Framework for Developing Organismal Biology - iPlant Pods

rapidparentBiotechnology

Dec 12, 2012 (4 years and 7 months ago)

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A. Here we propose a fresh framework for developing organismal biology.
[DEFINITIONAL; HOW ORGANISMS RESOLVE CHALLENGES &
OPPORTUNITIES]




Joel, Lou, Michael, Scott, Molly








The framework builds on the enormous technological advances that have
come through a combination of the 'omics and micro/nano
-
engineering




'OMICS: high throughput collection of data
--

typically about molecular
variables




Micro/nano
-
engineering


fa
brication of miniaturized devices used here
for data collection and organismal manipulation.




These technologies enable new approaches to old questions such as:




transcriptomics to examine whether similar environment


adaptation
relations are accompan
ied by comparable transcriptional signals




Can we define the genomic basis of adpatational costs and tradeoffs




___________








what potential for developing a unifying theoretical framework for
organismal biology?


A general theory for whole organi
sm for integrated model choice for designing
these data


A general theory of whole organism integrated physiology and behavior can
incorporate two aspects of multi
-
level data:


(i) model choice for combining these data and deceasing what state variable
s are
necessary to capture the phenomena of interest at whole organism scale; and


(ii) characterize the adaptive nature of whole organism response specifying what
control variables are critical to assess organism dynamic response to challenges
on multiple time scales.


Can we describe how within organism variation in development, metab
olism,
physiology and morphology are integrated to produce whole organism response
to environment.


The organism the central unit for integrating biology


focus on the phenotype


organism must be understood in terms of the environment from the perspectiv
e
of evolution, development and function.

Genotype


phenotype relations are contextually dependent

Evolution is the central guiding princip
al

organismal biology.

Variation in phenotype is a key theme


CHALLENGE: Bring the environment into the lab, inste
ad of the animal into the
lab


WHY THIS MUST OCCU
R? WHAT IT OFFERS? e.g., the study of
genomicly

engineered animals in relevant environments.


Can we describe how within org variation in metabolism, physiology, anatomy,
morphology are integrated to produ
ce whole organism resp
on
se to the
environment.

Use of transcriptomics to define tissue
-
specific responses and how these
responses contribute to the whole animal response to a specific
environmental signal

Use transcriptomics to define species
-
differences
in signal


adaptation
relati
o
ns: define transcriptional pathways to specific for
ms of adaptations
across specie
s.

These comments need not be considered only in terms of transcriptomics, but
rather to any “’omic” approaches


G
enetic engineering of crop
plants and insect pests: suggests that genetics
modifications targeting single genes/traits affects multiple

traits…understand
whole organisms to do this better. Does not work because traits work co
-
operatively…(correlated traits).

Functional
integration

Elelim: horned horned beetles trading
-
off horned size for eye development
(the transcriptional basis of trade
-
offs).

The ability of org
anismal

biologists to define

and study adpatati
onal costs.

List examples where organismal biology hig
hlights a trade
-
of
fs, adaptation
al
costs, pleiotropy,

The study of variation implies that the study must arrive at the whole
organism.

How do various sy
s
tems

functionally interact to produce a de
fined

outcome

The integration of systems and organismal biology: Permits allow
s
researchers to examine a signal


response tra
nsduction

and translational
to whole organisms re
sponses
.

The study of adaptational costs/tradeoffs at the levels of mechanism
allows us to understand constraints on adaptation…

comparative

Sub
-
theme: how
exposure to early life adversity lim
its

the capacity
for plasticity in later life; organismal biology provides a framework to
examine this happens.

Example of where organismal biology has contributed to clinical
med: fetal orig
i
ns of he
alth



importance of

thrifty phenotype
hypothesis.

,

It has long

been known by leading whole organismal

b
iologists

(e..g, Molly
Cummings) complex phenotypes do not have a simple genetic basis
: this
provides opportunities as

‘omics technology
with organismal biology
-
infored
approaches provide

the basis
for studies of
this issue.

As a corollary, the study of g
ene networks and their operation must be
understood at the level of the inte
grat
ed

system


within the context of the whole
organism and whole organism responses to rel
evant environmental conditions.

BUT….to systems biologists this will appear to diffuse and lacking in precision…


HO
WEVER….

Advances in sensor technology…real time measurement of
phenotypes….permits opportunites to characterize complex phenotypes in
divers
e environments over time (real time measurement


energy expenditure,
social structure affects phyisology/behaviour, integration of traits, defensive
responses over a broad set of challenges over time,