partite motif that wraps around the N-terminal LSM domain of LSM14. We also determined the crystal structure of LSM14 bound to the C-terminal RecA-like domain of DDX6...
March 6, 2018: EMBO Journal
Juliana M B Ricci, Emanuel R M Martinez, Arno J Butzge, Lucas B Doretto, Marcos A Oliveira, Robie Allan Bombardelli, Jan Bogerd, Rafael H Nóbrega
We have characterized the full-length vasa cDNA from Jundiá, Rhamdia quelen (Heptapteridae, Siluriformes). vasa encodes a member of the DEAD-box protein family of ATP-dependent RNA helicases. This protein is highly conserved among different organisms and its role is associated with RNA metabolism. In the majority of the investigated species, vasa is restricted to the germ cell lineage and its expression has been used to study germline development in many organisms, including fish. The deduced R. quelen vasa amino acid sequence displayed high similarity with Vasa protein sequences from other organisms, and did not cluster with PL10 or P68 DEAD-box protein subfamilies...
February 14, 2018: Gene
Kei Daizumoto, Tetsuro Yoshimaru, Yosuke Matsushita, Tomoya Fukawa, Hisaori Uehara, Masaya Ono, Masato Komatsu, Hiro-Omi Kanayama, Toyomasa Katagiri
The p53 and EGFR pathways are frequently altered in bladder cancers, yet their contributions to its progression remain elusive. Here we report that DEAD box polypeptide 31 (DDX31) plays a critical role in the multistep progression of muscle invasive bladder cancer (MIBC) through its sequential interactions with mutant p53 (mutp53) and EGFR. In early MIBC cells, nuclear DDX31 bound mutp53/SP1 and enhanced mutp53 transcriptional activation, leading to migration and invasion of MIBC. Cytoplasmic DDX31 also bound EGFR and phospho-nucleolin (p-NCL) in advanced MIBC, leading to EGFR-Akt signaling activation...
February 13, 2018: Cancer Research
Siying Tao, Zhenlong Jiao, Guigui Wen, Lihong Zhang, Guoxiu Wang
Ovomermis sinensis is a potentially-valuable nematode for controlling insect pests. The parasitic stage of the nematode absorbs nutrients in its host's hemolymph to maintain its growth development and then kills the host when it emerges. At present, little known about its reproductive development, particularly the responsible molecular mechanism. More detailed research on the genes of reproductive development will not only help us understand the mechanisms underlying sex differentiation in the nematode, but would also be valuable for successfully cultivating them in vitro and using them for biocontrol...
2018: PloS One
Will McIntyre, Rachel Netzband, Gaston Bonenfant, Jason M Biegel, Clare Miller, Gabriele Fuchs, Eric Henderson, Manoj Arra, Mario Canki, Daniele Fabris, Cara T Pager
More than 140 post-transcriptional modifications (PTMs) are known to decorate cellular RNAs, but their incidence, identity and significance in viral RNA are still largely unknown. We have developed an agnostic analytical approach to comprehensively survey PTMs on viral and cellular RNAs. Specifically, we used mass spectrometry to analyze PTMs on total RNA isolated from cells infected with Zika virus, Dengue virus, hepatitis C virus (HCV), poliovirus and human immunodeficiency virus type 1. All five RNA viruses significantly altered global PTM landscapes...
January 24, 2018: Nucleic Acids Research
Gregory L Dignon, Wenwei Zheng, Young C Kim, Robert B Best, Jeetain Mittal
Membraneless organelles important to intracellular compartmentalization have recently been shown to comprise assemblies of proteins which undergo liquid-liquid phase separation (LLPS). However, many proteins involved in this phase separation are at least partially disordered. The molecular mechanism and the sequence determinants of this process are challenging to determine experimentally owing to the disordered nature of the assemblies, motivating the use of theoretical and simulation methods. This work advances a computational framework for conducting simulations of LLPS with residue-level detail, and allows for the determination of phase diagrams and coexistence densities of proteins in the two phases...
January 2018: PLoS Computational Biology
Eliezer Calo, Bo Gu, Margot E Bowen, Fardin Aryan, Antoine Zalc, Jialiang Liang, Ryan A Flynn, Tomek Swigut, Howard Y Chang, Laura D Attardi, Joanna Wysocka
Many craniofacial disorders are caused by heterozygous mutations in general regulators of housekeeping cellular functions such as transcription or ribosome biogenesis. Although it is understood that many of these malformations are a consequence of defects in cranial neural crest cells, a cell type that gives rise to most of the facial structures during embryogenesis, the mechanism underlying cell-type selectivity of these defects remains largely unknown. By exploring molecular functions of DDX21, a DEAD-box RNA helicase involved in control of both RNA polymerase (Pol) I- and II-dependent transcriptional arms of ribosome biogenesis, we uncovered a previously unappreciated mechanism linking nucleolar dysfunction, ribosomal DNA (rDNA) damage, and craniofacial malformations...
February 1, 2018: Nature
Vanessa Khemici, Patrick Linder
RNA molecules have the tendency to fold into complex structures or to associate with complementary RNAs that exoribonucleases have difficulties processing or degrading. Therefore, degradosomes in bacteria and organelles as well as exosomes in eukaryotes have teamed-up with RNA helicases. Whereas bacterial degradosomes are associated with RNA helicases from the DEAD-box family, the exosomes and mitochondrial degradosome use the help of Ski2-like and Suv3 RNA helicases.
January 19, 2018: Biochemical Society Transactions
Emna Harigua-Souiai, Yosser Zina Abdelkrim, Imen Bassoumi-Jamoussi, Ons Zakraoui, Guillaume Bouvier, Khadija Essafi-Benkhadir, Josette Banroques, Nathan Desdouits, Hélène Munier-Lehmann, Mourad Barhoumi, N Kyle Tanner, Michael Nilges, Arnaud Blondel, Ikram Guizani
Leishmaniases are neglected parasitic diseases in spite of the major burden they inflict on public health. The identification of novel drugs and targets constitutes a research priority. For that purpose we used Leishmania infantum initiation factor 4A (LieIF), an essential translation initiation factor that belongs to the DEAD-box proteins family, as a potential drug target. We modeled its structure and identified two potential binding sites. A virtual screening of a diverse chemical library was performed for both sites...
January 18, 2018: PLoS Neglected Tropical Diseases
Ran Lee, Won-Young Lee, Hyun-Jung Park, Woo-Tae Ha, Jae-Seok Woo, Hak-Jae Chung, Ji-Heon Lee, Kwonho Hong, Hyuk Song
Spermatogenesis begins with spermatogonial stem cells (SSCs), which are located in the basement membrane of the adult testes. Previous studies have described specific biomarkers for undifferentiated porcine spermatogonia or SSCs; however, these markers are not sufficient to understand spermatogenesis at different developmental stages. The objective of this study was characterize the expression of DEAD-Box polypeptide 4 (DDX4, also known as VASA) and tyrosine-protein kinase kit (c-kit), as potential markers of male germ cells in the porcine testis...
December 30, 2017: Animal Reproduction Science
Yu He, Dan Zhang, Yanfang Yang, Xixi Wang, Xinyu Zhao, Peng Zhang, Hongxia Zhu, Ningzhi Xu, Shufang Liang
DEAD-box RNA helicase 3 (DDX3) is a highly conserved family member of DEAD-box proteins in all eukaryotes from yeasts to human beings. Accumulating studies have confirmed DDX3 has the ability to regulate different steps of RNA metabolism, including RNA splicing, RNA export, transcription and translation initiation. Moreover, DDX3 is involved in many biological processes, such as stress response, cell apoptosis, cell cycle regulation and virus infection. In recent years, DDX3 is getting increasing attention due to its essential roles in cancer progression...
January 9, 2018: Oncology Reports
(no author information available yet)
No abstract text is available yet for this article.
January 9, 2018: Journal of Cell Science
Kohei Taniguchi, Ayako Iwatsuki, Nobuhiko Sugito, Haruka Shinohara, Yuki Kuranaga, Yuki Oshikawa, Toshihiro Tajirika, Manabu Futamura, Kazuhiro Yoshida, Kazuhisa Uchiyama, Yukihiro Akao
Human DEAD-box RNA helicase gene DDX6 was cloned from B-cell lymphoma cell line RC-K8. Previously, we reported that DDX6 acts as oncogene in several cancers such as colorectal cancer and hepatocellular carcinoma. However, the detailed mechanism of DDX6 action in carcinogenesis is largely unknown. In this study, we examined the functions of DDX6 in clinical gastric cancer (GC) samples and GC cells. DDX6 protein expression levels of cancer samples were higher than those of the adjacent normal tissues in 25 clinical GC samples (median value: 1...
January 4, 2018: Molecular Carcinogenesis
Erica Silvestris, Paola Cafforio, Stella D'Oronzo, Claudia Felici, Franco Silvestris, Giuseppe Loverro
STUDY QUESTION: Are the large cells derived from cultured DEAD box polypeptide 4 (DDX4)-positive oogonial stem cells (OSCs), isolated from the ovarian cortex of non-menopausal and menopausal women, oocyte-like cells? SUMMARY ANSWER: Under appropriate culture conditions, DDX4-positive OSCs from non-menopausal and menopausal women differentiate into large haploid oocyte-like cells expressing the major oocyte markers growth differentiation factor 9 (GDF-9) and synaptonemal complex protein 3 (SYCP3) and then enter meiosis...
January 3, 2018: Human Reproduction
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