keyword
MENU ▼
Read by QxMD icon Read
search

RNA sequencing

keyword
https://www.readbyqxmd.com/read/28743023/principles-of-transgenerational-small-rna-inheritance-in-caenorhabditis-elegans
#1
REVIEW
Oded Rechavi, Itamar Lev
Examples of transgenerational inheritance of environmental responses are rapidly accumulating. In Caenorhabditis elegans nematodes, such heritable information transmits across generations in the form of RNA-dependent RNA polymerase-amplified small RNAs. Regulatory small RNAs enable sequence-specific gene regulation, and unlike chromatin modifications, can move between tissues, and escape from immediate germline reprogramming. In this review, we discuss the path that small RNAs take from the soma to the germline, and elaborate on the mechanisms that maintain or erase parental small RNA responses after a specific number of generations...
July 24, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28742933/gene-expression-is-more-strongly-influenced-by-age-than-caste-in-the-ant-lasius-niger
#2
Eric R Lucas, Jonathan Romiguier, Laurent Keller
Phenotypic plasticity, where a single genome can give rise to different phenotypes, underlies many remarkable features of the natural world and occurs in a wide range of organisms. Understanding the transcriptional differences that underlie plastic phenotypes remains a major unsolved problem in biology. In many ants, females can develop into either queens or workers, two phenotypes with different morphology, behaviour and longevity. In comparison to workers, queens are larger, more fecund and longer-lived. Here, we study gene expression differences between queens and workers in the ant Lasius niger...
July 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28742856/fit-for-genomic-and-proteomic-purposes-sampling-the-fitness-of-nucleic-acid-and-protein-derivatives-from-formalin-fixed-paraffin-embedded-tissue
#3
Anna Yakovleva, Jordan L Plieskatt, Sarah Jensen, Razan Humeida, Jonathan Lang, Guangzhao Li, Paige Bracci, Sylvia Silver, Jeffrey Michael Bethony
The demand for nucleic acid and protein derivatives from formalin-fixed paraffin-embedded (FFPE) tissue has greatly increased due to advances in extraction and purification methods, making these derivatives available for numerous genomic and proteomic platforms. Previously, DNA, RNA, microRNA (miRNA), or protein derived from FFPE tissue blocks were considered "unfit" for such platforms, as the process of tissue immobilization by FFPE resulted in cross-linked, fragmented, and chemically modified macromolecules...
2017: PloS One
https://www.readbyqxmd.com/read/28742285/variable-expressivity-and-incomplete-penetrance-in-a-large-family-with-non-classical-diamond-blackfan-anemia-associated-with-ribosomal-protein-l11-splicing-variant
#4
Colleen M Carlston, Zeinab A Afify, Janice C Palumbos, Heidi Bagley, Carlos Barbagelata, Whitney L Wooderchak-Donahue, Rong Mao, John C Carey
Diamond-Blackfan anemia (DBA) is a group of clinically and genetically heterogeneous bone marrow failure disorders with or without congenital anomalies. Variable expressivity and incomplete penetrance have been observed within affected families. Diamond-Blackfan anemia-7 (DBA7), caused by heterozygous mutations in ribosomal protein L11 (RPL11), accounts for approximately 5% of DBA. DBA7 is usually characterized by early-onset bone marrow failure often accompanied by congenital malformations, especially thumb defects...
July 25, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28742275/the-proteome-and-transcriptome-of-the-infectious-metacyclic-form-of-trypanosoma-brucei-define-quiescent-cells-primed-for-mammalian-invasion
#5
Romain Christiano, Nikolay G Kolev, Huafang Shi, Elisabetta Ullu, Tobias C Walther, Christian Tschudi
The infectious metacyclic forms of Trypanosoma brucei result from a complex development in the tsetse fly vector. When they infect mammals, they cause African sleeping sickness in humans. Due to scarcity of biological material and difficulties of the tsetse fly as an experimental system, very limited information is available concerning the gene expression profile of metacyclic forms. We used an in vitro system based on expressing the RNA binding protein 6 to obtain infectious metacyclics and determined their protein and mRNA repertoires by mass-spectrometry (MS) based proteomics and mRNA sequencing (RNA-Seq) in comparison to non-infectious procyclic trypanosomes...
July 25, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28742140/short-16-mer-locked-nucleic-acid-splice-switching-oligonucleotides-restore-dystrophin-production-in-duchenne-muscular-dystrophy-myotubes
#6
Vanessa Borges Pires, Ricardo Simões, Kamel Mamchaoui, Célia Carvalho, Maria Carmo-Fonseca
Splice-switching antisense oligonucleotides (SSOs) offer great potential for RNA-targeting therapies, and two SSO drugs have been recently approved for treating Duchenne Muscular Dystrophy (DMD) and Spinal Muscular Atrophy (SMA). Despite promising results, new developments are still needed for more efficient chemistries and delivery systems. Locked nucleic acid (LNA) is a chemically modified nucleic acid that presents several attractive properties, such as high melting temperature when bound to RNA, potent biological activity, high stability and low toxicity in vivo...
2017: PloS One
https://www.readbyqxmd.com/read/28742088/genome-wide-identification-of-hami-melon-mirnas-with-putative-roles-during-fruit-development
#7
Hong Zhang, Lan Yin, Huaisong Wang, Guangzhi Wang, Xinli Ma, Meihua Li, Haibo Wu, Qiushi Fu, Yi Zhang, Hongping Yi
MicroRNAs represent a family of small endogenous, non-coding RNAs that play critical regulatory roles in plant growth, development, and environmental stress responses. Hami melon is famous for its attractive flavor and excellent nutritional value, however, the mechanisms underlying the fruit development and ripening remains largely unknown. Here, we performed small RNA sequencing to investigate the roles of miRNAs during Hami melon fruit development. Two batches of flesh samples were collected at four fruit development stages...
2017: PloS One
https://www.readbyqxmd.com/read/28741180/loss-of-nhej1-protein-due-to-a-novel-splice-site-mutation-in-a-family-presenting-with-combined-immunodeficiency-microcephaly-and-growth-retardation-and-literature-review
#8
Farrukh Sheikh, Abbas Hawwari, Safa Alhissi, Sulaiman Al Gazlan, Hasan Al Dhekri, Agha M Rehan Khaliq, Esteban Borrero, Lina El-Baik, Rand Arnaout, Hamoud Al-Mousa, Anas M Alazami
INTRODUCTION: Non-homologous end joining gene 1 (NHEJ1) defect is a rare form of primary immune deficiency. Very few cases have been described from around the world. PURPOSE: We are reporting the first family from the Arabian Gulf with three siblings presenting with combined immunodeficiency (CID), microcephaly, and growth retardation due to a novel NHEJ1 splice site mutation, in addition to a review of the previously published literature on this subject. METHODS: Patients' clinical, immunological, and laboratory features were examined...
July 24, 2017: Journal of Clinical Immunology
https://www.readbyqxmd.com/read/28741097/distribution-and-phylogenetic-analysis-of-blastocystis-sp-subtypes-isolated-from-ibd-patients-and-healthy-individuals-in-iran
#9
H Mirjalali, M R Abbasi, N Naderi, Z Hasani, E S Mirsamadi, C R Stensvold, H Balaii, H Asadzadeh Aghdaei, M R Zali
Blastocystis is a single-celled intestinal parasite commonly found in humans and a broad range of animals all over the world. In humans, its role in health and disease remains unsettled. The aim of our study was to investigate the distribution of Blastocystis and Blastocystis subtypes (ST) in patients with inflammatory bowel disease (IBD) and control subjects. A total of 71 stool samples were collected from IBD patients, 69 and 2 of whom had ulcerative colitis (UC) and Crohn's Disease (CD), respectively. Moreover, 166 stool samples from healthy subjects were included as control samples...
July 25, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28740869/comparing-sequencing-assays-and-human-machine-analyses-in-actionable-genomics-for-glioblastoma
#10
Kazimierz O Wrzeszczynski, Mayu O Frank, Takahiko Koyama, Kahn Rhrissorrakrai, Nicolas Robine, Filippo Utro, Anne-Katrin Emde, Bo-Juen Chen, Kanika Arora, Minita Shah, Vladimir Vacic, Raquel Norel, Erhan Bilal, Ewa A Bergmann, Julia L Moore Vogel, Jeffrey N Bruce, Andrew B Lassman, Peter Canoll, Christian Grommes, Steve Harvey, Laxmi Parida, Vanessa V Michelini, Michael C Zody, Vaidehi Jobanputra, Ajay K Royyuru, Robert B Darnell
OBJECTIVE: To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each. METHODS: Tumor DNA was analyzed by a commercial targeted panel. In addition, tumor-normal DNA was analyzed by whole-genome sequencing (WGS) and tumor RNA was analyzed by RNA sequencing (RNA-seq). The WGS and RNA-seq data were analyzed by a team of bioinformaticians and cancer oncologists, and separately by IBM Watson Genomic Analytics (WGA), an automated system for prioritizing somatic variants and identifying drugs...
August 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28740759/a-positive-readout-single-transcript-reporter-for-site-specific-mrna-cleavage
#11
Nikolay Kandul, Ming Guo, Bruce A Hay
Cleavage of mRNA molecules causes their rapid degradation, thereby playing an important role in regulation of gene expression and host genome defense from viruses and transposons in bacterial and eukaryotic cells. Current negative-readout, and repressor-based positive-readout reporters of mRNA degradation have limitations. Here we report the development of a single transcript that acts as a positive reporter of mRNA cleavage. We show that placement of bacterial CopT and CopA hairpins into the 5' UTR and 3' UTR of an mRNA results in inhibition of translation of the intervening coding sequence in Drosophila...
2017: PeerJ
https://www.readbyqxmd.com/read/28740499/multi-omics-and-integrated-network-analyses-reveal-new-insights-into-the-systems-relationships-between-metabolites-structural-genes-and-transcriptional-regulators-in-developing-grape-berries-vitis-vinifera-l-exposed-to-water-deficit
#12
Stefania Savoi, Darren C J Wong, Asfaw Degu, Jose C Herrera, Barbara Bucchetti, Enrico Peterlunger, Aaron Fait, Fulvio Mattivi, Simone D Castellarin
Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28739829/inherent-oxidative-stress-in-lewis-rat-is-associated-with-resistance-to-toxoplasmosis
#13
William H Witola, Chi Yong Kim, Xuejin Zhang
The course of Toxoplasma gondii infection in rats closely resembles that in humans. However, compared to the Brown Norway (BN) rat, the Lewis (LEW) rat is extremely resistant to T. gondii infection. Thus, we performed RNA sequencing analysis of the LEW versus BN rat, with or without T. gondii infection, in order to unravel molecular factors directing robust and rapid early T. gondii-killing mechanisms in the LEW rat. We found that, compared to the uninfected BN rat, the uninfected LEW rat has inherently higher transcript levels of cytochrome enzymes [Cyp2d3, Cyp2d5 and Cybrd1 that catalyze generation of reactive oxygen species (ROS)], with concomitant higher levels of ROS...
July 24, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28739827/transcriptional-profiling-of-the-chicken-tracheal-response-to-virulent-mycoplasma-gallisepticum-strain-rlow
#14
J Beaudet, E R Tulman, K Pflaum, X Liao, G F Kutish, S M Szczepanek, L K Silbart, S J Geary
Mycoplasma gallisepticum, the primary etiologic agent of Chronic Respiratory Disease (CRD) in poultry, leads to prolonged recruitment and activation of inflammatory cells in the respiratory mucosa. This is consistent with the current model of immune dysregulation that ostensibly allows the organism to evade clearance mechanisms and establish chronic infection. To date, studies using qRT-PCR and microarrays have shown a significant transient up-regulation of cytokines and chemokines from tracheal epithelial cells (TECs) in vitro and tracheal tissue ex vivo in response to virulent strain Rlow, that contributes to the infiltration of inflammatory cells into the tracheal mucosa...
July 24, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28739824/epigenetic-mechanisms-regulate-innate-immunity-against-uropathogenic-and-commensal-like-escherichia-coli-in-the-surrogate-insect-model-galleria-mellonella
#15
Miriam Heitmueller, André Billion, Ulrich Dobrindt, Andreas Vilcinskas, Krishnendu Mukherjee
Innate immunity-related genes in humans are activated during urinary tract infections (UTIs) caused by pathogenic strains of Escherichia coli but are suppressed by commensals. Epigenetic mechanisms play a pivotal role in the regulation of gene expression in response to environmental stimuli. To determine whether epigenetic mechanisms can explain the different behaviors of pathogenic and commensal bacteria, we infected larvae of the greater wax moth Galleria mellonella, a widely-used model insect host, with a uropathogenic E...
July 24, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28739676/shape-analysis-of-the-htra-rna-thermometer-from-salmonella-enterica
#16
Edric K Choi, Kelsey A Ulanowicz, Yen Anh H Nguyen, Jane K Frandsen, Rachel M Mitton-Fry
RNA thermometers regulate expression of prokaryotic genes involved in heat shock response or in virulence of pathogenic bacteria such as Yersinia, Neisseria, and Salmonella They function through temperature-dependent conformational changes in the mRNAs in which they reside. Most RNA thermometers are found in the 5'-untranslated region (UTR) of the mRNA, where they modulate availability of the ribosome-binding site. We have used SHAPE (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension) assays to systematically characterize the structure and dynamics of the htrA thermometer of Salmonella enterica at single-nucleotide resolution...
July 24, 2017: RNA
https://www.readbyqxmd.com/read/28739599/evolutionary-dynamics-of-male-reproductive-genes-in-the-drosophila-virilis-subgroup
#17
Yasir H Ahmed-Braimah, Robert L Unckless, Andrew G Clark
Postcopulatory sexual selection (PCSS) is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs) are major players in postmating interactions, and are important targets of PCSS in males. The virilis subgroup of Drosophila exhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of PCSS and gametic isolation...
July 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28739526/chronic-mild-stress-exacerbates-severity-of-experimental-autoimmune-encephalomyelitis-in-association-with-altered-non-coding-rna-and-metabolic-biomarkers
#18
Brietta Gerrard, Vaibhav Singh, Olena Babenko, Isabelle Gauthier, V Wee Yong, Igor Kovalchuk, Artur Luczak, Gerlinde A S Metz
The causal factors determining the onset and severity of multiple sclerosis (MS) are not well understood. Here, we investigated the influence of chronic stress on clinical symptoms, metabolic and epigenetic manifestations of experimental autoimmune encephalomyelitis (EAE), a common animal model of MS. Lewis rats were immunized for monophasic EAE with MBP69-88 and were exposed to chronic stress for 37 days starting 7 days prior to immunization. The exposure to stress accelerated and exacerbated the clinical symptoms of EAE...
July 21, 2017: Neuroscience
https://www.readbyqxmd.com/read/28739339/challenges-in-defining-the-role-of-intron-retention-in-normal-biology-and-disease
#19
REVIEW
Darya P Vanichkina, Ulf Schmitz, Justin J-L Wong, John E J Rasko
RNA sequencing has revealed a striking diversity in transcriptomic complexity, to which alternative splicing is a major contributor. Intron retention (IR) is a conserved form of alternative splicing that was originally overlooked in normal mammalian physiology and development, due mostly to difficulties in its detection. IR has recently been revealed as an independent mechanism of controlling and enhancing the complexity of gene expression. IR facilitates rapid responses to biological stimuli, is involved in disease pathogenesis, and can generate novel protein isoforms...
July 21, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28739310/identification-of-new-tsga10-transcript-variants-in-human-testis-with-conserved-regulatory-rna-elements-in-5-untranslated-region-and-distinct-expression-in-breast-cancer
#20
Pouya Salehipour, Mahsa Nematzadeh, Maryam Beigom Mobasheri, Mandana Afsharpad, Mohammad Hossein Modarressi
Testis specific gene antigen 10 (TSGA10) is a cancer testis antigen involved in the process of spermatogenesis. TSGA10 could also play an important role in the inhibition of angiogenesis by preventing nuclear localization of HIF-1α. Although it has been shown that TSGA10 messenger RNA (mRNA) is mainly expressed in testis and some tumors, the transcription pattern and regulatory mechanisms of this gene remain largely unknown. Here, we report that human TSGA10 comprises at least 22 exons and generates four different transcript variants...
July 21, 2017: Biochimica et Biophysica Acta
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"