Elif Senem Köksal’s research while affiliated with University of Oslo and other places


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Publications (13)


Protocells: Milestones and Recent Advances (Small 18/2022)
  • Article

May 2022

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32 Reads

Small
Irep Gözen

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Elif Senem Köksal

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[...]

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Aldo Jesorka

Protocells Approximately 4 billion years ago, protocells are thought to have emerged as a precursor to life. In article number 2106624, Irep Gözen and co‐workers introduce protocell concepts, research and laboratory methods.


Spontaneous Formation of Prebiotic Compartment Colonies on Hadean Earth and Pre‐Noachian Mars
  • Article
  • Publisher preview available

April 2022

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21 Reads

The front cover artwork is provided by İrep Gözen group at the University of Oslo. The image shows primitive cell‐like compartments which have spontaneously emerged from a crack in rock‐forming mineral oligoclase. Read the full text of the Article at 10.1002/syst.202100040.

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Timeline of important events and conditions on the early Earth, which could have been influential for protocell formation and development. The timeline initiates with the formation of the Earth (≈4.5 Gya), continues with the formation of a stable hydrosphere (≈4.2 Gya) and the late heavy bombardment (≈4 Gya, end of Hadean eon). Before the presence of liquid water, several minerals and porous rocks were present, some of which could have acted as solid compartments for prebiotic reactions. Meteorites delivered during the LHB contained organic material, e.g., amphiphiles, nucleotides, amino acids. The emergence of liquid water and delivery of organic materials opened the possibility for the formation of coacervates and amphiphilic membranous compartments. The first living cells appeared most likely during the Eoarchean period (≈3.5 Gya).
Field experiments and search for extraterrestrial life. a) Bumpass Hell, a hydrothermal field on Mount Lassen in California proposed as an environment suitable for the origin of life. Adapted with permission.[⁵³] Copyright 2021, MDPI. b) Mixture of dodecanoic acid and dodecanoyl monoglyceride added to a hot spring water in the Yellowstone at two different pH values lead to self‐assembly of vesicular structures. Adapted with permission.[⁵⁴] Copyright 2018, MDPI. c) Microcavities in a Martian meteorite sample as solid compartments for prebiotic reactions. Adapted with permission.[⁵⁵] Copyright 2021, Mary Ann Liebert, Inc. d) Scanning electron microscopy image showing an interstellar dust particle (IDP). MET: metal, MGR: magnetite rim. Adapted with permission.[⁵⁶] Copyright 2017, Geological Society of America. e) Japanese Kibo module from the Tanpopo mission in search of evidence for panspermia, which collects IDPs in sample chambers exposed to the space environment. Public domain, NASA. f) Magnified view of the exterior of the sample chamber array. Adapted with permission.[⁵⁷] Copyright 2016, Mary Ann Liebert, Inc.
Prebiotically plausible key chemical reactions. a) Miller‐Urey synthesis of amino acids. b) Phospholipid synthesis. c,d) Fatty acid synthesis. e) Formose reaction and synthesis of ribose sugars. f) Ribonucleotide synthesis.
Compartment types. a) Microcavities in rocks constitute solid compartments. b) Phyllosilicates can accommodate chemical species in between smectic layers. c) Aqueous droplets are stabilized by a layer of nanoparticles (colloidosomes). d) The gas–water interface can provide two types of compartments: water particles suspended in air (aerosols), and gas bubbles suspended in water, which can accommodate biosurfactants at the interface. e) A frozen water‐ice matrix upconcentrates solutes. f) Gel‐like aqueous entities composed of macromolecules (coacervates). g) Spherical lipid bilayer compartments fully enclose and encapsulate an aqueous volume.
Subcompartmentalization of protocells. a,b) Lipid membrane‐bound two‐phase liquid coacervates. In (a) the condensed liquid phase is dextran, and in (b) the thermo‐responsive polymer PNIPAAm. Lipid nanotubes form between the droplet and the protocell membrane during phase transition of the polymer to a gel droplet. a) Adapted with permission.[¹¹⁶] Copyright 2012, American Chemical Society. b) Adapted with permission.[²⁰²] Copyright 2011, American Chemical Society. c) Multicompartmentalized/multivesicular giant unilamellar compartments. Adapted with permission.[²⁰³] Copyright 1994, American Chemical Society. d) Nanotube‐connected, membrane‐bound subcompartments inside a membranous protocell (dashed lines) formed via exposure of the membrane to a Ca²⁺ flow. Adapted with permission.[²⁰⁴] Copyright 2020, Springer Nature Limited. e) A “raspberry vesicle” with multiple, disconnected subcompartments. Adapted with permission.[²⁰⁵] Copyright 2002, Elsevier. f) Subcompartments formed at the basal membrane of a surface‐adhered lipid compartment. Adapted with permission.[²⁰⁶] Copyright 2021, John Wiley and Sons.

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Protocells: Milestones and Recent Advances

March 2022

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517 Reads

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62 Citations

The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, gain the structure and functions necessary to fulfill the criteria of life. Research addressing protocells as a central element in this transition is diverse and increasingly interdisciplinary. The authors review current protocell concepts and research directions, address milestones, challenges and existing hypotheses in the context of conditions on the early Earth, and provide a concise overview of current protocell research methods.


of the experiment. a) Earth surfaces (20 specimens) and one Martian meteorite NWA 7533 sample have been planarized to an even thickness of 170 μm. b) Photographs of two examples of natural surfaces: granite (top) and NWA 7533 (bottom), from top view. Scale bars: 1 cm. (cf. Figure S1 for photographs of other specimens) c) Schematic drawing showing the preparation of the sample chamber. The thin section has been gently mounted on a perforated glass cover slide (ID 0.5 cm). The hole allows direct contact with the oil objective of an inverted confocal microscope. The glass slide provides support for the thin fragile sections. d) A flat‐bottomed silicon frame is air‐sealed onto the glass cover slip and filled with an aqueous suspension of lipid reservoirs. For almost completely opaque samples, a standard cover slide with an upright confocal microscope was employed (not shown).
Formation of lipid nanotube‐protocell networks. a) Confocal micrograph showing the positive control: a lipid nanotube‐protocell network formed on a nano‐engineered SiO2 surface, from top view. b) Schematic drawing depicting the membrane configuration of the structure shown in a white dashed frame. A nanotube, a fraction of which is swelling as a lipid compartment, resides on a single bilayer. c–f) Confocal micrographs showing the phenomenon described in (a–b) on natural surfaces: c) olivine, d) fluorite, e) dolerite, f) picrite basalt. Scale bars: 10 μm.
Formation of protocell colonies on analogue Hadean materials. Confocal micrographs showing dense, protocell colonies, formed predominantly along the cracks and grain boundaries of the surfaces: a–c) olivine, d–f) oligoclase, g–i) nephelinite. Panels (a), (d) and (g) are epi‐fluorescence projections of the colonies while (b), (e) and (h) are cross sections (x–y plane). Panels (c), (f) and (i) show cross sections along the dashed lines in (b), (e) and (h), respectively (x–z plane). j) Granite, k) eclogite, l) fluorite. The foam‐like colonies grow in 2 days. Arrows in (e) and (f) point to encapsulated containers (surface‐adhered “sub‐compartments”).
Formation of protocells on the Martian meteorite NWA 7533 specimen. b) Confocal micrograph showing several foam‐like protocell colonies emerging on the proximal (lower) bilayer that is adhered onto the meteorite. The insets show the cross sectional profile of the colonies (xz plane) along the dashed lines. b) Confocal micrographs showing the division of the colonies after 4 days to smaller units. The original structures and their corresponding daughter structures have been labeled with identical numbers. c–d), close up confocal sections showing the nanotubular structures associated with the vesicles (white arrows). Pink arrows show the Y‐junctions, 3‐way tubular intersections typically associated with lipid nanotube networks. e) Confocal micrograph showing a double lipid bilayer (bright green) dewetting a single lipid bilayer (dark green), and small, nanotube‐attached vesicles adhered on the bilayer. The inset plot shows the fluorescence intensity profile over the dashed line. The two M‐shaped spikes correspond to the two vesicles on the single bilayer. f) Fluorescence micrograph of the membrane superimposed on the SEM image of the surface. Yellow frame represents (e). g–h) SEM‐EDX scans of the meteorite surface in (f) showing different elements. White dashed lines correspond to the contour of the fluorescence membrane micrograph in (f).
RNA and DNA encapsulation and non‐enzymatic DNA strand displacement reaction inside the protocells formed on natural surfaces. a) Schematic drawing showing the RNA encapsulation via transient pores. b–d) Confocal micrographs showing protocells (red fluorescence) before (b), during (c) and after (d) RNA (green fluorescence) superfusion. Panels (b) and (d) represent the area framed in black dashed lines in (c). e) Fluorescence intensity of the regions of interest in (d) (circles with continuous lines) over time. The center vesicle takes up the RNA and maintains it over 4 minutes. The sharp drop in ambient RNA intensity corresponds to the termination of controlled superfusion. f) Schematic drawing showing the encapsulation of ssDNA as part of a non‐enzymatic, entropy‐driven DNA reaction. The entry of the ssDNA leads to melting of annealed dsDNA previously encapsulated inside the protocells and hybridization of one of the strands with the newly entering ssDNA (strand displacement). The released ssDNA becomes no longer quenched and starts to fluoresce. g–j) Confocal micrographs corresponding to (f). i–j) Represents the region framed in white dashed line in (h). k) Fluorescence intensity inside the ROIs circled in j, versus time. The vesicles and colonies shown in this figure were formed on granite.
Spontaneous Formation of Prebiotic Compartment Colonies on Hadean Earth and Pre‐Noachian Mars

February 2022

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68 Reads

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6 Citations

Prominent among the models for protocells is the spherical biosurfactant shell, freely suspended in aqueous media. This model explains initial, but not subsequent events in the development process towards structured protocells. Taking into consideration the involvement of naturally occurring surfaces, which were abundant on the early Earth, feasible and productive pathways for the development of primitive cells are reported. Surfaces intrinsically possess energy, easily utilized by the interfacing amphiphiles, such as lipids, to attain self‐organization and spontaneous transformations. This work shows that the physical interaction of phospholipid pools with 20 Hadean Earth analogue materials as well as a Martian meteorite composed of fused regolith representing the ancient crust of Mars consistently lead to the shape transformation and autonomous formation of surfactant compartment assemblies. Dense, colony‐like protocell populations grow from these lipid deposits, predominantly at the grain boundaries or cleavages of the investigated natural surfaces, and remain there for several days. The model protocells in this study are able to autonomously develop, transform and pseudo‐divide, and encapsulate RNA as well as DNA. Moreover, they can accommodate non‐enzymatic, DNA strand displacement reactions. These findings suggest a feasible route towards the transformation from non‐living to living entities, and provide fresh support for the ‘Lipid World’ hypothesis.


Mixed fatty acid-phospholipid protocell networks

November 2021

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30 Reads

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5 Citations

Physical Chemistry Chemical Physics

Self-assembled membranes composed of both fatty acids and phospholipids are permeable for solutes and structurally stable, which was likely an advantageous combination for the development of primitive cells on the early Earth. Here we report on the solid surface-assisted formation of primitive mixed-surfactant membrane compartments, i.e. model protocells, from multilamellar lipid reservoirs composed of different ratios of fatty acids and phospholipids. Similar to the previously discovered enhancement of model protocell formation on solid substrates, we achieve spontaneous multi-step self-transformation of mixed surfactant reservoirs into closed surfactant containers, interconnected via nanotube networks. Some of the fatty acid-containing compartments in the networks exhibit colony-like growth. We demonstrate that the compartments generated from fatty acid-containing phospholipid membranes feature increased permeability coefficients for molecules in the ambient solution, for fluorescein up to 7 × 10-6 cm s-1 and for RNA up to 3.5 × 10-6 cm s-1. Our findings indicate that surface-assisted autonomous protocell formation and development, starting from mixed amphiphiles, is a plausible scenario for the early stages of the emergence of primitive cells.


Protocells: Subcompartmentalization and Pseudo‐Division of Model Protocells (Small 2/2021)

January 2021

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21 Reads

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1 Citation

In article number 2005320, Irep Gözen and co‐workers demonstrate that the spontaneous subcompartmentalization of model protocells is governed by the physicochemical interaction of the protocell membranes with mineral‐like solid interfaces. In the described experiments, several tens of compartments emerge on the basal membrane of each adhered model protocell. They are able to encapsulate small molecules from the external environment and maintain them within. The compartments become isolated daughter protocells when the enveloping membrane ruptures, which can be perceived as a form of primitive division.


Subcompartmentalization and Pseudo‐Division of Model Protocells

November 2020

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51 Reads

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23 Citations

Membrane enclosed intracellular compartments have been exclusively associated with the eukaryotes, represented by the highly compartmentalized last eukaryotic common ancestor. Recent evidence showing the presence of membranous compartments with specific functions in archaea and bacteria makes it conceivable that the last universal common ancestor and its hypothetical precursor, the protocell, may have exhibited compartmentalization. To the authors’ knowledge, there are no experimental studies yet that have tested this hypothesis. They report on an autonomous subcompartmentalization mechanism for protocells which results in the transformation of initial subcompartments to daughter protocells. The process is solely determined by the fundamental materials properties and interfacial events, and does not require biological machinery or chemical energy supply. In the light of the authors’ findings, it is proposed that similar events may have taken place under early Earth conditions, leading to the development of compartmentalized cells and potentially, primitive division.


Protocells: Rapid Growth and Fusion of Protocells in Surface‐Adhered Membrane Networks (Small 38/2020)

September 2020

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17 Reads

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1 Citation

In article number 2002529, Irep Gozen and co‐workers present experimental evidence that nucleation and growth of protocell‐like membrane compartments from surface‐adhered lipid nanotube networks are significantly enhanced at temperatures between 40 and 70 °C, and fusion can be initiated at ≈90 °C. They show that the microcontainers (5–15 μm) formed in this manner encapsulate and redistribute RNA, and corroborate that lipid nanotube–interconnected neighboring vesicles join and fuse more rapidly than in bulk suspensions.


Heat‐induced protocell formation from surface‐adhered lipid nanotubes. a,b) Schematic drawing summarizing the experiment. (a) Network of hollow lipid nanotubes (inset) is residing on a SiO2‐adhered bilayer. (b) Rapid formation of protocells from the nanotubes as a result of mild heating. Inset on the lower right corner shows the confocal image of protocells formed as a result of this process. All experiments have been performed in biological buffers. c–e) Laser scanning confocal microscopy time series of the process schematically described in (a) and (b). f–k) Confocal images showing that the formed compartments and the nanotubes have colocalized. During growth, the compartments maintain their positions. (i) The outline of the nanotubes in panel (f). (j) The positions of the nucleation sites in (g), indicated with the red circles, are superimposed on the network outlined in (i). (k) The positions of the nucleation sites in (g and j) are superimposed on the image in (h). l–m) Schematic drawing depicting the transformation from a nanotube to a vesicular compartment.
Characterization of protocell formation and growth induced by a mild heat gradient. a) laser scanning confocal image of a large membrane region with nucleating protocells. The area exposed to the IR laser is split to 31 hypothetical elliptical rings, the minor radius of which is expressed as rx and the major radius, ry. A quarter of the outline of each ring is shown in yellow dashed lines. rx of the outmost ring is 77.5 µm. b) Plot showing the protocell density over distance rx. The protocell density is calculated as the number of protocells in each individual elliptical ring. c–f) Confocal images of a nanotube network leading to nucleation and growth of protocells exposed to heat gradients for 10 min. c) Nanotube network before local heat exposure (d) cross‐section of protocell sample from the equator after heat exposure (top view). (e) Cross‐section of sample close to the surface after heat exposure (top view). (f) 3D reconstruction of the formed protocells. Plot showing g) the number and h) the average diameter of the protocells formed in (c–f) over 10 min. i) The histograms depicting the size distribution of protocells over time. Each color represents the size distribution at a given time point. j) Plots showing total membrane area and total membrane volume of the protocells in (c–f) during their formation and growth.
Heat induced protocell fusion. a,b) Confocal images showing the fusion of several protocells formed out of a lipid nanotube network upon exposure to the IR laser. The blue color assigned to the labeled lipid membranes is resulting from the false coloring of the gray scale images of the fluorescence signals, and is assigned arbitrarily. (a) The group of protocells which later merge after exposure to heat gradient, are encircled with dashed lines. Each encircled region is numbered. (b) The merged protocells. Each protocell has been formed or grown as a result of the fusion of the multiple, originally separated protocells shown in (a). The group of protocells and their fused version are numbered identically in (a) and (b). c) Plots showing the number of protocells (orange graph) and average protocell diameter (blue graph) over the complete course of the experiment partly shown in (a and b). d–k) Protocell fusion on same nanotube. (d–g) and (h–k) Two different fusion events in which the protocells on the same nanotube rapidly merge. l–u) Fusion of protocells which are originally located on separate nanotubes. (l–p) and (q–u) Two different events during which vesicular compartments, originally located on different nanotubes, later fuse.
Mathematical model for fusion. Two compartments of equal size are connected to a membrane tube with diameter 2rt. Simulation snapshots are shown as the compartments fuse either a) at the compartments’ equator region or b) at the connecting tube. The outer left snapshots on (a) and (b) show a side view parallel to the membrane tube, while the other snapshots are tilted to better illustrate the expansion of the fusion neck. c) The bending energy E, rescaled by the bending energy of the spherical compartment Esph, decreases as the length of the contact line Δln increases. d) If the compartments fuse initially at their equator, a cavity forms between the fusion site and the membrane tube, with a stable diameter d that is similar to the diameter of the membrane tube.
RNA encapsulation and redistribution. a,b) Schematic drawing showing the experimental setup. (a) An open‐space microfluidic device is used for the superfusion of RNA‐oligonucleotides with a designated membrane area populated with protocells. (b) IR laser is activated to induce fusion, leading to the redistribution of pre‐encapsulated RNA into the fused protocell. c,d) RNA uptake. (c) Confocal image of a membrane area with the microfluidic pipette recirculating RNA above it (top view). The protocells in the recirculation zone appear as black dots. (d) Magnified view of the blue frame in (c) after termination of recirculation. Two protocells contain RNA. e–m) Laser scanning confocal microscopy images showing the fusion of RNA encapsulating protocells and redistribution of contents upon fusion. (e–g) Membrane, RNA fluorescence, and bright field channels are overlaid. (h–j) Membrane fluorescence channel only. (k–m) RNA fluorescence channel only. n–p) Plots showing the fluorescence intensity over the white dashed arrows in (k), (l), and (m), respectively. r–t) Laser scanning confocal microscopy images showing the fusion of RNA‐encapsulating protocells and redistribution of contents upon fusion. Membrane, RNA fluorescence, and bright field channels are overlaid.
Rapid Growth and Fusion of Protocells in Surface‐Adhered Membrane Networks

August 2020

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55 Reads

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12 Citations

Elevated temperatures might have promoted the nucleation, growth, and replication of protocells on the early Earth. Recent reports have shown evidence that moderately high temperatures not only permit protocell assembly at the origin of life, but can have actively supported it. Here, the fast nucleation and growth of vesicular compartments from autonomously formed lipid networks on solid surfaces, induced by a moderate increase in temperature, are shown. Branches of the networks, initially consisting of self‐assembled interconnected nanotubes, rapidly swell into microcompartments which can spontaneously encapsulate RNA fragments. The increase in temperature further causes fusion of adjacent network‐connected compartments, resulting in the redistribution of the RNA. The experimental observations and the mathematical model indicate that the presence of nanotubular interconnections between protocells facilitates the fusion process.


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Citations (10)


... A spectacular presence was reported in the Murchison meteorite, estimated 7 billion years old, which contains particles of SiC [16]. The transition of abiotic compartments to primitive biological cells is currently an unanswered scientific question; a possible involvement of natural solid surfaces in this transition has been suggested [17,18]. ...

Reference:

Complete de-wetting of lipid membranes on silicon carbide
Spontaneous Formation of Prebiotic Compartment Colonies on Hadean Earth and Pre‐Noachian Mars
  • Citing Article
  • April 2022

... [166][167][168][169][170] These division processes can be used for self-reproduction in protocells. [171][172][173] In molecular simulations, reactions can be treated by force fields and MC methods. For atomistic molecular dynamics simulations, a force field called ReaxFF (reactive force field) has been developed to simulate bond breaking/formation based on quantum me-chanics calculations. ...

Protocells: Milestones and Recent Advances

... 14 Most recently, we showed the formation of colony-like model protocells emerging from the molecular lipid films on early Earth minerals and a Martian meteorite. 15 Here we report the stepwise formation and growth of protocell superstructures containing tens to thousands of membranous compartments, originating from a single onionshell lipid reservoir. Inside a lipid compartment, several layers of smaller vesicles grow from the surface up, leading to a densely packed pool of compartments of similar shape and size, reminiscent of bacterial colonies. ...

Spontaneous Formation of Prebiotic Compartment Colonies on Hadean Earth and Pre‐Noachian Mars

... membrane composition, lipid phase, chain length, sterol type. Permeability coefficients of different lipid membranes have been reported [9][10][11][12] . across a DMPC:DPPC (50:50) bilayer was calculated as 0.2 × 10 −9 / for ATP. of fluorescein through GUVs composed of DPPC, DOPC and cholesterol (1:1:1) was determined as 19.4 ± 1.8 × 10 −6 / by Li et al. 12 . ...

Mixed fatty acid-phospholipid protocell networks

Physical Chemistry Chemical Physics

... The supplied cargo molecules were ATTO 488 (Fig. 2a), a 10-base RNA labeled with fluorescein amidite (FAM), or a 20-base single stranded DNA, also labeled with FAM. During superfusion, these molecules passed the membrane and entered the protocellnanotube networks through transient nano-pores 10,20 . The concentration of FAM-RNA and FAM-ssDNA inside the compartments after 4 min. of superfusion was observed to be lower compared to ATTO 488 (Fig. S1). ...

Protocells: Subcompartmentalization and Pseudo‐Division of Model Protocells (Small 2/2021)
  • Citing Article
  • January 2021

... This indicates that another adhesion-controlling factor influences the transformation, which we attribute to differences in the number of pinning sites in each patch. Reduction of the adhesion strength by a temperature increase, as reported in references [13,32] is therefore only partly decisive of the transformation outcome. The availability of the pinning sites, evident through the occurrence of fractal ruptures, which we earlier associated with strong inter-bilayer pinning by divalent ions [33,34], prevents excessive de-wetting and transformation into vesicles. ...

Subcompartmentalization and Pseudo‐Division of Model Protocells

... Despite their proximity, spontaneous fusion between the compartments is not likely, as energy input is required to create pores in initially isolated bilayers. Fusion in PNNs induced by external cues was previously observed, and characterized with a mathematical model 13 . It is expected that if the two compartments fuse at their equator, they will rapidly form a larger compartment containing a stable circular pore (Fig. S7b-d). ...

Protocells: Rapid Growth and Fusion of Protocells in Surface‐Adhered Membrane Networks (Small 38/2020)
  • Citing Article
  • September 2020

... In order to exert control over the wetting and de-wetting behavior of the lipid films, we utilized temperature regulation by means of a focused IR-B laser integrated into the laser-induced fluorescence imaging setup. Heating as an effective means of adhesion control has been established earlier [13,26,27]. Depending on the nature (A, B). ...

Rapid Growth and Fusion of Protocells in Surface‐Adhered Membrane Networks

... Previous studies have demonstrated that even small quantities of polymer can lead to pore formation in lipid bilayers. These pores may subsequently compromise the stability of the formed vesicles [42,43], potentially contributing to the observed irregularities and deformations during the cryo-TEM sample preparation processes and explain the poor GUV release efficiency at high SMALP concentrations. Additionally, the reduced vesicle stability was observed by centrifugation (1000 g for 10 min) of the vesicles, which SMALP formed vesicles could not withstand but electroformed vesicles can. ...

Styrene maleic acid copolymer induces pores in biomembranes

Soft Matter

... Preparation of Lipid Vesicles. The dehydration and rehydration method 79,80 was used to prepare the lipid suspensions. Briefly, lipids (99 wt %) and lipid-conjugated fluorophores (1 wt %) were dissolved in chloroform to a final concentration of 10 mg/mL (cf . ...

Spontaneous Formation and Rearrangement of Artificial Lipid Nanotube Networks as a Bottom-Up Model for Endoplasmic Reticulum

Journal of Visualized Experiments