bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Nov. 23, 2023
Microfluidic
platforms
enable
long-term
quantification
of
stochastic
behaviors
individual
bacterial
cells
under
precisely
controlled
growth
conditions.
Yet,
quantitative
comparisons
physiological
parameters
and
cell
different
microorganisms
in
experimental
device
modalities
is
not
readily
possible
owing
to
experiment-specific
details
affecting
physiology
confounding
ways.
To
rigorously
assess
the
effects
mechanical
confinement,
we
designed,
engineered,
performed
side-by-side
experiments
otherwise
identical
conditions
Mother
Machine
(with
confinement)
SChemostat
(without
confinement),
using
latter
as
ideal
comparator.
We
established
a
protocol
cultivate
suitably
engineered
rod-shaped
mutant
Caulobacter
crescentus
Machine,
benchmarked
differences
division
dynamics
with
respect
SChemostat.
While
single-cell
rate
distributions
are
remarkably
similar,
mechanically
confined
experience
substantial
increase
interdivision
times.
However,
find
that
ratio
distribution
compensates
for
this
times,
which
turn
reflects
emergent
simplicities
governing
intergenerational
homeostasis
sizes
across
configurations,
provided
appropriately
mean-rescaled
each
condition.
Our
results
provide
insights
into
nature
robustness
machinery.
Sensors and Actuators A Physical,
Journal Year:
2024,
Volume and Issue:
376, P. 115625 - 115625
Published: June 24, 2024
The
integration
of
CRISPR
technology
with
microfluidic-based
biosensors
has
greatly
expanded
its
applications
in
medicine
and
molecular
biology.
This
combination
offers
enhanced
sensitivity
selectivity
medical
diagnostics.
CRISPR-powered
microfluidics
enables
the
accurate
quantification
DNA
RNA
associated
diseases
such
as
cancer,
viral
infections,
bacterial
diseases.
precise
targeting
capabilities
allow
for
detection
specific
genetic
sequences,
aiding
early
diagnosis,
disease
monitoring,
treatment
assessment.
improves
specificity
by
leveraging
programmable
nature
coupling
it
signal
readouts.
However,
challenges
assay
optimization,
standardization,
device
fabrication
need
to
be
addressed.
Additionally,
complexity
presents
potential
limitations
terms
off-target
effects
unintended
modifications.
Overall,
holds
tremendous
diagnostics,
but
further
research
development
are
required
fully
exploit
benefits
clinical
settings.
SoftwareX,
Journal Year:
2024,
Volume and Issue:
26, P. 101638 - 101638
Published: Feb. 1, 2024
Automated
microscopy
techniques
combined
with
high-throughput
microfluidic
cultivation
systems
provide
unique
insights
into
living
microorganisms,
enabling
hundreds
of
experiments
to
be
performed
in
parallel.
Such
setups
generate
large
data
sets
rich
cellular
features
that
need
extracted
arrive
at
quantitative
insights.
The
sheer
amount
recorded
time-lapse
images
requires
reliable
automated
processing.
While
recent
advances
deep
learning
methods
have
enabled
processing,
these
rely
on
large-scale
and
precisely
annotated
sets,
often
not
available
for
new
organisms
or
custom
imaging
modalities.To
overcome
the
bottleneck,
particularly
microbial
domain,
we
present
open-source
ObiWan-Microbi
platform
providing
a
fast
workflow
annotation
up
hundred
thousands
segmentation
tracking
annotations
data.
focuses
easy-to-use
semi-automated
browser
eliminating
local
installation
accelerator
hardware,
encourages
FAIR
management
using
OMERO,
provides
convenient
collaborative
cloud
deployment
simplify
creation
long-term
development
sets.
public
availability
such
benchmark
has
potential
improve
data-driven
methods,
increase
comparability
among
them,
is
an
essential
step
towards
image
processing
live-cell
microscopy.
International Journal of Biological Sciences,
Journal Year:
2024,
Volume and Issue:
20(6), P. 2151 - 2167
Published: Jan. 1, 2024
Immunotherapy
plays
a
key
role
in
cancer
treatment,
however,
responses
are
limited
to
small
number
of
patients.The
biological
basis
for
the
success
immunotherapy
is
complex
interaction
between
tumor
cells
and
immune
microenvironment
(TIME).Historically,
research
on
constitution
was
analysis
one
or
two
markers,
more
novel
technologies
needed
interpret
interactions
TIME.In
recent
years,
major
advances
have
already
been
made
depicting
TIME
at
considerably
elevated
degree
throughput,
dimensionality
resolution,
allowing
dozens
markers
be
labeled
simultaneously,
analyzing
heterogeneity
tumour-immune
infiltrates
detail
single
cell
level,
spatial
landscape
entire
microenvironment,
as
well
applying
artificial
intelligence
(AI)
large
amount
data
from
this
review,
we
summarized
emerging
that
contributions
field
TIME,
provided
prospects
future
research.
npj Aging,
Journal Year:
2024,
Volume and Issue:
10(1)
Published: Nov. 26, 2024
Aging
has
profound
effects
on
the
body,
most
notably
an
increase
in
prevalence
of
several
diseases.
An
important
aging
hallmark
is
presence
senescent
cells
that
no
longer
multiply
nor
die
off
properly.
Another
characteristic
altered
immune
system
fails
to
properly
self-surveil.
In
this
multi-player
process,
cellular
senescence
induces
a
change
secretory
phenotype,
known
as
senescence-associated
phenotype
(SASP),
many
with
intention
recruiting
accelerate
clearance
these
damaged
cells.
However,
SASP
results
inducing
secondary
nearby
cells,
resulting
those
becoming
senescent,
and
improper
activation
state
chronic
inflammation,
called
inflammaging,
Senescence
termed
immunosenescence,
further
dysregulation
system.
interdisciplinary
approach
needed
physiologically
assess
changes
at
tissue
level.
Thus,
intersection
biomaterials,
microfluidics,
spatial
omics
great
potential
collectively
model
immunosenescence.
Each
approaches
mimics
unique
aspects
body
undergoes
part
aging.
This
perspective
highlights
key
how
biomaterials
provide
non-cellular
cues
cell
aging,
microfluidics
recapitulate
flow-induced
multi-cellular
dynamics,
analyses
dissect
coordination
biomarkers
function
interactions
distinct
environments.
overview
play
role
organ
cancer,
wound
healing,
Alzheimer's,
osteoporosis
included.
To
illuminate
societal
impact
increasing
trend
anti-senescence
anti-aging
interventions,
including
pharmacological
medical
procedures,
lifestyle
discussed,
context
senescence.
Lab on a Chip,
Journal Year:
2024,
Volume and Issue:
24(11), P. 2834 - 2860
Published: Jan. 1, 2024
Synthetic
biology
is
the
design
and
modification
of
biological
systems
for
specific
functions,
integrating
several
disciplines
like
engineering,
genetics,
computer
science.
The
field
synthetic
to
understand
processes
within
host
organisms
through
manipulation
regulation
their
genetic
pathways
addition
biocontrol
circuits
enhance
production
capabilities.
This
pursuit
serves
address
global
challenges
spanning
diverse
domains
that
are
difficult
tackle
conventional
routes
production.
Despite
its
impact,
achieving
precise,
dynamic,
high-throughput
still
challenging.
Microfluidics
offers
a
solution
those
challenges,
enabling
controlled
fluid
handling
at
microscale,
offering
lower
reagent
consumption,
faster
analysis
biochemical
reactions,
automation,
high
throughput
screening.
In
this
review,
we
diverge
from
focus
on
automating
design-build-test-learn
cycle,
instead,
microfluidic
platforms
role
in
advancing
integration
with
-
bacterial
cells,
yeast,
fungi,
animal
cells
cell-free
systems.
review
illustrates
how
devices
have
been
instrumental
understanding
by
showcasing
microfluidics
as
an
essential
tool
create
circuits,
pathways,
environments.
conclusion,
show
expedite
applications
across
including
but
not
limited
personalized
medicine,
bioenergy,
agriculture.
Molecular Biology of the Cell,
Journal Year:
2024,
Volume and Issue:
35(6)
Published: April 10, 2024
Microfluidic
platforms
enable
long-term
quantification
of
stochastic
behaviors
individual
bacterial
cells
under
precisely
controlled
growth
conditions.
Yet,
quantitative
comparisons
physiological
parameters
and
cell
different
microorganisms
in
experimental
device
modalities
is
not
available
due
to
experiment-specific
details
affecting
physiology.
To
rigorously
assess
the
effects
mechanical
confinement,
we
designed,
engineered,
performed
side-by-side
experiments
otherwise
identical
conditions
Mother
Machine
(with
confinement)
SChemostat
(without
confinement),
using
latter
as
ideal
comparator.
We
established
a
protocol
cultivate
suitably
engineered
rod-shaped
mutant
Characterizing
and
manipulating
cellular
behaviour
requires
a
mechanistic
understanding
of
the
causal
interactions
between
components.
We
present
an
approach
to
detect
genes
without
need
perturb
physiological
state
cells.
This
exploits
naturally
occurring
cell-to-cell
variability
which
is
experimentally
accessible
from
static
population
snapshots
genetically
identical
cells
follow
over
time.
Our
main
contribution
simple
mathematical
relation
that
constrains
propagation
gene
expression
noise
through
biochemical
reaction
networks.
allows
us
rigorously
interpret
fluctuation
data
even
when
only
small
part
complex
regulatory
process
can
be
observed.
show
how
this
can,
in
theory,
exploited
by
synthetically
engineering
passive
reporter
expression,
akin
established
“dual
as-say”.
While
focus
our
theoretical,
we
also
experimental
proof-of-principle
demonstrate
real-world
applicability
certain
circumstances.
suggest
method
specific
synthetic
circuits
E.
coli
confirming
theoretical
result
narrow
set
controlled
settings.
Further
work
needed
practical
on
large
scale,
with
networks,
or
organisms
other
than
.
Despite
much
progress,
image
processing
remains
a
significant
bottleneck
for
high-throughput
analysis
of
microscopy
data.
One
popular
platform
single-cell
time-lapse
imaging
is
the
mother
machine,
which
enables
long-term
tracking
microbial
cells
under
precisely
controlled
growth
conditions.
While
several
machine
pipelines
have
been
developed
in
past
years,
adoption
by
non-expert
audience
challenge.
To
fill
this
gap,
we
implemented
our
own
software,
MM3,
as
plugin
multidimensional
viewer
napari.
napari-MM3
complete
and
modular
pipeline
data,
takes
advantage
high-level
interactivity
Here,
give
an
overview
test
it
against
well-designed
widely
used
pipelines,
including
BACMMAN
DeLTA.
Researchers
often
analyze
data
with
custom
scripts
using
varied
methods,
but
quantitative
comparison
output
different
has
lacking.
end,
show
that
key
physiological
parameter
correlations
distributions
are
robust
to
choice
method.
However,
also
find
small
changes
thresholding
parameters
can
systematically
alter
extracted
from
experiments.
Moreover,
explicitly
deep
learning-based
segmentation,
'what
you
put
what
get'
(WYPIWYG)
-
is,
pixel-level
variation
training
cell
segmentation
propagate
model
bias
spatial
temporal
measurements.
Finally,
while
primary
purpose
work
introduce
software
over
last
decade
lab,
provide
information
those
who
want
implement
machine-based
methods
their
research.
Physical Biology,
Journal Year:
2023,
Volume and Issue:
20(4), P. 045006 - 045006
Published: May 24, 2023
Recently,
there
has
been
an
increasing
need
for
tools
to
simulate
cell
size
regulation
due
important
applications
in
proliferation
and
gene
expression.
However,
implementing
the
simulation
usually
presents
some
difficulties,
as
division
a
cycle-dependent
occurrence
rate.
In
this
article,
we
gather
recent
theoretical
framework
IOP Conference Series Earth and Environmental Science,
Journal Year:
2024,
Volume and Issue:
1342(1), P. 012015 - 012015
Published: May 1, 2024
Abstract
Challenges
of
stability
and
specificity
associated
with
early
generation
sensors
necessitate
the
fabrication
optimization
microbial
biosensors.
More
so,
global
biosensors
market
size
currently
valued
at
USD25.5
billion
in
2021
is
expected
to
grow
a
compound
annual
growth
rate
(CAGR)
7.5%
USD36.7
2026.
Microbial
are
bioanalytical
systems
that
integrate
microorganisms
physical
transducer
generate
signals,
thus,
aiding
identification
analytes.
The
fabricated
through
series
steps
comprising
microbe
selection,
immobilization
onto
matrix,
microfabrication,
calibration,
validation.
transducers
integrated
quantifiable
enabling
real-time
monitoring
diversity
analytes
within
food
samples.
strategies
scrutinized,
particular
focus
on
integration
sundry
nanoparticles,
such
as
magnetic,
gold,
quantum-dot
which
enhance
sensor
performance.
Distinct
advantages
offered
by
promise
revolutionize
quality
assessment
via
cost-effectiveness,
rapid
sample
testing,
ability
provide
access
data.
Literature
have
highlighted
certain
limitations
including
interference
from
complex
matrices,
instability
microorganisms,
lifespan.
In
assessing
their
economic
importance,
comparative
analysis
presented
against
conventional
analytical
methods
like
ELISA,
PCR,
HPLC;
highlighting
unique
strengths
future
perspectives
potential
technology
addressing
need
for
continuous
challenges,
research
further
improvements
biocompatibility
processes
long-term
reusability.