Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Microscopic structure of the polymer-induced liquid precursor for calcium carbonate

Many biomineral crystals form complex non-equilibrium shapes, often via transient amorphous precursors. Also in vitro crystals can be grown with non-equilibrium morphologies, such as thin films or nanorods. In many cases this involves charged polymeric additives that form a polymer-induced liquid precursor (PILP). Here, we investigate the CaCO3 based PILP process with a variety of techniques including cryoTEM and NMR. The initial products are 30–50 nm amorphous calcium carbonate (ACC) nanoparticles with ~2 nm nanoparticulate texture. We show the polymers strongly interact with ACC in the early stages, and become excluded during crystallization, with no liquid–liquid phase separation detected during the process. Our results suggest that “PILP” is actually a polymer-driven assembly of ACC clusters, and that its liquid-like behavior at the macroscopic level is due to the small size and surface properties of the assemblies. We propose that a similar biopolymer-stabilized nanogranular phase may be active in biomineralization

Effect of surface modification on magnetization of iron oxide nanoparticle colloids

Magnetic iron oxide nanoparticles have numerous applications in the biomedical field, some more mature, such as contrast agents in magnetic resonance imaging (MRI), and some emerging, such as heating agents in hyperthermia for cancer therapy. In all of these applications, the magnetic particles are coated with surfactants and polymers to enhance biocompatibility, prevent agglomeration, and add functionality. However, the coatings may interact with the surface atoms of the magnetic core and form a magnetically disordered layer, reducing the total amount of the magnetic phase, which is the key parameter in many applications. In the current study, amine and carboxyl functionalized and bare iron oxide nanoparticles, all suspended in water, were purchased and characterized. The presence of the coatings in commercial samples was verified with X-ray photoelectron spectroscopy (XPS). The class of iron oxide (magnetite) was verified via Raman spectroscopy and X-ray diffraction. In addition to these, in-house prepared iron oxide nanoparticles coated with oleic acid and suspended in heptane and hexane were also investigated. The saturation magnetization obtained from vibrating sample magnetometry (VSM) measurements was used to determine the effective concentration of magnetic phase in all samples. The Tiron chelation test was then utilized to check the real concentration of the iron oxide in the suspension. The difference between the concentration results from VSM and the Tiron test confirmed the reduction of magnetic phase of magnetic core in the presence of coatings and different suspension media. For the biocompatible coatings, the largest reduction was experienced by amine particles, where the ratio of the effective weight of magnetic phase reported to the real weight was 0.5. Carboxyl-coated samples experienced smaller reduction with a ratio of 0.64. Uncoated sample also exhibits a reduction with a ratio of 0.6. Oleic acid covered samples show a solvent-depended reduction with a ratio of 0.5 in heptane and 0.4 in hexane. The corresponding effective thickness of the nonmagnetic layer between magnetic core and surface coating was calculated by fitting experimentally measured magnetization to the modified Langevin equation

Poly(acrylic acid)-directed synthesis of colloidally stable single domain magnetite nanoparticles via partial oxidation

\u3cp\u3eOctahedral, single domain magnetite nanoparticles with average size of ~55 nm were synthesized through oxidative aging of a ferrous hydroxide (Fe(OH)\u3csub\u3e2\u3c/sub\u3e) precursor at high pH in water. The synthesis was also carried out in the presence of the hydrophilic polymer poly(acrylic acid). Presence of the polymer changed the particle morphology from octahedral to spherical while average size decreased to 40-50 nm. Although these particles have a tendency to precipitate due to their high magnetic moment, dispersions of these particles were obtained in the presence of this particular polymer which made the particles stable in water for several days making them suitable for various biotechnological applications such as cell separation owing to their low toxicity.\u3c/p\u3