keyword
MENU ▼
Read by QxMD icon Read
search

Transcriptome

keyword
https://www.readbyqxmd.com/read/28449399/comparative-transcriptomic-analysis-of-bombyx-mori-fat-body-tissue-following-dietary-restriction
#1
Ye Pan, Peng Lü, Qinyun Wang, Feifei Zhu, Chengjun Li, Yuanqing He, Keping Chen
Dietary restriction (DR) refers to a reduction in food intake to induce undernutrition but not malnutrition, which extends the lifespan of multiple species. Although there are invertebrate aging models, such as the Caenorhabditis elegans and Drosophila melanogaster, aging studies in Lepidoptera are few in number and the underlying life-extending molecular mechanisms are not clear. Research on a broader range of animals is necessary to support generalizations on mechanisms of aging and rates of aging. The aim of this study was to further investigate genes and pathways associated with DR in Bombyx mori...
May 2017: Archives of Insect Biochemistry and Physiology
https://www.readbyqxmd.com/read/28449359/transcriptomic-responses-of-solanum-dulcamara-to-natural-and-simulated-herbivory
#2
Tobias Lortzing, Vivien Firtzlaff, Duy Nguyen, Ivo Rieu, Sandra Stelzer, Martina Schad, Jim Kallarackal, Anke Steppuhn
Plants are attacked by diverse herbivores and respond with manifold defense responses. To study transcriptional and other early regulation events of these plant responses, herbivory is often simulated to standardize the temporal and spatial dynamics that vary tremendously for natural herbivory. Yet to what extent such simulations of herbivory are able to elicit the same plant response as real herbivory remains largely undetermined. We examined the transcriptional response of a wild model plant to herbivory by lepidopteran larvae and to a commonly used herbivory simulation by applying the larvae's oral secretions to standardized wounds...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449301/the-profile-and-dynamics-of-rna-modifications-in-animals
#3
Pieter van Delft, Alper Akay, Sabrina M Huber, Christoph Bueschl, Konrad L M Rudolph, Tomás Di Domenico, Rainer Schuhmacher, Eric A Miska, Shankar Balasubramanian
More than a hundred distinct modified nucleosides have been identified in RNA, but little is known about their distribution across different organisms, their dynamic nature and their response to cellular and environmental stress. Mass-spectrometry-based methods have been at the forefront of identifying and quantifying modified nucleosides. However, they often require synthetic reference standards, which do not exist in the case of many modified nucleosides, and this therefore impedes their analysis. Here we use a metabolic labelling approach to achieve rapid generation of bio-isotopologues of the complete Caenorhabditis elegans transcriptome and its modifications and use them as reference standards to characterise the RNA modification profile in this multicellular organism through an untargeted liquid-chromatography tandem high-resolution mass spectrometry (LC-HRMS) approach...
March 16, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28449243/pathologic-features-of-mycobacteriosis-in-naturally-infected-syngnathidae-and-novel-transcriptome-assembly-in-association-with-disease
#4
S B Fogelson, M D Fast, J Leary, A C Camus
Syngnathidae (seahorses, seadragons and pipefish) suffer significant losses from non-tuberculous mycobacteria. However, they produce markedly different lesions in response to the disease compared to other teleost species, notably infrequent granuloma formation. This study evaluated 270 syngnathid fish, from which 92 were diagnosed with mycobacteriosis by histopathology, culture or both. Microscopic lesions variably consisted of random foci of coagulative necrosis in multiple organs, containing high numbers of free bacteria and large aggregates or sheets of macrophages with cytoplasm laden with acid-fast bacilli...
April 27, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28449211/operational-tolerance-in-kidney-transplantation-and-associated-biomarkers
#5
REVIEW
Annick Massart, Lidia Ghisdal, Marc Abramowicz, Daniel Abramowicz
In the 1960s, our predecessors won a historical battle against acute rejection and ensured that transplantation became a common life-saving treatment. In parallel to this success, or perhaps because of it, we lost the battle for long-lived transplants, being overwhelmed with chronic immune insults and the toxicities of immunosuppression. It is likely that current powerful treatments block acute rejection, but at the same time condemn the few circulating donor cells that would have been able to elicit immunoregulatory host responses towards the allograft...
April 27, 2017: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/28449108/poly-a-clickseq-click-chemistry-for-next-generation-3%C3%AE-end-sequencing-without-rna-enrichment-or-fragmentation
#6
Andrew Routh, Ping Ji, Elizabeth Jaworski, Zheng Xia, Wei Li, Eric J Wagner
The recent emergence of alternative polyadenylation (APA) as an engine driving transcriptomic diversity has stimulated the development of sequencing methodologies designed to assess genome-wide polyadenylation events. The goal of these approaches is to enrich, partition, capture and ultimately sequence poly(A) site junctions. However, these methods often require poly(A) enrichment, 3΄ linker ligation steps, and RNA fragmentation, which can necessitate higher levels of starting RNA, increase experimental error and potentially introduce bias...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449102/enhancing-expression-of-ssu1-genes-in-saccharomyces-uvarum-leads-to-an-increase-in-sulfite-tolerance-and-transcriptome-profiles-change
#7
X Z Liu, M Sang, X A Zhang, T K Zhang, H Y Zhang, X He, S X Li, X D Sun, Z M Zhang
Saccharomyces uvarum is a good wine yeast species which may have great potential for the future. However, sulfur tolerance of most S. uvarum strains is very poor. In addition there is still little information about the SSU1 gene of S. uvarum. In order to analyze the function of SSU1 genes, two expression vectors which contained different SSU1 genes were constructed and transferred into a sulfite-tolerant S. uvarum strain A9. Then sulfite tolerance, PCR analysis, sequencing analysis, SO2 output production analysis, RT-qPCR analysis and transcriptome analysis were used to access the function of the S...
April 25, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28449042/long-noncoding-rna-a-crosslink-in-biological-regulatory-network
#8
Yuwei Zhang, Yang Tao, Qi Liao
Long noncoding RNAs (lncRNAs) had been defined as a novel class of functional RNAs longer than 200 nucleotides around a decade ago. It is widely acknowledged that lncRNAs play a significant role in regulation of gene expression, but the biological and molecular mechanisms are diverse and complex, and remain to be determined. Especially, the regulatory network of lncRNAs associated with other biological molecules is still a controversial matter, thus becoming a new frontier of the studies on transcriptome. Recent advance in high-throughput sequencing technologies and bioinformatics approaches may be an accelerator to lift the mysterious veil...
April 24, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28449035/identification-and-expression-profiling-of-odorant-binding-proteins-and-chemosensory-proteins-of-daktulosphaira-vitifoliae-hemiptera-phylloxeridae
#9
Jing-Jing Zhao, Yue Zhang, Dong-Sheng Fan, Ji-Nian Feng
In insects, odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) are primary peripheral olfactory proteins playing critical roles in odorant detection. In this study, we present the first identification of OBPs and CSPs from the transcriptome of grape phylloxera Daktulosphaira vitifoliae Fitch, an important pest that damages both roots and leaves of grapes. The OBPs contained six conserved cysteine residues and the CSPs contained four conserved cysteine residues in this insect. Phylogenetic analysis showed that most of the olfactory proteins were closely related to OBPs and CSPs from other aphids...
April 25, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28448797/the-single-cell-yin-and-yang-of-live-imaging-and-transcriptomics
#10
Michael Tsabar, Galit Lahav
A new approach to monitoring both signaling over time and a global gene expression profile from the same cell establishes a functional role for NF-κB dynamics in transcription.
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28448552/transcriptomic-analysis-of-the-hepatic-response-to-stress-in-the-red-cusk-eel-genypterus-chilensis-insights-into-lipid-metabolism-oxidative-stress-and-liver-steatosis
#11
Sebastian Naour, Brisa M Espinoza, Jorge E Aedo, Rodrigo Zuloaga, Jonathan Maldonado, Macarena Bastias-Molina, Herman Silva, Claudio Meneses, Cristian Gallardo-Escarate, Alfredo Molina, Juan Antonio Valdés
Teleosts exhibit a broad divergence in their adaptive response to stress, depending on the magnitude, duration, and frequency of stressors and the species receiving the stimulus. We have previously reported that the red cusk-eel (Genypterus chilensis), an important marine farmed fish, shows a physiological response to stress that results in increased skeletal muscle atrophy mediated by over-expression of components of the ubiquitin proteasome and autophagy-lysosomal systems. To better understand the systemic effects of stress on the red cusk-eel metabolism, the present study assessed the transcriptomic hepatic response to repetitive handling-stress...
2017: PloS One
https://www.readbyqxmd.com/read/28448519/zika-infection-of-neural-progenitor-cells-perturbs-transcription-in-neurodevelopmental-pathways
#12
Lynn Yi, Harold Pimentel, Lior Pachter
BACKGROUND: A recent study of the gene expression patterns of Zika virus (ZIKV) infected human neural progenitor cells (hNPCs) revealed transcriptional dysregulation and identified cell cycle-related pathways that are affected by infection. However deeper exploration of the information present in the RNA-Seq data can be used to further elucidate the manner in which Zika infection of hNPCs affects the transcriptome, refining pathway predictions and revealing isoform-specific dynamics. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed data published by Tang et al...
2017: PloS One
https://www.readbyqxmd.com/read/28448512/suppression-of-the-escherichia-coli-dnaa46-mutation-by-changes-in-the-activities-of-the-pyruvate-acetate-node-links-dna-replication-regulation-to-central-carbon-metabolism
#13
Joanna Tymecka-Mulik, Lidia Boss, Monika Maciąg-Dorszyńska, João F Matias Rodrigues, Lidia Gaffke, Anna Wosinski, Grzegorz M Cech, Agnieszka Szalewska-Pałasz, Grzegorz Węgrzyn, Monika Glinkowska
To ensure faithful transmission of genetic material to progeny cells, DNA replication is tightly regulated, mainly at the initiation step. Escherichia coli cells regulate the frequency of initiation according to growth conditions. Results of the classical, as well as the latest studies, suggest that the DNA replication in E. coli starts at a predefined, constant cell volume per chromosome but the mechanisms coordinating DNA replication with cell growth are still not fully understood. Results of recent investigations have revealed a role of metabolic pathway proteins in the control of cell division and a direct link between metabolism and DNA replication has also been suggested both in Bacillus subtilis and E...
2017: PloS One
https://www.readbyqxmd.com/read/28448505/polyphenolic-extract-of-insp-5-ptase-expressing-tomato-plants-reduce-the-proliferation-of-mcf-7-breast-cancer-cells
#14
Mohammad Alimohammadi, Mohamed Hassen Lahiani, Diamond McGehee, Mariya Khodakovskaya
In recent years, by extensive achievements in understanding the mechanisms and the pathways affected by cancer, the focus of cancer research is shifting from developing new chemotherapy methods to using natural compounds with therapeutic properties to reduce the adverse effects of synthetic drugs on human health. We used fruit extracts from previously generated human type I InsP 5-ptase gene expressing transgenic tomato plants for assessment of the anti-cancer activity of established genetically modified tomato lines...
2017: PloS One
https://www.readbyqxmd.com/read/28448473/transcriptomic-analysis-of-calcium-remodeling-in-colorectal-cancer
#15
Enrique Pérez-Riesgo, Lucía G Gutiérrez, Daniel Ubierna, Alberto Acedo, Mary P Moyer, Lucía Núñez, Carlos Villalobos
Colorectal cancer (CRC) cells undergo the remodeling of intracellular Ca(2+) homeostasis, which contributes to cancer hallmarks such as enhanced proliferation, invasion and survival. Ca(2+) remodeling includes critical changes in store-operated Ca(2+) entry (SOCE) and Ca(2+) store content. Some changes have been investigated at the molecular level. However, since nearly 100 genes are involved in intracellular Ca(2+) transport, a comprehensive view of Ca(2+) remodeling in CRC is lacking. We have used Next Generation Sequencing (NGS) to investigate differences in expression of 77 selected gene transcripts involved in intracellular Ca(2+) transport in CRC...
April 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28448468/transcriptome-analysis-of-core-dinoflagellates-reveals-a-universal-bias-towards-gc-rich-codons
#16
Ernest Williams, Allen Place, Tsvetan Bachvaroff
Although dinoflagellates are a potential source of pharmaceuticals and natural products, the mechanisms for regulating and producing these compounds are largely unknown because of extensive post-transcriptional control of gene expression. One well-documented mechanism for controlling gene expression during translation is codon bias, whereby specific codons slow or even terminate protein synthesis. Approximately 10,000 annotatable genes from fifteen "core" dinoflagellate transcriptomes along a range of overall guanine and cytosine (GC) content were used for codonW analysis to determine the relative synonymous codon usage (RSCU) and the GC content at each codon position...
April 27, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28448034/using-a-fluorescent-pcr-capillary-gel-electrophoresis-technique-to-genotype-crispr-cas9-mediated-knockout-mutants-in-a-high-throughput-format
#17
Muhammad Khairul Ramlee, Jing Wang, Alice M S Cheung, Shang Li
The development of programmable genome-editing tools has facilitated the use of reverse genetics to understand the roles specific genomic sequences play in the functioning of cells and whole organisms. This cause has been tremendously aided by the recent introduction of the CRISPR/Cas9 system-a versatile tool that allows researchers to manipulate the genome and transcriptome in order to, among other things, knock out, knock down, or knock in genes in a targeted manner. For the purpose of knocking out a gene, CRISPR/Cas9-mediated double-strand breaks recruit the non-homologous end-joining DNA repair pathway to introduce the frameshift-causing insertion or deletion of nucleotides at the break site...
April 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28448031/transcriptomic-analysis-of-c-elegans-rna-sequencing-data-through-the-tuxedo-suite-on-the-galaxy-project
#18
Francis R G Amrit, Arjumand Ghazi
Next generation sequencing (NGS) technologies have revolutionized the nature of biological investigation. Of these, RNA Sequencing (RNA-Seq) has emerged as a powerful tool for gene-expression analysis and transcriptome mapping. However, handling RNA-Seq datasets requires sophisticated computational expertise and poses inherent challenges for biology researchers. This bottleneck has been mitigated by the open access Galaxy project that allows users without bioinformatics skills to analyze RNA-Seq data, and the Database for Annotation, Visualization, and Integrated Discovery (DAVID), a Gene Ontology (GO) term analysis suite that helps derive biological meaning from large data sets...
April 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28448019/a-tandem-liquid-chromatography-mass-spectrometry-based-approach-for-metabolite-analysis-of-staphylococcus-aureus
#19
David J Samuels, Zhe Wang, Kyu Y Rhee, Shaun R Brinsmade
In an effort to thwart bacterial pathogens, hosts often limit the availability of nutrients at the site of infection. This limitation can alter the abundances of key metabolites to which regulatory factors respond, adjusting cellular metabolism. In recent years, a number of proteins and RNA have emerged as important regulators of virulence gene expression. For example, the CodY protein responds to levels of branched-chain amino acids and GTP and is widely conserved in low G+C Gram-positive bacteria. As a global regulator in Staphylococcus aureus, CodY controls the expression of dozens of virulence and metabolic genes...
March 28, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28447797/signal-transductions-of-beas-2b-cells-in-response-to-carcinogenic-pm2-5-exposure-based-on-microfluidic-system
#20
Lulu Zheng, Sixiu Liu, Guoshun Zhuang, Jian Xu, Qi Liu, Xinlian Zhang, Congrui Deng, Zhigang Guo, Wang Zhao, Tingna Liu, Yiqi Wang, Yuxiao Zhang, Jing Lin, Qiongzhen Wang, Guodong Sui
PM2.5 (particulate matter less than 2.5 micrometers in diameter) is considered as a harmful carcinogen. Determining the precise relationship between the chemical constituents of PM2.5 in the air and cancer progression could aid the treatment of environment related disease and establishing risk reduction strategies. Herein, we used transcriptomics (RNA-seq) and integrated microfluidic system to identify the global gene expression and differential target proteins expression induced by ambient fine particles collected from the heavy haze in China...
April 27, 2017: Analytical Chemistry
keyword
keyword
13493
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"