Molecular architectonics of DNA for functional nanoarchitectures

• Debasis Ghosh,
• Lakshmi P. Datta and
• Thimmaiah Govindaraju

Beilstein J. Nanotechnol. 2020, 11, 124–140, doi:10.3762/bjnano.11.11

• siRNA-loaded tetrahedrons at the tumor surface 25 min after injection. The siRNA-mediated gene silencing feature was monitored by performing an in vivo firefly luciferase gene expression analysis. The remarkable feature of this study was the one-step synthesis of hybrid DNA–siRNA tetrahedron

pH-Controlled fluorescence switching in water-dispersed polymer brushes grafted to modified boron nitride nanotubes for cellular imaging

• Saban Kalay,
• Yurij Stetsyshyn,
• Volodymyr Donchak,
• Khrystyna Harhay,
• Ostap Lishchynskyi,
• Halyna Ohar,
• Yuriy Panchenko,
• Stanislav Voronov and
• Mustafa Çulha

Beilstein J. Nanotechnol. 2019, 10, 2428–2439, doi:10.3762/bjnano.10.233

• biocompatibility, molecular recognition, chemical stability, and ability to be taken up in cells, etc. [55]. It is known that in living cells, both pH and temperature fluctuations are experienced during cellular processes such as endosytosis, gene expression, enzymatic reactions and metabolism [56][57]. Abnormal

Synthesis and potent cytotoxic activity of a novel diosgenin derivative and its phytosomes against lung cancer cells

• Liang Xu,
• Dekang Xu,
• Ziying Li,
• Yu Gao and
• Haijun Chen

Beilstein J. Nanotechnol. 2019, 10, 1933–1942, doi:10.3762/bjnano.10.189

• anticancer activities, such as restraining the hTERT gene expression in A549 lung cancer cells [3], inhibiting breast cancer stem-like cells via Wnt β-catenin signaling [4], impeding hepatocellular carcinoma cells by increasing DDX3 expression [5], and inducing apoptosis of prostate cancer cells through

Scavenging of reactive oxygen species by phenolic compound-modified maghemite nanoparticles

• Małgorzata Świętek,
• Yi-Chin Lu,
• Rafał Konefał,
• Liliana P. Ferreira,
• M. Margarida Cruz,
• Yunn-Hwa Ma and
• Daniel Horák

Beilstein J. Nanotechnol. 2019, 10, 1073–1088, doi:10.3762/bjnano.10.108

• Reactive oxygen species (ROS) play a critical role in maintaining homeostasis in living organisms because they participate in cell-signaling pathways that control programmed cell death, gene expression, and mechanisms of immune defense [1][2]. Excessive ROS are undesirable because they lead to oxidative

Characterization and influence of hydroxyapatite nanopowders on living cells

• Przemyslaw Oberbek,
• Tomasz Bolek,
• Adrian Chlanda,
• Seishiro Hirano,
• Sylwia Kusnieruk,
• Julia Rogowska-Tylman,
• Ganna Nechyporenko,
• Viktor Zinchenko,
• Wojciech Swieszkowski and
• Tomasz Puzyn

Beilstein J. Nanotechnol. 2018, 9, 3079–3094, doi:10.3762/bjnano.9.286

• induction of stress inside the cell and the activation of the tumour-suppressor gene p53 [73][74], which promotes the downstream gene expression finally leading to an apoptosis. Gene p53 is also activated by phosphorylation, that is, the attachment of the phosphate group (PO43−) to the protein chain [75][76

Enhanced antineoplastic/therapeutic efficacy using 5-fluorouracil-loaded calcium phosphate nanoparticles

• Shanid Mohiyuddin,
• Saba Naqvi and
• Gopinath Packirisamy

Beilstein J. Nanotechnol. 2018, 9, 2499–2515, doi:10.3762/bjnano.9.233

• transcription polymerase chain reaction assay for gene expression studies The apoptotic induction capability of CaP@5-FU NPs in HCT-15 cells was further validated by gene expression. For this, a semiquantitative polymerase chain reaction (PCR) analysis of antiapoptotic genes and proapoptotic genes in CaP@5-FU

• in the semiquantitative PCR analysis for gene expression studies further confirmed the apoptosis events during the CaP@5-FU NP treatment. Additionally, the intensified apoptotic expression in the cell population during the cell cycle analysis elucidated the role of CaP@5-FU NPs in apoptotic induction

Nano- and microstructured materials for in vitro studies of the physiology of vascular cells

• Alexandra M. Greiner,
• Adria Sales,
• Hao Chen,
• Sarah A. Biela,
• Dieter Kaufmann and
• Ralf Kemkemer

Beilstein J. Nanotechnol. 2016, 7, 1620–1641, doi:10.3762/bjnano.7.155

• the feature geometry and size. Some studies reported that proliferation of SMCs was negatively affected by PDMS microgrooves [204][205] and titanium oxide (TiO2) nanotube surfaces [31]. However, nanopits positively regulated SMC proliferation and gene expression [30]. In other studies, human SMCs from

• regulated their gene expression [197]. On titanium oxide (TiO2) nanotube surfaces, vascular SMCs expressed more SMC α-actin (a marker of differentiation) [129]. YAP/TAZ (Yes-associated protein/transcriptional coactivator with PDZ-binding motif) is a protein complex that induces the expression of

• study the influence of nucleus morphology in vascular cells gene expression and the role of mechanotransduction mechanisms involving gene regulation. Moreover, a study correlating actin-mediated cell tension, with nuclei deformation and genetic expression changes would be of interest, since it was

Tight junction between endothelial cells: the interaction between nanoparticles and blood vessels

• Yue Zhang and
• Wan-Xi Yang

Beilstein J. Nanotechnol. 2016, 7, 675–684, doi:10.3762/bjnano.7.60

• induce brain dysfunction and pathology [25] and in some cases have an impact on gene expression in neural cells [26]. CuO NPs reduce cell viability and also cause oxidative stress in human bronchial epithelial cells [27]. Interaction between NPs and blood circulatory system The circulatory system or

Unraveling the neurotoxicity of titanium dioxide nanoparticles: focusing on molecular mechanisms

• Bin Song,
• Yanli Zhang,
• Jia Liu,
• Xiaoli Feng,
• Ting Zhou and
• Longquan Shao

Beilstein J. Nanotechnol. 2016, 7, 645–654, doi:10.3762/bjnano.7.57

• associated with poor performance in the Morris water maze test and passive avoidance test [58]. Maternal exposure to TiO2 NPs can also affect the production of dopamine and its metabolites, as determined by high performance liquid chromatography (HPLC) [59], and alter gene expression related to dopamine

• expression not caused through changes to the DNA sequence itself, but rather arise during development and cell proliferation [13][14]. In other words, the epigenetics represents the interactions between gene expression and environmental factors, and the relationship between genes, which were modulated during

• delivered to the lysosome. Autophagy also acts as a dynamic recycling system wherein new building blocks and energy, for cellular renovation and homeostasis, are produced [12]. The literal meaning of “epigenetics” is “outside conventional genetics”, which is defined as all heritable alternations in gene

Mismatch detection in DNA monolayers by atomic force microscopy and electrochemical impedance spectroscopy

• Maryse D. Nkoua Ngavouka,
• Pietro Capaldo,
• Elena Ambrosetti,
• Giacinto Scoles,
• Loredana Casalis and
• Pietro Parisse

Beilstein J. Nanotechnol. 2016, 7, 220–227, doi:10.3762/bjnano.7.20

• SNP, confirming the relevance of immobilized DNA on solid supports in life science studies, including single cell RNA characterization, gene expression profile and genetic variability. Moreover, the complementarity of the two techniques (one more sensitive to the morphological and mechanical changes

Nanoinformatics for environmental health and biomedicine

• Rong Liu and
• Yoram Cohen

Beilstein J. Nanotechnol. 2015, 6, 2449–2451, doi:10.3762/bjnano.6.253

• nanoparticles, carbon black, and carbon nanotubes) were also identified using biclustering of gene expression data and gene set enrichment analysis methods [16]. Various visual analytical approaches (e.g., bipartite graphs, log-ratio analysis, and multidimensional scaling) are demonstrated in another study for

Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials

• Andrew Williams and
• Sabina Halappanavar

Beilstein J. Nanotechnol. 2015, 6, 2438–2448, doi:10.3762/bjnano.6.252

• were examined and functionally related biclusters of genes showing similar expression profiles were identified. The identified biclusters were then used to conduct a gene set enrichment analysis on pulmonary gene expression profiles derived from mice exposed to nano-titanium dioxide (nano-TiO2), carbon

• advantage of using a data-driven approach to identify novel, functionally related gene sets. The results can be used in future gene set enrichment analysis studies involving NMs or as features for clustering and classifying NMs of diverse properties. Keywords: gene expression; risk assessment

• ; toxicogenomics; Introduction Metadata analysis that leverages genomics data has become increasingly popular as more experiments populate publicly available data repositories such as the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) and European Bioinformatics Institute (EBI; https

Experiences in supporting the structured collection of cancer nanotechnology data using caNanoLab

• Stephanie A. Morris,
• Sharon Gaheen,
• Michal Lijowski,
• Mervi Heiskanen and
• Juli Klemm

Beilstein J. Nanotechnol. 2015, 6, 1580–1593, doi:10.3762/bjnano.6.161

• need for standards and databases to house the extensive amount of data generated by gene expression and sequencing experiments, yielding such efforts as the development of the minimum information about a microarray experiment (MIAME) [16]. As a result, the MIAME guideline, and others, have been adopted

PLGA nanoparticles as a platform for vitamin D-based cancer therapy

• Maria J. Ramalho,
• Joana A. Loureiro,
• Bárbara Gomes,
• Manuela F. Frasco,
• Manuel A. N. Coelho and
• M. Carmo Pereira

Beilstein J. Nanotechnol. 2015, 6, 1306–1318, doi:10.3762/bjnano.6.135

• targeting gene expression via both genomic and nongenomic pathways [1]. Although known as an important regulator of calcium homeostasis and bone mineralization [3], several studies support that vitamin D also plays a major role in tumor pathogenesis, progression and therapy [2]. Calcitriol is also regarded

Hematopoietic and mesenchymal stem cells: polymeric nanoparticle uptake and lineage differentiation

• Ivonne Brüstle,
• Thomas Simmet,
• Gerd Ulrich Nienhaus,
• Katharina Landfester and
• Volker Mailänder

Beilstein J. Nanotechnol. 2015, 6, 383–395, doi:10.3762/bjnano.6.38

• the complex process of hMSC and hHSC differentiation, it is hard to determine at which point the particle influence takes place. As we observed some gene expression changes, a closer look at the molecular level of the interaction between nanoparticles and cells should be the aim of future research to

• normalize the gene expression level in hHSCs. For hMSCs, expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and β2 microglobulin (B2M) was used to normalize the gene expression level. The relative difference in the expression level was calculated using the ΔΔCT method, setting the expression in

Synthesis of boron nitride nanotubes and their applications

• Saban Kalay,
• Zehra Yilmaz,
• Ozlem Sen,
• Melis Emanet,
• Emine Kazanc and
• Mustafa Çulha

Beilstein J. Nanotechnol. 2015, 6, 84–102, doi:10.3762/bjnano.6.9

• -embedded polylactide-polycaprolactone (PLC–BNNT) in orthopedic implants [75]. Using real-time PCR methods, they studied the RunX2 gene expression profile, which is a transcription factor responsible for enhancing the cell proliferation. The results of the experiments showed that the PLC–BNNTs increased the

• RunX2 gene expression of the osteoblast cells up to sevenfold. It was concluded that the positive effect of the BNNTs embedded into the scaffold on the cell proliferation was due to the natural affinity of proteins to the hydrophobic BNNTs [75]. Ciofani et al. investigated the cytotoxicity of GC–BNNTs

• of a scaffold and up regulated the gene expression for increased cell viability for orthopedic applications [75]. Hydroxypatite (HA) is an important material used in orthopedic implant applications [89]. 4 wt % of BNNTs were added into HA to improve its mechanical properties. It was found that

Anticancer efficacy of a supramolecular complex of a 2-diethylaminoethyl–dextran–MMA graft copolymer and paclitaxel used as an artificial enzyme

• Yasuhiko Onishi,
• Yuki Eshita,
• Rui-Cheng Ji,
• Masayasu Onishi,
• Takashi Kobayashi,
• Masaaki Mizuno,
• Jun Yoshida and
• Naoji Kubota

Beilstein J. Nanotechnol. 2014, 5, 2293–2307, doi:10.3762/bjnano.5.238

• effects were revealed by gene expression array analysis [5]. Remarkably, AP-GA-treated cells exhibited an increased expression of HSP70 and HSP27 compared to cells treated with GA and P[AP-GA] [5]. It was proposed that the conjugation of AP-GA to the N-(2-hydroxypropyl)methacrylamide copolymer resulted in

• -degrading enzyme dextransucrase. The polymer micelle of DDMC forms a complex with DNA, undergoes endocytosis, and a small proportion of the complex is transported to the nucleus. However, analysis of gene expression by using DDMC/DNA has revealed that the majority of the complex is found not in the nucleus

• convex survival curve in Figure 5a. This convex survival curve is considered to be the product of gene expression at low concentrations of PTX (event A) and a factor negatively associated with survival at higher concentrations of PTX (event B). It is assumed that event A is related to the MDR of the

Effect of silver nanoparticles on human mesenchymal stem cell differentiation

• Christina Sengstock,
• Jörg Diendorf,
• Matthias Epple,
• Thomas A. Schildhauer and
• Manfred Köller

Beilstein J. Nanotechnol. 2014, 5, 2058–2069, doi:10.3762/bjnano.5.214

• monodispersed silver nanoparticles. In summary, Ag-NP exert multiple effects on cellular physiology and signal transduction, which can lead to alterations in gene expression. The adipogenic and osteogenic differentiation of hMSCs is clearly down-regulated even at subtoxic concentrations of Ag-NP. Conclusion In

Carbon-based smart nanomaterials in biomedicine and neuroengineering

• Antonina M. Monaco and
• Michele Giugliano

Beilstein J. Nanotechnol. 2014, 5, 1849–1863, doi:10.3762/bjnano.5.196

• of NDs has been proposed by several research groups, who monitored gene expression of cells. No significant change in the expression of Bcl-x and TNF-α genes [65] was found, while a decreased expression of genes responding to genotoxic compounds was described; in addition, no effects on the

Biocompatibility of cerium dioxide and silicon dioxide nanoparticles with endothelial cells

• Claudia Strobel,
• Martin Förster and
• Ingrid Hilger

Beilstein J. Nanotechnol. 2014, 5, 1795–1807, doi:10.3762/bjnano.5.190

• been derived from different tissue types. Interestingly, the gene expression profiles of microvascular and macrovascular endothelial cells are different between each other; the expression patterns are also determined by the respective tissue from which they have been derived [38][39]. Therefore, it is

• conceivable that the observed differences in sensitivity of the two endothelial cell types in our study (HMEC-1: immortalized, microvascular; HUVEC: primary, macrovascular) to CeO2 nanoparticle exposure is a result of different gene expression patterns. Furthermore, the difference in the stability of actin

Silica nanoparticles are less toxic to human lung cells when deposited at the air–liquid interface compared to conventional submerged exposure

• Alicja Panas,
• Andreas Comouth,
• Harald Saathoff,
• Thomas Leisner,
• Marco Al-Rawi,
• Michael Simon,
• Gunnar Seemann,
• Olaf Dössel,
• Sonja Mülhopt,
• Hanns-Rudolf Paur,
• Susanne Fritsch-Decker,
• Carsten Weiss and
• Silvia Diabaté

Beilstein J. Nanotechnol. 2014, 5, 1590–1602, doi:10.3762/bjnano.5.171

• of ZnO particles under submerged and ALI conditions. Interestingly, the response (LDH release, HO-1 induction) occurred more rapidly at the ALI but to a similar extend [37]. Similarly, exposure of A549 cells to ZnO particles at the ALI provoked a stronger increase in pro-inflammatory gene expression

• confirm a reduced toxicity of NPs at the ALI in general or rather to identify a NP-specific behaviour that depends on the exposure method. Furthermore, it is possible that at the ALI gene expression will change compared to submerged cultures, a topic which warrants further investigations. Indeed, human

In vitro interaction of colloidal nanoparticles with mammalian cells: What have we learned thus far?

• Moritz Nazarenus,
• Qian Zhang,
• Mahmoud G. Soliman,
• Pablo del Pino,
• Beatriz Pelaz,
• Susana Carregal-Romero,
• Joanna Rejman,
• Barbara Rothen-Rutishauser,
• Martin J. D. Clift,
• Reinhard Zellner,
• G. Ulrich Nienhaus,
• James B. Delehanty,
• Igor L. Medintz and
• Wolfgang J. Parak

Beilstein J. Nanotechnol. 2014, 5, 1477–1490, doi:10.3762/bjnano.5.161

• has to be assessed. In the context of this review we have focused on in vitro studies. The advantage of such studies is the easy screening capability and the possibility to monitor in detail biomolecular pathways and changes in gene expression as a measure of a possible biologically adverse response

The cell-type specific uptake of polymer-coated or micelle-embedded QDs and SPIOs does not provoke an acute pro-inflammatory response in the liver

• Markus Heine,
• Alexander Bartelt,
• Oliver T. Bruns,
• Denise Bargheer,
• Artur Giemsa,
• Barbara Freund,
• Ludger Scheja,
• Christian Waurisch,
• Alexander Eychmüller,
• Rudolph Reimer,
• Horst Weller,
• Peter Nielsen and
• Joerg Heeren

Beilstein J. Nanotechnol. 2014, 5, 1432–1440, doi:10.3762/bjnano.5.155

• process that is dependent on the LDL receptor and apolipoprotein E, by hepatocytes. Gene expression analysis of pro-inflammatory markers such as tumor necrosis factor alpha (TNFα) or chemokine (C-X-C motif) ligand 10 (Cxcl10) indicated that 48 h after injection internalized nanocrystals did not provoke

• , we measured pro-inflammatory markers by gene expression analysis after the injection of SPIO nanocrystals embedded by different coats. Intravenous injection of Ferinject® (contains ferric carboxymaltose that is commonly given to treat iron deficits) at high doses caused a significant induction of pro

• intracellular multiprotein oligomer, the so-called-inflammasome [31], which can be activated by intracellular aggregates such as ureate or cholesterol crystals [32]. Notably, hepatic internalization of Ferinject® or SPIOs delivered by polymer or lipid micelles did not influence Il1b gene expression underlining

Mimicking exposures to acute and lifetime concentrations of inhaled silver nanoparticles by two different in vitro approaches

• Fabian Herzog,
• Kateryna Loza,
• Sandor Balog,
• Martin J. D. Clift,
• Matthias Epple,
• Peter Gehr,
• Alke Petri-Fink and
• Barbara Rothen-Rutishauser

Beilstein J. Nanotechnol. 2014, 5, 1357–1370, doi:10.3762/bjnano.5.149

• could be observed when simultaneously exposed with Ag NPs. Ag NPs were not found to interfere with the ELISA assay (data not shown). Gene expression of pro-inflammatory and oxidative stress markers As described in [44], the total RNA content of the triple cell co-cultures was collected 4 and 24 h after

Molecular biology approaches in bioadhesion research

• Marcelo Rodrigues,
• Birgit Lengerer,
• Thomas Ostermann and
• Peter Ladurner

Beilstein J. Nanotechnol. 2014, 5, 983–993, doi:10.3762/bjnano.5.112

• temporary adhesives that contain a significant carbohydrate fraction usually also rely on proteins for adhesion. Review 1. Transcriptome sequencing and differential gene expression 1.1 What is a transcriptome? A transcriptome represents the entirety of RNA molecules expressed in an organism, a tissue or a

• differential RNA-seq experiment can be compared to the established transcriptome database. 3. Spatial gene expression 3.1 Aim of in situ hybridization For detecting the spatial (and temporal) expression of genes within a tissue, ISH is a widespread and straightforward method. The principle of ISH can be used

• validate the expression of an adhesion-related candidate transcript list that resulted from previous mass spectrometry or differential gene expression experiments. For high-throughput approaches, in situ robots such as “InsituPro VSi” from Invatis AG are available. For medium scale ISH screenings, a manual