keyword
MENU ▼
Read by QxMD icon Read
search

rna sequence

keyword
https://www.readbyqxmd.com/read/29679834/microeukaryotic-biogeography-in-the-typical-subtropical-coastal-waters-with-multiple-environmental-gradients
#1
Huajun Zhang, Xiaolin Huang, Lei Huang, Fangjian Bao, Shangling Xiong, Kai Wang, Demin Zhang
The determinants of microeukaryotic biogeography in coastal waters at a regional scale remain largely unclear. The coastal northern Zhejiang (in the East China Sea) is a typical subtropical marine ecosystem with multiple environmental gradients that has been extensively perturbed by anthropogenic activities. Thus, it is a valuable region to investigate the key drivers that shape microbial biogeography. We investigated microeukaryotic communities in surface waters from 115 stations in this region using 18S ribosomal RNA gene amplicon sequencing...
April 18, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29679637/recent-stimulant-use-and-leukocyte-gene-expression-in-methamphetamine-users-with-treated-hiv-infection
#2
Adam W Carrico, Annesa Flentje, Kord Kober, Sulggi Lee, Peter Hunt, Elise D Riley, Steven Shoptaw, R N Elena Flowers, Samantha E Dilworth, Savita Pahwa, Bradley E Aouizerat
Stimulant use may accelerate HIV disease progression through biological and behavioral pathways. However, scant research with treated HIV-positive persons has examined stimulant-associated alterations in pathophysiologic processes relevant to HIV pathogenesis. In a sample of 55 HIV-positive, methamphetamine-using sexual minority men with a viral load less than 200 copies/mL, we conducted RNA sequencing to examine patterns of leukocyte gene expression in participants who had a urine sample that was reactive for stimulants (n = 27) as compared to those who tested non-reactive (n = 28)...
April 18, 2018: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/29679569/ddx1-regulates-alternative-splicing-and-insulin-secretion-in-pancreatic-%C3%AE-cells
#3
Wen Zhong, Zonghong Li, Maoge Zhou, Tao Xu, You Wang
DEAD-box helicase 1 (DDX1) is a multifunction protein involved in diverse cellular processes including transcription, viral replication, mRNA/miRNA processing, and tRNA splicing. Here, we report a novel function of DDX1 in mRNA alternative splicing in pancreatic β cells. By performing integrated data analysis of high-throughput RNA sequencing (RNA-Seq), and cross-linking and immunoprecipitation coupled with deep sequencing (CLIP-Seq), we identify hundreds of alternative splicing genes that are targeted by DDX1...
April 18, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29679562/myotube-derived-factor-promotes-oligodendrocyte-precursor-cell-proliferation
#4
Akino Nakasone, Rieko Muramatsu, Yuki Kato, Yukio Kawahara, Toshihide Yamashita
Muscle cells secrete numerous molecules that function as endocrine hormones and regulate the functions of distant organs. Myelination in the central nervous system (CNS) is regulated by peripheral hormones. However, the effects of muscle-derived molecules on myelination have not been sufficiently analyzed. In this study, we show that muscle-releasing factors promote proliferation of oligodendrocyte precursor cells (OPCs), which is an element of myelination process. Supernatants of mouse myotube cultures stimulated bromodeoxyuridine (BrdU) incorporation into mouse OPCs...
April 18, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29679497/ewsr1-patz1-gene-fusion-may-define-a-new-glioneuronal-tumor-entity
#5
Aurore Siegfried, Audrey Rousseau, Claude-Alain Maurage, Sarah Pericart, Yvan Nicaise, Frederic Escudie, David Grand, Alix Delrieu, Anne Gomez-Brouchet, Sophie Le Guellec, Camille Franchet, Sergio Boetto, Matthieu Vinchon, Jean-Christophe Sol, Franck-Emmanuel Roux, Valerie Rigau, Anne-Isabelle Bertozzi, David Tw Jones, Dominique Figarella-Branger, Emmanuelle Uro-Coste
We investigated the challenging diagnostic case of a ventricular cystic glioneuronal tumor with papillary features, by RNA sequencing using the Illumina TruSight RNA Fusion panel. We did not retrieve the SLC44A1-PRKCA fusion gene specific for papillary glioneuronal tumor, but an EWSR1-PATZ1 fusion transcript. RT-PCR followed by Sanger sequencing confirmed the EWSR1-PATZ1 fusion. It matched with canonic EWSR1 fusion oncogene, juxtaposing the entire N terminal transcriptional activation domain of EWSR1 gene and the C terminal DNA binding domain of a transcription factor gene, PATZ1...
April 21, 2018: Brain Pathology
https://www.readbyqxmd.com/read/29679401/translational-regulation-of-ribosomal-protein-s15-drives-characteristic-patterns-of-protein-mrna-epistasis
#6
Saurav Mallik, Sudipto Basu, Suman Hait, Sudip Kundu
Do coding and regulatory segments of a gene co-evolve with each-other? Seeking answers to this question, here we analyze the case of Escherichia coli ribosomal protein S15, that represses its own translation by specifically binding its messenger RNA (rpsO mRNA) and stabilizing a pseudoknot structure at the upstream untranslated region, thus trapping the ribosome into an incomplete translation initiation complex. In the absence of S15, ribosomal protein S1 recognizes rpsO and promotes translation by melting this very pseudoknot...
April 21, 2018: Proteins
https://www.readbyqxmd.com/read/29679251/repressible-transgenic-sterilization-in-channel-catfish-ictalurus-punctatus-by-knockdown-of-primordial-germ-cell-genes-with-copper-sensitive-constructs
#7
Hanbo Li, Baofeng Su, Guyu Qin, Zhi Ye, Ahmed Elaswad, Ahmed Alsaqufi, Dayan A Perera, Zhenkui Qin, Ramji Odin, Khoi Vo, David Drescher, Dalton Robinson, Sheng Dong, Dan Zhang, Mei Shang, Nermeen Abass, Sanjay K Das, Max Bangs, Rex A Dunham
Repressible knockdown approaches were investigated to manipulate for transgenic sterilization in channel catfish, Ictalurus punctatus. Two primordial germ cell (PGC) marker genes, nanos and dead end, were targeted for knockdown and an off-target gene, vasa, was monitored. Two potentially copper-sensitive repressible promoters, yeast ctr3 (M) and ctr3-reduced (Mctr), were coupled with four knockdown strategies separately including: ds-sh RNA targeting the 5' end (N1) or 3' end (N2) of channel catfish nanos, full-length cDNA sequence of channel catfish nanos for overexpression (cDNA), and ds-sh RNA-targeting channel catfish dead end (DND)...
April 20, 2018: Marine Biotechnology
https://www.readbyqxmd.com/read/29679239/comparative-analysis-of-the-root-transcriptomes-of-cultivated-and-wild-rice-varieties-in-response-to-magnaporthe-oryzae-infection-revealed-both-common-and-species-specific-pathogen-responses
#8
Lei Tian, Shaohua Shi, Fahad Nasir, Chunling Chang, Weiqiang Li, Lam-Son Phan Tran, Chunjie Tian
BACKGROUND: Magnaporthe oryzae, the causal fungus of rice blast disease, negatively impacts global rice production. Wild rice (Oryza rufipogon), a relative of cultivated rice (O. sativa), possesses unique attributes that enable it to resist pathogen invasion. Although wild rice represents a major resource for disease resistance, relative to current cultivated rice varieties, no prior studies have compared the immune and transcriptional responses in the roots of wild and cultivated rice to M...
April 20, 2018: Rice
https://www.readbyqxmd.com/read/29679055/towards-annotating-the-plant-epigenome-the-arabidopsis-thaliana-small-rna-locus-map
#9
Thomas J Hardcastle, Sebastian Y Müller, David C Baulcombe
Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29678912/characterizing-the-ecology-of-vibrio-in-the-neuse-river-estuary-north-carolina-using-heat-shock-protein-60-hsp60-next-generation-amplicon-sequencing
#10
Kelsey J Jesser, Rachel T Noble
Of marine eubacteria, the genus Vibrio is intriguing because member species are relevant to both marine ecology and human health. Many have touted the relationships of Vibrio to environmental factors, especially temperature and salinity, to predict total Vibrio abundance, but these studies lacked the taxonomic resolution to identify relationships among species and key drivers of Vibrio dynamics. In order to improve NGS surveys of Vibrio, we have conducted both 16S small subunit ribosomal RNA (rRNA) and heat shock protein 60 ( hsp60 ) amplicon sequencing of water samples collected at two well-studied locations in the Neuse River Estuary, NC...
April 20, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29678725/cloning-and-characterization-of-a-second-lamprey-pituitary-glycoprotein-hormone-thyrostimulin-gpa2-gpb5
#11
Krist N Hausken, Belen Tizo, Michal Shpilman, Shannon Barton, Wayne Decatur, David Plachetzki, Scott Kavanaugh, Sabah Ul-Hasan, Berta Levavi-Sivan, Stacia A Sower
A novel heterodimeric glycoprotein hormone (GpH) comprised of alpha (GpA2) and beta (GpB5) subunits was discovered in 2002 and called thyrostimulin for its ability to activate the TSH receptor in mammals, but its central function in vertebrates has not been firmly established. We report here the cloning and expression of lamprey (l)GpB5, and its ability to heterodimerize with lGpA2 to form a functional l-thyrostimulin. The full-length cDNA of lGpB5 encodes 174 amino acids with ten conserved cysteine residues and one glycosylation site that is conserved with other vertebrate GpB5 sequences...
April 17, 2018: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/29678692/nucpospred-predicting-species-specific-genomic-nucleosome-positionin-g-via-four-different-modes-of-general-pseknc
#12
Cangzhi Jia, Qing Yang, Quan Zou
The nucleosome is the basic structure of chromatin in eukaryotic cells, with essential roles in the regulation of many biological processes, such as DNA transcription, replication and repair, and RNA splicing. Because of the importance of nucleosomes, the factors that determine their positioning within genomes should be investigated. High-resolution nucleosome-positioning maps are now available for organisms including Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans, enabling the identification of nucleosome positioning by application of computational tools...
April 17, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29678584/genome-wide-profiles-of-metastasis-associated-mrnas-and-micrornas-in-salivary-adenoid-cystic-carcinoma
#13
Shubin Wang, Lei Zhang, Pengwei Shi, Yuanyuan Zhang, Hong Zhou, Xuanping Cao
Salivary adenoid cystic carcinoma (SACC) is often accompanied with poor prognosis due to local recurrence, distant metastasis, and perineural invasion. The mechanism involved in SACC metastasis is not yet fully understood. In this study, we profiled the expression of messenger RNA (mRNA) and microRNA (miRNA) in an SACC cell line, ACC-2, and a highly metastatic SACC cell line, ACC-M, using high-throughput sequencing. We discovered that: (1) differentially expressed (DE) mRNAs and DE miRNAs are potentially involved in SACC metastasis; (2) multiple regulatory interactions between DE miRNAs and DE mRNAs exist; and (3) miR-338-5p/3p target LAMC2 to impair motility and invasion of ACC-M and MDA-MB-231 cells...
April 17, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29678567/germ-cell-specific-apoptosis-by-extracellular-clusterin-in-cryptorchid-dog-testes
#14
Hyunjhung Jhun, Hyun-Jung Park, Ran Lee, Hyuk Song, Tai-Young Hur, Seunghoon Lee, Jin-Ki Park, Won-Young Lee
Mammalian testes are maintained at a relatively lesser temperature than the abdominal region so that normal spermatogenesis can occur. Germ cell apoptosis has resulted in heat-damaged testes that occurs as a result of cryptorchidism, but the mechanism is not yet fully understood. To elucidate the cause of germ-cell death by cryptorchidism, cryptorchidism was surgically induced in dog testes and histological and molecular analyses were performed. Histological data indicated that the seminiferous tubules of cryptorchid testes and epididymis contained fewer germ cells...
April 13, 2018: Animal Reproduction Science
https://www.readbyqxmd.com/read/29678492/hmga1a-induces-alternative-splicing-of-estrogen-receptor-alpha-in-mcf-7-human-breast-cancer-cells
#15
Kenji Ohe, Shinsuke Miyajima, Tomoko Tanaka, Yuriko Hamaguchi, Yoshihiro Harada, Yuta Horita, Yuki Beppu, Fumiaki Ito, Takafumi Yamasaki, Hiroki Terai, Masayoshi Mori, Yusuke Murata, Makito Tanabe, Kenji Ashida, Munechika Enjoji, Toshihiko Yanase, Nobuhiro Harada, Toshiaki Utsumi, Akila Mayeda
The high-mobility group A protein 1a (HMGA1a) protein is known as an oncogene whose expression level in cancer tissue correlates with the malignant potential, and known as a component of senescence-related structures connecting it to tumor suppressor networks in fibroblasts. HMGA1 protein binds to DNA, but recent studies have shown it exerts novel functions through RNA-binding. Our previous studies have shown that sequence-specific RNA-binding of HMGA1a induces exon-skipping of Presenilin-2 exon 5 in sporadic Alzheimer disease...
April 17, 2018: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29677513/nuclear-import-receptor-inhibits-phase-separation-of-fus-through-binding-to-multiple-sites
#16
Takuya Yoshizawa, Rustam Ali, Jenny Jiou, Ho Yee Joyce Fung, Kathleen A Burke, Seung Joong Kim, Yuan Lin, William B Peeples, Daniel Saltzberg, Michael Soniat, Jordan M Baumhardt, Rudolf Oldenbourg, Andrej Sali, Nicolas L Fawzi, Michael K Rosen, Yuh Min Chook
Liquid-liquid phase separation (LLPS) is believed to underlie formation of biomolecular condensates, cellular compartments that concentrate macromolecules without surrounding membranes. Physical mechanisms that control condensate formation/dissolution are poorly understood. The RNA-binding protein fused in sarcoma (FUS) undergoes LLPS in vitro and associates with condensates in cells. We show that the importin karyopherin-β2/transportin-1 inhibits LLPS of FUS. This activity depends on tight binding of karyopherin-β2 to the C-terminal proline-tyrosine nuclear localization signal (PY-NLS) of FUS...
April 19, 2018: Cell
https://www.readbyqxmd.com/read/29677213/ifn-%C3%AE-and-micrornas-are-important-modulators-of-the-pulmonary-innate-immune-response-against-influenza-a-h1n2-infection-in-pigs
#17
Louise Brogaard, Lars E Larsen, Peter M H Heegaard, Christian Anthon, Jan Gorodkin, Ralf Dürrwald, Kerstin Skovgaard
The innate immune system is paramount in the response to and clearance of influenza A virus (IAV) infection in non-immune individuals. Known factors include type I and III interferons and antiviral pathogen recognition receptors, and the cascades of antiviral and pro- and anti-inflammatory gene expression they induce. MicroRNAs (miRNAs) are increasingly recognized to participate in post-transcriptional modulation of these responses, but the temporal dynamics of how these players of the antiviral innate immune response collaborate to combat infection remain poorly characterized...
2018: PloS One
https://www.readbyqxmd.com/read/29677157/molecular-characterization-and-the-function-of-argonaute3-in-rnai-pathway-of-plutella-xylostella
#18
Muhammad Salman Hameed, Zhengbing Wang, Liette Vasseur, Guang Yang
Argonaute (Ago) protein family plays a key role in the RNA interference (RNAi) process in different insects including Lepidopteran. However, the role of Ago proteins in the RNAi pathway of Plutella xylostella is still unknown. We cloned an Argonaute3 gene in P. xylostella ( PxAgo3 ) with the complete coding sequence of 2832 bp. The encoded protein had 935 amino acids with an expected molecular weight of 108.9 kDa and an isoelectric point of 9.29. It contained a PAZ (PIWI/Argonaute/Zwile) domain and PIWI (P-element-induced whimpy testes) domain...
April 20, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29677136/cytoplasmic-translocation-of-nucleolar-protein-nop53-promotes-viral-replication-by-suppressing-host-defense
#19
Wen Meng, Shi-Chong Han, Cui-Cui Li, Hui-Jun Dong, Jian-Yu Chang, Hwa-Chain Robert Wang, Xiao-Jia Wang
NOP53 is a tumor suppressor protein located in the nucleolus and is translocated to the cytoplasm during infection by vesicular stomatitis virus (VSV) and herpes simplex virus type 1 (HSV-1), as shown in our previous study. Cytoplasmic NOP53 interacts with the retinoic acid-inducible gene I (RIG-I) to remove its K63-linked ubiquitination, leading to attenuation of type I interferon IFN-β. In the present study, we found no obvious translocation of NOP53 in infection by a mutant virus lacking ICP4 (HSV-1/d120, replication inadequate)...
April 20, 2018: Viruses
https://www.readbyqxmd.com/read/29676772/functional-roles-of-eriocalyxin-b-in-zebrafish-revealed-by-transcriptome-analysis
#20
Xunian Zhou, Cyanne Ye Cao, Angel Tsz-Yau Wan, Grace Gar-Lee Yue, Frankie Hin-Fai Kwok, Kwok-Pui Fung, Handong Sun, Clara Bik-San Lau, Pema-Tenzin Puno, Stephen Kwok-Wing Tsui
BACKGROUND: Eriocalyxin B (EriB) is a natural ent-kaurane diterpenoid obtained from Isodon eriocalyx var. laxiflora (family Lamiaceae), which has multiple biological activities (e.g. anti-tumor and anti-inflammatory) via the alteration of gene expression and signaling transduction. Recently, RNA sequencing (RNA-seq) has been developed as a dynamic transcriptome approach to analyze the transcriptional profile and in addition use such gene expression profiles to identify novel candidate genes in a zebrafish model...
April 20, 2018: Molecular omics
keyword
keyword
60921
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"