Coupling of aptamers with reduced graphene oxide for detection of herpes simplex virus 2 protein marker
Fullerenes Nanotubes and Carbon Nanostructures,
Год журнала:
2025,
Номер
unknown, С. 1 - 12
Опубликована: Апрель 3, 2025
Язык: Английский
Biosensors Characterisation: Formal methods from the Perspective of Proteome Fractions
Synthetic Biology,
Год журнала:
2025,
Номер
10(1)
Опубликована: Янв. 1, 2025
Abstract
Many
studies
characterize
transcription
factors
and
other
regulatory
elements
to
control
gene
expression
in
recombinant
systems.
However,
most
lack
a
formal
approach
analyse
the
inherent
context-specific
variations
of
these
components.
This
study
addresses
this
gap
by
establishing
framework
from
which
convenient
methods
are
inferred
circuits.
We
modelled
bacterial
cell
as
collection
proteome
fractions.
Deriving
time-dependent
fraction,
we
obtained
general
theorem
that
describes
its
change
function
specific
portion
total
biosynthesis
flux
cell.
Formal
deduction
reveals
when
fraction
reaches
maximum,
it
becomes
equivalent
fraction.
equation
enables
reliable
measurement
through
direct
protein
quantification.
In
addition,
experimental
data
demonstrate
linear
correlation
between
production
rate
growth
over
significant
time
period.
suggests
constant
within
window.
For
an
Isopropyl
β-
d-1-thiogalactopyranoside
(IPTG)
biosensor,
five
cellular
contexts,
fractions
determined
maximum
method
slope
produced
strikingly
similar
dose–response
parameters
independently
fit
Hill
function.
Furthermore,
analysing
two
more
biosensors,
for
mercury
cumate
detection,
can
be
applied
effectively
various
Therefore,
concepts
presented
here
provide
obtaining
parameters,
clearly
defining
interval
their
validity
offering
interpreting
typical
biosensor
outputs
terms
physiology.
Graphical
Nutrients,
transformed
action
Nutrient
Fixators
(purple
arrow),
used
at
ρ
Protein
biosynthesis.
The
is
multiplied
fR,
fC,
fH,
fQ
obtain
(black
arrows)
each
ΦR,
ΦC,
ΦH,
ΦQ,
respectively.
graph
Growth
versus
Proteome
Fraction
Production
Rate,
(green
lines)
observed,
equal
condition.
Язык: Английский
Harnessing Synthetic Biology for Sustainable Industrial Innovation: Advances, Challenges, and Future Direction
Biochemical Engineering Journal,
Год журнала:
2025,
Номер
unknown, С. 109777 - 109777
Опубликована: Май 1, 2025
Язык: Английский
A generalizable approach for programming protease-responsive conformationally inhibited artificial transcriptional factors
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Май 17, 2025
Synthetic
genetic
circuits
that
harness
programmable
protein
modules
and
artificial
transcription
factors
(ATF)
to
devise
event-triggerable
cascaded
pathways
represent
an
essential
class
of
tools
for
studying
cell
biology.
Fine-tuning
the
general
structural
functionality
ATFs
is
important
constructing
orthogonal
composable
transcriptional
regulators.
Here,
we
report
design
a
protease-responsive
conformationally
inhibited
system
(PRCIS).
By
intramolecularly
linking
free
DNA-binding
domains
ATF
confined
dimerized
regions,
binding
inactivated.
The
function
DNA
reinstated
upon
proteolytic
cleavage
linkages,
activating
downstream
gene
expressions.
versatility
PRCIS
demonstrated
through
its
adaptability
various
proteases,
showcasing
high
activation
ratios
specificity.
Furthermore,
development
PRCIS-based
triple-orthogonal
dual-orthogonal
chemical-inducible
platforms
Boolean
logic
operations
are
elaborated
in
this
paper,
providing
generalizable
synthetic
Язык: Английский
Genetically Encoded, Noise-Tolerant, Auxin Biosensors in Yeast
ACS Synthetic Biology,
Год журнала:
2024,
Номер
13(9), С. 2804 - 2819
Опубликована: Авг. 28, 2024
Auxins
are
crucial
signaling
molecules
that
regulate
the
growth,
metabolism,
and
behavior
of
various
organisms,
most
notably
plants
but
also
bacteria,
fungi,
animals.
Many
microbes
synthesize
perceive
auxins,
primarily
indole-3-acetic
acid
(IAA,
referred
to
as
auxin
herein),
prevalent
natural
auxin,
which
influences
their
ability
colonize
Understanding
biosynthesis
in
fungi
may
allow
us
better
control
interkingdom
relationships
microbiomes
from
agricultural
soils
human
gut.
Despite
this
importance,
a
biological
tool
for
measuring
with
high
spatial
temporal
resolution
has
not
been
engineered
fungi.
In
study,
we
present
suite
genetically
encoded,
ratiometric,
protein-based
biosensors
designed
model
yeast
Язык: Английский
Biosensor‐Guided Engineering of a Baeyer‐Villiger Monooxygenase for Aliphatic Ester Production
ChemBioChem,
Год журнала:
2024,
Номер
26(1)
Опубликована: Сен. 25, 2024
Abstract
Esters
are
valuable
aroma
compounds
and
can
be
produced
enzymatically
by
Baeyer‐Villiger
monooxygenases
(BVMOs)
from
(aliphatic)
ketone
precursors.
However,
a
genetically
encoded
biosensor
system
for
the
assessment
of
BVMO
activity
detection
reaction
products
is
missing.
In
this
work,
we
assembled
synthetic
enzyme
cascade
–
featuring
an
esterase,
alcohol
dehydrogenase,
LuxAB
in
heterologous
host
Escherichia
coli
.
Target
esters
BVMO,
subsequently
cleaved,
corresponding
oxidized
through
artificial
pathway.
Ultimately,
aldehyde
detected
vivo
LuxAB,
luciferase
Photorhabdus
luminescens
that
emits
bioluminescence
upon
oxidation
aldehydes
to
carboxylates.
This
greatly
accelerated
screening
selection
active
variants
focused
library,
omitting
commonly
used
low‐throughput
chromatographic
analysis.
Engineered
enzymes
accepted
linear
aliphatic
ketones
such
as
2‐undecanone
2‐dodecanone
exhibited
improved
ester
formation.
Язык: Английский
Biological Switches: Past and Future Milestones of Transcription Factor-Based Biosensors
ACS Synthetic Biology,
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 22, 2024
Since
the
description
of
Язык: Английский
Genetically Encoded Fluorogenic DNA Aptamers for Imaging Metabolite in Living Cells
Journal of the American Chemical Society,
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 31, 2024
Genetically
encoded
fluorescent
protein
and
fluorogenic
RNA
sensors
are
indispensable
tools
for
imaging
biomolecules
in
cells.
To
expand
the
toolboxes
improve
generalizability
stability
of
this
type
sensor,
we
report
herein
a
genetically
DNA
aptamer
(GEFDA)
sensor
by
linking
dimethylindole
red
with
an
ATP
aptamer.
The
design
enhances
fluorescence
4-fold
at
650
nm
presence
ATP.
Additionally,
upon
dimerization,
it
improves
signal-to-noise
ratio
2-3
folds.
We
further
integrated
into
plasmid
to
create
GEFDA
sensing
live
bacterial
mammalian
This
work
expanded
employing
aptamers,
which
offer
enhanced
over
proteins
RNAs,
providing
novel
tool
real-time
monitoring
even
broader
range
small
molecular
metabolites
biological
systems.
Язык: Английский
Genetically encoded biosensors for the circular plastics bioeconomy
Metabolic Engineering Communications,
Год журнала:
2024,
Номер
19, С. e00255 - e00255
Опубликована: Ноя. 28, 2024
Язык: Английский
Biosensors Characterization: Formal methods from the Perspective of Proteome Fractions
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Дек. 1, 2023
Abstract
Many
studies
characterize
transcription
factors
and
other
regulatory
elements
to
control
the
expression
of
heterologous
genes
in
recombinant
systems.
However,
most
lack
a
formal
approach
analyse
parameters
context-specific
variations
these
components.
This
study
addresses
this
gap
by
establishing
convenient
methods
for
characterising
circuits.
We
model
bacterial
cell
as
collection
small
number
proteome
fractions.
Then,
we
derive
fraction
over
time
obtain
general
theorem
describing
its
change
function
fraction,
which
represents
specific
portion
total
biosynthesis
flux
cell.
Formal
deduction
reveals
that
when
reaches
maximum,
it
becomes
equivalent
fraction.
equation
enables
reliable
measurement
through
direct
protein
quantification.
In
addition,
experimental
data
demonstrate
linear
correlation
between
production
rate
growth
significant
period.
suggests
constant
within
window.
The
fractions
estimated
from
slopes
intervals
those
obtained
maximum
amount
points
can
both
be
independently
fitted
Hill
function.
case
an
IPTG
biosensor,
five
cellular
contexts,
determined
method
slope
produced
similar
dose-response
parameters.
Additionally,
analysing
two
more
biosensors,
mercury
cumate
detection,
effectively
applied
various
systems,
generating
Язык: Английский