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https://www.readbyqxmd.com/read/28938616/identification-of-potential-cancer-related-pseudogenes-in-lung-adenocarcinoma-based-on-cerna-hypothesis
#1
Yunzhen Wei, Zhiqiang Chang, Cheng Wu, Yinling Zhu, Kun Li, Yan Xu
Pseudogenes are initially regarded as non-functional genomic fossils resulted from inactivating gene mutations during evolution. Far from being silent, pseudogenes are proved to regulate the expression of protein-coding genes through function as microRNA sponge in vivo. The aim of our study was to propose an integrative systems biology approach to identify disease pseudogenes base on competitive endogenous RNA (ceRNA) hypothesis. Here, we applied our method to lung adenocarcinoma (LUAD) RNASeq data from TCGA and identified 33 candidate pseudogenes...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938466/optogenetic-analysis-of-depolarization-dependent-glucagon-like-peptide-1-release
#2
Catalin Chimerel, Cristian Riccio, Keir Murison, Fiona M Gribble, Frank Reimann
Incretin hormones play an important role in the regulation of food intake and glucose homeostasis. Glucagon-like peptide-1 (GLP-1) secreting cells have been demonstrated to be electrically excitable and to fire action potentials (APs) with increased frequency in response to nutrient exposure. However, nutrients can also be metabolised or activate G-protein-coupled receptors, thus potentially stimulate GLP-1 secretion independent of their effects on the plasma membrane potential. Here we used channelrhodopsins to manipulate the membrane potential of GLUTag cells, a well established model of GLP-1 secreting enteroendocrine L-cells...
July 28, 2017: Endocrinology
https://www.readbyqxmd.com/read/28938067/a-single-chain-photoswitchable-crispr-cas9-architecture-for-light-inducible-gene-editing-and-transcription
#3
Xin X Zhou, Xinzhi Zou, Hokyung K Chung, Yuchen Gao, Yanxia Liu, Lei S Qi, Michael Z Lin
Optical control of CRISPR-Cas9-derived proteins would be useful for restricting gene editing or transcriptional regulation to desired times and places. Optical control of Cas9 functions has been achieved with photouncageable unnatural amino acids or by using light-induced protein interactions to reconstitute Cas9-mediated functions from two polypeptides. However, these methods have only been applied to one Cas9 species and have not been used for optical control of different perturbations at two genes. Here, we use photodissociable dimeric fluorescent protein domains to engineer single-chain photoswitchable Cas9 (ps-Cas9) proteins in which the DNA-binding cleft is occluded at baseline and opened upon illumination...
September 22, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28938006/association-between-circulating-mirnas-and-spinal-involvement-in-patients-with-axial-spondyloarthritis
#4
Klára Prajzlerová, Kristýna Grobelná, Markéta Hušáková, Šárka Forejtová, Astrid Jüngel, Steffen Gay, Jiří Vencovský, Karel Pavelka, Ladislav Šenolt, Mária Filková
OBJECTIVES: Dysregulation of miRNAs and their target genes contributes to the pathophysiology of autoimmune diseases. Circulating miRNAs may serve as diagnostic/prognostic biomarkers. We aimed to investigate the association between circulating miRNAs, disease activity and spinal involvement in patients with axial spondyloarthritis (AxSpA). METHODS: Total RNA was isolated from the plasma of patients with non-radiographic (nr)AxSpA, patients with ankylosing spondylitis (AS) and healthy controls (HC) via phenol-chloroform extraction...
2017: PloS One
https://www.readbyqxmd.com/read/28936334/synthesis-of-bioactive-and-stabilized-cyclic-peptides-by-macrocyclization-using-c-sp-3-h-activation
#5
Jian Tang, Yadong He, Hongfei Chen, Wangjian Sheng, Huan Wang
Cyclic peptides have attracted increasing attention in recent years due to their ability to inhibit protein-protein interactions. Current strategies to prepare cyclic peptides often rely on functional amino acid side chains or the incorporation of unnatural amino acids, thus limiting their structural diversity. Here, we describe the development of a highly versatile peptide macrocyclization strategy through a palladium-catalyzed C(sp(3))-H activation and the synthesis of cyclic peptides featuring unique hydrocarbon linkages between the β-carbon of amino acids and the aromatic side chains of Phe and Trp...
June 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28936181/novel-heparin-receptor-transmembrane-protein-184a-regulates-angiogenesis-in-the-adult-zebrafish-caudal-fin
#6
Sara Lynn N Farwell, Kimberly G Reylander, M Kathryn Iovine, Linda J Lowe-Krentz
Transmembrane protein 184A (TMEM184A) was recently identified as the heparin receptor in vascular cells. Heparin binds specifically to TMEM184A and induces anti-proliferative signaling in vitro. Though it is highly conserved, the physiological function of TMEM184A remains unknown. The objective of this study was to investigate the expression and effects on vascular regeneration of TMEM184A using the adult zebrafish regenerating caudal fin as an in vivo model. Here, we show that Tmem184a is expressed in vascular endothelial cells (ECs) of mature and regenerating zebrafish fins...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28935957/modulation-of-cyclic-nucleotide-mediated-cellular-signaling-and-gene-expression-using-photoactivated-adenylyl-cyclase-as-an-optogenetic-tool
#7
Meenakshi Tanwar, Lohit Khera, Nemneineng Haokip, Rajeev Kaul, Aruna Naorem, Suneel Kateriya
Cyclic nucleotide signaling pathway plays a significant role in various biological processes such as cell growth, transcription, inflammation, in microbial pathogenesis, etc. Modulation of cyclic nucleotide levels by optogenetic tools has overcome certain limitations of studying transduction cascade by pharmacological agents and has allowed several ways to modulate biological processes in a spatiotemporal manner. Here, we have shown the optogenetic modulation of the cyclooxygenase 2 (Cox-2) gene expression and their downstream effector molecule (PGE2) in HEK-293T cells and the development process of Dictyostelium discoideum via modulating the cyclic nucleotide (cAMP) signaling pathway utilizing photoactivated adenylyl cyclases (PACs) as an optogenetic tool...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935940/layer-and-cell-type-selective-co-transmission-by-a-basal-forebrain-cholinergic-projection-to-the-olfactory-bulb
#8
Daniel T Case, Shawn D Burton, Jeremy Y Gedeon, Sean-Paul G Williams, Nathaniel N Urban, Rebecca P Seal
Cholinergic neurons in the basal forebrain project heavily to the main olfactory bulb, the first processing station in the olfactory pathway. The projections innervate multiple layers of the main olfactory bulb and strongly influence odor discrimination, detection, and learning. The precise underlying circuitry of this cholinergic input to the main olfactory bulb remains unclear, however. Here, we identify a specific basal forebrain cholinergic projection that innervates select neurons concentrated in the internal plexiform layer of the main olfactory bulb...
September 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28935857/sensorimotor-computation-underlying-phototaxis-in-zebrafish
#9
Sébastien Wolf, Alexis M Dubreuil, Tommaso Bertoni, Urs Lucas Böhm, Volker Bormuth, Raphaël Candelier, Sophia Karpenko, David G C Hildebrand, Isaac H Bianco, Rémi Monasson, Georges Debrégeas
Animals continuously gather sensory cues to move towards favourable environments. Efficient goal-directed navigation requires sensory perception and motor commands to be intertwined in a feedback loop, yet the neural substrate underlying this sensorimotor task in the vertebrate brain remains elusive. Here, we combine virtual-reality behavioural assays, volumetric calcium imaging, optogenetic stimulation and circuit modelling to reveal the neural mechanisms through which a zebrafish performs phototaxis, i.e...
September 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28935174/timp-3-mrna-expression-levels-positively-correlates-with-levels-of-mir-21-in-in-situ-bc-and-negatively-in-pr-positive-invasive-bc
#10
Nina Petrovic, Ahmad Sami, Jelena Martinovic, Marina Zaric, Irina Nakashidze, Silvana Lukic, Snezana Jovanovic-Cupic
BACKGROUND: Breast carcinomas (BC) belong to a heterogeneous group of malignant diseases. Correct categorization of BC based on molecular biomarkers has a very important role in deciding the proper course of therapy for each patient. It has been already shown that the decrease of TIMP metalloproteinase inhibitor 3 (TIMP-3) together with overexpression of microRNA-21 (miR-21) might be involved in the process of BC invasion. This is the first study that examined relationship among miR-21, TIMP-3 mRNA and TIPM-3 protein levels in BC groups formed according to invasiveness...
September 6, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28935113/directed-evolution-of-glycopeptides-using-mrna-display
#11
Satoru Horiya, Jennifer K Bailey, Isaac J Krauss
Directed evolution is a useful method for the discovery of nucleic acids, peptides, or proteins that have desired binding abilities or functions. Because of the abundance and importance of glycosylation in nature, directed evolution of glycopeptides and glycoproteins is also highly desirable. However, common directed evolution platforms such as phage-, yeast-, or mammalian-cell display are limited for these applications by several factors. Glycan structure at each glycosylation site is not genetically encoded, and yeast and mammalian cells produce a heterogeneous mixture of glycoforms at each site on the protein...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28934937/mir-9-mir-21-and-mir-155-as-potential-biomarkers-for-hpv-positive-and-negative-cervical-cancer
#12
Sunyoung Park, Kiyoon Eom, Jungho Kim, Hyeeun Bang, Hye-Young Wang, Sungwoo Ahn, Geehyuk Kim, Hyoungsoon Jang, Sunghyun Kim, Dongsup Lee, Kwang Hwa Park, Hyeyoung Lee
BACKGROUND: Cervical cancer is the second leading cause of death among female patients with cancer in the world. High risk human papillomavirus has causal roles in cervical cancer initiation and progression by deregulating several cellular processes. However, HPV infection is not sufficient for cervical carcinoma development. Therefore, other genetic and epigenetic factors may be involved in this complex disease, and the identification of which may lead to better diagnosis and treatment...
September 21, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28934717/expression-of-c-ebp%C3%AE-in-myeloid-progenitors-during-sepsis-promotes-immunosuppression
#13
Jun Dai, Ajinkya Kumbhare, Dima Youssef, Zhi Q Yao, Charles E McCall, Mohamed El Gazzar
Sepsis-induced myeloid-derived suppressor cells (MDSCs) contribute to immunosuppression associated with sepsis. We reported that the CCAAT enhancer-binding protein C/EBPβ activates microRNA (miR)-21 and miR-181b expressions, which induce transcription factor NFI-A to support the generation and expansion of MDSCs in the bone marrow and spleens of septic mice. Here, using a conditional knockout mouse model lacking C/EBPβ in the myeloid lineage, we find that without C/EBPβ, myeloid progenitor cells could not express miR-21 or miR-181b, and ectopic expression of C/EBPβ in the C/EBPβ-deficient myeloid progenitors activated the expression of the two miRNAs...
September 18, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28934490/number-of-inadvertent-rna-targets-for-morpholino-knockdown-in-danio-rerio-is-largely-underestimated-evidence-from-the-study-of-ser-arg-rich-splicing-factors
#14
Marine Joris, Marie Schloesser, Denis Baurain, Marc Hanikenne, Marc Muller, Patrick Motte
Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the programmable site-specific nucleases. Consistent with previous research, we revealed discrepancies between the mutant and morphant phenotypes and we show that these inconsistencies may result from a large number of unsuspected inadvertent morpholino RNA targets...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934466/cohesin-acetyltransferase-esco2-regulates-sac-and-kinetochore-functions-via-maintaining-h4k16-acetylation-during-mouse-oocyte-meiosis
#15
Yajuan Lu, Xiaoxin Dai, Mianqun Zhang, Yilong Miao, Changyin Zhou, Zhaokang Cui, Bo Xiong
Sister chromatid cohesion, mediated by cohesin complex and established by the acetyltransferases Esco1 and Esco2, is essential for faithful chromosome segregation. Mutations in Esco2 cause Roberts syndrome, a developmental disease characterized by severe prenatal retardation as well as limb and facial abnormalities. However, its exact roles during oocyte meiosis have not clearly defined. Here, we report that Esco2 localizes to the chromosomes during oocyte meiotic maturation. Depletion of Esco2 by morpholino microinjection leads to the precocious polar body extrusion, the escape of metaphase I arrest induced by nocodazole treatment and the loss of BubR1 from kinetochores, indicative of inactivated SAC...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28933779/genetically-encoded-releasable-photo-cross-linking-strategies-for-studying-protein-protein-interactions-in-living-cells
#16
Yi Yang, Haiping Song, Dan He, Shuai Zhang, Shizhong Dai, Xiao Xie, Shixian Lin, Ziyang Hao, Huangtao Zheng, Peng R Chen
Although protein-protein interactions (PPIs) have crucial roles in virtually all cellular processes, the identification of more transient interactions in their biological context remains challenging. Conventional photo-cross-linking strategies can be used to identify transient interactions, but these approaches often suffer from high background due to the cross-linked bait proteins. To solve the problem, we have developed membrane-permeable releasable photo-cross-linkers that allow for prey-bait separation after protein complex isolation and can be installed in proteins of interest (POIs) as unnatural amino acids...
October 2017: Nature Protocols
https://www.readbyqxmd.com/read/28933778/synthesis-of-a-hycosul-peptide-substrate-library-to-dissect-protease-substrate-specificity
#17
Marcin Poreba, Guy S Salvesen, Marcin Drag
Many biologically and chemically based approaches have been developed to design highly active and selective protease substrates and probes. It is, however, difficult to find substrate sequences that are truly selective for any given protease, as different proteases can demonstrate a great deal of overlap in substrate specificities. In some cases, better enzyme selectivity can be achieved using peptide libraries containing unnatural amino acids such as the hybrid combinatorial substrate library (HyCoSuL), which uses both natural and unnatural amino acids...
October 2017: Nature Protocols
https://www.readbyqxmd.com/read/28933518/mir-564-promotes-hypertrophic-scar-via-up-regulating-tgf-%C3%AE-1
#18
Long Xiao, Tianyi Tang, Yu Huang, Jianxing Guo
BACKGROUND: To evaluate the role of microRNA564 (miR-564) in the development of hypertrophic scar and investigate the possible mechanism of this process. METHODS: The hypertrophic scar (HS) tissues and adjacent normal skin (NS) tissues were selected from 10 patients. The fibrosis-related proteins were detected via hematoxylin eosin (HE) staining, Masson staining and immunohistochemical detection. The relative expression difference of miR-564 in NS tissues and HS tissues was detected via reverse transcription-polymerase chain reaction (RT-PCR)...
September 20, 2017: Giornale Italiano di Dermatologia e Venereologia: Organo Ufficiale, Società Italiana di Dermatologia e Sifilografia
https://www.readbyqxmd.com/read/28933150/an-ultra-flexible-transparent-oxide-metal-oxide-stack-electrode-with-low-sheet-resistance-for-electrophysiological-measurements
#19
Yasutoshi Jimbo, Naoji Matsuhisa, Wonryung Lee, Peter Zalar, Hiroaki Jinno, Tomoyuki Yokota, Masaki Sekino, Takao Someya
Flexible, transparent electrodes are a crucial component for future implantable and wearable systems. For practical applications, conductivity and flexibility should be further improved to prevent signal attenuation, heat generation, and disconnection. Herein, we fabricate an ultra-flexible transparent electrode with low sheet resistance (8.6 Ω/sq) using an indium-tin-oxide/Au/indium-tin-oxide multilayer on a 1 µm-thick parylene substrate. The electrodes were foldable, and when compared to pristine ITO displayed greater mechanical robustness...
September 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28932769/microrna-expression-in-a-phosphaturic-mesenchymal-tumour
#20
Darrell Green, Irina Mohorianu, Isabelle Piec, Jeremy Turner, Clare Beadsmoore, Andoni Toms, Richard Ball, John Nolan, Iain McNamara, Tamas Dalmay, William D Fraser
Phosphaturic mesenchymal tumours are a heterogeneous set of bone and soft tissue neoplasms that can cause a number of paraneoplastic syndromes such as tumour induced osteomalacia. The term phosphaturic comes from the common finding that these tumours secrete high levels of fibroblast growth factor 23 which causes renal phosphate wasting leading to hypophosphatemia. Phosphaturic mesenchymal tumours are rare and diagnosis is difficult. A very active 68 year old male presented with bone pain and muscle weakness...
December 2017: Bone Reports
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