bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2022,
Volume and Issue:
unknown
Published: Aug. 29, 2022
Abstract
To
analyze
and
visualize
comprehensive
gene
expression
patterns
in
the
phytopathogenic
fungus
Botrytis
cinerea
,
we
developed
BEB
—
a
web-based
B.
browser.
This
tool
associated
databases
(DB)
contain
manually-curated
RNA-Seq
experiments
conducted
.
allows
easy
analyses
of
genes
interest
under
different
culture
conditions
by
providing
publication-ready
heatmaps
depicting
transcripts
levels.
is
computationally-inexpensive
application
DB
that
effortless
visualization
transcript
levels
without
needing
advanced
computational
skills.
also
provides
details
each
experiment
analysis
user-defined
clustering
options.
If
needed,
tables
values
can
be
downloaded
for
further
exploration,
employing
more
sophisticated
bioinformatics
tools.
The
implementation
based
on
open-source
technologies
easily
deployed
other
organisms
with
little
additional
effort.
demonstrate
BEB’s
usability
potential,
selected
to
determine
their
across
conditions.
We
thus
focused
our
secondary
metabolite
clusters,
chromosome-wide
expression,
previously
described
virulence
factors,
reference
genes,
leading
overview
these
groups
this
relevant
fungal
phytopathogen.
Journal of Fungi,
Journal Year:
2023,
Volume and Issue:
9(1), P. 84 - 84
Published: Jan. 6, 2023
For
comprehensive
gene
expression
analyses
of
the
phytopathogenic
fungus
Botrytis
cinerea,
which
infects
a
number
plant
taxa
and
is
cause
substantial
agricultural
losses
worldwide,
we
developed
BEB,
web-based
B.
cinerea
Expression
Browser.
This
computationally
inexpensive
application
its
associated
database
contain
manually
curated
RNA-Seq
data
for
cinerea.
BEB
enables
genes
interest
under
different
culture
conditions
by
providing
publication-ready
heatmaps
depicting
transcript
levels,
without
requiring
advanced
computational
skills.
also
provides
details
each
experiment
user-defined
clustering
visualization
options.
If
needed,
tables
values
can
be
downloaded
further
exploration,
including,
instance,
determination
differentially
expressed
genes.
The
implementation
based
on
open-source
technologies
that
deployed
other
organisms.
In
this
case,
new
will
limited
only
transcriptomic
experiments
are
incorporated
into
platform.
To
demonstrate
usability
value
analyzed
patterns
across
conditions,
with
focus
secondary
metabolite
clusters,
chromosome-wide
expression,
previously
described
virulence
factors,
reference
genes,
first
overview
these
groups
in
relevant
fungal
phytopathogen.
We
expect
tool
to
broadly
useful
research,
basis
comparative
transcriptomics
candidate
identification
functional
assays.
Microbial Cell Factories,
Journal Year:
2023,
Volume and Issue:
22(1)
Published: Aug. 17, 2023
Sm1
and
Chit42
of
Trichoderma
have
been
universally
confirmed
as
crucial
biocontrol
factors
against
pathogen
infection
through
induced
resistance
mycoparasitism,
respectively.
However,
not
enough
work
has
conducted
to
understand
the
novel
function
fused
expression
these
two
proteins
in
Trichoderma.
The
results
this
study
demonstrated
that
Sm1-Chit42
protein
(SCf)
engineered
T.
afroharzianum
strain
OE:SCf
exerted
synergistic
inhibition
Botrytis
cinerea
growth
at
multiple
stages
mycoparasitic
interaction
B.
including
chemotropism
sensing,
hyphal
coiling,
hydrophobicity
modulation,
cell
wall
adhesion,
virulence
reduction
killing
by
ROS.
These
highlight
a
system
strains
with
chimeric
combat
reproduction,
which
would
lay
strong
foundation
for
exploring
new
biofungicide
created
future.
BioEssays,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Dec. 18, 2024
Circadian
rhythms
are
∼24-h
biological
oscillations
that
enable
organisms
to
anticipate
daily
environmental
cycles,
so
they
may
designate
appropriate
day/night
functions
align
with
these
changes.
The
molecular
clock
in
animals
and
fungi
consists
of
a
transcription-translation
feedback
loop,
the
plant
is
comprised
multiple
interlocking
feedback-loops,
cyanobacterial
driven
by
phosphorylation
cycle
involving
three
main
proteins.
Despite
divergent
core
mechanisms
across
systems,
all
circadian
clocks
able
buffer
period
length
against
changes
ambient
growth
environment,
such
as
temperature
nutrients.
This
defining
capability,
termed
compensation,
critical
proper
timekeeping,
yet
underlying
mechanism(s)
remain
elusive.
Here
we
examine
known
players
in,
current
models
for,
compensation
five
systems.
While
systems
not
unified,
common
themes
exist
them,
including
regulation
via
temperature-dependent
post-translational
modifications.
Journal of Fungi,
Journal Year:
2024,
Volume and Issue:
11(1), P. 9 - 9
Published: Dec. 26, 2024
Secondary
metabolism
is
one
of
the
main
mechanisms
Trichoderma
uses
to
explore
and
colonize
new
niches,
6-pentyl-α-pyrone
(6-PP)
an
important
secondary
metabolite
in
this
process.
This
work
focused
on
standardizing
a
method
investigate
production
6-PP.
Ethanol
ethyl
acetate
were
both
effective
solvents
for
quantifying
6-PP
solution
had
limited
solubility
potato–dextrose–broth
media.
The
extraction
using
provided
rapid
efficient
process
recover
metabolite.
was
readily
produced
during
development
atroviride
growing
dark,
but
light
suppressed
its
production.
purified,
spectrum
by
nuclear
magnetic
resonance
mass
spectroscopy
identical
that
commercial
Light
also
induced
or
other
unidentified
metabolites
several
species
Trichoderma.
antagonistic
activity
T.
influenced
light,
as
suppression
plant
pathogens
greater
dark.
secreted
potato–dextrose–agar
differentially
regulated
indicating
with
against
pathogens.
has
influence
Trichoderma,
trait
key
relevance
selecting
strains
protection.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2022,
Volume and Issue:
unknown
Published: Aug. 29, 2022
Abstract
To
analyze
and
visualize
comprehensive
gene
expression
patterns
in
the
phytopathogenic
fungus
Botrytis
cinerea
,
we
developed
BEB
—
a
web-based
B.
browser.
This
tool
associated
databases
(DB)
contain
manually-curated
RNA-Seq
experiments
conducted
.
allows
easy
analyses
of
genes
interest
under
different
culture
conditions
by
providing
publication-ready
heatmaps
depicting
transcripts
levels.
is
computationally-inexpensive
application
DB
that
effortless
visualization
transcript
levels
without
needing
advanced
computational
skills.
also
provides
details
each
experiment
analysis
user-defined
clustering
options.
If
needed,
tables
values
can
be
downloaded
for
further
exploration,
employing
more
sophisticated
bioinformatics
tools.
The
implementation
based
on
open-source
technologies
easily
deployed
other
organisms
with
little
additional
effort.
demonstrate
BEB’s
usability
potential,
selected
to
determine
their
across
conditions.
We
thus
focused
our
secondary
metabolite
clusters,
chromosome-wide
expression,
previously
described
virulence
factors,
reference
genes,
leading
overview
these
groups
this
relevant
fungal
phytopathogen.
