New Phytologist,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 24, 2025
Summary
Temperature
is
a
critical
environmental
factor
affecting
nearly
all
plant
processes,
including
growth,
development,
and
yield.
Yet,
despite
decades
of
research,
we
lack
the
ability
to
predict
performance
at
different
temperatures,
limiting
development
climate‐resilient
crops.
Further,
there
pressing
need
bridge
gap
between
prediction
physiological
molecular
traits
improve
our
understanding
manipulation
temperature
responses.
Here,
developed
first
enzyme‐constrained
model
Arabidopsis
thaliana
's
metabolism,
facilitating
predictions
growth‐related
phenotypes
temperatures.
We
showed
that
can
be
employed
for
in
silico
identification
genes
affect
growth
suboptimal
temperature.
Using
mutant
lines,
validated
predicted
demonstrating
potential
metabolic
modeling
accurately
predicting
thermal
The
temperature‐dependent
provides
template
used
developing
sophisticated
strategies
engineer
Deleted Journal,
Journal Year:
2024,
Volume and Issue:
2(2)
Published: March 25, 2024
Abstract
Body
temperature
variations,
including
the
generation,
transfer,
and
dissipation
of
heat,
play
an
important
role
throughout
life
participate
in
all
biological
events.
Cellular
information
is
indispensable
link
comprehensive
understanding
science
processes,
but
traditional
testing
strategies
cannot
provide
sufficient
due
to
their
low
precision
inefficient
cellular‐entrance.
In
recent
years,
with
help
luminescent
nanomaterials,
a
variety
new
thermometers
have
been
developed
achieve
real‐time
measurement
at
micro/nano
scale.
this
review,
we
summarized
latest
advances
several
nanoparticles
for
cellular
detection
related
applications
revealing
cell
metabolism
disease
diagnosis.
Furthermore,
review
proposed
few
challenges
nano‐thermometry,
expecting
spark
novel
thought
push
forward
its
preclinical
translational
uses.
Fermentation,
Journal Year:
2025,
Volume and Issue:
11(5), P. 249 - 249
Published: May 1, 2025
Vibrio
natriegens
(V.
natriegens)
is
an
emerging
synthetic
biology
chassis
characterized
by
rapid
growth,
and
its
potential
for
the
synthesis
of
sesquiterpenes
(such
as
pentalenene)
has
not
been
developed.
In
this
study,
heterologous
pentalenene
biosynthesis
was
successfully
established
in
V.
via
metabolic
engineering.
The
optimization
gene
dosage
culture
conditions
led
to
increase
yield
from
0.75
mg/L
39.4
mg/L,
representing
highest
titer
reported
date,
though
still
markedly
lower
than
yields
achieved
conventional
microbial
hosts.
Transcriptome
analysis
demonstrated
that
exogenous
mevalonate
(MVA)
pathway
effectively
activated
terpenoid
precursor
synthesis,
evidenced
up-regulation
key
genes.
However,
endogenous
methylerythritol
4-phosphate
(MEP)
remained
inactive,
genes
involved
oxidative
phosphorylation,
pentose
phosphate
pathway,
thiamine
were
down-regulated,
leading
limited
availability
ATP,
NADPH,
acetyl-CoA.
Competition
cofactors,
particularly
further
constrained
supply
efficiency.
This
study
confirmed
a
production
platform
revealed
bottleneck,
providing
theoretical
basis
subsequent
engineering
optimization.
Briefings in Bioinformatics,
Journal Year:
2023,
Volume and Issue:
25(1)
Published: Nov. 13, 2023
Environmental
perturbations
are
encountered
by
microorganisms
regularly
and
will
require
metabolic
adaptations
to
ensure
an
organism
can
survive
in
the
newly
presenting
conditions.
In
order
study
mechanisms
of
adaptation
such
conditions,
various
experimental
computational
approaches
have
been
used.
Genome-scale
models
(GEMs)
one
most
powerful
metabolism,
providing
a
platform
systems
level
different
environments
which
could
otherwise
be
infeasible
experimentally.
this
review,
we
describing
application
GEMs
understanding
how
microbes
reprogram
their
system
as
result
environmental
variation.
particular,
provide
details
model
reconstruction
approaches,
algorithms
tools
for
simulation,
consequences
genetic
perturbations,
integration
'-omics'
datasets
creating
context-specific
studying
due
change
PLoS Computational Biology,
Journal Year:
2023,
Volume and Issue:
19(10), P. e1011549 - e1011549
Published: Oct. 19, 2023
Protein
allocation
determines
the
activity
of
cellular
pathways
and
affects
growth
across
all
organisms.
Therefore,
different
experimental
machine
learning
approaches
have
been
developed
to
quantify
predict
protein
abundance
how
they
are
allocated
functions,
respectively.
Yet,
despite
advances
in
quantification,
it
remains
challenging
condition-specific
enzymes
metabolic
networks.
Here,
using
protein-constrained
models,
we
propose
a
family
constrained-based
approaches,
termed
PARROT,
much
each
enzyme
is
used
based
on
principle
minimizing
difference
between
reference
an
alternative
condition.
To
this
end,
PARROT
variants
model
minimization
reallocation
four
(combinations
of)
distance
functions.
We
demonstrate
that
variant
minimizes
Manhattan
condition
outperforms
existing
parsimonious
distribution
fluxes
or
for
both
Escherichia
coli
Saccharomyces
cerevisiae.
Further,
show
combined
flux
adjustment
leads
inconsistent
predictions.
Together,
our
findings
indicate
rather
than
redistribution
governing
determining
steady-state
pathway
microorganism
grown
conditions.
Microorganisms,
Journal Year:
2023,
Volume and Issue:
11(9), P. 2149 - 2149
Published: Aug. 24, 2023
Secondary
metabolites
are
not
essential
for
the
growth
of
microorganisms,
but
they
play
a
critical
role
in
how
microbes
interact
with
their
surroundings.
In
addition
to
this
important
ecological
role,
secondary
also
have
variety
agricultural,
medicinal,
and
industrial
uses,
thus
examination
metabolism
plants
is
growing
scientific
field.
While
chemical
production
certain
possible,
industrial-scale
microbial
green
economically
attractive
alternative.
This
even
more
true,
given
advances
bioengineering
that
allow
us
alter
workings
order
increase
compounds
interest.
type
engineering
requires
detailed
knowledge
"chassis"
organism's
metabolism.
Since
resources
catalytic
capacity
enzymes
finite,
it
examine
tradeoffs
between
various
bioprocesses
an
engineered
system
its
working
manner
minimally
perturbs
robustness
while
allowing
maximum
product
The
silico
multi-objective
analysis
using
genome-scale
models
ideal
method
such
examinations.
International Journal of Molecular Sciences,
Journal Year:
2023,
Volume and Issue:
24(23), P. 16955 - 16955
Published: Nov. 29, 2023
Temperature
is
a
crucial
regulator
of
the
rate
and
direction
biochemical
reactions
cell
processes.
The
recent
data
indicating
presence
local
thermal
gradients
associated
with
sites
high-rate
thermogenesis,
on
one
hand,
demonstrate
possibility
for
existence
"thermal
signaling"
in
and,
other,
are
criticized
basis
thermodynamic
calculations
models.
Here,
we
review
main
thermometric
techniques
sensors
developed
determination
temperature
inside
living
cells
diverse
intracellular
compartments.
A
comparative
analysis
conducted
results
obtained
using
these
methods
cytosol,
nucleus,
endo-/sarcoplasmic
reticulum,
mitochondria,
as
well
their
biological
consistency.
Special
attention
given
to
limitations,
possible
sources
errors
ambiguities
sensor's
responses.
issue
limits
organelles
considered.
It
concluded
that
elaboration
experimental
protocols
ultralocal
measurements
take
into
account
both
characteristics
systems,
properties
limitations
each
type
sensor
critical
importance
generation
reliable
further
progress
this
field.
