peering-at-brain-polysomes-with-atomic-force-microscopy

Peering at Brain Polysomes with Atomic Force Microscopy

The translational machinery, i.e., the polysome or polyribosome, is one of the biggest and most complex cytoplasmic machineries in cells. Polysomes, ...

Fondazione Bruno Kessler

A steady-state kinetic study of bovine serum amine oxidase activity was performed, over a wide range of pH values (5.4-10.2) and ionic strength (10-200 mM), using various (physiological and analogue) substrates as specific probes of the active-site binding region. Relatively small changes in k (cat) values (approx. one order of magnitude) accompanied by marked changes in K(m) and k(cat)/K(m) values (approx. six orders of magnitude) were observed. This behaviour was correlated with the presence of positively charged groups or apolar chains in the substrates. In particular, it was found that the docking of the physiological polyamines, i.e. spermidine and spermine, appears to be modulated by three amino acid residues of the active site, which we have named L(-)H(+), G(-)H(+) and IH(+), characterized by p K (a) values of 6.2+/-0.2 [Di Paolo, Scarpa, Corazza, Stevanato and Rigo (2002) Biophys. J. 83, 2231-2239], 8.2+/-0.3 and 7.8+/-0.4 respectively. The electrostatic interaction between the protonated substrates and the enzyme containing the residues L(-)H(+), G(-)H(+) and IH(+) in the deprotonated form, the on/off role of the IH(+) residue and the role of hydrophobic interactions with substrates characterized by apolar chains are discussed.

Electrostatic compared with hydrophobic interactions between bovine serum amine oxidase and its substrates.

The study of the adhesion of lipid vesicles on surfaces is of increasing interest in the field of medical implants and tissue engineering (protein-resistant surfaces), drug delivery, biosensors, and biochips. In this work, lipid coverage was developed from PEG-coated vesicles (with sizes from 100 to 300 nm) by covalently binding poly(ethylene glycol)-alpha-disteroylphosphatidylethanolamine-omega-benzotriazole carbonate (DSPE-PEG-BTC) molecules onto the surface amine groups by carbamate chemistry. Lipid surface density and the surface structure of multilamellar (MLVs) and extruded unilamellar (LUVs) vesicles deposited on three types of polystyrene (PS) well-plates were probed by fluorescence and atomic force microscopy (AFM) imaging. A significant difference in the vesicle surface coverage of PS substrates was observed with a substantial increase in lipid multilayers on the amine-enriched PS surface using both unilamellar and multilamellar vesicles.

Covalently anchored lipid structures on amine-enriched polystyrene.

In this study we analyzed the surface properties of different silicon-based materials used for micro-electro-mechanical systems (MEMS) production, such as thermally grown silicon oxide, plasma-enhanced chemical vapor deposition (PECVD)-treated silicon oxide, reactive-ion etch (RIE)-treated silicon oxide, and Pyrex. Substrates were characterized by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS) to define the surface chemical and morphological properties, and by fluorescence microscopy to directly assess the absorption of the different polymerase chain reaction (PCR) components. By using microchips fabricated with the same materials we investigated their compatibility with PCR reactions, exploiting the use of different enzymes and reagents or proper surface treatments. We established the best conditions for DNA amplification in silicon/Pyrex microdevices depending on the type of device and fabrication method used and the quality of reagents, rather than on the passivation treatment or increment in standard Taq polymerase concentration.

Effect of materials for micro-electro-mechanical systems on PCR yield.

In this study the initial reactions of different carbon-based materials with human blood were investigated by short-time exposure to platelet poor plasma (PPP). Extent of protein adsorption and conformational changes of proteins adsorbed on material surfaces are known to be keys factors affecting further biological reactions. Plasma protein adsorption on multi-walled carbon nanotubes (MWCNTs), highly oriented pyrolytic graphite (HOPG) and nanocrystalline graphite (NG) were investigated and the results obtained on these materials were compared with those obtained studying pyrolytic carbon (PyC), a material showing good anti-trombogenic properties. The quantification of adsorbed plasma proteins on sample surfaces was obtained by Micro BCA Protein Assay, while immunofluorescence analysis was employed to monitor the surface density and distribution of two selected proteins, namely fibrinogen (Fg) and Hageman factor (FXII), proteins playing a leading role in mediating platelet adhesion. The dependence of the biological response on the surface chemical and morphological properties were also investigated and data obtained using X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and atomic force microscopy (AFM) are presented. After PPP incubation PyC is characterized by the presence of low level of whole proteins and FXII adsorption, in contrast to a high adhesion of Fg. Compared to PyC the analysis of the other carbon-based materials result in a higher whole protein adsorption with an increasing trend moving from MWCNTs, NG and HOPG respectively. The Fg surface density on PyC, NG and MWCNTs is about four times higher than on HOPG while only HOPG show a detectable fluorescent signal of FXII. If AFM data indicate that surface morphology does not play a crucial role in protein adhesion, XPS analysis show chemical differences that can be correlated with this biological response.

Human plasma protein adsorption on carbon-based materials.

In this paper we report an innovative use of Poly(DiMethyl)Siloxane (PDMS) to design a microfluidic device that combines, for the first time, in one single reaction chamber, DNA purification from a complex biological sample (blood) without elution and PCR without surface passivation agents. This result is achieved by exploiting the spontaneous chemical structure and nanomorphology of the material after casting. The observed surface organization leads to spontaneous DNA adsorption. This property allows on-chip complete protocols of purification of complex biological samples to be performed directly, starting from cells lysis. Amplification by PCR is performed directly on the adsorbed DNA, avoiding the elution process that is normally required by DNA purification protocols. The use of one single microfluidic volume for both DNA purification and amplification dramatically simplifies the structure of microfluidic devices for DNA preparation. X-Ray Photoelectron Spectroscopy (XPS) was used to analyze the surface chemical composition. Atomic Force Microscopy (AFM) and Field Emission Scanning Electron Microscopy (FESEM) were employed to assess the morphological nanostructure of the PDMS-chips. A confocal fluorescence analysis was utilized to check DNA distribution inside the chip.

Solid phase DNA extraction on PDMS and direct amplification.

The cytotoxic cell granule secretory pathway is essential for immune defence. How the pore-forming protein perforin (PFN) facilitates the cytosolic delivery of granule-associated proteases (granzymes) remains enigmatic. Here we show that PFN is able to induce invaginations and formation of complete internal vesicles in giant unilamellar vesicles. Formation of internal vesicles depends on native PFN and calcium and antibody labeling shows the localization of PFN at the invaginations. This vesiculation is recapitulated in large unilamellar vesicles and in this case PFN oligomers can be seen associated with the necks of the invaginations. Capacitance measurements show PFN is able to increase a planar lipid membrane surface area in the absence of pore formation, in agreement with the ability to induce invaginations. Finally, addition of PFN to Jurkat cells causes the formation of internal vesicles prior to pore formation. PFN is capable of triggering an endocytosis-like event in addition to pore formation, suggesting a new paradigm for its role in delivering apoptosis-inducing granzymes into target cells.

Perforin activity at membranes leads to invaginations and vesicle formation.

Whispering gallery mode resonators (WGMR), as silica microspheres, have been recently proposed as an efficient tool for the realisation of optical biosensors. In this work we present a functionalization procedure based on the DNA-aptamer sequence immobilization on WGMR, able to recognize specifically thrombin or VEGF protein, preserving a high Q factor. The protein binding was optically characterized in terms of specificity in buffer solution or in 10% diluted human serum. Simulation of the protein flow was found in good agreement with experimental data. The aptasensor was also chemically regenerated and tested again, demonstrating the reusability of our system.

Whispering gallery mode aptasensors for detection of blood proteins.

There is an increasing interest in circulating microRNAs (miRNAs) as potential minimally invasive diagnostic biomarkers in oncology. Considerable efforts are being made in the development of lab-on-a-chip devices for biomedical applications to purify and detect miRNAs from biological fluids. Here, we report the development of an innovative polydimethylsiloxane (PDMS)-based parallel device whose internal surface can opportunely be functionalized with positively charged 3-aminopropyltriethoxysilane (APTES) alone or mixed with two different neutral poly(ethylene glycol) silanes (PEG-s). The differently functionalized internal surfaces of the PDMS chip were characterized with s-SDTB (sulfosuccinimidyl-4-o-(4,4-dimethoxytrityl) butyrate) and the portion of the surface able to adsorb a synthetic fluorescently labeled miRNA was determined. Interestingly, the adsorbed miRNA (both synthetic and cell supernatant-derived) was found mainly on the bottom surface of the chip and could be reverse transcribed into cDNA directly on the same PDMS chip used for its purification, saving hours with respect to the use of standard purification kits. We identified 0.1% APTES/0.9% PEG-silane as the most efficient PDMS functionalization to capture both synthetic and extracellular miRNA. Moreover, the amount of captured miRNA was increased by treating the cell supernatant with a commercially available lysis buffer for RNA extraction. We assessed that the available miRNA binding sites on the functionalized surface were efficiently saturated with only one incubation, shortening the time and greatly simplifying the protocol for miRNA purification from biological samples. Finally, the extracellular miRNA purification efficiency of the PDMS functionalized multichip determined via real-time quantitative polymerase chain reaction (RT-qPCR) was confirmed by droplet digital PCR (ddPCR) quantification. This work shows an innovative, rapid and easy to use microdevice for the purification and reverse transcription of circulating miRNAs, approaching the realization of diagnostic and prognostic oncomiR-based assays.

OncomiR detection in circulating body fluids: a PDMS microdevice perspective.

The need for decentralized clinical tests together with the concept of time and cost saving are pushing the development of portable, miniaturized, compact biosensors with diagnostic and prognostic purpose. Here, we propose an innovative detection system based on a Single Photon Avalanche Diode (SPAD) with high sensitivity and low noise, crucial features for an efficient chemiluminescence biosensor. The SPAD detector, having 60 µm diameter, has a Photon Detection Efficiency higher than 55% at 425 nm and a Dark Count Rate lower than 100 Hz at room temperature. Our design allows a good optical coupling efficiency between sample and detector. A specific biofunctional surface was implemented taking advantage of aptamers, short DNA sequences having high selectivity and affinity toward their targets. We successfully detected physiological levels of Vascular Endothelial Growth Factor (VEGF), a circulating protein biomarker highly correlated with cancer. The SPAD aptasensor showed a Limit of Detection (LoD) in the pM range, stability (up to 42 days) and re-usability (up to seven cycles). This compact biosensor is therefore a promising step toward the actual use of portable microdevices in diagnostics.

SPAD aptasensor for the detection of circulating protein biomarkers.

Translation is increasingly recognized as a central control layer of gene expression in eukaryotic cells. The overall organization of mRNA and ribosomes within polysomes, as well as the possible role of this organization in translation are poorly understood. Here we show that polysomes are primarily formed by three distinct classes of ribosome assemblies. We observe that these assemblies can be connected by naked RNA regions of the transcript. We show that the relative proportions of the three classes of ribosome assemblies reflect, and probably dictate, the level of translational activity. These results reveal the existence of recurrent supra-ribosomal building blocks forming polysomes and suggest the presence of unexplored translational controls embedded in the polysome structure.

Three distinct ribosome assemblies modulated by translation are the building blocks of polysomes.

In stressed organisms, strategic proteins are selectively translated even if the global process of protein synthesis is compromised. The determination of protein concentrations in tissues of non-model organisms (thus with limited genomic information) is challenging due to the absence of specific antibodies. Moreover, estimating protein levels quantifying transcriptional responses may be misleading, because translational control mechanisms uncouple protein and mRNAs abundances. Translational control is increasingly recognized as a hub where regulation of gene expression converges to shape proteomes, but it is almost completely overlooked in molecular ecology studies. An interesting approach to study translation and its control mechanisms is the analysis of variations of gene-specific translational efficiencies by quantifying mRNAs associated to ribosomes. In this paper, we propose a robust and streamlined pipeline for purifying ribosome-associated mRNAs and calculating global and gene-specific translation efficiencies from non-model insect's species. This method might found applications in molecular ecology to study responses to environmental stressors in non-model organisms.

Studying translational control in non-model stressed organisms by polysomal profiling.

Pore formation of cellular membranes is an ancient mechanism of bacterial pathogenesis that allows efficient damaging of target cells. Several mechanisms have been described, however, relatively little is known about the assembly and properties of pores. Listeriolysin O (LLO) is a pH-regulated cholesterol-dependent cytolysin from the intracellular pathogen Listeria monocytogenes, which forms transmembrane β-barrel pores. Here we report that the assembly of LLO pores is rapid and efficient irrespective of pH. While pore diameters at the membrane surface are comparable at either pH 5.5 or 7.4, the distribution of pore conductances is significantly pH-dependent. This is directed by the unique residue H311, which is also important for the conformational stability of the LLO monomer and the rate of pore formation. The functional pores exhibit variations in height profiles and can reconfigure significantly by merging to other full pores or arcs. Our results indicate significant plasticity of large β-barrel pores, controlled by environmental cues like pH.

Plasticity of lysteriolysin O pores and its regulation by pH and unique histidine.

The introduction of new compact systems for sensitive, fast and simplified analysis is currently playing a substantial role in the development of point-of-care solutions aimed to assist both prognosis and diagnosis. Here we report a simple and low cost biosensor based on Surface Plasmon Resonance (SPR) taking advantage of a plastic optical fiber (POF) for the detection of Vascular endothelial growth factor (VEGF), selected as a circulating protein potentially associated with cancer. Our system is based onto two crucial aspects. By one hand, the functional layer which allows the transduction signal is based on DNA aptamers, short oligonucleotide sequences that bind to non-nucleic acid targets with high affinity and specificity. By the other hand, the light guiding structure is based on a POF with a planar gold layer as the sensing region, which is particularly suitable for bioreceptors implementation. The sensor revealed to be really useful in the interface characterization. The developed system is relatively easy to realize and could well address the development of a rapid, portable and low cost diagnostic platform, with a sensitivity in the nanomolar range.

An easy way to realize SPR aptasensor: A multimode plastic optical fiber platform for cancer biomarkers detection.

Fluctuations in mRNA levels only partially contribute to determine variations in mRNA availability for translation, producing the well-known poor correlation between transcriptome and proteome data. Recent advances in microscopy now enable researchers to obtain high resolution images of ribosomes on transcripts, providing precious snapshots of translation in vivo. Here we propose RiboAbacus, a mathematical model that for the first time incorporates imaging data in a predictive model of transcript-specific ribosome densities and translational efficiencies. RiboAbacus uses a mechanistic model of ribosome dynamics, enabling the quantification of the relative importance of different features (such as codon usage and the 5' ramp effect) in determining the accuracy of predictions. The model has been optimized in the human Hek-293 cell line to fit thousands of images of human polysomes obtained by atomic force microscopy, from which we could get a reference distribution of the number of ribosomes per mRNA with unmatched resolution. After validation, we applied RiboAbacus to three case studies of known transcriptome-proteome datasets for estimating the translational efficiencies, resulting in an increased correlation with corresponding proteomes. RiboAbacus is an intuitive tool that allows an immediate estimation of crucial translation properties for entire transcriptomes, based on easily obtainable transcript expression levels.

Article	Year
Electrostatic compared with hydrophobic interactions between bovine serum amine oxidase and its substrates. The Biochemical journal\| PubMed ID: 12529179	2003
Covalently anchored lipid structures on amine-enriched polystyrene. Langmuir : the ACS journal of surfaces and colloids\| PubMed ID: 16114940	2005
Effect of materials for micro-electro-mechanical systems on PCR yield. European biophysics journal : EBJ\| PubMed ID: 19455320	2010
Human plasma protein adsorption on carbon-based materials. Journal of nanoscience and nanotechnology\| PubMed ID: 19504920	2009
Solid phase DNA extraction on PDMS and direct amplification. Lab on a chip\| PubMed ID: 21989780	2011
Perforin activity at membranes leads to invaginations and vesicle formation. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 22173634	2011
Whispering gallery mode aptasensors for detection of blood proteins. Journal of biophotonics\| PubMed ID: 22461241	2012
OncomiR detection in circulating body fluids: a PDMS microdevice perspective. Lab on a chip\| PubMed ID: 25178053	2014
SPAD aptasensor for the detection of circulating protein biomarkers. Biosensors & bioelectronics\| PubMed ID: 25636022	2015
Three distinct ribosome assemblies modulated by translation are the building blocks of polysomes. The Journal of cell biology\| PubMed ID: 25713412	2015
Studying translational control in non-model stressed organisms by polysomal profiling. Journal of insect physiology\| PubMed ID: 25796968	2015
Plasticity of lysteriolysin O pores and its regulation by pH and unique histidine. Scientific reports\| PubMed ID: 25854672	2015
An easy way to realize SPR aptasensor: A multimode plastic optical fiber platform for cancer biomarkers detection. Talanta\| PubMed ID: 26048828	2015
RiboAbacus: a model trained on polyribosome images predicts ribosome density and translational efficiency from mammalian transcriptomes. Nucleic acids research\| PubMed ID: 26240374	2015
Corrigendum: Plasticity of Listeriolysin O Pores and its Regulation by pH and Unique Histidine. Scientific reports\| PubMed ID: 26543014	2015

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