Non-3D pore descriptors

LOVAMAP analyzes more than just 3-D pores. For example, we study paths that course throughout the void space of a scaffold. (You can see a distinct path highlighted in red below.) The measurements taken for a path give rise to some of our non-3D pore descriptors.

3-D pore descriptors

3-D pores (or pockets of open void space) form such weird shapes!! How do you describe something that looks so weird? If someone asked you to come up with different ways to measure a cube, that’s easy – you could measure length, volume, corner angles, etc. 🥱 But for these 3-D pores, it’s more complicated. So we came up with 30 different measurements to describe them, like reporting their volume or the number of surrounding particles that form the space. We also distinguish between 3-D pores that are completely inside of the scaffold vs. those that are touching the edge (like the massive purple one below).

Global descriptors

LOVAMAP computes 20 global descriptors for each scaffold. ‘Global’ refers to the fact that a single value is reported for the descriptor, which captures information spanning the entire scaffold. For example, the most common global descriptor reported in the literature for granular biomaterials is Void-Volume Fraction, where the top of the fraction is the volume of scaffold that’s occupied by empty space and the bottom of the fraction is the total volume of the scaffold.

This collaborative project has been a challenging journey for sure, but we are on our way to exciting results! If you are a student interested in working at the intersection between hydrogels and active immunotherapy for enhanced tissue healing, contact us and add in the message that you are interested in my project! #pablo #mapfibers

My research interest is to subvert solid organ rejection by masking donor antigen or even disguising foreign tissues as “self.” I am working to do this by utilizing novel, synthetic cell surfaces and by developing organ-specific drug delivery methods. Through this work, we hope to reduce the burden of system immunosuppression, enhance donor organ function, and prolong survival following organ transplantation.

If you’re a student who is intrigued by stealth-ing of antigens or tissue-targeting therapies, contact us and add in the message that you’re interested in my project! #sydney #immunecloacking

My project is to leverage this plasticity window with a ‘repair soup’ to promote healing after stroke. In particular, I am working on strategies that would trap locally-secreted plasticity-proteins into our biomaterial in an effort to extend the window of cellular change. The end goal of course is to reduce physical impairment caused by stroke.

After talking with Prof. Segura, I also learned that the brain is 50% lipids by weight. Lipids do much more than make us fat – they’re active players in signaling and normal tissue function. I’ll be reading and learning about lipid biology, especially in the context of stroke, so that I can guide my synthesis to include brain-active materials. By using self-assembling lipids, I aim to make nanoparticles that are entirely bioactive.

Hydrogel microparticles (HMPs)

The first step is to design the particles that compose our MAP material. Each particle is actually a network of entangled polymers (like a microscopic hairball), and we typically work with hydrogel polymers that swell in water – hence the term HMPs (also referred to as µgels). The process starts with some good ‘ole polymer chemistry, where we customize our material to fit the therapeutic application. Once the polymers are just right, we form them into the desired shape, then lock the shape into place through a process called polymerization. Most of our MAP experiments use spherical HMPs produced through emulsion or microfluidic techniques, but we’ve been experimenting with other shapes as well. (I know we just dropped some technical terms, so if you’re unfamiliar and want to learn more about HMPs, click here, we won’t tell anyone 🤫)

Generate images & GIFs

Part of LOVAMAP’s power is its ability to offer visual insight into all that is void space. Visualization is an important aspect of science communication, and we put a lot of effort into making beautiful images and videos that help the scientific community see what we’re talking about. Below we’re highlighting a single 3-D pore that represents a pocket of empty space surrounded by particles.

Segment void space

Our goal is to isolate all of the distinct pockets of empty space throughout the scaffold – seems like the obvious way to break up the space, right? But doing this accurately is so much more complicated than you might think. LOVAMAP uses the spatial landmarks as a basis for segmenting the void space into these natural open pockets, which we called ‘3-D pores.’ Below you can get a taste for how crazy and diverse pore shapes can be!

I was so intrigued by how such a small change in material composition could influence the regenerative properties of a material with that magnitude, so it’s become my goal to understand the mechanisms of this phenomenon and leverage this knowledge to improve wound healing.

If you’re interested in working on a skin project that studies chirality of biomaterials, regeneration, and the immune system, contact us and add in the message that you’re interested in my project! #elle #chiralityandregeneration

The brain does try to repair some of these connections after stroke but can only do so for a limited amount of time. My project investigates whether our MAP material can serve as a scaffold for synapse formation, and I’m incorporating different factors to help boost stable connections. That way, stroke patients will have more time to reform those neural circuits and eventually regain their mobility.

If you’re interested in connecting with me (pun intended) to study neural plasticity in the brain, contact us and add in the message that you’re interested in my project! #nhi #synapticmaterials

Extract spatial landmarks

LOVAMAP relies on accurately identifying key spatial landmarks within the void space of MAP scaffolds. These landmarks are subtypes of the medial axis, which are central locations in space, and they serve as a starting point to orient LOVAMAP to the space. Our custom algorithms are highly effective at locating these landmarks because we take advantage of information stored in the graphical representation of granular material. Once the information has been stored, we’re ready to start dissecting and analyzing the MAP scaffold.

The work presented here is a visually-rich dissertation that covers our approach for analyzing the void space of packed particles. We use techniques from computational geometry and graph theory to develop a robust methodology for segmenting the void space into natural pockets of open space and outputting a set of descriptors that characterize the space. Our methods are developed using simulated MAP scaffolds covering a range of particle compositions, including mixed particle sizes, stiffnesses, and shapes. Our software, called LOcal Void Analysis of MAP scaffolds (LOVAMAP), has allowed us to study many aspects of void space, including global descriptors like void volume fraction, local ‘pore’ measurements of size and shape, and additional features like ligand availability, paths, isotropy/anisotropy, and available regions for unhindered migration based on size. LOVAMAP is an enabling technology that can be used for analyzing real scaffolds or studying simulated scaffolds to inform material design. It serves as a platform for void space analysis that can easily be built upon to encompass ever-growing innovations in scaffold characterization.

Read the full dissertation here: https://dukespace.lib.duke.edu/dspace/handle/10161/25268

We hypothesized that our microparticles may be dissipating the energy exerted by cells, which in turn influences cell behavior. Prof. Segura suggested studying fibroblasts since these cells are involved in skin wound healing and are very susceptible to mechanical cues. Once fibroblasts receive mechanical (and chemical) cues, they ‘activate’ into another cell type called myofibroblasts, which secrete collagen and other components of the extracellular matrix as well as contract the wound. This process is a feedback loop known as the fibroblast-myofibroblast transition, and it controls the balance between regeneration and scarring. My project is to study this process and investigate whether our material can modulate the communication between fibroblasts and myofibroblasts.

But if you’re interested in working on a skin project that studies my favorite cells, contact us and add in the message that you’re interested in my project! #alejandra #reducingstress

My current disease-focus is on ischemic stroke, and I am trying to develop MAP-based materials that incorporate several glycans shown to be important in the pathophysiology of stroke. I hope to synergize the power of glycans with that of our MAP scaffolds in order to develop a platform that can dynamically address a multitude of stroke symptoms – leading to more comprehensive recovery in patients.

If you’re a student interested in working at the junction between glycotherapuetics and brain tissue engineering, contact us and add in the message that you’re interested in my project! #yunxin #sugarmap

We have designed a biocompatible biomaterial from macroporous annealed particles (MAP) hydrogels for injection into the stroke core five days after a photothrombotic stroke. Our hyaluronic acid-based material has been modified to dictate NPC fate in vitro through maintained stemness and the formation of neurospheres or towards Tuj1 positive NPCs, as well as enhance angiogenesis and the recruitment of endogenous NPCs after stroke. Within only 10 days after injection, we have observed the first case of NPC differentiation, enhanced recruitment, and angiogenesis after stroke, and at 30 days after injection we observe significant angiogenesis throughout the entire stroke core.

Read the full dissertation here: TBD

We uncovered that a fine balance between pro-regenerative and pro-inflammatory macrophage phenotypes in MAPS with D-amino acid-based crosslinker was an indicator for regenerative scaffolds in a subcutaneous implantation model. We also discovered that scaffolds comprised of large microgels with pore sizes that can accommodate ~40 µm diameter spheres induced a more balanced pro-regenerative macrophage response and better wound healing outcomes with more mature collagen regeneration and reduced inflammation level. The role of spatial confinement on macrophage response was further explored in vitro, where we demonstrated that size-dependent macrophage response to M1/M2 cytokine stimulations was tied to the change in cell morphology and motility.  This work offers valuable insights into the dynamic immune response to synthetic porous scaffolds with a specific focus on macrophages and establishes a foundation for further optimization of immunomodulatory pro-regenerative outcomes for wound healing and biomaterial implants.

Read the full dissertation here: TBD

Skin grafting (my current topic) is a cornerstone of reconstructive surgery. Over 160,000 skin grafts are performed annually for patients after burns, trauma or vascular disease (Serebrakian, et al. Plast Reconstr Surg Glob Open, 2018). Despite various FDA-approved dressings, up to half of skin grafts are rejected. Repeated skin grafting requires multiple surgeries, which increases risk of morbidity and mortality. Although a variety of cadaveric and synthetic alternatives exist, they are limited by allogeneic responses, dysregulated inflammatory reactions, worse scarring, poor functional outcome, and just overall lower quality of life. My research aims to improve the outcome of soft tissue reconstruction through the development of hydrogel biomaterials that can coordinate the interactions of immune cells to improve tolerance in the wound bed of allotransplantation.

If working on a biomaterials-based approach to promote tolerance in soft tissue transplants is of interest to you, contact us and add in the message that you’re interested in my project! #holly #culturingtolerance

Extending the window for cellular change

We’ve explored this approach the most. During the latter stages of wound healing, the microenvironment is in a state of endogenous plasticity, which means the tissue is still undergoing changes as it heals. The goal here is to place materials into wounds that extend the plastic time period by recruiting progenitor cells and other important factors. We primarily do this by designing materials that promote blood vessel formation. Blood vessels are a key component in tissue repair – they deliver important nutrients, regulate the immune response, and guide cell migration and tissue deposition. By maintaining and controlling the process of vessel formation with our materials, we’re thinking we can extend the window of plasticity and promote tissue regeneration. You can learn more about our approaches to promote vessel formation by reading the articles on Our Publications page that deal with therapeutic angiogenic material (filter by Topic: angiogenesis)!

Another way we’re extending endogenous plasticity is by designing materials that allow for rapid cellular infiltration while maintaining structural support. We do this by forming a microscopic scaffold made of packed hydrogel microparticles that are stuck together, which forms pockets of void space that are large enough for cells to fit. Alright, you guessed it – we’re describing MAP… you might as well read about it here.

Re-opening the window for cellular change

The most difficult wounds to treat are those that are chronic or well-past the phase of endogenous plasticity – when tissue is still being remodeled. For these wounds, we want to re-activate plasticity so that the body has another opportunity to heal itself properly. As you can imagine, this is harder to achieve than when wounds are still fresh in the acute or sub-acute phase. Our strategy is to first identify the molecules that are present in wounds during endogenous plasticity. We will then introduce materials that induce blood vessel formation as a source for replenishing the molecules that are present during plasticity. The goal is to determine the minimum molecular signals needed to re-open the window for cellular change.

Injectability

In the same way that it would be difficult to fit a sponge into a needle, it’s difficult for a non-granular matrix to be injected. And if something can’t be injected, then getting it to the right place might require some surgery. Luckily MAP is granular, so all of the tiny particles can fit inside a syringe. And – thanks to the concept of particle jamming – after injection, the particles reform into a scaffold that perfectly conforms to the shape of the wound. Once the material has been deposited, the last step is to perform some chemistry magic to interlink the particles so they don’t go anywhere. The injectability of MAP makes it much more convenient for physician’s to use, and patients can avoid undergoing unnecessary surgery – everyone wins!

My lab has worked for over a decade on approaches to deliver genetic material from hydrogel biomaterials (heck even my advisor’s thesis was on this topic, along with past lab members Leo, Quinn, Talar, Anandika, Cynthia, and Norman). These approaches have led to high levels of protein expression in vitro, but not in test animals. Also, previous approaches did not load genetic material into injectable gels…and just like a vaccine, if our gene therapy isn’t injectable, it limits applicability. My thesis work is focused on improving our delivery strategies to achieve effective genetic material delivery from injectable hydrogels into the brain. Once this is achieved, my goal is to express proteins that can regulate endogenous protein expression of pro-repair factors to promote recovery after stroke.

If you’re a student who recognizes that non-viral gene delivery is trending, contact us and add in the message that you’re interested in my project! #evan #genedelivery

Inner porosity

The picture below really says it all! MAP is designed so that the space between the particles is large enough to fit cells. Back in the day, researchers would create materials that resemble… Jello swiss cheese 🤔 The idea was to create a material that’s filled with interconnected holes (or ‘pores), which would allow cells to move around freely. The structure of MAP is essentially the opposite of that! The holes are now the particles, and the cheese(?) is now empty void space. Cells can still move around freely, and in fact, they seem to prefer the concave surface of the particles. We want to create materials that keep cells happy and push them toward healing wounds, so this is good news.

Outer porosity

Let’s first cover what MAP is not – MAP is not a solid hunk of material, like Jello. Imagine a cell approaching a giant wall of Jello. It would have to eat away at the material in order to get inside and hang out. We want to make our materials inviting to cells so that there’s minimal effort for them to get right in and start healing that wound. MAP is genius in that way because it’s made of a bunch of microscopic particles of Jello packed together, and the space between the particles is also on the micron-scale. Do you know what else is on the micron-scale? Cells. So with MAP, the micron-sized openings (or ‘pores) allow cells to easily crawl into the scaffold without wasting time and energy degrading the material first. This process of cell movement is called ‘cell infiltration,’ and the structure of MAP makes for some effortless cell infiltration. Do you see those brain cells stained in red making their way into the MAP stained in green?

I am interested in understanding how glycosylation changes with aging and after a stroke, and I want to understand if part of the success of our previous materials are because of changes in the glycosylation profile. My ultimate goal is to design novel glycan-decorated materials to promote recovery after stroke.

If you’re a student who agrees that glycans > proteins and nucleic acids and you’re interested in their impact on stroke recovery, contact us and add in the message that you’re interested in my project! #juhi #sweetbrain

Microporous annealed particles (MAP) scaffolds

The magic of MAP comes from interlinking the HMPs in a granular scaffold so that the particles get stuck in place. There are many, many different techniques for doing this, but the very first MAP scaffold was designed to naturally crosslink in the body. This was great because it meant we could load a syringe with HMPs, inject into the body to form a granular scaffold, then wait for the body’s natural clotting factor to chemically link the particles together. Since then, we’ve also become fond of interlinking using UV light. The benefit of interlinking (or annealing) HMPs is that we create a stable structure that sticks around for longer and makes cells extra happy. We’ve seen MAP scaffolds promote aspects of wound healing in disease models like stroke, myocardial infarction, skin wounds, and spinal cord injury. And once the MAP scaffold has completed its job, it naturally gets degraded by the body.

Return descriptor data

LOVAMAP does some powerful computing to generate an ever-growing list of descriptors that quantitatively characterize the MAP scaffold. These measurements describe features of the void space between the particles, the pathways throughout the scaffold, integrin-binding hotspots, and more. By quantifying the microarchitecture of our scaffolds, researchers can study how scaffold geometry affects other measurable properties, like infiltrating cell behavior and material mechanics. Ultimately, these types of analyses will help us optimize our material for the best possible therapeutic effect.

Generate images and GIFs

Coming soon!

Granular scaffolds

The word ‘scaffold’ implies a supporting structure or framework, so at this step, we’re creating a framework using the HMPs as building blocks. The term ‘granular’ has a specific definition as well, but we’ll leave you to read this review for the nitty-gritty details. The take-home point is that granular materials transition from a ‘liquid-like’ state to a ‘solid-like’ state when particle jamming occurs – so to create a solid structure from HMPs, we pack them together. Now we have a granular scaffold with empty space in between the particles to support cell ingrowth. But remember, a granular scaffold is just a collection of particles jammed together, so it’s still a dynamic system where everything can slosh around.

Wound healing

We are inspired by our body’s ability to heal. This occurs through a process called endogenous regeneration, which takes advantage of the activation of ‘plasticity’ upon injury. Plasticity is the ability to transform local cells into tissue factories that produce extracellular matrix and other multicellular structures that got destroyed. The goal of plasticity is to produce brand-spanking-new tissue. As you may have guessed, these pathways are usually dormant and only awaken once the body recognizes that an injury has occurred. So this begs the question – if tissues have the ability to fix themselves back to working order, why do some injuries cause permanent damage? This is because there are two competing forces in healing: plasticity and scarring. Scarring is a pro-survival mechanism that evolved to ensure that we survive an injury. Regenerating tissue takes time and resources – time that we may not have if the injury starts inhibiting important bodily functions or introducing deadly bacterial infections. Thus, at the same time that pro-regenerative pathways are activated to promote functional recovery, there are also pro-survival mechanisms activated that favor a quick-fix. Usually, scarring wins, and scar tissue gets deposited that is not completely functional.

Our main goals are to 1) scale-down scarring so that our tissues have a chance to regrow, and 2) deliver key signals that promote tissue regeneration. Luckily we know that our body actively works to repair itself after injury, so we only have to deliver the pro-healing components that are low or lacking in the wound environment. And the good news is that biomaterials can be designed to do just that – modulate the pathways that are responsible for scarring, while at the same time deliver key therapeutics to promote functional tissue deposition.

Heterogeneity

MAP is a collection of tiny particles, but nobody says we have to use the SAME particles throughout our scaffold. In fact, having the option to easily combine different types of particles into one scaffold is a big plus with our material. We can include particles of different shapes, sizes, and stiffnesses…made from different polymers…with different degradation rates…carrying different types of drugs… Really the world is our MAP-oyster! And not only can we precisely choose the proportion of these particle types, but we can also vary where in the scaffold they lie. Do you want everything to be mixed like rainbow Dippin’ Dots? Do you want particle types to be nicely layered like a cake? You choose. This is all to say, the heterogeneity offered by MAP allows for a highly personalized, versatile therapeutic material.

Aside from sex and age, my work focuses on further development of a dual-function angiogenic biomaterial, CLUVENA, that previous lab members developed (Sean, Shiva, and Lina). When injected intracranially into the stroke cavity, CLUVENA can both restore blood vessel density and decrease inflammation. This material was also able to reduce physical disability in a rodent model of stroke. My goal is to better understand the mechanism of action of CLUVENA in order to design a novel approach that further reduces physical disability. I also want to make sure our materials can be easily manufactured, shipped, and stored.

If you’re a student who wants to work on cutting-edge technology in the stroke recovery space, contact us and add in the message that you are interested in my project! #kevin #stroke

Ninjabyte Computing

If you’ve ever watched a Marvel movie or played a video game like Witcher 3, you know graphics have come a long way. But you may not know how much serious math and research goes into 3D animation. Technologies in simulation and visual effects are incredibly powerful, yet most scientists don’t have access to them because software engineers in animation don’t often chill with scientists. Ninjabyte Computing was founded to connect the science community with high-performance animation tools used in industry.

The company is headed by Peter Cheng, PhD, who offers the perfect blend of expertise in mathematics, computer science, and animation. Ninjabyte Computing uses professional visual effects software, like SideFX Houdini, to generate physically-accurate simulations of randomly packed particles with varying shapes, sizes, stiffness, and textures. These simulations are fantastic mimics of a range of MAP scaffold types, which makes the data perfect to analyze with LOVAMAP in order to study our scaffolds. Ninjabyte Computing also renders beautiful images and videos of our material to help explain our work. One of their images was featured on the cover of Nature Materials!

While our collaboration focuses on MAP simulations, this only scratches the surface of animation technology. We’re happy to share the love for Ninjabyte, and we recommend reaching out to ninjabytecomputing@gmail.com for any inquiries.

Biomaterial scaffold

A biomaterial scaffold is exactly what it sounds like – a structure made from building blocks that provides support. In this case, the building blocks we use are nanoscopically small because our scaffolds interact with tissue at the microscopic level. The scaffolds act as a supplemental extracellular matrix that provides physical support in compromised tissue, and they also serve as a framework to help nearby cells move around and do their job. You can see below that a typical scaffold looks like a little slab of clear Jello.

The scaffold itself can also behave as a drug and influence biological processes in the tissue surrounding it. This is possible because cells in the tissue are mechanoresponsive, which means that they can sense the structural features around them and respond to any changes. We can engineer the structural features of our scaffold to influence cell behavior, which leads to therapeutic action.

When we make scaffolds out of hydrogel microparticles and link these particles together, we create MAP – but you can read more about that here.

Read in formatted data

LOVAMAP is a software designed for analyzing granular material. For this reason, LOVAMAP takes in a specific data format that highlights individual particles – basically each voxel (3D pixel) associated with a particular particle should be labeled with a unique identifying number. This ensures that our software is analyzing exactly what you intended. Alternatively, if you’re simulating spherical particles with a known center and radius, go ahead and input the sphere data – our code can handle it.

Tweaking the immune system

The goal with this approach is to design materials that communicate with our body’s immune system and urge it to generate a lasting pro-regenerative response in the wound. The immune system is most commonly known for helping us fight disease. When external objects enter our body, specialized cells will recognize them as foreign and trigger a specific immune response depending on the type of invader. Viruses, for example, often trigger a danger! danger! response that causes the immune system to produce antibodies against the virus for long-lasting defense. This means you’re protected from getting sick if you get infected with the same virus again. Materials made in lab, however, don’t always elicit the same immune response, which means our materials can be explicitly engineered to tweak the immune system in a certain direction.

Since MAP scaffolds are a highly versatile biomaterial that have been shown to support cell growth, we are hoping they can be used to combat cancer as well. So far, we have experimented with different polymer types, as well as varying material stiffness, and our custom MAP scaffolds are already showing promising results – with more functionality on the way.

Our focus is on glioblastoma multiform, an aggressive brain cancer with particularly low survival rates. If you’re a student with a passion to fight cancer using pro-repair matrices, contact us and add in the message that you are interested in my project! #alex #healingcancer

Since the amniotic membrane is used to promote healing of non-healing wounds, I will incorporate components of the amniotic membrane – which I will produce recombinantly – into HA hydrogels.

If you’re a student who’s excited about scarless healing and synthetic placenta biomaterials, contact us and add in the message that you’re interested in my project! #drew #syntheticplacenta

Modified building blocks

Our starting materials are hydrogel polymers, such as

• hyaluronic acid
• polyethylene glycol
• poly(propylene sulfide)
• heparin
• poly(allyl mercaptan)

We chemically engineer these polymers to precisely fit our needs, like adding handles that allow the strands to link to one another and form a gel. Our polymer modifications include end-group modifications, side-chain modifications, and even attachment of biologically relevant ligands that make our materials more biocompatible and useful for therapeutic applications. We also use these polymers to create higher-level building blocks called hydrogel microparticles, which you can read more about on our MAP Scaffolds page.

In vivo work

In vivo studies are performed in a living organism and are an essential and exciting part of the research we do. These types of experiments are invaluable because they not only teach us about biocompatibility, but we also get the full effect of a living tissue. This means we gain access to the complicated signaling pathways that would be impossible to recreate in a test tube, and therefore, we get a complete picture of the healing process. Understanding our in vivo results bring us one step closer to developing a product that can help real patients.

In vitro work

In vitro studies are performed in the lab outside of a living organism – think test tubes and petri dishes. These types of experiments allow us to characterize important properties of our scaffolds, like how much they deform or how well the molecules we’ve attached get released. It also offers us the luxury of studying the effects of our material on specific phenomenon, like cell behavior and vessel growth, in a controlled environment. It’s basically Step 1 in understanding what we’ve created.

Although their name would imply that NPCs become neural cells (e.g., nerves), I am interested in how these cells also play a role in blood vessel formation. There is a synergistic relationship between growing blood vessels in the brain and NPCs. Low blood vessel growth results in low NPC migration, but also NPCs secrete factors that are essential for blood vessel sprouting and maturation. My studies revolve around the use of MAP scaffolds as well as our VEGF delivery technology CLUVENA to promote NPC migration and vascularization. In addition, I am changing the physical and biochemical cues of the scaffold to modulate NPC phenotype and mature vessel formation.

If you’re interested in working on strategies to promote recovery after stroke focusing on NPCs and vascularization, contact us and add in the message that you’re interested in my project! #kat #brainheroes

Stem cell delivery

Tbd

Wound healing

Tbd

Bells and whistles

We hate to be boring, so we’re always exploring new features to incorporate into our materials. Most of our scaffolds include additional bioactive signals that help make our material more effective at promoting healing, like:

• peptides / proteins
• nucleic acids
• small molecules
• cells

These additions can be used to attract and influence cells that make their way into the scaffold, or the material can be designed as a drug depot that releases factors at desired time points.