Molecule-level imaging of Pax6 mRNA distribution in mouse embryonic neocortex by molecular interaction force microscopy

Comprehensive analysis of mRNAs in the cerebral cortex in APP/PS1 double-transgenic mice with Alzheimer's disease based on high-throughput sequencing of N4-acetylcytidine

N4-acetylcytidine (ac4C), a significant modified nucleoside, participates in the development of many diseases. Messenger RNAs (mRNAs) contain most of the information of the genome and are the molecules that transmit information from genes to proteins. Alzheimer's disease (AD) is a progressive neurodegenerative disease in which fibrillar amyloid plaques are present. However, it remains unknown how mRNA ac4C modification affects the development of AD. In the current study, ac4C-modified mRNAs were comprehensively analyzed in AD mice by ac4C-RIP-seq and RNA-seq. Next, a protein-protein interaction (PPI) network was constructed to examine the relationships between the genes with differential ac4C modification levels and their RNA expression levels. The differentially expressed genes (DEGs) acquired above were subjected to Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to further analyze the molecular mechanisms in AD. In total, 3312 significant ac4C peaks were found on 2512 mRNAs, 1241 of which were hyperacetylated and 1271 of which were hypoacetylated. In addition, 956 mRNAs with differential expression were found, including 520 upregulated mRNAs and 436 downregulated mRNAs. Overall, 134 mRNAs with simultaneous changes at the ac4C levels as well as RNA expression levels were identified via joint analysis. Then, through PPI network construction and functional enrichment analysis, 37 key mRNAs were screened, which were predominantly enriched in GABAergic synapses and the PI3K/AKT signaling pathway. The significant difference in the abundance of mRNA ac4C modification indicates that this modification is associated with AD progression, which may provide insight for more investigations of the potential mechanisms.

Ascent of atomic force microscopy as a nanoanalytical tool for exosomes and other extracellular vesicles

Over the last 30 years, atomic force microscopy (AFM) has made several significant contributions to the field of biology and medicine. In this review, we draw our attention to the recent applications and promise of AFM as a high-resolution imaging and force sensing technology for probing subcellular vesicles: exosomes and other extracellular vesicles. Exosomes are naturally occurring nanoparticles found in several body fluids such as blood, saliva, cerebrospinal fluid, amniotic fluid and urine. Exosomes mediate cell-cell communication, transport proteins and genetic content between distant cells, and are now known to play important roles in progression of diseases such as cancers, neurodegenerative disorders and infectious diseases. Because exosomes are smaller than 100 nm (about 30-120 nm), the structural and molecular characterization of these vesicles at the individual level has been challenging. AFM has revealed a new degree of complexity in these nanosized vesicles and generated growing interest as a nanoscale tool for characterizing the abundance, morphology, biomechanics, and biomolecular make-up of exosomes. With the recent interest in exosomes for diagnostic and therapeutic applications, AFM-based characterization promises to contribute towards improved understanding of these particles at the single vesicle and sub-vesicular levels. When coupled with complementary methods like optical super resolution STED and Raman, AFM could further unlock the potential of exosomes as disease biomarkers and as therapeutic agents.

Atomic force microscopy of RNA: State of the art and recent advancements

The atomic force microscope (AFM) has become a powerful tool for the visualization, probing and manipulation of RNA at the single molecule level. AFM measurements can be carried out in buffer solution in a physiological medium, which is crucial to study the structure and function of biomolecules, also allowing studying them at work. Imaging the specimen in its native state is a great advantage compared to other high resolution methods such as electron microscopy and X-ray diffraction. There is no need to stain, freeze or crystallize biological samples. Moreover, compared to NMR spectroscopy for instance, for AFM studies the size of the biomolecules is not limiting. Consequently the AFM allows one also to investigate larger RNA molecules. In particular, structural studies of nucleic acids and assemblies thereof, have been carried out by AFM routinely including ssRNA, dsRNA and nucleoprotein complexes thereof, as well as RNA aggregates and 2D RNA assemblies. These are becoming increasingly important as novel unique building blocks in the emerging field of RNA nanotechnology. In particular by AFM unique information can be obtained on these RNA based assemblies. Moreover, the AFM is of fundamental relevance to study biological relevant RNA interactions and dynamics. In this short review a brief overview will be given on structural studies that have been done related to AFM topographic imaging of RNA, RNA assemblies and aggregates. Finally, an overview on AFM beyond imaging will be provided. This includes force spectroscopy of RNA under physiological conditions in aqueous buffer to probe RNA interaction with proteins and ligands as well as other AFM tip based RNA probing. Important applications include the detection and quantification of RNA in biological samples. A selection of recent highlights and breakthroughs will be provided related to structural and functional studies by AFM. The main intention of this short review to provide the reader with a flavor of what AFM is able to contribute to RNA research and engineering.

Spatially nanoscale-controlled functional surfaces toward efficient bioactive platforms

Interest in well-defined surface architectures has shown a steady increase, particularly among those involved in biological applications where the reactivity of functional groups on the surface is desired to be close to that of the solution phase. Recent research has demonstrated that utilizing the self-assembly process is an attractive and viable choice for the fabrication of two-dimensional nanoscale-controlled architectures. This review highlights representative examples for controlling the spatial placement of reactive functional groups in the optimization of bioactive surfaces. While the selection is not comprehensive, it becomes evident that surface architecture is one of the key components in allowing efficient biomolecular interactions with surfaces and that the optimized lateral spacing between the immobilized molecules is crucial and even critical in some cases.

Imaging a specific mRNA in pollen with atomic force microscopy

Distribution of ammonium transporter mRNA in a sectioned pollen is studied at the higher resolution, and localization of the mRNA in the nucleus of the sperm cells is observed.

Direct quantitative analysis of HCV RNA by atomic force microscopy without labeling or amplification

Force-based atomic force microscopy (AFM) was used to detect HCV (hepatitis C virus) RNA directly and to quantitatively analyse it without the need for reverse transcription or amplification. Capture and detection DNA probes were designed. The former was spotted onto a substrate with a conventional microarrayer, and the latter was immobilized on an AFM probe. To control the spacing between the immobilized DNAs on the surface, dendron self-assembly was employed. Force-distance curves showed that the mean force of the specific unbinding events was 32 ± 5 pN, and the hydrodynamic distance of the captured RNA was 30-60 nm. Adhesion force maps were generated with criteria including the mean force value, probability of obtaining the specific curves and hydrodynamic distance. The maps for the samples whose concentrations ranged from 0.76 fM to 6.0 fM showed that cluster number has a linear relationship with RNA concentration, while the difference between the observed number and the calculated one increased at low concentrations. Because the detection limit is expected to be enhanced by a factor of 10 000 when a spot of 1 micron diameter is employed, it is believed that HCV RNA of a few copy numbers can be detected by the use of AFM.

Atomic force microscopy on chromosomes, chromatin and DNA: a review

The purpose of this review is to discuss the achievements and progress that has been made in the use of atomic force microscopy in DNA related research in the last 25 years. For this review DNA related research is split up in chromosomal-, chromatin- and DNA focused research to achieve a logical flow from large- to smaller structures. The focus of this review is not only on the AFM as imaging tool but also on the AFM as measuring tool using force spectroscopy, as therein lays its greatest advantage and future. The amazing technological and experimental progress that has been made during the last 25 years is too extensive to fully cover in this review but some key developments and experiments have been described to give an overview of the evolution of AFM use from 'imaging tool' to 'measurement tool' on chromosomes, chromatin and DNA.

Ferritin-based new magnetic force microscopic probe detecting 10 nm sized magnetic nanoparticles

A single-molecule ferritin picking-up process was realized with the use of AFM, which was enhanced by employing controlled dendron surface chemistry. The approach enabled the placement of a single ferritin protein molecule at the very end of an AFM tip. When used for magnetic force microscopy (MFM) imaging, the tips were able to detect magnetic interactions of approximately 10 nm sized magnetic nanoparticles. The single ferritin tip also showed the characteristics of a "multifunctional" MFM probe that can sense the magnetic force from magnetic materials as well as detect the biomolecular interaction force with DNAs on the surface. The multifunctional tip enabled us not only to investigate the specific molecular interaction but also to image the magnetic interaction between the probe and the substrate, in addition to allowing the common capability of topographic imaging. Because the protein engineering of ferritin and the supporting coordination and conjugation chemistry are well-established, we envisage that it would be straightforward to extend this approach to the development of various single magnetic particle MFM probes of different compositions and sizes.

Molecular imaging of membrane proteins and microfilaments using atomic force microscopy

Atomic force microscopy (AFM) is an emerging technique for a variety of uses involving the analysis of cells. AFM is widely applied to obtain information about both cellular structural and subcellular events. In particular, a variety of investigations into membrane proteins and microfilaments were performed with AFM. Here, we introduce applications of AFM to molecular imaging of membrane proteins, and various approaches for observation and identification of intracellular microfilaments at the molecular level. These approaches can contribute to many applications of AFM in cell imaging.

Phloem cytochemical modification and gene expression following the recovery of apple plants from apple proliferation disease

Recovery of apple trees from apple proliferation was studied by combining ultrastructural, cytochemical, and gene expression analyses to possibly reveal changes linked to recovery-associated resistance. When compared with either healthy or visibly diseased plants, recovered apple trees showed abnormal callose and phloem-protein accumulation in their leaf phloem. Although cytochemical localization detected Ca(2+) ions in the phloem of all the three plant groups, Ca(2+) concentration was remarkably higher in the phloem cytosol of recovered trees. The expression patterns of five genes encoding callose synthase and of four genes encoding phloem proteins were analyzed by quantitative real-time reverse transcription-polymerase chain reaction. In comparison to both healthy and diseased plants, four of the above nine genes were remarkably up-regulated in recovered trees. As in infected apple trees, phytoplasma disappear from the crown during winter, but persist in the roots, and it is suggested that callose synthesis/deposition and phloem-protein plugging of the sieve tubes would form physical barriers preventing the recolonization of the crown during the following spring. Since callose deposition and phloem-protein aggregation are both Ca(2+)-dependent processes, the present results suggest that an inward flux of Ca(2+) across the phloem plasma membrane could act as a signal for activating defense reactions leading to recovery in phytoplasma-infected apple trees.

Interactions between signal-transducing proteins measured by atomic force microscopy

Atomic force microscopy (AFM) has been used to study the specific interactions between the signal-transducing proteins mammalian phospholipase D1 (PLD1), phospholipase C-gamma1 (PLC-gamma1), and Munc-18-1. To record the forces between them, the Phox homology (PX) domain of PLD1, the Src homology (SH3) domain of PLC-gamma1, and Munc-18-1 were fused with glutathione S-transferase (GST) and immobilized onto reduced glutathione (GSH)-tethered surfaces. In order to enhance the recognition efficiency and avoid undesirable complications, both AFM tips and substrates were first modified with dendrons of two different sizes. Under the employed conditions, the probability of observing an unbinding event increased, most force-distance curves showed the single rupture events, and the unbinding forces were 51 +/- 2 pN for PX-(Munc-18-1) and 42 +/- 2 pN for PX-SH3. To investigate dynamics of these biomolecular interactions, we measured the loading rate dependence of the unbinding forces. The unbinding forces increased linearly with the logarithm of the loading rate, indicating the presence of a single potential barrier in the dissociation energy landscape. The measured off-rate constants (k(off)) at 15 degrees C were 10(-3.4 +/- 0.3) s(-1) for PX-(Munc-18-1) and 10(-1.7 +/- 0.1) s(-1) for PX-SH3. Further, we elucidated the influence of free SH3 and Munc-18-1 on the specific PX-(Munc-18-1) and PX-SH3 interaction, respectively.