keyword
MENU ▼
Read by QxMD icon Read
search

RNA profile

keyword
https://www.readbyqxmd.com/read/29792950/transcriptome-profile-analysis-reveals-the-ontogenesis-of-rooted-chichi-in-ginkgo-biloba-l
#1
Xiaojing Liu, Limin Sun, Qikui Wu, Xiaoyan Men, Linmei Yao, Shiyan Xing
The Ginkgo biloba L. chichi is a unique organ. To explore the molecular mechanisms underlying the ontogenesis of G. biloba chichi, we used RNA-seq to analyse the transcriptome profile of rooted chichi at two developmental stages (ch1 and ch2) and nearby tissues (ck), and each sample had three biological replicates. A total of 57.74 Gb of clean bases were generated in nine cDNA libraries. These bases were de novo assembled into 68,277 unigenes with average length of 844 bp, and 51.47% of the unigenes had a match in at least one public database...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29792949/srnaome-and-transcriptome-analysis-provide-insight-into-chilling-response-of-cowpea-pods
#2
Jinhua Zuo, Yunxiang Wang, Benzhong Zhu, Yunbo Luo, Qing Wang, Lipu Gao
Cowpea is an important horticultural crop in tropical and subtropical areas of Asia, Africa, and Latin America, as well as parts of southern Europe and Central and South America. Chilling injury is a common physiological hazard of cowpea in cold chain logistics which reduce the cowpea pod's nutritional quality and product value. However, the molecular mechanism involved in chilling injury remains unclear in cowpea pods. RNA-Seq and sRNA-Seq technologies were employed to decipher the miRNAs and mRNAs expression profiles and their regulatory networks in cowpea pods involved in chilling stress...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29792762/genetic-profiling-in-acute-myeloid-leukemia-a-path-to-predicting-treatment-outcome
#3
Giuseppe Visani, Federica Loscocco, Alessandro Isidori, Pier Paolo Piccaluga
Despite substantial progresses in acute myeloid leukemia (AML) diagnosis and treatment, at least half of patient will eventually die for the disease. In the last decades, the use of genetic and genomic approaches allowed the identification of patients with higher risk of recurrence after and/or resistance to CHT. However, though many novel drugs have been proposed and tested, only little clinical improvements have been made concerning the treatment of the so called 'high risk' patients. Areas covered: In this article, the authors, based on their own experience and the most updated literature, review the basic knowledge of AML prognostication and treatment prediction developed throughout genetic and genomic profiling, and focus on the use of gene expression profiling as a promising predictive tool...
May 24, 2018: Expert Review of Hematology
https://www.readbyqxmd.com/read/29791589/non-invasive-messenger-rna-transcriptional-evaluation-in-human-kidney-allograft-dysfunction
#4
G Joelsons, T Domenico, L F Gonçalves, R C Manfro
The aim of the present study was to evaluate messenger RNA expression in kidney allograft recipients. Forty-four kidney transplant recipients were evaluated up to three months after grafting. After transplantation, peripheral blood samples were drawn sequentially for real-time polymerase chain reaction analyses of perforin and TIM-3 genes. Biopsies were obtained to evaluate acute graft dysfunction and interpreted according to the Banff classification. Eight patients presented episodes of acute rejection. Recipients with rejection had significantly higher levels of TIM-3 mRNA transcripts compared to those without rejection (median gene expression 191...
2018: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/29790987/structural-accommodations-accompanying-splicing-of-a-group-ii-intron-rnp
#5
Xiaolong Dong, Srivathsan Ranganathan, Guosheng Qu, Carol Lyn Piazza, Marlene Belfort
Group II introns, the putative progenitors of spliceosomal introns and retrotransposons, are ribozymes that are capable of self-splicing and DNA invasion. In the cell, group II introns form ribonucleoprotein (RNP) complexes with an intron-encoded protein, which is essential to folding, splicing and retromobility of the intron. To understand the structural accommodations underlying splicing, in preparation for retromobility, we probed the endogenously expressed Lactococcus lactis Ll.LtrB group II intron RNP using SHAPE...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29790929/mir172-downregulates-the-translation-of-cleistogamy-1-in-barley
#6
Nadia Anwar, Masaru Ohta, Takayuki Yazawa, Yutaka Sato, Chao Li, Akemi Tagiri, Mari Sakuma, Thomas Nussbaumer, Phil Bregitzer, Mohammad Pourkheirandish, Jianzhong Wu, Takao Komatsuda
Background and Aims: Floret opening in barley is induced by the swelling of the lodicule, a trait under the control of the cleistogamy1 (cly1) gene. The product of cly1 is a member of the APETALA2 (AP2) transcription factor family, which inhibits lodicule development. A sequence polymorphism at the miR172 target site within cly1 has been associated with variation in lodicule development and hence with the cleistogamous phenotype. It was unclear whether miR172 actually functions in cly1 regulation and, if it does, which miR172 gene contributes to cleistogamy...
May 22, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29789704/single-cell-rna-sequencing-for-the-study-of-development-physiology-and-disease
#7
REVIEW
S Steven Potter
An ongoing technological revolution is continually improving our ability to carry out very high-resolution studies of gene expression patterns. Current technology enables the global gene expression profiles of single cells to be defined, facilitating dissection of heterogeneity in cell populations that was previously hidden. In contrast to gene expression studies that use bulk RNA samples and provide only a virtual average of the diverse constituent cells, single-cell studies enable the molecular distinction of all cell types within a complex population mix, such as a tumour or developing organ...
May 22, 2018: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/29789577/long-non-coding-rna-gm2199-rescues-liver-injury-and-promotes-hepatocyte-proliferation-through-the-upregulation-of-erk1-2
#8
Qiang Gao, Yunyan Gu, Yanan Jiang, Li Fan, Zixiang Wei, Haobin Jin, Xirui Yang, Lijuan Wang, Xuguang Li, Sheng Tai, Baofeng Yang, Yan Liu
Long non-coding RNAs (lncRNAs) are a new class of regulators of various human diseases. This study was designed to explore the potential role of lncRNAs in experimental hepatic damage. In vivo hepatic damage in mice and in vitro hepatocyte damage in AML12 and NCTC1469 cells were induced by carbon tetrachloride (CCl4 ) treatments. Expression profiles of lncRNAs and mRNAs were analyzed by microarray. Bioinformatics analyses were conducted to predict the potential functions of differentially expressed lncRNAs with respect to hepatic damage...
May 22, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29789409/characterization-of-an-activating-r1353h-insulin-like-growth-factor-1-receptor-variant-in-a-male-with-extreme-tall-height
#9
Yingbo Lin, Hermine A van Duyvenvoorde, Hong Liu, Chen Yang, Dudi Warsito, Chang Yin, Sarina G Kant, Felix Haglund, Jan M Wit, Olle Larsson
OBJECTIVE: The Insulin-like growth factor 1 receptor (IGF-1R) is important in growth and development, and inactivating IGF1R mutations cause short stature and relatively high levels of serum IGF-I. We identified an unclassified IGF1R R1353H variant in a male with extreme tall height, very low levels of serum IGF-I and delayed and prolonged growth spurt. The index case's mother and three sons all carried the variant, but so far only the eldest son (age 18) presented with tall height. We hypothesized that the variant could constitute an activating mutation...
May 22, 2018: European Journal of Endocrinology
https://www.readbyqxmd.com/read/29788408/effects-of-4-hydroxy-2-3-3-4-5-pentachlorobiphenyl-4-oh-cb107-on-liver-transcriptome-in-rats-implication-in-the-disruption-of-circadian-rhythm-and-fatty-acid-metabolism
#10
Mari Ochiai, Midori Iida, Tetsuro Agusa, Kohki Takaguchi, Satoshi Fujiic, Kei Nomiyama, Hisato Iwata
Polychlorinated biphenyls (PCBs) and their hydroxylated metabolites (OH-PCBs) have been detected in tissues of both wild animals and humans. Several previous studies have suggested adverse effects of OH-PCBs on the endocrine and nervous systems in mammals. However, there have been no studies on transcriptome analysis of the effects of OH-PCBs, and thus, the whole picture and mechanisms underlying the adverse effects induced by OH-PCBs are still poorly understood. We therefore investigated the mRNA expression profile in the liver of adult male Wistar rats treated with 4-hydroxy-2,3,3',4',5-pentachlorobiphenyl (4-OH-CB107) to explore the genes responsive to OH-PCBs and to understand the potential effects of the chemical...
May 21, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29787824/discovery-and-expression-analysis-of-novel-transcripts-of-the-human-sr-related-ctd-associated-factor-1-scaf1-gene-in-human-cancer-cells-using-next-generation-sequencing
#11
Panagiotis G Adamopoulos, Georgios D Raptis, Christos K Kontos, Andreas Scorilas
The human SR-related CTD associated factor 1 (SCAF1) gene is a new member of the human SR (Ser/Arg-rich) superfamily of pre-mRNA splicing factors, which has been discovered and cloned by members of our lab. SCAF1 interacts with the CTD domain of the RNA polymerase II polypeptide A and is firmly involved in pre-mRNA splicing. Although it was found to be expressed widely in multiple human tissues, its mRNA levels vary a lot. The significant relation of SCAF1 with cancer has been confirmed by many studies, since SCAF1 mRNA transcript was found to be overexpressed in breast and ovarian tumors, confirming its significant prognostic value as a cancer biomarker in both these human malignancies...
May 19, 2018: Gene
https://www.readbyqxmd.com/read/29787779/stichodactyla-helianthus-de-novo-transcriptome-assembly-discovery-of-a-new-actinoporin-isoform
#12
Esperanza Rivera-de-Torre, Álvaro Martínez-Del-Pozo, Jessica E Garb
Transcriptomic profiling of venom producing tissues from different animals is an effective approach for discovering new toxins useful in biotechnological and pharmaceutical applications, as well in evolutionary comparative studies of venomous animals. Stichodactyla helianthus is a Caribbean sea anemone which produces actinoporins as part of its toxic venom. This family of pore forming toxins is multigenic and at least two different isoforms, encoded by separate genes, are produced by S. helianthus. These isoforms, sticholysins I and II, share 93% amino acid identity but differ in their pore forming activity and act synergistically...
May 19, 2018: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/29787577/analysis-of-micrornas-in-familial-mediterranean-fever
#13
Gil Amarilyo, Nir Pillar, Ilan Ben-Zvi, Daphna Weissglas-Volkov, Jonatan Zalcman, Liora Harel, Avi Livneh, Noam Shomron
OBJECTIVES: Although Familial Mediterranean fever (FMF) is categorized as autosomal recessive, frequent exceptions to this model exist and therefore we aimed to search epigenetic modifications in this disease. METHODS: Ten M694V homozygous FMF patients (the most severe phenotype) were recruited for this study. Patients with inflammatory flare were excluded. Total RNA was extracted from peripheral blood, and microRNA expression profiled using NanoString nCounter technology...
2018: PloS One
https://www.readbyqxmd.com/read/29787292/signature-microrna-expression-profile-is-associated-with-spontaneous-hypertension-in-african-green-monkey
#14
Xiaojun Zhou, Jin Wang, Yunzhi Fa, Huahu Ye
Chlorocebus aethiops sabaeus, the African Green monkey (AGM), has been proved to exhibit renal vascular remodeling and spontaneous hypertension. However, little is known about the roles of microRNAs (miRNAs) in this process.Using small RNA deep sequencing, we compared the plasma miRNA expression patterns between hypertensive (HT) AGMs and normotensive (NT) AGMs. Expression of miRNAs (miR-122, miR-339, miR-296-5p) was validated independently in plasma samples from 10 HT AGMs and 10 NT AGMs (fold changes are 2...
May 22, 2018: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/29786565/modelling-non-alcoholic-fatty-liver-disease-in-human-hepatocyte-like-cells
#15
Marcus J Lyall, Jessy Cartier, John P Thomson, Kate Cameron, Jose Meseguer-Ripolles, Eoghan O'Duibhir, Dagmara Szkolnicka, Baltasar Lucendo Villarin, Yu Wang, Giovanny Rodriguez Blanco, Warwick B Dunn, Richard R Meehan, David C Hay, Amanda J Drake
Non-alcoholic fatty liver disease (NAFLD) is the most common cause of liver disease in developed countries. An in vitro NAFLD model would permit mechanistic studies and enable high-throughput therapeutic screening. While hepatic cancer-derived cell lines are a convenient, renewable resource, their genomic, epigenomic and functional alterations mean their utility in NAFLD modelling is unclear. Additionally, the epigenetic mark 5-hydroxymethylcytosine (5hmC), a cell lineage identifier, is rapidly lost during cell culture, alongside expression of the Ten-eleven-translocation ( TET ) methylcytosine dioxygenase enzymes, restricting meaningful epigenetic analysis...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29786556/assessment-of-stem-cell-differentiation-based-on-genome-wide-expression-profiles
#16
REVIEW
Patricio Godoy, Wolfgang Schmidt-Heck, Birte Hellwig, Patrick Nell, David Feuerborn, Jörg Rahnenführer, Kathrin Kattler, Jörn Walter, Nils Blüthgen, Jan G Hengstler
In recent years, protocols have been established to differentiate stem and precursor cells into more mature cell types. However, progress in this field has been hampered by difficulties to assess the differentiation status of stem cell-derived cells in an unbiased manner. Here, we present an analysis pipeline based on published data and methods to quantify the degree of differentiation and to identify transcriptional control factors explaining differences from the intended target cells or tissues. The pipeline requires RNA-Seq or gene array data of the stem cell starting population, derived 'mature' cells and primary target cells or tissue...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29786096/reversal-of-sirna-mediated-gene-silencing-in-vivo
#17
Ivan Zlatev, Adam Castoreno, Christopher R Brown, June Qin, Scott Waldron, Mark K Schlegel, Rohan Degaonkar, Svetlana Shulga-Morskaya, Huilei Xu, Swati Gupta, Shigeo Matsuda, Akin Akinc, Kallanthottathil G Rajeev, Muthiah Manoharan, Martin A Maier, Vasant Jadhav
We report rapid, potent reversal of GalNAc-siRNA-mediated RNA interference (RNAi) activity in vivo with short, synthetic, high-affinity oligonucleotides complementary to the siRNA guide strand. We found that 9-mers with five locked nucleic acids (LNAs) have the highest potency across several targets. Our modular, sequence-specific approach, named REVERSIR, may enhance the therapeutic profile of any long-acting GalNAc-siRNA (short interfering RNA) conjugate by enabling control of RNAi pharmacology.
May 14, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29784986/a-workflow-for-the-integrative-transcriptomic-description-of-molecular-pathology-and-the-suggestion-of-normalizing-compounds-exemplified-by-parkinson-s-disease
#18
Mohamed Hamed, Yvonne Gladbach, Steffen Möller, Sarah Fischer, Mathias Ernst, Stephan Struckmann, Alexander Storch, Georg Fuellen
The volume of molecular observations on human diseases in public databases is continuously increasing at accelerating rates. A bottleneck is their computational integration into a coherent description, from which researchers may derive new well-founded hypotheses. Also, the need to integrate data from different technologies (genetics, coding and regulatory RNA, proteomics) emerged in order to identify biomarkers for early diagnosis and prognosis of complex diseases and therefore facilitating the development of novel treatment approaches...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784930/comparative-mrna-and-mirna-expression-in-european-mouflon-ovis-musimon-and-sheep-ovis-aries-provides-novel-insights-into-the-genetic-mechanisms-for-female-reproductive-success
#19
Ji Yang, Xin Li, Yin-Hong Cao, Kisun Pokharel, Xiao-Ju Hu, Ze-Hui Chen, Song-Song Xu, Jaana Peippo, Mervi Honkatukia, Juha Kantanen, Meng-Hua Li
Prolific breeds of domestic sheep (Ovis aries) are important genetic resources due to their reproductive performance, which is characterized by multiple lambs per birth and out-of-season breeding. However, the lack of a comprehensive understanding of the genetic mechanisms underlying the important reproductive traits, particularly from the evolutionary genomics perspective, has impeded the efficient advancement of sheep breeding. Here, for the first time, by performing RNA-sequencing we built a de novo transcriptome assembly of ovarian and endometrial tissues in European mouflon (Ovis musimon) and performed an mRNA-miRNA integrated expression profiling analysis of the wild species and a highly prolific domestic sheep breed, the Finnsheep...
May 21, 2018: Heredity
https://www.readbyqxmd.com/read/29784918/early-lineage-segregation-of-multipotent-embryonic-mammary-gland-progenitors
#20
Aline Wuidart, Alejandro Sifrim, Marco Fioramonti, Shigeru Matsumura, Audrey Brisebarre, Daniel Brown, Alessia Centonze, Anne Dannau, Christine Dubois, Alexandra Van Keymeulen, Thierry Voet, Cédric Blanpain
The mammary gland is composed of basal cells and luminal cells. It is generally believed that the mammary gland arises from embryonic multipotent progenitors, but it remains unclear when lineage restriction occurs and what mechanisms are responsible for the switch from multipotency to unipotency during its morphogenesis. Here, we perform multicolour lineage tracing and assess the fate of single progenitors, and demonstrate the existence of a developmental switch from multipotency to unipotency during embryonic mammary gland development...
May 21, 2018: Nature Cell Biology
keyword
keyword
44220
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"