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How these London scientists make body parts in a lab - The Times Herald

How these London scientists make body parts in a lab - The Times Herald | SynBioFromLeukipposInstitute | Scoop.it
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How these London scientists make body parts in a lab
The Times Herald
How these London scientists make body parts in a lab.
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The Biohacking Hobbyist § SEEDMAGAZINE.COM

The Biohacking Hobbyist § SEEDMAGAZINE.COM | SynBioFromLeukipposInstitute | Scoop.it
Why does all biology happen in academic or industrial labs? Mac Cowell, cofounder of DIYbio, seeks to change that.
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Bio is the new digital

Bio is the new digital | SynBioFromLeukipposInstitute | Scoop.it
How long can we teach science and math as if time stopped centuries ago?
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Engineering of gentiopicroside-producing yeast strain using low-energy ion implantation mediated synthetic biology

Engineering of gentiopicroside-producing yeast strain using low-energy ion implantation mediated synthetic biology | SynBioFromLeukipposInstitute | Scoop.it
To obtain an alternative source for the production of gentiopicroside, here genomic DNA segments of the medicinal plant Gentiana macrophylla were randomly transferred into Hansenula polymorpha by 25 KeV nitrogen ions (N+) at a dose of 2.5 × 1016 ions/cm2 under vacuum pressure of 1 × 10−3 Pa. To screen for potential gentiopicroside-producing recombinant yeast strains, geraniol 10-hydroxylase (G10H) and secologanin synthase (SLS) involved in the gentiopicroside biosynthesis pathway were used as molecular markers. Based on the conserved protein sequences of G10H and SLS, degenerate primers were designed and used for colony polymerase chain reaction (PCR). PCR-positive results for both the G10H and SLS genes were obtained in 79 out of 653 transformants by low-energy ion beam-mediated transformation. These 79 potential gentiopicroside-producing strains were further analysed by Fehling's test, thin-layer chromatography, high performance liquid chromatography and high performance liquid chromatography-mass spectrometry. The results showed that the retention time and ion peaks of the sample from one stable recombinant strain designated as DL67 were consistent with those of the gentiopicroside standard. The corresponding gentiopicroside yield was 8.41 mg/g dry cell weight after strain DL67 was cultured for 96 h. This could offer a new starting point for the construction of recombinant yeasts for production of medicinal plant compounds.
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Biological Materials Have Potential For Custom Applications

Biological Materials Have Potential For Custom Applications | SynBioFromLeukipposInstitute | Scoop.it
The emerging science of synthetic biology promises innovative advances in bio-based materials development.
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The "first man-made biological leaf" could enable humans to colonise space

RCA graduate Julian Melchiorri says the synthetic biological leaf he developed, which absorbs water and carbon dioxide to produce oxygen just like a plant, could…
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Powered by Biology

Powered by Biology | SynBioFromLeukipposInstitute | Scoop.it
RT @MiriamDelirium8: https://t.co/5NUJFwLTWM The #FloatingFabLab is using #biology to build a #sustainable #future. #biosensor #biorobots h…
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Scientists Create the World’s Smallest Thermometer Out of DNA

Scientists Create the World’s Smallest Thermometer Out of DNA | SynBioFromLeukipposInstitute | Scoop.it
Scientists Create the World’s Smallest Thermometer Out of DNA
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Toolbox for Exploring Modular Gene Regulation in Synthetic Biology Training 

We report a toolbox for exploring the modular tuning of genetic circuits, which has been specifically optimized for widespread deployment in STEM environments through a combination of bacterial strain engineering and distributable hardware development. The transfer functions of sixteen genetic switches, programmed to express a GFP reporter under the regulation of the (acyl-homoserine lactone) AHL-sensitive luxR transcriptional activator, can be parametrically tuned by adjusting high/low degrees of transcriptional, translational, and post-translational processing. Strains were optimized to facilitate daily large-scale preparation and reliable performance at room temperature in order to eliminate the need for temperature controlled apparatuses, which are both cost-limiting and space-constraining. The custom-designed, automated, and web-enabled fluorescence documentation system allows time-lapse imaging of AHL-induced GFP expression on bacterial plates with real-time remote data access, thereby requiring trainees to only be present for experimental setup. When coupled with mathematical models in agreement with empirical data, this toolbox expands the scalability and scope of reliable synthetic biology experiments for STEM training.
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DNA Nanostructures on Membranes as Tools for Synthetic Biology

DNA Nanostructures on Membranes as Tools for Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
Over the last decade, functionally designed DNA nanostructures applied to lipid membranes prompted important achievements in the fields of biophysics and synthetic biology. Taking advantage of the universal rules for self-assembly of complementary oligonucleotides, DNA has proven to be an extremely versatile biocompatible building material on the nanoscale. The possibility to chemically integrate functional groups into oligonucleotides, most notably with lipophilic anchors, enabled a widespread usage of DNA as a viable alternative to proteins with respect to functional activity on membranes. As described throughout this review, hybrid DNA-lipid nanostructures can mediate events such as vesicle docking and fusion, or selective partitioning of molecules into phase-separated membranes. Moreover, the major benefit of DNA structural constructs, such as DNA tiles and DNA origami, is the reproducibility and simplicity of their design. DNA nanotechnology can produce functional structures with subnanometer precision and allow for a tight control over their biochemical functionality, e.g., interaction partners. DNA-based membrane nanopores and origami structures able to assemble into two-dimensional networks on top of lipid bilayers are recent examples of the manifold of complex devices that can be achieved. In this review, we will shortly present some of the potentially most relevant avenues and accomplishments of membrane-anchored DNA nanostructures for investigating, engineering, and mimicking lipid membrane-related biophysical processes.
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How To Start A Biotech Company On A Dime

How To Start A Biotech Company On A Dime | SynBioFromLeukipposInstitute | Scoop.it
After doing some research into affordable ways to set up a new lab, we came across two new pieces of equipment – the Bento Lab and the MinION – which are ideal for multiple biotech applications.
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The crystal structure of Cpf1 in complex with CRISPR RNA 

The crystal structure of Cpf1 in complex with CRISPR RNA  | SynBioFromLeukipposInstitute | Scoop.it
The CRISPR–Cas systems, as exemplified by CRISPR–Cas9, are RNA-guided adaptive immune systems used by bacteria and archaea to defend against viral infection1, 2, 3, 4, 5, 6, 7. The CRISPR–Cpf1 system, a new class 2 CRISPR–Cas system, mediates robust DNA interference in human cells1, 8, 9, 10. Although functionally conserved, Cpf1 and Cas9 differ in many aspects including their guide RNAs and substrate specificity. Here we report the 2.38 Å crystal structure of the CRISPR RNA (crRNA)-bound Lachnospiraceae bacterium ND2006 Cpf1 (LbCpf1). LbCpf1 has a triangle-shaped architecture with a large positively charged channel at the centre. Recognized by the oligonucleotide-binding domain of LbCpf1, the crRNA adopts a highly distorted conformation stabilized by extensive intramolecular interactions and the (Mg(H2O)6)2+ ion. The oligonucleotide-binding domain also harbours a looped-out helical domain that is important for LbCpf1 substrate binding. Binding of crRNA or crRNA lacking the guide sequence induces marked conformational changes but no oligomerization of LbCpf1. Our study reveals the crRNA recognition mechanism and provides insight into crRNA-guided substrate binding of LbCpf1, establishing a framework for engineering LbCpf1 to improve its efficiency and specificity for genome editing.
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Limits to Creating Artificial Biological Systems

Limits to Creating Artificial Biological Systems | SynBioFromLeukipposInstitute | Scoop.it
Assessing the organs design limits by introducing a parameter space that includes all forms of possible biological functions.

SPAIN – Over the past decade we have gone to simulate biological systems on the computer to build them in the laboratory with a level that was previously difficult to imagine. Synthetic biology has allowed, for example, making human kidneys using 3D printers, synthesizing antibiotics, or genetically engineer bacteria to degrade plastic polymers. We are crossing borders that until recently were considered unthinkable.
But are all of these conceivable viable biological structures? What are the limits in the design of new organs and organisms? What are the restrictions? In a recent study, a group of scientists from the University Pompeu Fabra of Barcelona led by Ricard Solé proposed using synthetic biology as a tool to investigate those paths unexplored by evolutionary approach of the response of such unknowns.
To do this, researchers have defined a theoretical parameter space that includes all forms and possible biological functions that organizes the universe of possible natural and artificial organs. The conclusions are published in the journal Integrative Biology.
So far, the progress of synthetic biology and tissue engineering has been based on creating structures that mimic natural organs. But, according to the authors, “there is no reason to limit ourselves to manufacture organs and tissues as they exist in nature. We might think of the creation of new bodies to improve the functions of existing bodies. If we liberate the limits linked to the embryonic processes come into play perhaps affordable new rules for biological engineering.”
This new approach could lead to developing completely new functions or even design new methods to diagnose and cure diseases. An existing example is the generation of bionic ear with an antenna integrated coil. Apart from the ethical considerations, this context is also linked to certain biological constraints. According to the authors, should not be diffident when designing complex cellular structures, but it is necessary to establish what the limits associated with the organization of biological structures are.
This is where the idea comes in building his work: morphospace. Researchers have known structures categorized according to a set of variables. These variables define the morphospace, in which structures are ordered in those regions forgotten by evolution. The three axes that make it up are the complexity of development, cognitive complexity and fitness.
The development degrees of complexity ranging from mixtures of cells that do not interrelate to fully developed organs, cells interact and perform the same function (as, for example, in the liver). Furthermore, the degree of cognitive complexity is defined as the ability of the organs to receive and process information. The brain and the immune system would be two examples of the highest degree of such complexity. Finally, the third axis of morphospace, physical condition, is referencing the phases of inorganic matter and is intended to describe the mobility of the components of organs and organelles.
According to the authors, the morphospace could become a good tool to raise the chances of success would be the new biological designs. One of its most interesting features is the presence of a disturbing empty space inside. One explanation for this gap is that it is not possible for that region combination. Another interpretation, however, would be that it is inaccessible designs for evolution under natural conditions, but maybe it could be achieved through bioengineering strategies.
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mSBW3 – The Third International Mammalian Synthetic Biology Workshop

mSBW3 – The Third International Mammalian Synthetic Biology Workshop | SynBioFromLeukipposInstitute | Scoop.it
The SBC@MIT is pleased to invite you to participate in the Third International Mammalian Synthetic Biology Workshop (mSBW 3.0). Following the first and second mSBW meetings, the potential to the field of synthetic biology is gaining extensive interest and this conference will provide the latest foundational advances in mammalian synthetic biology and their diverse applications.

The mSBW 3.0 will be held at Wong Auditorium at MIT on May 21-22, 2016
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Artificial organs: where are the limits?

Artificial organs: where are the limits? | SynBioFromLeukipposInstitute | Scoop.it
The creation of new organisms is the final goal of synthetic biology. This field of science emerged at the beginning of 21 st   century and, since then, we hav
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Biochemical Dissection of the Natural Diversification of Microcystin Provides Lessons for Synthetic Biology of NRPS

Biochemical Dissection of the Natural Diversification of Microcystin Provides Lessons for Synthetic Biology of NRPS | SynBioFromLeukipposInstitute | Scoop.it
The cyanobacterial hepatotoxin microcystin is assembled at a non-ribosomal peptide synthetase (NRPS) complex. The enormous structural diversity of this peptide, which is also found in closely related strains, is the result of frequent recombination events and point mutations. Here, we have compared the in vitro activation profiles of related monospecific and multispecific modules that either strictly incorporate leucine or arginine or incorporate chemically diverse amino acids in parallel into microcystin. By analyzing di- and tri-domain proteins we have dissected the role of adenylation and condensation domains for substrate specificity. We have further analyzed the role of subdomains and provide evidence for an extended gatekeeping function for the condensation domains of multispecific modules. By reproducing natural point mutations, we could convert a monospecific module into a multispecific module. Our findings may inspire novel synthetic biology approaches and demonstrate how recombination platforms of NRPSs have developed in nature.
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DNA Hard Drives? | PLOS Synthetic Biology Community

n 2013, 5 exabytes of content were created each day, that is 5 x 10^18, or five quintillion bytes or 1000000000000000000B! – every day! and the amount is only increasing.

How we store this information is becoming a big challenge.

Storage of information in DNA is proposed as one solution. The idea has been around for a long time (first recorded in the USSR in the 1960s), but has only really begun to take off with the fall in price of DNA synthesis. One of the first major examples of synthetic DNA data storage was performed by George Church’s lab in 2012. On Jake Beal’s blog he reports from a two-day workshop investigating the latest prospects and challenges for an exciting field.

To read more you can visit  http://jakebeal.blogspot.co.uk/
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Protocell Self repairing Trainers

Protocell Self repairing Trainers | SynBioFromLeukipposInstitute | Scoop.it
London designer and researcher Shamees Aden is developing a concept for running shoes that would be 3D-printed from synthetic biological material and could repair themselves overnightThe Protocell trainer would be 3D-printed to the exact size of...
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MIT Team bioLogic Wins Multiple Design Awards with Extraordinary Living Textile that Transform Based on Users' Needs

MIT Team bioLogic Wins Multiple Design Awards with Extraordinary Living Textile that Transform Based on Users' Needs | SynBioFromLeukipposInstitute | Scoop.it
The award winning synthetic bio-skin reacts to body heat and sweat, causing flaps around heat zones to open, enabling sweat to evaporate and cool down the body through an organic material flux.
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Gene-trification? Inside the Brooklyn lab where you can splice your own DNA

Gene-trification? Inside the Brooklyn lab where you can splice your own DNA | SynBioFromLeukipposInstitute | Scoop.it
n a crowded stretch of Flatbush Avenue in Brooklyn, on the seventh floor of a building gentrification forgot, is a place where you can dabble in genetic engineering. Genspace, a kind of co-working lab for scientists, offers a fully equipped research laboratory available for public use for a modest monthly fee.

It was the first of its kind to open its doors back in 2010 and signaled the rebirth of the gentleman (or gentlewoman) scientist. Since then, BioCurious, another DIY lab, has opened in Silicon Valley, allowing hobbyist biologists to fiddle with their own DNA and titrate their own blood samples. A number of startups like Bento Lab have popped up to serve the DIY Bio movement, making compact desktop versions of traditional biology lab equipment small enough to set up anywhere at home.

Above the din of rumbling trucks and screaming teenagers strolling home from nearby schools, the noise in the Genspace lab that is troubling founder Ellen Jorgensen is a centrifuge. It’s too loud and she is not sure if it is safe to use. The equipment in the lab was donated or purchased secondhand to keep costs down.


Biohackers push life to the limits with DIY biology
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In one corner near the communal table that serves as an office sits a small aquarium of the type that usually houses hamsters in elementary schools. It is now home to a few enormous South American cockroaches. A DIY neuroscience company called Backyard Brains used to teach workshops at the lab using a SpikerBox, a device that picks up and displays nerve signals. The easiest way to show those nerve signals is to tear the leg off one of the roaches, attach it to the SpikerBox and stimulate it to show the nerve signals being sent from the leg on an app. Backyard Brains has not run the workshop in a while so the lab inherited the roaches, which Jorgensen has become attached to since she started feeding them. They’re practically pets at this point. “I don’t know how I would feel about the legs coming off,” she says.

Many different people have rotated through the lab, from those needing gel electrophoresis equipment to others looking for low-temperature storage. There are people working on an RNA-based therapy, on genetically engineering E coli to produce cellulose, on trying to turn spent grain from the brewing industry into feed using a fungus and on stabilization work for personal care products. While lab members are all adults, teenagers rotate through as well for science projects and internships.
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Data Integration and Mining for Synthetic Biology Design

One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterised parts and devices. However, there is a wealth of existing biological information, which can be used to identify and characterise biological parts, and their design constraints in the literature and numerous biological databases. However, this information is spread amongst these databases in many different formats. New computational approaches are required to make this information available in an integrated format that is more amenable to data mining. A tried and tested approach to this problem is to map disparate data sources into a single dataset, with common syntax and semantics, to produce a data warehouse or knowledge base. Ontologies have been used extensively in the life sciences, providing this common syntax and semantics as a model for a given biological domain, in a fashion that is amenable to computational analysis and reasoning. Here, we present an ontology for applications in synthetic biology design, SyBiOnt, which facilitates the modelling of information about biological parts and their relationships. SyBiOnt was used to create the SyBiOntKB knowledge base, incorporating and building upon existing life sciences ontologies and standards. The reasoning capabilities of ontologies were then applied to automate the mining of biological parts from this knowledge base. We propose that this approach will be useful to speed up synthetic biology design and ultimately help facilitate the automation of the biological engineering life cycle.
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Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory

Synthetic constructs in biotechnology, biocomputing, and modern gene therapy interventions are often based on plasmids or transfected circuits which implement some form of "on-off" switch. For example, the expression of a protein used for therapeutic purposes might be triggered by the recognition of a specific combination of inducers (e.g., antigens), and memory of this event should be maintained across a cell population until a specific stimulus commands a coordinated shut-off. The robustness of such a design is hampered by molecular ("intrinsic") or environmental ("extrinsic") noise, which may lead to spontaneous changes of state in a subset of the population and is reflected in the bimodality of protein expression, as measured for example using flow cytometry. In this context, a "majority-vote" correction circuit, which brings deviant cells back into the required state, is highly desirable, and quorum-sensing has been suggested as a way for cells to broadcast their states to the population as a whole so as to facilitate consensus. In this paper, we propose what we believe is the first such a design that has mathematically guaranteed properties of stability and auto-correction under certain conditions. Our approach is guided by concepts and theory from the field of "monotone" dynamical systems developed by M. Hirsch, H. Smith, and others. We benchmark our design by comparing it to an existing design which has been the subject of experimental and theoretical studies, illustrating its superiority in stability and self-correction of synchronization errors. Our stability analysis, based on dynamical systems theory, guarantees global convergence to steady states, ruling out unpredictable ("chaotic") behaviors and even sustained oscillations in the limit of convergence. These results are valid no matter what are the values of parameters, and are based only on the wiring diagram. The theory is complemented by extensive computational bifurcation analysis, performed for a biochemically-detailed and biologically-relevant model that we developed. Another novel feature of our approach is that our theorems on exponential stability of steady states for homogeneous or mixed populations are valid independently of the number N of cells in the population, which is usually very large (N ≫ 1) and unknown. We prove that the exponential stability depends on relative proportions of each type of state only. While monotone systems theory has been used previously for systems biology analysis, the current work illustrates its power for synthetic biology design, and thus has wider significance well beyond the application to the important problem of coordination of toggle switches.
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The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA 

The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA  | SynBioFromLeukipposInstitute | Scoop.it
CRISPR–Cas systems that provide defence against mobile genetic elements in bacteria and archaea have evolved a variety of mechanisms to target and cleave RNA or DNA1. The well-studied types I, II and III utilize a set of distinct CRISPR-associated (Cas) proteins for production of mature CRISPR RNAs (crRNAs) and interference with invading nucleic acids. In types I and III, Cas6 or Cas5d cleaves precursor crRNA (pre-crRNA)2, 3, 4, 5 and the mature crRNAs then guide a complex of Cas proteins (Cascade-Cas3, type I; Csm or Cmr, type III) to target and cleave invading DNA or RNA6, 7, 8, 9, 10, 11, 12. In type II systems, RNase III cleaves pre-crRNA base-paired with trans-activating crRNA (tracrRNA) in the presence of Cas9 (refs 13, 14). The mature tracrRNA–crRNA duplex then guides Cas9 to cleave target DNA15. Here, we demonstrate a novel mechanism in CRISPR–Cas immunity. We show that type V-A Cpf1 from Francisella novicida is a dual-nuclease that is specific to crRNA biogenesis and target DNA interference. Cpf1 cleaves pre-crRNA upstream of a hairpin structure formed within the CRISPR repeats and thereby generates intermediate crRNAs that are processed further, leading to mature crRNAs. After recognition of a 5′-YTN-3′ protospacer adjacent motif on the non-target DNA strand and subsequent probing for an eight-nucleotide seed sequence, Cpf1, guided by the single mature repeat-spacer crRNA, introduces double-stranded breaks in the target DNA to generate a 5′ overhang16. The RNase and DNase activities of Cpf1 require sequence- and structure-specific binding to the hairpin of crRNA repeats. Cpf1 uses distinct active domains for both nuclease reactions and cleaves nucleic acids in the presence of magnesium or calcium. This study uncovers a new family of enzymes with specific dual endoribonuclease and endonuclease activities, and demonstrates that type V-A constitutes the most minimalistic of the CRISPR–Cas systems so far described.
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The quiet revolutionary: How the co-discovery of CRISPR explosively changed Emmanuelle Charpentier’s life

The quiet revolutionary: How the co-discovery of CRISPR explosively changed Emmanuelle Charpentier’s life | SynBioFromLeukipposInstitute | Scoop.it
The quiet revolutionary: How the co-discovery of CRISPR explosively changed Emmanuelle Charpentier’s life
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DNA Nanostructures on Membranes as Tools for Synthetic Biology

Over the last decade, functionally designed DNA nanostructures applied to lipid membranes prompted important achievements in the fields of biophysics and synthetic biology. Taking advantage of the universal rules for self-assembly of complementary oligonucleotides, DNA has proven to be an extremely versatile biocompatible building material on the nanoscale. The possibility to chemically integrate functional groups into oligonucleotides, most notably with lipophilic anchors, enabled a widespread usage of DNA as a viable alternative to proteins with respect to functional activity on membranes. As described throughout this review, hybrid DNA-lipid nanostructures can mediate events such as vesicle docking and fusion, or selective partitioning of molecules into phase-separated membranes. Moreover, the major benefit of DNA structural constructs, such as DNA tiles and DNA origami, is the reproducibility and simplicity of their design. DNA nanotechnology can produce functional structures with subnanometer precision and allow for a tight control over their biochemical functionality, e.g., interaction partners. DNA-based membrane nanopores and origami structures able to assemble into two-dimensional networks on top of lipid bilayers are recent examples of the manifold of complex devices that can be achieved. In this review, we will shortly present some of the potentially most relevant avenues and accomplishments of membrane-anchored DNA nanostructures for investigating, engineering, and mimicking lipid membrane-related biophysical processes.
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