A myeloid leukemia factor homolog involved in encystation-induced protein metabolism in Giardia lamblia

BackgroundGiardia lamblia differentiates into resistant cysts as an established model for dormancy. Myeloid leukemia factor (MLF) proteins are important regulators of cell differentiation. Giardia possesses a MLF homolog which was up-regulated during encystation and localized to unknown cytosolic vesicles named MLF vesicles (MLFVs).MethodsWe used double staining for visualization of potential factors with role in protein metabolism pathway and a strategy that employed a deletion mutant, CDK2m3, to test the protein degradation pathway. We also explored whether autophagy or proteasomal degradation are regulators of Giardia encystation by treatment with MG132, rapamycin, or chloroquine.ResultsDouble staining of MLF and ISCU or CWP1 revealed no overlap between their vesicles. The aberrant CDK2m3 colocalized with MLFVs and formed complexes with MLF. MG132 increased the number of CDK2m3-localized vesicles and its protein level. We further found that MLF colocalized and interacted with a FYVE protein and an ATG8-like (ATG8L) protein, which were up-regulated during encystation and their expression induced Giardia encystation. The addition of MG132, rapamycin, or chloroquine, increased their levels and the number of their vesicles, and inhibited the cyst formation. MLF and FYVE were detected in exosomes released from culture.ConclusionsThe MLFVs are not mitosomes or encystation-specific vesicles, but are related with degradative pathway for CDK2m3. MLF, FYVE, and ATG8L play a positive role in encystation and function in protein clearance pathway, which is important for encystation and coordinated with Exosomes.General significanceMLF, FYVE, and ATG8L may be involved an encystation-induced protein metabolism during Giardia differentiation.     

New approaches in the chemical design of gd-containing liposomes for use in magnetic resonance imaging of lymph nodes

Abstract

Several approaches to Improve Gd-containing liposomes as magnetic resonance contrast medium for the visualization of lymph nodes are discussed. The modification of the liposome surface with a polymer was chosen as a chemical solution to control the contrast enhancement properties of the medium. It was found that liposome modification with Gd-diethylenetriaminepentaacetic acid (DTPA)-polylysine-based chelating polymer can increase several fold the metal load per vesicle, while surface modification with polyethylene glycol (PEG) might lead to the increased relaxivity of paramagnetic vesicles. Examples are given on how chemical modification of the liposome surface can improve the performance of Gd-containing liposomes in the visualization of lymph nodes.     

Steric and Electronic Properties of the 3′-spiro Moiety of TSAO-T and Analogues

Abstract

The synthesis and study of geometrical and stereoelectronic properties of the spiro moiety of tof novel TSAO analogues modified at the 3′-spiro moiety is described.     

Can the molecules carried by extracellular vesicles help to diagnose pancreatic cancer early?

BackgroundPancreatic cancer is a deadly malignancy mainly because of its asymptomatic onset which prevents the implementation of the primary tumour's resection surgery, leading to metastatic spread resistant to chemotherapy. Early-detection of this cancer in its initial stage would represent a game changer in the fight against this disease. The few currently available biomarkers detectable in patients' body fluids lack sensitivity and specificity.Scope of reviewThe recent discovery of extracellular vesicles and their role in promoting cancer's advancement has boosted interest in researching their cargo, to find reliable early detection biological markers. This review examines the most recent discoveries in the analysis of potential extra vesicle-carried biological markers for the early detection of pancreatic cancer.Major conclusionsDespite the advantages of using extracellular vesicles for early diagnosis, and the promising findings of extracellular vesicle-carried molecules possibly functional as biomarkers, until now there are no validated markers derived from extracellular vesicles available to be used in the clinic.General significanceFurther studies in this direction are urgently required to provide what would be a major asset for defeating pancreatic cancer.     

Towards reconstitution of membrane fusion mediated by SNAREs and other synaptic proteins

Abstract

Proteoliposomes have been widely used for in vitro studies of membrane fusion mediated by synaptic proteins. Initially, such studies were made with large unsynchronized ensembles of vesicles. Such ensemble assays limited the insights into the SNARE-mediated fusion mechanism that could be obtained from them. Single particle microscopy experiments can alleviate many of these limitations but they pose significant technical challenges. Here we summarize various approaches that have enabled studies of fusion mediated by SNAREs and other synaptic proteins at a single-particle level. Currently available methods are described and their advantages and limitations are discussed.     

Nanomechanical characterization of exosomes and concomitant nanoparticles from blood plasma by PeakForce AFM in liquid

BackgroundTo date, EVs characterization techniques are extremely diverse. The contribution of AFM, in particular, is often confined to size distribution. While AFM provides a unique possibility to carry out measurements in situ, nanomechanical characterization of EVs is still missing.MethodsBlood plasma EVs were isolated by ultracentrifugation, analyzed by flow cytometry and NTA. Followed by cryo-EM, we applied PeakForce AFM to assess morphological and nanomechanical properties of EVs in liquid.ResultsNanoparticles were subdivided by their size estimated for their suspended state into sub-sets of small S1-EVs (< 30 nm), S2-EVs (30–50 nm), and sub-set of large ones L-EVs (50–170 nm). Non-membranous S1-EVs were distinguished by higher Young's modulus (10.33(7.36;15.25) MPa) and were less deformed by AFM tip (3.6(2.8;4.4) nm) compared to membrane exosomes S2-EVs (6.25(4.52;8.24) MPa and 4.8(4.3;5.9) nm). L-EVs were identified as large membrane exosomes, heterogeneous by their nanomechanical properties (22.43(8.26;53.11) MPa and 3.57(2.07;7.89) nm). Nanomechanical mapping revealed a few non-deformed L-EVs, of which Young's modulus rose up to 300 MPa. Taken together with cryo-EM, these results lead us to the suggestion that two or more vesicles could be contained inside a large one being a multilayer vesicle.ConclusionsWe identified particles similar in morphology and showed differences in nanomechanical properties that could be attributed to the features of their inner structure.General significanceOur results further elucidate the identification of EVs and concomitant nanoparticles based on their nanomechanical properties.     

Matrix vesicles from chondrocytes and osteoblasts: Their biogenesis,properties, functions and biomimetic models

BackgroundMatrix vesicles (MVs) are released from hypertrophic chondrocytes and from mature osteoblasts, the cells responsible for endochondral and membranous ossification. Under pathological conditions, they can also be released from cells of non-skeletal tissues such as vascular smooth muscle cells. MVs are extracellular vesicles of approximately 100–300 nm diameter harboring the biochemical machinery needed to induce mineralization.Scope of the reviewThe review comprehensively delineates our current knowledge of MV biology and highlights open questions aiming to stimulate further research. The review is constructed as a series of questions addressing issues of MVs ranging from their biogenesis and functions, to biomimetic models. It critically evaluates experimental data including their isolation and characterization methods, like lipidomics, proteomics, transmission electron microscopy, atomic force microscopy and proteoliposome models mimicking MVs.Major conclusionsMVs have a relatively well-defined function as initiators of mineralization. They bind to collagen and their composition reflects the composition of lipid rafts. We call attention to the as yet unclear mechanisms leading to the biogenesis of MVs, and how minerals form and when they are formed. We discuss the prospects of employing upcoming experimental models to deepen our understanding of MV-mediated mineralization and mineralization disorders such as the use of reconstituted lipid vesicles, proteoliposomes and, native sample preparations and high-resolution technologies.General significanceMVs have been extensively investigated owing to their roles in skeletal and ectopic mineralization. MVs serve as a model system for lipid raft structures, and for the mechanisms of genesis and release of extracellular vesicles.     

Interactions Between non-ionic Surfactant Vesicles and human stratum corneum in vitro.

Abstract

The effects of non-ionic surfactant vesicles (NSVs) on human skin in vitro were studied in relation to the physico-chemical properties of the vesicles. The interactions between NSVs and skin were visualized using both freeze fracture electron microscopy and confocal laser scanning microscopy. The physico-chemical properties of the NSVs were varied in a systematic way, using a broad series of polyoxyethylene monoalkyl ether type surfactants (C_nEO_m). The number of oxyethylene units (m) was varied between 3, 7 and 10, and the number of carbon atoms (n) was either 12 or 18. Both the effects of liquid state vesicles composed of ^C12^Eo3,7 ^and C9=9^EO10 surfactants and gel state vesicles (C18EO37) were investigated. After the application of the NS V suspension on the stratum corneum surface two essentially different types of vesicle-skin interactions were visualized. Firstly, an interfacial interaction, involving the adsorption of vesicles, and the deposition of bilayer sheets on the outermost layers of the stratum corneum observed for all NSV formulations tested in this study. Secondly, effects on the ultrastructure of the stratum corneum were observed: the appearance of water pools observed for the liquid state vesicles only, and ultrastructural changes of the intercellular lipid domains are induced only observed after treatment with C₁₂EO₃ NSVs. Neither changes in the ultrastructure of the viable epidermis, nor changes in deeper skin layers were observed.     

Post-implant evaluation of the anastomotic mechanical and geometrical coupling between human native arteries and arterial cryografts implanted in lower-limb: mechanical, histological and ultraestructural studies of implanted cryografts

BackgroundThere is an urgent need of vascular substitutes (VS) to be used in lower limb revascularization procedures when autologous veins are not available and synthetic prosthesis are contraindicated. Since the mechanical differences with respect to native vessels are determinants of the VS failure, the substitutes should have mechanical properties similar to those of the recipient vessels. The use of cryopreserved arteries (cryografts) could overcome limitations of available VS. These work aims were to characterize (a) native vessels/implanted cryografts mechanical and geometrical coupling, (b) cryografts capability to ensure mismatch levels lesser than those expected for expanded polytetrafluoroethylene (ePTFE), (c) cryografts functional properties considering their histological and ultra-structural characteristics.MethodsInstantaneous pressure (mechano-transducers) and diameter (B-mode echography) were obtained in implanted femoro-popliteal, ileo-femoro-popliteal and axilo-humeral cryografts (n = 8), in femoral arteries from recipients (n = 8), recipient-like (n = 15) and multiorgan donors-like (n = 15) subjects, and in ePTFE segments (n = 10). Calculus: (a) Mechanical parameters: elastic modulus, arterial compliance, distensibility and characteristic impedance; (b) Arterial remodeling: diameter, wall thickness, cross-sectional area and wall-to-lumen ratio; (c) Native vessels/VS coupling. Histological and structural analysis were done in explanted femoro-popliteal and axilo-humeral cryografts (n = 7).ResultsPost-implant the cryografts remodeled. Their stiffness increased and the conduit function diminished. Remodeling resulted in an improvement in native vessels/cryograft coupling, which was always better than native vessels/ePTFE coupling.ConclusionsPost-implant cryograft remodeling improved native vessels/cryografts coupling. Cryografts would have mechanical and geometrical advantages over ePTFE. Anastomotic cryograft remodeling differed from that expected only due to haemodynamic factors. The structural properties of the remodeled cryografts contribute to explain their functional characteristics.     

Dynamin regulates the fusion pore of endo- and exocytotic vesicles as revealed by membrane capacitance measurements

BackgroundDynamin is a multidomain GTPase exhibiting mechanochemical and catalytic properties involved in vesicle scission from the plasmalemma during endocytosis. New evidence indicates that dynamin is also involved in exocytotic release of catecholamines, suggesting the existence of a dynamin-regulated structure that couples endo- to exocytosis.MethodsThus we here employed high-resolution cell-attached capacitance measurements and super-resolution structured illumination microscopy to directly examine single vesicle interactions with the plasmalemma in cultured rat astrocytes treated with distinct pharmacological modulators of dynamin activity. Fluorescent dextrans and the lipophilic plasmalemmal marker DiD were utilized to monitor uptake and distribution of vesicles in the peri-plasmalemmal space and in the cell cytosol.ResultsDynamin inhibition with Dynole™-34-2 and Dyngo™-4a prevented vesicle internalization into the cytosol and decreased fusion pore conductance of vesicles that remained attached to the plasmalemma via a narrow fusion pore that lapsed into a state of repetitive opening and closing - flickering. In contrast, the dynamin activator Ryngo™-1-23 promoted vesicle internalization and favored fusion pore closure by prolonging closed and shortening open fusion pore dwell times. Immunocytochemical staining revealed dextran uptake into dynamin-positive vesicles and increased dextran uptake into Syt4- and VAMP2-positive vesicles after dynamin inhibition, indicating prolonged retention of these vesicles at the plasmalemma.ConclusionsOur results have provided direct evidence for a role of dynamin in regulation of fusion pore geometry and kinetics of endo- and exocytotic vesicles, indicating that both share a common dynamin-regulated structural intermediate, the fusion pore.     

Best practice of identification and proteomic analysis of extracellular vesicles in human health and disease

Introduction: Extracellular vesicles are emerging sources of biomarkers for modern preventive and precision medicine. Extracellular vesicles in body fluids offer a unique opportunity for integrative biomarker approaches due to their complex biocargo that includes proteins, lipids, nucleic acids and metabolites. Mass spectrometry-based proteomics data suggest that a significant portion of human proteins are sorted into extracellular vesicles and amenable for biomarker discovery schemes.

Areas covered: this review focuses on key aspects of isolation, quality control and subsequent analysis of blood plasma- and conditioned medium-derived extracellular vesicle proteins, and summarizes the current state-of-the-art in the field. Furthermore, it provides introduction and guidelines for mass spectrometry-based proteomic analysis of extracellular vesicles.

Expert commentary: Comparison of newly developed isolation and purification techniques with classical ultracentrifugation-based approaches are highly recommended. It is also essential to use multiple analytical approaches to characterize the isolated extracellular vesicles prior to characterization of their biocargo. Rigor in data reproducibility, critical data analysis, awareness of potential pitfalls, standardization and benchmarking are required for extracellular vesicle research to fulfil the current expectation that these subcellular structures can become a valid source of next generation biomarkers.     

Covalent Interaction of Proteins and Nucleic Acids. Synthetic and Natural Nucleotide-Peptides

Abstract

The review reports data on the occurrence, structure and functions of covalent nucleotide and NA-protein complexes. Methods of synthesis of model nucleotide-peptides with phosphoester and phosphoamide bonds and their hydrolytic properties are discussed. Separate sections are devoted to methods of specific cleavage of phosphoamide and phosphoester bonds in nucleotide-peptides and their application in biochemistry.     

Dynamics of Interaction of Phosphatidylcholine/Octadecylamine Liposomes with Human Erythrocyte Membranes: Electron Microscopic Study

Abstract

The interactions of octadecylamine and of positively charged liposomes (egg phosphatidylcholine/octadecylamine in molar ratio from 7:5 to 7:0.5) with human erythrocyte membrane have been studied by freeze-fracture and thin-section electron microscopy.

For the first time a very fast adsorption of liposomes to the cell membranes (less than 1 sec) is shown, and their intensive incorporation into plasma membrane (probably within the first 2-5 sec) without visible changes in cell morphology.

The prolonged incubation of the cells with liposomes results in certain morphologic changes: the transition of diskocytes to stomatocytes (30-80 sec) accompanied by the formation of isolated membrane vesicles in cell matrix (80-120 sec); the formation of pentalaminar contacts between plasma membrane of spherocytes and the membrane of isolated matrix vesicles (2.5-3 min); and the incorporation of matrix vesicle membranes into the spherocyte membranes (5 min+).

Possible molecular mechanisms underlying the observed structural changes are discussed briefly.     

Structures of Non-canonical Tandem Base Pairs in RNA Helices: Review

Abstract

The structures of tandem non-canonical base pairs, a frequently recurring motif in RNA molecules, are reviewed and analysed. The tandem non-canonical base pair motifs can be roughly divided in three groups, containing seven subgroups based on their base pairing patterns and local geometries. Structural details and helical parameters that can be used to numerically distinguish between the subgroups are tabulated. Remarkably, while the individual helical twists of the tandem and adjacent base pair steps can be substantially smaller or larger than the typical A-form value of 32.7°, the average value is close to A-form. This and other striking regularities resulting from compensating geometrical adjustments, important for understanding and predicting the configurations of non-canonical base pairs geometries are discussed.     

Fine structure studies on phragmoplast and cell plate formation

Formation and development of phragmoplast and cell plate were studied in endosperm of Haemanthus katherinae Bak. The same cells were studied with the light and electron microscope. Several cells were studied with time-lapse microcinematography before fixation. This permitted comparison of structures during their development on both the light and electron microscope level. Movements of fibrillar components of the phragmoplast and spindle were analyzed and their transport properties were correlated with formation of the cell plate. Change of arrangement of microtubules, transport of vesicles which form the cell plate, and formation of vesicles and microtubules has also been discussed.     

Barrier properties of glycophorin-phospholipid systems prepared by different methods

Glycophorin was incorporated into large unilamellar dioleoylphosphatidylcholine vesicles by either a detergent dialysis method using octylglucoside or a method avoiding the use of detergents. The vesicles were characterized and the permeability properties and transbilayer movement of lipids in both vesicles were investigated as a function of the protein concentration and were compared to protein-free vesicles. An insight in the permeability properties of the vesicles was obtained by monitoring the ratio potassium (permeant): dextran (impermeant) trap immediately after separation of the vesicles from the external medium. Glycophorin incorporated without the use of detergents in 1:300 protein:lipid molar ratio induces a high potassium permeability for the majority of the vesicles as judged from the low potassium trap (K⁺:dextran trap = 0.21). In contrast, the vesicles in which glycophorin is incorporated via the octylglucoside method (1:500 protein:lipid molar ratio) are much less permeable to potassium (K⁺:dextran trap = 0.67 and $\text{t}\text{1}\text{2}$ of potassium efflux at 22°C is 7.5 h.). The relationship between protein-induced bilayer permeability and lipid transbilayer movement in both vesicle preparations is discussed. Addition of wheat-germ agglutinin to glycophorin-containing vesicles comprised of dioleoylphosphatidylcholine and total erythrocyte lipids caused no or just a small effect (less than 20% release of potassium) on the potassium permeability of these vesicles. Also, addition of lectin to dioleoylphosphatidylethanolamine-glycophorin bilayer vesicles in a 25:1 lipid:glycophorin molar ratio had no effect on the permeability characteristics of the vesicles. In contrast, addition of wheat-germ agglutinin to bilayer vesicles made of dioleoylphosphatidylethanolamine and glycophorin in a 200:1 molar ratio resulted in a release of 74% of the enclosed potassium by triggering a bilayer to hexagonal (H_II) phase transition. The role of protein aggregation and the formation of defects in the lipid bilayer on membrane permeability and lipid transbilayer movement is discussed.     

Polyhedron geometry of skeletons of Mesozoic radiolarian Pantanellium

We considered the geometrical properties of skeletons of the genus Pantanellium, a type of Mesozoic radiolarian. We constructed four 3D models of fossil specimens of Pantanellium, using X-ray Micro-CT and layered manufacturing technology. Focusing on cortical shells, we approximated the skeletal structures with convex polyhedrons and investigated their geometrical properties. We summarized these properties using planar graphs. The geometrical properties differ for fossils that are believed to belong to the same species. The results of numerical simulations based on a mathematical model for spherical radiolarians were partially consistent with the skeletal structures of the specimens. We conclude that the skeletal structure of the genus Pantanellium is not fixed and is not completely optimized from the viewpoint of symmetry.     

The golgi-mediated scale production in the marine haptophycean alga Ochrosphaera neapolitana Schussnig

Abstract

Some ultrastructural features of cells of the marine haptophycean alga, Ochrosphaera neapolitana Schussnig in the palmelloid stage were examined. Chloroplasts which are contained in a compartment isolated from the cytoplasm by ER profiles and nuclear envelope, display trilamellated thylakoids running along the major axis. The stalked pyrenoid with inner bilamellated thylakoids, protrudes in a large membrane-bounded vacuole. Other structures, as the haptonematic and flagellar bases, autophagic vacuoles and mitochondria, are typical of the chrysophycean and haptophycean genera so far investigated.

The Golgi apparatus is represented by a single dictyosome composed of stacked cisternae fonctioning in a way that they form organic scales which constitute the main part of the cell covering. The scales, build up of microfibrils disposed parallel each to other, lie in cisternal lumina of the dictyosomal maturing face; scaly cisternae are numerous in the peripheral cytoplasm and are observed merging in the plasma membrane and discharging the content outside the protoplast.

Dictyosomal activity is evidenced morphologically by massive vesicle production. Three kinds of membrane-bounded vesicles were identified in the present material: i) inner-granulated vesicles, arising from the maturation face; ii) coated vesicles, scattered in the cytoplasm or at the periphery of the golgi body, and iii) dense-cored vesicles, present in the proximity of the maturation face. The possible functional relationships related to scale production and assembly outside the protoplast, and between the nucleus and dictyosome are discussed.     

Fluorescent 3-hydroxy-4-pyridinone hexadentate iron chelators: intracellular distribution and the relevance to antimycobacterial properties

Abstract  

We report the synthesis and characterization of a fluorescent iron chelator (4), shown to be effective in inhibiting the growth of Mycobacterium avium in macrophages, together with the synthesis and characterization of two unsuccessful analogues selected to facilitate identification of the molecular properties responsible for the antimicrobial activity. Partition of the chelators in liposomes was investigated and the compounds were assessed with respect to uptake by macrophages, responsiveness to iron overload/iron deprivation and intracellular distribution by flow cytometry and confocal microscopy. The synthesis of the hexadentate chelators is based on a tetrahedral structure to which three bidentate 3-hydroxy-4-pyridinone chelating units are linked via amide bonds. The structure is synthetically versatile, allowing further addition of functional groups such as fluorophores. Here, we analyse the non-functionalized hexadentate unit (3) and the corresponding rhodamine B (4) and fluorescein (5) labelled chelators. The iron(III) stability constant was determined for 3 and the values log β = 34.4 and pFe³⁺ = 29.8 indicate an affinity for iron of the same order of magnitude as that of mycobacteria siderophores. Fluorescence properties in the presence of liposomes show that 4 strongly interacts with the lipid phase, whereas 5 does not. Such different behaviour may explain their distinct intracellular localization as revealed by confocal microscopy. The flow cytometry and confocal microscopy studies indicate that 4 is readily engulfed by macrophages and targeted to cytosol and vesicles of the endolysosomal continuum, whereas 5 is differentially distributed and only partially colocalizes with 4 after prolonged incubation. Differential distribution of the compounds is likely to account for their different efficacy against mycobacteria.