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Leveraging understudied spider species to uncover novel biology

Backed by David Lang
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  • $10
    pledged
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  • 43
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About This Project

Over $1.425B has been invested into spider silk companies, yet less than 20 annotated spider genomes are available on NCBI, and current spider research is phylogenetically skewed. This is prohibiting the scientific community from identifying novel traits in non-orb weaving spiders. By sequencing and annotating a whole genome of an understudied spider, the local community can interact closely with biology while contributing to the collective pool of knowledge.

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What is the context of this research?

Recombinant spider silk proteins — spidroins — that are comparable to native spidroins have been sought after for decades due to their strength, toughness and elasticity. Recognizing the potential textile, medical and beauty applications of spidroins, companies have sprinted to commercialize these proteins.

Over $1.425B has been raised with the hopes of capturing a majority of the projected $1.984B spidroin market, yet much is to be discovered about spiders more broadly. Most research efforts have been placed on studying and recombinantly expressing major and minor ampullate silks given their contribution to the strength and elasticity of orb webs for Araneidae spiders. Thus, non-Araneidae spiders are understudied despite their unique traits and uses for silk.

What is the significance of this project?

Although we have seen a meteoric rise in investor interest and available spider silk datasets such as the Spider Silkome Database, there are roughly 15 available annotated spider genomes available on NCBI and most of these are for orb-weaving (Araneidae) spiders. In an effort to quickly replicate this remarkable material by way of fermentation, we’ve neglected to consider how the potential commercial applications have shaped how basic research of spiders is conducted.

In fact, non-Araneidae spiders may be a source of overlooked novelty. For example, the ogre spider regrows its super-sensitive retinas daily. What can we learn about vision and regeneration that could lead to insights in human health?

What are the goals of the project?

This project aims to uncover basic science insights about a non-Araneidae spider species and to facilitate project-based learning of molecular biology, biochemistry and microscopy. Perhaps most importantly, the research will be published on an open and alternative platform and serve as an experiment to better identify how the Community Bio ecosystem can share, enhance and interact with research that emerges from community labs.

More explicitly, we aim to:

  1. Sequence and annotate the whole genome of an understudied non-Araneidae spider species

  2. Submit the annotations to NCBI and openly publish the methods and pipelines that led to the predicted annotations

  3. Learn about the principles of Raman spectroscopy and convey those learnings to Genspace members and the community bio ecosystem

Budget

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The Nanopore MiniION will generate long-read sequencing data while the Illumina MiniSeq will generate short-read sequencing data. Both datasets will increase our likelihood of creating high-quality genome annotations.

Although it is possible to evaluate DNA concentration from library preps with Nanodrop or Qubit, we will build a Raman microscope (OpenRAMAN) in order to teach the principles of spectroscopy to the community and compare the spectra to Qubit quantitation data. This will also make non-destructive chemical analysis available for other Genspace members.

We’ve established relationships with scientists studying arachnids such as Joe Arguelles, a PhD student in Cheryl Hayashi’s lab. Reserving funds for advisor compensation will improve the quality of our methods and ensure we have an “internal reviewer” while preparing for publication.

By publishing on PubPub, we’ll be able to receive a DOI and feedback from the scientific community directly on the “manuscript.”

Endorsed by

I'm thrilled about this project taking off! Not only will it fill a gap in the study of non-Araneidae spider species, but it will also be led by a group of amazing people with diverse expertise, creating the perfect team. Having met at Genspace, a community bio lab, they discovered their shared interests and developed this idea. This project will provide valuable insights into the spider genome and establish a workflow for Raman microscopy (it hasn’t been done at Genspace) that can be replicated and taught across the community bio space.
As a leader of a community project at Genspace to express insulin in Marchantia polymorpha, I have worked with all of the people who are on this project. You won't find a smarter, more capable or more committed group. Looking where people haven't looked before - in this case the non-orb weaving spiders - is going to turn up a lot of new and interesting information. I'm excited that the team will be bringing a new technique, Raman spectroscopy, to the Genspace community.

Project Timeline

In order to ensure that the community has the ability to learn about molecular biology, biochemistry and microscopy by participating in this community project, research will not begin until June 2024. The months of April and May will focus on explaining foundational concepts in phylogenomics, next-generation sequencing, Raman spectroscopy and more so that community members are empowered to significantly contribute to the scientific direction and research methods.

Jun 10, 2024

Project Launched

Jun 30, 2024

Literature review and phylogenetic analysis of represented spiders (whole genome and spider silkome)

Aug 16, 2024

Selected spider sequencing completed

Sep 30, 2024

Genome annotations completed

Oct 31, 2024

Results are published on PubPub

Meet the Team

Jasmine Neal
Jasmine Neal
Engineered Matter Lab Lead
Sally Kong
Sally Kong

Affiliates

Genspace
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Meghan Kane
Meghan Kane
Research Assistant, Computational Biology

Affiliates

Max Planck Institute for Molecular Genetics, Genspace
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Casey Lardner
Casey Lardner
Lab & Operations Manager

Affiliates

Genspace
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Kathy Mu
Kathy Mu

Affiliates

Genspace
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Team Bio

EML's multifaceted expertise positions them to bring the project's goals to life. Jasmine's biochemistry expertise, including in spider silk, provides a strong foundation for designing and steering robust experiments. Kathy's molecular biology lab skills are essential for leading these experiments at the bench. Sally's lab automation skills streamline conducting a variety of assays efficiently. Meghan's computational biology experience enables comprehensive sequence analyses and other modeling.

Jasmine Neal

Jasmine is an ASAPbio Fellow and Entrepreneur in Residence at Arcadia Science, focusing on the intersection of basic science research and translation. Some of her current research interests pertain to preeclampsia, female sexual desire for pre- and post-menopausal women, and enhanced rock weathering.

She also leads Engineered Matter Labs (EML) — a community protein-based materials design team focusing on engineering spider silk-inspired proteins to serve as a humectant in skin care and researching understudied spider species that can serve as sources of novelty.

Previously, she was the Co-Founder leading product and operations at TUNE, where some of their clients included lululemon, Google, Northwell Health, and JW Marriott.

Sally Kong

Sally is a software engineer, artist, and educator based in Brooklyn, NY. After studying computer science and robotics, she has built automation pipelines and artist tools for 3D animated feature films and games at Disney’s Blue Sky Studios, Netflix, and Rockstar Games. She has been an active member of Genspace since 2022 as part of the Engineered Matter Labs team, and is also a global teaching assistant for MIT Media Lab’s synthetic biology course, "How To Grow Almost Anything."

Meghan Kane

Meghan is currently a computational biology research assistant at the Max Planck Institute for Molecular Genetics modeling high-risk viral mutations with respect to antigenic fitness (immune escape) taking into account insights learned from phylogenetics, biophysics, and epidemiology. Since 2022, she's been a part of the vibrant Engineered Matter Labs team at Genspace NYC working to understand the remarkable properties of spider silk and design proteins inspired by it. She also helps as a global teaching assistant for MIT Media Lab's synthetic biology course during spring semester, "How To Grow Almost Anything."

Before working in computational biology, she worked as a software developer at companies such as SoundCloud. Her educational background is in computer science and mathematics.

Casey Lardner

Casey Lardner (she/her) is the Lab & Operations Manager at Genspace, the world's first community biology lab. She holds a Ph.D. in Neuroscience from the Icahn School of Medicine at Mount Sinai and completed postdoctoral research at Columbia University. Building on a background in ecology and evolutionary biology, much of her research used next-generation sequencing in mice and wild, urban rats to model and understand the human brain. As a graduate student, she co-directed an outreach group called “MINDS” and produced a science storytelling show called Studying the Brain. After her postdoc, she pursued full-time science communication and informal science education as a program coordinator in the Neuroscience Institute at NYU Langone. She is the president of BraiNY, a regional organization of the Society for Neuroscience in NYC and is enamored with all brains and minds – whether they belong to mice, pizza rats, people, or other living things.

Kathy Mu

Kathy works as an architect and has been a member of Genspace since 2019. She is interested in the use of biomaterials in the built environment and how the incorporation of these materials impacts building lifecycles and sustainability. At Genspace, Kathy is a co-lead for the Engineered Matters Lab developing protocols for experiments to potentially produce spider silk synthetically.

Lab Notes

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