AG2PI Field Day #20 - August 17, 2022


Industry Showcase

August 17, 2022 @ 10:30 AM - 12:00 PM (US Central Time)
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August 17, 2022
10:30 AM - 12:00 PM
(US Central Time)

Purpose

To share new technologies developed via industry that could be applied to genomic research.

Registration

(Virtual Zoom Meeting)

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Join the AG2PI Field Days Slack channel to post a question and receive responses from the speakers

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Chat Questions

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Phenospex: Combining 3D & Gravimetric Data to Breed Climate-Smart Crops

Restricting transpiration under high vapor pressure defcit (VPD) is a promising water-saving trait for drought adaptation. However, it is often measured under controlled conditions and at very low throughput, unsuitable for breeding. A few high-throughput phenotyping (HTP) studies exist, and have considered only maximum transpiration rate in analyzing genotypic differences in this trait.


Presenter

Paul McMahon

With a master's degree in crop breeding, Paul McMahon has been working with Phenospex for seven years. He provides business development for digital plant phenotyping solutions to plant researchers.


EpiCypher: Beyond the Genome: Leveraging Epigenomic Mapping to Uncover Phenotypic Determinants

Phenotypic outcomes are intrinsically linked to chromatin dynamics. Understanding how chromatin integrates genetic and environmental factors to mediate gene expression can inform robust biological predictors, but advances have been hampered by current approaches. EpiCypher's CUTANA CUT&RUN and CUT&Tag technologies enable high resolution mapping of chromatin features using a fraction of the cells and sequencing depth compared to ChIP-seq, the historical approach for epigenomic mapping. While CUT&RUN and CUT&Tag have been primarily applied for human disease research, this presentation will illustrate how these ultra-sensitive and scalable technologies can unlock the full potential of epigenomics for agricultural research.


Presenter

Dr. Andrea Johnstone

Andrea Johnstone, Ph.D., is the Senior Director of Product Development at EpiCypher, a pioneer of innovative research solutions to advance chromatin science.


Chat Questions

Are images available from this system?
Dr. Paul McMahon

In our software, you can visualize in the point cloud, you visualize through our software. You can also use tools like Cloud Compare, which is an open format.


How well does it work when the plants start to overlap? How well does it work when the wind is blowing and the plant leaves are moving?
Dr. Paul McMahon

The way we set-up the system, we divide into sectors. If the plants overlap, it will consider that to be part of the next zone. So there are issues with that. You can cluster plants together and analyze them together to get an average. And with wind, there's a wind threshold, both indoors and outdoors. We track environmental data, so above a certain threshold, it affects the quality of the image, but that data can be screened out.


What is digital biomass exactly? It is plant area/volume?
Dr. Paul McMahon

Digital biomass is a combination of plant height and 3D leaf area. Give a volume estimation or as we call it digital biomass

Follow-up Question: What is 3D leaf area? Area is always 2D

3D leaf area takes the curvature of the leaves into account.

Follow-up Question: By this concept, can you give a mathematical formulation to calculate digital biomass using RGB images?

The leaf area and plant height measurements are generated from our laser line measurements.


Are there opportunities to use this with animals?
Dr. Paul McMahon

We focus on plants, but there was interest in using this type of technology at a meat processing facility to measure the uniformity of chicken breasts. I'm not sure with large-scale, live animals.


We work with farmers in the field and are concerned about the cost of the system. We work with RGB multi-spectral data and digital biomass. Is there a way to measure this using RGB? If we have RGB images, is it possible to calculate the digital biomass?
Dr. Paul McMahon

Not using our system. Ours is designed mainly for research environments. Our system is designed for controlled environments.


With this device, you can record the process of accumulation of dry manure in different organs of the plant?
Dr. Paul McMahon

That would depend on whether it displays a color difference. We could develop indices. We have a greenness index that is reflective of nitrogen, but it would depend on how it manifests itself.


Can the accumulation of dry matter in different organs of the plant be measured in different stages?
Dr. Paul McMahon

We're not at that point where we're distinguishing between different organs.


Most of the examples you showed were where the scanner takes a view from the top. Are there cases where you also need to look at it from different angles?
Dr. Paul McMahon

We have the dual scan, which is at a 20 degree angle. We've tested scenarios for right angles. Theoretically, it's possible to do that to get a top scan and a side scan. Theoretically, you could do it at any angle.


How does the quality of the data from the system compare to other systems?
Dr. Paul McMahon

Our resolution is high, at a millimeter level. I'm not sure since, not having used other systems. There is a facility in the Netherlands where they have multiple systems for multiple vendors. They may be the best place to make that determination.


Is there a need to calibrate this system?
Dr. Paul McMahon

It is calibrated before delivery and the system is designed to be used with multiple species.


How often per day do they scan?
Dr. Paul McMahon

On a given plot, is usually scanned once per day or multiple times a day. I think one scan rate was 55 millimeters per second. We've since increased that. And it depends on the experiment.


The antibodies you talked about, a lot of them are not very specific. When you get to these more specific antibodies, are they specific to a species or can they be applied across species?
Dr. Andrea Johnstone

It depends on the homology. The antibodies we work on are to histone modification where histones are widely conserved across species. We're evolving, validating them in human and mouse cells. But based on the sequence conservation, I predict they would work also in plants and other animals.


Would you recommend to always to the spike-in?
Dr. Andrea Johnstone

Yes. Regardless of whether the antibody is validated by us or anyone else, still using the spike-in every time you are running the antibody it's a good idea.


Do you also use the spike-in data in the analysis?
Dr. Andrea Johnstone

We use it as a quality control check. We use it for troubleshooting.


You mentioned you do 496 well plates per week. How big of a set up would that involve?
Dr. Andrea Johnstone

We have one robot for Cut and Run and a separate one for library prep. But you can do this type of set-up using various robots.


If you don't use robotics and have a small lab, how many samples could a technician run?
Dr. Andrea Johnstone

Our kits come with 8 strip PCR tubes that are designed for multi-channel pipetting, meaning that one experimenter can easily process in-house. Starting with 8-16 is reasonable. All of our kids come in a 48-reaction format, compared to CHiP, which is normally like 16-24 reaction.


The tissue samples are very heterogenous. Are you using it for sorted cells?
Dr. Andrea Johnstone

We have a collaboration with a consortium Engine, which is similar to Encode. They generate functional reference maps of different types of immune cells. They've FACS-sorted them, they send to us, we do Cut and Run on the automated platform and it works fine.