cell specific networks in plants · cell specific networks in plants author: nyu subject:...

Systems Biology and Agriculture: Cell-Specific Networks in Plants

Kenneth D. Birnbaum

New York University

Center for Genomics

& Systems Biology

Biofuels

Drought

Yield

The Power of Cellular Approaches controlling growth with plant stem cells

Above ground

Biofuels -- Biomass

Food -- Edible mass

Below ground

Drought tolerence - tap roots

Food -- storage roots

Environment -- Nutrient uptake

Systems Biology Cycle

Data generation New Technology

High thru-put analysisCell-sorting

Data analysisNew Theory

Math & PhysicsCell-specificity index

Dynamic imagingNew Technology

Real-time morphometricsCandidate validation

Data ModelingPredictionsComputation

Useful Traits

New Technology New Data Targeted Approach

Cellular Level Resolution is Essential for understanding function

Why Cell-Specific Circuits?

1. Reduce pleiotropy – unwanted effects2. Understand cellular networks

growth cellular patterncell

identity

cell wall

The Stem Cell Niche

Quiescent Center (QC)

stem cells

A Genomic View of Cell Identity

Birnbaum et al, Science 2003

Cell Type: Xy Par Per End E/Cor Epi LRC Col QC

GFP marked cell lines

FACS Cell sorting

Cell-specific transcriptomics

Cellular Transcriptome

Isolated cell type

Rice lines

Presenter

Presentation Notes

Tool to evaluate the entire identity, not only a few markers








Data ModelingNew PredictionsComputation


New Theory: Cell Specificity Index

12 cell types

cell type A

enriched

enriched

Gene X

Gene Y

non-specific

specific

Gene Specificity and Noise12 cell types

cell type A

enriched

enriched

Gene X

Gene Y

non-specific

specificNoise: One of three replicates shows expression

Specificity Index: Quantify Specificity as Information

Gene Y

expression level

frequ

ency

0 0 0.2 0.2 0.2 0.2 0 0.2 0.2 0.2 0.7 0.7Spec Index

Nspec = 2.5

Information TheoryKullback-Leibler

DivergenceEdo Kussell

NYU Biology & Physics

Gene Y

frequ

ency

Confidence Limits on Specificity

A Cell is Born dynamics of cell-type assembly on a molecular scale

Control hormone treated

QC marker

Hypothesize the Transcriptional Cascade by Correlation Analysis

0hr 24hr 48hr 72hr 96hr

Cells in transition from endodermis to QC Genes groupedModel Patterns

t

t

t

Presenter

Presentation Notes

The second question. Quantitative way by correlation with model patterns Statistics is coming. We are interested in genes induced early, especially TFs.

“Drive Through” Plant Genetics

Protoplasts

Rapid Genetic Assays in Plant Cells

Gene YGene X ?

Rice and Arabidopsis

Combinatorial Auxin Code for QC

EARLY MIDDLE LATE

ARF5

ARF6

ARF7

ARF9

ARF2

ARF1

ARF18

ARF19

ARF16

IAA8,12,13,16,18,26,27,30

IAA1,2,17,19

PLT

SCR

PAN*

ERFa*

Dynamic view of a growing root

Sena,G., Frentz,Z., Birnbaum, K.D., Leibler, S. (in preparation)

6

Giovanni Sena, postdoc

Presenter

Presentation Notes

This is a normally growing root where we can already recognize several cell divisions occurring.

•

positions of nuclei trajectories in time (velocities, etc.)

•

cell divisions (location, orientation)

•

spatial and temporal correlations among division events (patterning!)

•

large scale, collective motions (stretching and torsion)

Examples of quantitative measures:

trajectories

20 μm

velocities

20 μm

0 0.2μm/min

cell division

2

hrs

10 μm

8

Presenter

Presentation Notes

These are examples of the quantitative measurements that can be extracted from this data. For the first time we will be able to track the position of each nucleus and to built their trajectories in time, upon which calculating various physical quantities such as their velocities. From this data, the location and orientation of each cell division can be extracted, and their temporal and spatial correlation could be calculated, which will give us a novel and detailed view on the dynamics of patterning As an example from real preliminary data, here I am showing you vector a field of nuclei velocities color-coded by their speed, nuclei trajectories projected on the cross plane of the root, and a cell division as it appears as a nuclear trajectory branching in time.









Useful Traits


Potential Applications: Controlling Stem Cell Activity in Roots

Maintaining the Stem Cell Niche

and Growth

Controlling Cap Growth for

Hydroponics

drought environment hydroponics

Fine root proliferation timed with fertilization

Genomics of Regeneration

Giovanni Sena, postdoc

Cellular Networks

Bastiaan Bargmann, postdoc

Collaborators

•Edo Kussell, NYU Biology & Physics

•Gloria Coruzzi, NYU Center for Genomics and Systems Biology

•Dennis Shasha, NYU Courant Institute

•Stan Leibler, Rockefeller University

Lihua Shen, graduate student

Shuai Yuan, graduate student

Plant meristem evolution

Alison Mello, graduate student

Genomics of Cell-Cell Signaling

Tal Nawy, postdoc

Pui-Leng Ip, technician

cell specific networks in plants · cell specific networks in plants author: nyu subject:...

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