ACS Synthetic Biology,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 8, 2025
Natural
biological
systems
use
feedback
regulation
to
effectively
respond
and
adapt
their
changing
environment.
Even
though
in
engineered
we
understand
how
accurate
can
be
depending
on
the
electronic
or
mechanical
parts
that
it
is
implemented
with,
largely
lack
a
similar
theoretical
framework
study
systems.
Specifically,
not
fully
understood
quantified
robust
implementation
of
actually
is.
In
this
paper,
sensitivity
variations
biochemical
parameters
using
five
example
circuits:
positive
autoregulation,
negative
double-positive
feedback,
positive-negative
double-negative
(the
toggle
switch).
We
find
some
these
examples
are
subjected
fundamental
performance
trade-offs,
propose
multi-objective
optimization
as
properties.
The
impact
work
improve
circuit
design
for
synthetic
biology
our
understanding
biology.
Nature Communications,
Год журнала:
2022,
Номер
13(1)
Опубликована: Июнь 27, 2022
Abstract
Cell
interactions
determine
phenotypes,
and
intercellular
communication
is
shaped
by
cellular
contexts
such
as
disease
state,
organismal
life
stage,
tissue
microenvironment.
Single-cell
technologies
measure
the
molecules
mediating
cell–cell
communication,
emerging
computational
tools
can
exploit
these
data
to
decipher
communication.
However,
current
methods
either
disregard
context
or
rely
on
simple
pairwise
comparisons
between
samples,
thus
limiting
ability
complex
across
multiple
time
points,
levels
of
severity,
spatial
contexts.
Here
we
present
Tensor-cell2cell,
an
unsupervised
method
using
tensor
decomposition,
which
deciphers
context-driven
simultaneously
accounting
for
stages,
states,
locations
cells.
To
do
so,
Tensor-cell2cell
uncovers
patterns
associated
with
different
phenotypic
states
determined
unique
combinations
cell
types
ligand-receptor
pairs.
As
such,
robustly
improves
upon
extends
analytical
capabilities
existing
tools.
We
show
identify
modules
distinct
processes
(e.g.,
participating
pairs)
linked
severities
Coronavirus
Disease
2019
Autism
Spectrum
Disorder.
Thus,
introduce
effective
easy-to-use
strategy
understanding
diverse
conditions.
Trends in biotechnology,
Год журнала:
2024,
Номер
42(7), С. 895 - 909
Опубликована: Фев. 5, 2024
Cells
provide
dynamic
platforms
for
executing
exogenous
genetic
programs
in
synthetic
biology,
resulting
highly
context-dependent
circuit
performance.
Recent
years
have
seen
an
increasing
interest
understanding
the
intricacies
of
circuit–host
relationships,
their
influence
on
bioengineering
workflow,
and
devising
strategies
to
alleviate
undesired
effects.
We
overview
how
emerging
interactions,
such
as
growth
feedback
resource
competition,
impact
both
deterministic
stochastic
behaviors.
also
emphasize
control
mitigating
these
unwanted
This
review
summarizes
latest
advances
current
state
host-aware
resource-aware
design
gene
circuits.
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Янв. 16, 2025
Plants,
with
intricate
molecular
networks
for
environmental
adaptation,
offer
groundbreaking
potential
reprogramming
predictive
genetic
circuits.
However,
realizing
this
goal
is
challenging
due
to
the
long
cultivation
cycle
of
plants,
as
well
lack
reproducible,
quantitative
methods
and
well-characterized
parts.
Here,
we
establish
a
rapid
(~10
days),
quantitative,
framework
in
plants.
A
group
orthogonal
sensors,
modular
synthetic
promoters,
NOT
gates
are
constructed
quantitatively
characterized.
model
developed
predict
designed
circuits'
behavior
accurately.
Our
versatile
robust
framework,
validated
by
constructing
21
two-input
circuits
high
prediction
accuracy
(R2
=
0.81),
enables
multi-state
phenotype
control
both
Arabidopsis
thaliana
Nicotiana
benthamiana
response
chemical
inducers.
study
achieves
predictable
design
application
offering
valuable
tools
engineering
plant
traits
biotechnology
agriculture.
The
gene
plants
has
been
lagging
behind
other
organisms.
authors
report
designing
reprograming
expression
hypersensitive
response.
Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Дек. 18, 2023
As
synthetic
biology
permeates
society,
the
signal
processing
circuits
in
engineered
living
systems
must
be
customized
to
meet
practical
demands.
Towards
this
mission,
novel
regulatory
mechanisms
and
genetic
with
unprecedented
complexity
have
been
implemented
over
past
decade.
These
mechanisms,
such
as
transcription
translation
control,
could
integrated
into
hybrid
termed
"multi-level
circuits".
The
multi-level
circuit
design
will
tremendously
benefit
current
paradigm,
from
modifying
basic
dynamics
facilitating
real-world
applications,
unleashing
our
capabilities
customize
cellular
address
global
challenges
through
biology.
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Янв. 2, 2025
Abstract
Degradation
tags,
otherwise
known
as
degrons,
are
portable
sequences
that
can
be
used
to
alter
protein
stability.
Here,
we
report
degron-tagged
proteins
compete
for
cellular
degradation
resources
in
engineered
mammalian
cells
leading
coupling
of
the
rates
independently
expressed
when
constitutively
targeted
human
degrons
adopted.
We
show
effect
this
competition
dependent
on
context
degrons.
By
considering
different
proteins,
degron
position
and
hosts,
highlight
how
impact
both
strength
resource
changes,
with
identification
orthogonal
combinations.
adopting
inducible
bacterial
plant
also
controlled
uncoupling
synthetic
construct
from
native
machinery
achieved.
then
build
a
genomically
integrated
capacity
monitor
tagged
confirm
between
genomic
transiently
DNA
constructs.
This
work
expands
characterisation
including
systems,
providing
framework
optimisation
heterologous
expression
systems
advance
applications
fundamental
applied
biological
research.
