keyword
MENU ▼
Read by QxMD icon Read
search

RNA sequencing

keyword
https://www.readbyqxmd.com/read/28231302/bioinformatic-prediction-of-g-protein-coupled-receptor-encoding-sequences-from-the-transcriptome-of-the-foreleg-including-the-haller-s-organ-of-the-cattle-tick-rhipicephalus-australis
#1
Sergio Munoz, Felix D Guerrero, Anastasia Kellogg, Andrew M Heekin, Ming-Ying Leung
The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. The Haller's organ, located in the tick's forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we aimed to sequence and annotate the transcriptome of the R. australis forelegs and associated tissues, including the Haller's organ. As G protein-coupled receptors (GPCRs) are an important family of eukaryotic proteins studied as pharmaceutical targets in humans, we prioritized the identification and classification of the GPCRs expressed in the foreleg tissues...
2017: PloS One
https://www.readbyqxmd.com/read/28231257/targeted-sequencing-identifies-a-novel-sh2d1a-pathogenic-variant-in-a-chinese-family-carrier-screening-and-prenatal-genetic-testing
#2
Jun-Yu Zhang, Song-Chang Chen, Yi-Yao Chen, Shu-Yuan Li, Lan-Lan Zhang, Ying-Hua Shen, Chun-Xin Chang, Yu-Qian Xiang, He-Feng Huang, Chen-Ming Xu
X-linked lymphoproliferative disease type 1 (XLP1) is a rare primary immunodeficiency characterized by a clinical triad consisting of severe EBV-induced hemophagocytic lymphohistiocytosis, B-cell lymphoma, and dysgammaglobulinemia. Mutations in SH2D1A gene have been revealed as the cause of XLP1. In this study, a pregnant woman with recurrence history of birthing immunodeficiency was screened for pathogenic variant because the proband sample was unavailable. We aimed to clarify the genetic diagnosis and provide prenatal testing for the family...
2017: PloS One
https://www.readbyqxmd.com/read/28230851/using-hiclip-to-identify-rna-duplexes-that-interact-with-a-specific-rna-binding-protein
#3
Yoichiro Sugimoto, Anob M Chakrabarti, Nicholas M Luscombe, Jernej Ule
The structure of RNA molecules has a critical role in regulating gene expression, largely through influencing their interactions with RNA-binding proteins (RBPs). RNA hybrid and individual-nucleotide resolution UV cross-linking and immunoprecipitation (hiCLIP) is a transcriptome-wide method of monitoring these interactions by identifying RNA duplexes bound by a specific RBP. The hiCLIP protocol consists of the following steps: in vivo cross-linking of RBPs to their bound RNAs; partial RNA digestion and purification of RNA duplexes interacting with the specific RBP using immunoprecipitation; ligation of the two arms of RNA duplexes via a linker; reverse transcription; cDNA library amplification; and finally high-throughput DNA sequencing...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28230789/fungal-ribotoxins-a-review-of-potential-biotechnological-applications
#4
REVIEW
Miriam Olombrada, Rodrigo Lázaro-Gorines, Juan C López-Rodríguez, Álvaro Martínez-Del-Pozo, Mercedes Oñaderra, Moisés Maestro-López, Javier Lacadena, José G Gavilanes, Lucía García-Ortega
Fungi establish a complex network of biological interactions with other organisms in nature. In many cases, these involve the production of toxins for survival or colonization purposes. Among these toxins, ribotoxins stand out as promising candidates for their use in biotechnological applications. They constitute a group of highly specific extracellular ribonucleases that target a universally conserved sequence of RNA in the ribosome, the sarcin-ricin loop. The detailed molecular study of this family of toxic proteins over the past decades has highlighted their potential in applied research...
February 21, 2017: Toxins
https://www.readbyqxmd.com/read/28230734/deep%C3%A2-transcriptome%C3%A2-sequencing%C3%A2-of%C3%A2-two%C3%A2-green%C3%A2-algae-chara%C3%A2-vulgaris%C3%A2-and%C3%A2-chlamydomonas%C3%A2-reinhardtii-%C3%A2-provides%C3%A2-no%C3%A2-evidence%C3%A2-of%C3%A2-organellar%C3%A2-rna%C3%A2-editing
#5
A Bruce Cahoon, John A Nauss, Conner D Stanley, Ali Qureshi
Nearly all land plants post-transcriptionally modify specific nucleotides within RNAs, a process known as RNA editing. This adaptation allows the correction of deleterious mutations within the asexually reproducing and presumably non-recombinant chloroplast and mitochondrial genomes. There are no reports of RNA editing in any of the green algae so this phenomenon is presumed to have originated in embryophytes either after the invasion of land or in the now extinct algal ancestor of all land plants. This was challenged when a recent in silico screen for RNA edit sites based on genomic sequence homology predicted edit sites in the green alga Chara vulgaris, a multicellular alga found within the Streptophyta clade and one of the closest extant algal relatives of land plants...
February 20, 2017: Genes
https://www.readbyqxmd.com/read/28229366/mining-cancer-transcriptomes-bioinformatic-tools-and-the-remaining-challenges
#6
Thomas Milan, Brian T Wilhelm
The development of next-generation sequencing technologies has had a profound impact on the field of cancer genomics. With the enormous quantities of data being generated from tumor samples, researchers have had to rapidly adapt tools or develop new ones to analyse the raw data to maximize its value. While much of this effort has been focused on improving specific algorithms to get faster and more precise results, the accessibility of the final data for the research community remains a significant problem. Large amounts of data exist but are not easily available to researchers who lack the resources and experience to download and reanalyze them...
February 22, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28229336/relevant-principal-factors-affecting-the-reproducibility-of-insect-primary-culture
#7
Norichika Ogata, Kikuo Iwabuchi
The primary culture of insect cells often suffers from problems with poor reproducibility in the quality of the final cell preparations. The cellular composition of the explants (cell number and cell types), surgical methods (surgical duration and surgical isolation), and physiological and genetic differences between donors may be critical factors affecting the reproducibility of culture. However, little is known about where biological variation (interindividual differences between donors) ends and technical variation (variance in replication of culture conditions) begins...
February 22, 2017: In Vitro Cellular & Developmental Biology. Animal
https://www.readbyqxmd.com/read/28229213/development-of-a-rapid-identification-method-for-the-differentiation-of-enterococcus-species-using-a-species-specific-multiplex-pcr-based-on-comparative-genomics
#8
Jongbin Park, Gwi-Deuk Jin, Jae In Pak, Jihyun Won, Eun Bae Kim
Enterococci are lactic acid bacteria that are commonly found in food and in animal gut. Since 16 S ribosomal RNA (rRNA) sequences, genetic markers for bacterial identification, are similar among several Enterococcus species, it is very difficult to determine the correct species based on only 16 S rRNA sequences. Therefore, we developed a rapid method for the identification of different Enterococcus species using comparative genomics. We compared 38 genomes of 13 Enterococcus species retrieved from the National Center of Biotechnology Information database and identified 25,623 orthologs...
February 22, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28229116/short-and-long-term-changes-in-sugarbeet-beta-vulgaris-l-gene-expression-due-to-postharvest-jasmonic-acid-treatment-data
#9
Lucilene Silva de Oliveira, Karen Klotz Fugate, Jocleita Perruzo Ferrareze, Melvin D Bolton, Edward L Deckard, Fernando L Finger
Jasmonic acid is a natural plant hormone that induces native defense responses in plants. Sugarbeet (Beta vulgaris L.) root unigenes that were differentially expressed 2 and 60 days after a postharvest jasmonic acid treatment are presented. Data include changes in unigene expression relative to water-treated controls, unigene annotations against nonredundant (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) protein databases, and unigene annotations with Gene Ontology (GO) terms...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28228849/considerations-and-complications-of-mapping-small-rna-high-throughput-data-to-transposable-elements
#10
Alexandros Bousios, Brandon S Gaut, Nikos Darzentas
BACKGROUND: High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), or when such genomes are large, as is often the case in plants...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28228764/de-novo-transcriptome-assembly-of-chinese-kale-and-global-expression-analysis-of-genes-involved-in-glucosinolate-metabolism-in-multiple-tissues
#11
Shuanghua Wu, Jianjun Lei, Guoju Chen, Hancai Chen, Bihao Cao, Changming Chen
Chinese kale, a vegetable of the cruciferous family, is a popular crop in southern China and Southeast Asia due to its high glucosinolate content and nutritional qualities. However, there is little research on the molecular genetics and genes involved in glucosinolate metabolism and its regulation in Chinese kale. In this study, we sequenced and characterized the transcriptomes and expression profiles of genes expressed in 11 tissues of Chinese kale. A total of 216 million 150-bp clean reads were generated using RNA-sequencing technology...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28228611/anti-diabetic-action-of-all-trans-retinoic-acid-and-the-orphan-g-protein-coupled-receptor-gprc5c-in-pancreatic-%C3%AE-cells
#12
Stefan Amisten, Israa Mohammad Al-Amily, Arvind Soni, Ross Hawkes, Patricio Atanes, Shanta Jean Persaud, Patrik Rorsman, Albert Salehi
Pancreatic islets express high levels of the orphan G-protein coupled receptor C5C (GPRC5C), the function of which remains to be established. Here we have examined the role of GPRC5C in the regulation of insulin secretion and β-cell survival and proliferation using human and mouse pancreatic islets. The expression of GPRC5C was analysed by RNA-sequencing, qPCR, western blotting and confocal microscopy. Insulin secretion and cell viability were determined by RIA and MTS assays, respectively. GPRC5C mRNA expression and protein level were reduced in the islets from type-2 diabetic donors...
February 22, 2017: Endocrine Journal
https://www.readbyqxmd.com/read/28228493/hepatitis-e-virus-detection-and-quantification-by-an-rt-qpcr-assay-calibrated-to-the-world-health-organization-standard-for-hev-rna
#13
Jeffrey J Germer, Irina Ankoudinova, Yevgeniy S Belousov, Walt Mahoney, Chen Dong, Jihong Meng, Jayawant N Mandrekar, Joseph D Yao
Hepatitis E virus (HEV) has emerged as a cause of chronic hepatitis among immunocompromised patients. Molecular assays have become important tools for the diagnosis and management of these chronically-infected patients. A reverse transcription, real-time PCR (RT-qPCR) assay utilizing Pleiades probe chemistry and an RNA internal control for simultaneous detection and quantification of HEV RNA in human serum was developed based on adaptation of a previously described and broadly reactive primer set targeting the overlapping open reading frame (ORF) 2/3 nucleotide sequence of HEV...
February 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28228255/can1-arginine-permease-deficiency-extends-yeast-replicative-lifespan-via-translational-activation-of-stress-response-genes
#14
Carine Beaupere, Brian M Wasko, Jared Lorusso, Brian K Kennedy, Matt Kaeberlein, Vyacheslav M Labunskyy
Transcriptional regulation plays an important role in the control of gene expression during aging. However, translation efficiency likely plays an equally important role in determining protein abundance, but it has been relatively understudied in this context. Here, we used RNA sequencing (RNA-seq) and ribosome profiling to investigate the role of translational regulation in lifespan extension by CAN1 gene deletion in yeast. Through comparison of the transcriptional and translational changes in cells lacking CAN1 with other long-lived mutants, we were able to identify critical regulatory factors, including transcription factors and mRNA-binding proteins, that coordinate transcriptional and translational responses...
February 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28228215/hnrnpk-regulated-ptov1-as1-modulates-heme-oxygenase-1-expression-via-mir-1207-5p
#15
Chang Hoon Shin, Seongho Ryu, Hyeon Ho Kim
Antisense transcripts were initially identified as transcriptional noise, but have since been reported to play an important role in the quality control of miRNA functions. In this report, we tested the hypothesis that hnRNPK regulates miRNA function via competitive endogenous RNAs, such as pseudogenes, long non-coding RNAs, and antisense transcripts. Based on analyses of RNA sequencing data, the knockdown of hnRNPK decreased antisense PTOV1-AS1 transcript, which harbors five binding sites for miR-1207-5p. We identified heme oxygenase-1 (HO-1) mRNA as a novel target of miR-1207-5p by western blotting and Ago2 immunoprecipitation...
February 23, 2017: BMB Reports
https://www.readbyqxmd.com/read/28228093/comparative-profiling-of-hepatopancreas-transcriptomes-in-satiated-and-starving-pomacea-canaliculata
#16
Lei Yang, Tian-Yin Cheng, Fei-Yan Zhao
BACKGROUND: Although Pomacea canaliculata is native to South and Central America, it has become one of the most abundant invasive species worldwide and causes extensive damage to agriculture and horticulture. Conventional physical and chemical techniques have been used to eliminate P. canaliculata, but the effects are not ideal. Therefore, it is important to devise a new method based on a greater understanding of the biology of P. canaliculata. However, the molecular mechanisms underlying digestion and absorption in P...
February 22, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28228091/exploring-the-transcriptome-of-non-model-oleaginous-microalga-dunaliella-tertiolecta-through-high-throughput-sequencing-and-high-performance-computing
#17
Lina Yao, Kenneth Wei Min Tan, Tin Wee Tan, Yuan Kun Lee
BACKGROUND: RNA-Seq technology has received a lot of attention in recent years for microalgal global transcriptomic profiling. It is widely used in transcriptome-wide analysis of gene expression., particularly for microalgal strains with potential as biofuel sources. However, insufficient genomic or transcriptomic information of non-model microalgae has limited the understanding of their regulatory mechanisms and hampered genetic manipulation to enhance biofuel production. As such, an optimal microalgal transcriptomic database construction is a subject of urgent investigation...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28227013/pan-cancer-analysis-for-studying-cancer-stage-using-protein-and-gene-expression-data
#18
Sameer Mishra, Chanchala D Kaddi, May D Wang, Sameer Mishra, Chanchala D Kaddi, May D Wang, Sameer Mishra, Chanchala D Kaddi, May D Wang
Pan-cancer analyses attempt to discover similar features among multiple cancers to identify fundamental patterns common to cancer development and progression. A pan-cancer analysis integrating both protein expression and transcriptomic data is important because it can identify genes that are linked to proteins potentially responsible for a patient's status. This study aims to identify differentially expressed (DE) genes between early and advanced cases of multiple cancer types through the usage of RNA sequencing data...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226240/position-and-hippo-signaling-dependent-plasticityduring-lineage-segregation-in-the-early-mouse-embryo
#19
Eszter Posfai, Sophie Petropoulos, Flavia Ro de Barros, John Paul Schell, Igor Jurisica, Rickard Sandberg, Fredrik Lanner, Janet Rossant
The segregation of the trophectoderm (TE) from the inner cell mass (ICM) in the mouse blastocyst is determined by position-dependent Hippo signaling. However, the window of responsiveness to Hippo signaling, the exact timing of lineage commitment and the overall relationship between cell commitment and global gene expression changes are still unclear. Single-cell RNA sequencing during lineage segregation revealed that the TE transcriptional profile stabilizes earlier than the ICM and prior to blastocyst formation...
February 22, 2017: ELife
https://www.readbyqxmd.com/read/28225830/ex-vivo-activation-of-cd4-t-cells-from-donors-on-suppressive-art-can-lead-to-sustained-production-of-infectious-hiv-1-from-a-subset-of-infected-cells
#20
John K Bui, Elias K Halvas, Elizabeth Fyne, Michele D Sobolewski, Dianna Koontz, Wei Shao, Brian Luke, Feiyu F Hong, Mary F Kearney, John W Mellors
The fate of HIV-infected cells after reversal of proviral latency is not well characterized. Simonetti, et al. recently showed that CD4+ T-cells containing intact proviruses can clonally expand in vivo and produce low-level infectious viremia. We hypothesized that reversal of HIV latency by activation of CD4+ T-cells can lead to the expansion of a subset of virus-producing cells rather than their elimination. We established an ex vivo cell culture system involving stimulation of CD4+ T-cells from donors on suppressive antiretroviral therapy (ART) with PMA/ionomycin (day 1-7), followed by rest (day 7-21), and then repeat stimulation (day 21-28), always in the presence of high concentrations of raltegravir and efavirenz to effectively block new cycles of viral replication...
February 22, 2017: PLoS Pathogens
keyword
keyword
38600
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"