Transcriptome Profile Alterations with Carbon Nanotubes, Quantum Dots, and Silver Nanoparticles: A Review

Next-generation sequencing (NGS) technology has revolutionized sequence-based research. In recent years, high-throughput sequencing has become the method of choice in studying the toxicity of chemical agents through observing and measuring changes in transcript levels. Engineered nanomaterial (ENM)-toxicity has become a major field of research and has adopted microarray and newer RNA-Seq methods. Recently, nanotechnology has become a promising tool in the diagnosis and treatment of several diseases in humans. However, due to their high stability, they are likely capable of remaining in the body and environment for long periods of time. Their mechanisms of toxicity and long-lasting effects on our health is still poorly understood. This review explores the effects of three ENMs including carbon nanotubes (CNTs), quantum dots (QDs), and Ag nanoparticles (AgNPs) by cross examining publications on transcriptomic changes induced by these nanomaterials.

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Identification of conserved hepatic transcriptomic responses to 17β-estradiol using high-throughput sequencing in brown trout

Physiological Genomics ◽

10.1152/physiolgenomics.00123.2014 ◽

2015 ◽

Vol 47 (9) ◽

pp. 420-431 ◽

Cited By ~ 8

Author(s):

Tamsyn M. Uren Webster ◽

Janice A. Shears ◽

Karen Moore ◽

Eduarda M. Santos

Keyword(s):

High Throughput ◽

Brown Trout ◽

Ribosome Biogenesis ◽

Molecular Mechanisms ◽

High Throughput Sequencing ◽

Cellular Proliferation ◽

Sequence Information ◽

Rna Seq ◽

Mechanisms Of Toxicity ◽

17Β Estradiol

Estrogenic chemicals are major contaminants of surface waters and can threaten the sustainability of natural fish populations. Characterization of the global molecular mechanisms of toxicity of environmental contaminants has been conducted primarily in model species rather than species with limited existing transcriptomic or genomic sequence information. We aimed to investigate the global mechanisms of toxicity of an endocrine disrupting chemical of environmental concern [17β-estradiol (E2)] using high-throughput RNA sequencing (RNA-Seq) in an environmentally relevant species, brown trout ( Salmo trutta). We exposed mature males to measured concentrations of 1.94, 18.06, and 34.38 ng E2/l for 4 days and sequenced three individual liver samples per treatment using an Illumina HiSeq 2500 platform. Exposure to 34.4 ng E2/L resulted in 2,113 differentially regulated transcripts (FDR < 0.05). Functional analysis revealed upregulation of processes associated with vitellogenesis, including lipid metabolism, cellular proliferation, and ribosome biogenesis, together with a downregulation of carbohydrate metabolism. Using real-time quantitative PCR, we validated the expression of eight target genes and identified significant differences in the regulation of several known estrogen-responsive transcripts in fish exposed to the lower treatment concentrations (including esr1 and zp2.5). We successfully used RNA-Seq to identify highly conserved responses to estrogen and also identified some estrogen-responsive transcripts that have been less well characterized, including nots and tgm2l. These results demonstrate the potential application of RNA-Seq as a valuable tool for assessing mechanistic effects of pollutants in ecologically relevant species for which little genomic information is available.

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Transcriptomic Changes in Broiler Chicken Hypothalamus during Growth and Development

International Journal of Genomics ◽

10.1155/2018/6049469 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10 ◽

Cited By ~ 3

Author(s):

Katarzyna Piórkowska ◽

Kacper Żukowski ◽

Katarzyna Połtowicz ◽

Joanna Nowak ◽

Dorota Wojtysiak ◽

...

Keyword(s):

Differentially Expressed Gene ◽

Structural Complexity ◽

Rna Seq ◽

Physiological Processes ◽

Sequencing Method ◽

Avian Hypothalamus ◽

Vessel Development ◽

Next Generation Sequencing Ngs ◽

Transcriptomic Changes ◽

Intensive Growth

The hypothalamus plays an overarching role that is reflected in the physiological processes observed in the entire organism. The hypothalamus regulates selected metabolic processes and activities of the autonomic nervous system. The avian hypothalamus due to the structural complexity is not well described and has a slightly different function than the mammalian hypothalamus that is the subject of numerous studies. The present study evaluated activities of hypothalamic genes in fast-growing chickens during development (at the 1st day and 3rd and 6th weeks after hatching). The hypothalamic transcriptomes for 3- and 6-week-old cockerels were analysed using an RNA sequencing method in next-generation sequencing (NGS) technology. The differentially expressed gene analysis was conducted using DESeq2 software. In younger 22-day-old cockerels, 389 genes showed higher expression (fold change > 1.5) than that in 45-day-old birds. These genes played a role in several biological processes because they encoded proteins involved in integrin signalling, regulation of hormone levels, camera-type eye development, and blood vessel development. Moreover, surprisingly in the hypothalamus of 3-week-old cockerels, transcripts were identified for proteins involved in both anorexigenic (POMC, NMU) and orexigenic (PMCH, ALDH1A1, LPL, and GHRH) pathways. The RNA-seq results were confirmed by qPCR methods. In summary, the intensive growth of 3-week-old chickens was reflected in hypothalamic activities because the genes associated with the somatotropin axis and regulation of satiety centre showed increased expression.

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Carbon Nanotubes, Quantum Dots and Dendrimers as Potential Nanodevices for Nanotechnology Drug Delivery Systems

International Journal of Pharmaceutical Sciences and Nanotechnology ◽

10.37285/ijpsn.2013.6.3.2 ◽

2013 ◽

Vol 6 (3) ◽

pp. 2113-2124

Author(s):

Prashant Malik ◽

Neha Gulati ◽

Raj Kaur Malik ◽

Upendra Nagaich

Keyword(s):

Carbon Nanotubes ◽

Drug Delivery ◽

Quantum Dots ◽

Self Assembly ◽

Drug Delivery Systems ◽

Delivery Systems ◽

Atomic Scale ◽

Sustained Drug Delivery ◽

Pharmaceutical Nanotechnology ◽

Conventional Device

Nanotechnology deal with the particle size in nanometers. Nanotechnology is ranging from extensions of conventional device physics to completely new approaches based upon molecular self assembly, from developing new materials with dimensions on the nanoscale to direct control of matter on the atomic scale. In nanotechnology mainly three types of nanodevices are described: carbon nanotubes, quantum dots and dendrimers. It is a recent technique used as small size particles to treat many diseases like cancer, gene therapy and used as diagnostics. Nanotechnology used to formulate targeted, controlled and sustained drug delivery systems. Pharmaceutical nanotechnology embraces applications of nanoscience to pharmacy as nanomaterials and as devices like drug delivery, diagnostic, imaging and biosensor materials. Pharmaceutical nanotechnology has provided more fine tuned diagnosis and focused treatment of disease at a molecular level.

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Effect of Dapagliflozin on Intestinal Flora in MafA-deficient Mice

Current Pharmaceutical Design ◽

10.2174/1381612824666180912143434 ◽

2018 ◽

Vol 24 (27) ◽

pp. 3223-3231 ◽

Cited By ~ 3

Author(s):

Luyao Li ◽

Shiyao Xu ◽

Tingting Guo ◽

Shouliang Gong ◽

Chuan Zhang

Keyword(s):

Blood Glucose ◽

High Throughput Sequencing ◽

Fatty Acid Content ◽

Fasting Blood Glucose ◽

Intestinal Flora ◽

Short Chain Fatty Acids ◽

The Body ◽

Short Chain ◽

Control Group ◽

Deficient Mice

Objective: To investigate the effect of dapagliflozin on intestinal microflora in MafA-deficient mice using an animal model of diabetes. Methods: Male MafA-deficient mice were administered dapagliflozin (1.0 mg/kg/d) intragastrically for 6 weeks. Mouse body weights and fasting blood glucose levels were measured, and intestinal short-chain fatty acids were measured by gas chromatography. A series of methods was used to analyse the number of primary harmful bacteria in the faeces, and high-throughput sequencing was used to sequence the changes in intestinal flora. Results: The weight of the mice decreased after dapagliflozin gavage, and fasting blood glucose was significantly lower than that in the control group (P < 0.001). Acetic acid and butyric acid contents in the intestinal tracts of the mice increased, and the growth of harmful microorganisms, such as Clostridium perfringens, enterococci, Enterobacteriaceae, and intestinal enterococci, was inhibited. Blautia is a species found in the experimental group and was significantly different from the control and blank groups as determined by the LDA score from highthroughput sequencing. Conclusion: Dapagliflozin can reduce fasting blood glucose, decrease body weight, increase short-chain fatty acid content, regulate the intestinal microecological balance of the body and promote blood glucose and energy homeostasis.

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Toxicology

10.1093/oso/9780190662677.003.0007 ◽

2017 ◽

Author(s):

Robert Laumbach ◽

Michael Gochfeld

Keyword(s):

Molecular Mechanisms ◽

Molecular Targets ◽

Toxicity Testing ◽

The Body ◽

Toxic Substances ◽

Basic Principles ◽

Practical Applications ◽

Mechanisms Of Toxicity ◽

Body Distribution ◽

Threshold Doses

This chapter describes the basic principles of toxicology and their application to occupational and environmental health. Topics covered include pathways that toxic substances may take from sources in the environment to molecular targets in the cells of the body where toxic effects occur. These pathways include routes of exposure, absorption into the body, distribution to organs and tissues, metabolism, storage, and excretion. The various types of toxicological endpoints are discussed, along with the concepts of dose-response relationships, threshold doses, and the basis of interindividual differences and interspecies differences in response to exposure to toxic substances. The diversity of cellular and molecular mechanisms of toxicity, including enzyme induction and inhibition, oxidative stress, mutagenesis, carcinogenesis, and teratogenesis, are discussed and the chapter concludes with examples of practical applications in clinical evaluation and in toxicity testing.

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Potential use of molecular and structural characterization of the gut bacterial community for postmortem interval estimation in Sprague Dawley rats

Scientific Reports ◽

10.1038/s41598-020-80633-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Huan Li ◽

Siruo Zhang ◽

Ruina Liu ◽

Lu Yuan ◽

Di Wu ◽

...

Keyword(s):

High Throughput Sequencing ◽

Interval Estimation ◽

The Body ◽

Taxon Richness ◽

Time Since Death ◽

Sprague Dawley ◽

Sprague Dawley Rats ◽

Level Data ◽

Species Taxon

AbstractOnce the body dies, the indigenous microbes of the host begin to break down the body from the inside and play a key role thereafter. This study aimed to investigate the probable shift in the composition of the rectal microbiota at different time intervals up to 15 days after death and to explore bacterial taxa important for estimating the time since death. At the phylum level, Proteobacteria and Firmicutes showed major shifts when checked at 11 different intervals and emerged at most of the postmortem intervals. At the species level, Enterococcus faecalis and Proteus mirabilis showed a downward and upward trend, respectively, after day 5 postmortem. The phylum-, family-, genus-, and species-taxon richness decreased initially and then increased considerably. The turning point occurred on day 9, when the genus, rather than the phylum, family, or species, provided the most information for estimating the time since death. We constructed a prediction model using genus-level data from high-throughput sequencing, and seven bacterial taxa, namely, Enterococcus, Proteus, Lactobacillus, unidentified Clostridiales, Vagococcus, unidentified Corynebacteriaceae, and unidentified Enterobacteriaceae, were included in this model. The abovementioned bacteria showed potential for estimating the shortest time since death.

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Present trends in the encapsulation of anticancer drugs

Physical Sciences Reviews ◽

10.1515/psr-2020-0080 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Xavier Montané ◽

Karolina Matulewicz ◽

Karolina Balik ◽

Paulina Modrakowska ◽

Marcin Łuczak ◽

...

Keyword(s):

Carbon Nanotubes ◽

Drug Toxicity ◽

Recent Progress ◽

Polymeric Micelles ◽

Drug Loading ◽

The Body ◽

Inorganic Nanoparticles ◽

Hybrid Nanoparticles ◽

Traditional Medicines ◽

Low Solubility

Abstract Different nanomedicine devices that were developed during the recent years can be suitable candidates for their application in the treatment of various deadly diseases such as cancer. From all the explored devices, the nanoencapsulation of several anticancer medicines is a very promising approach to overcome some drawbacks of traditional medicines: administered dose of the drugs, drug toxicity, low solubility of drugs, uncontrolled drug delivery, resistance offered by the physiological barriers in the body to drugs, among others. In this chapter, the most important and recent progress in the encapsulation of anticancer medicines is examined: methods of preparation of distinct nanoparticles (inorganic nanoparticles, dendrimers, biopolymeric nanoparticles, polymeric micelles, liposomes, polymersomes, carbon nanotubes, quantum dots, and hybrid nanoparticles), drug loading and drug release mechanisms. Furthermore, the possible applications in cancer prevention, diagnosis, and cancer therapy of some of these nanoparticles have been highlighted.

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Differential Expression Analysis of Phytohormone-Related Genes of Korean Wheat (Triticum aestivum) in Response to Preharvest Sprouting and Abscisic Acid (ABA)

Applied Sciences ◽

10.3390/app11083562 ◽

2021 ◽

Vol 11 (8) ◽

pp. 3562

Author(s):

Yong Jin Lee ◽

Sang Yong Park ◽

Dae Yeon Kim ◽

Jae Yoon Kim

Keyword(s):

Abscisic Acid ◽

Differential Expression Analysis ◽

Preharvest Sprouting ◽

Global Changes ◽

Rna Seq ◽

Hormone Metabolism ◽

Global Issue ◽

End Use ◽

Transcriptomic Changes

Preharvest sprouting (PHS) is a key global issue in production and end-use quality of cereals, particularly in regions where the rainfall season overlaps the harvest. To investigate transcriptomic changes in genes affected by PHS-induction and ABA-treatment, RNA-seq analysis was performed in two wheat cultivars that differ in PHS tolerance. A total of 123 unigenes related to hormone metabolism and signaling for abscisic acid (ABA), gibberellic acid (GA), indole-3-acetic acid (IAA), and cytokinin were identified and 1862 of differentially expressed genes were identified and divided into 8 groups by transcriptomic analysis. DEG analysis showed the majority of genes were categorized in sugar related processes, which interact with ABA signaling in PHS tolerant cultivar under PHS-induction. Thus, genes related to ABA are key regulators of dormancy and germination. Our results give insight into global changes in expression of plant hormone related genes in response to PHS.

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