CellSP: Module discovery and visualization for subcellular spatial transcriptomics data
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 15, 2025
Spatially
resolved
transcriptomics
has
made
it
possible
to
study
the
subcellular
organization
of
mRNA,
a
critical
aspect
cellular
function.
However,
there
is
dearth
analytical
tools
identify
and
interpret
functional
significance
spatial
distribution
patterns.
To
address
this,
we
present
CellSP,
computational
framework
for
identifying,
visualizing,
characterizing
consistent
patterns
mRNA.
CellSP
introduces
concept
"gene-cell
modules"
uncover
gene
sets
with
non-random
transcript
distributions
in
many
cells.
provides
intuitive
visualizations
captured
offers
insights
into
genes
cells
comprising
each
discovered
module.
We
demonstrate
that
reliably
identifies
functionally
significant
modules
across
various
tissues
reveals
changes
associated
phenotypic
variation.
Language: Английский
Myelin: A possible proton capacitor for energy storage during sleep and energy supply during wakefulness
Progress in Biophysics and Molecular Biology,
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 1, 2025
There
are
several
physiological
reasons
why
biological
organisms
sleep.
One
key
one
concerns
brain
metabolism.
In
our
article
we
discuss
the
role
of
metabolism
in
myelin,
based
on
recent
discovery
that
myelin
contains
mitochondrial
components
enable
production
adenosine
triphosphate
(ATP)
via
oxidative
phosphorylation
(OXPHOS).
These
probably
originate
from
vesiculation
membranes
form
derived
vesicles
(MDVs).
We
hypothesize
acts
as
a
proton
capacitor,
accumulating
energy
protons
during
sleep
and
converting
it
to
ATP
OXPHOS
wakefulness.
Empirical
evidence
supporting
hypothesis
is
discussed,
including
data
metabolic
activity,
MDVs,
allometric
scaling
between
white
matter
volume
duration
mammals.
Language: Английский
Perspective Strategies for Interventions in Parkinsonism: Remedying the Neglected Role of TPPP
Cells,
Journal Year:
2024,
Volume and Issue:
13(4), P. 338 - 338
Published: Feb. 14, 2024
Neurological
disorders
such
as
Parkinsonism
cause
serious
socio-economic
problems
there
are,
at
present,
only
therapies
that
treat
their
symptoms.
The
well-established
hallmark
alpha-synuclein
(SYN)
is
enriched
in
the
inclusion
bodies
characteristic
of
Parkinsonism.
We
discovered
a
prominent
partner
SYN,
termed
Tubulin
Polymerization
Promoting
Protein
(TPPP),
which
has
important
physiological
and
pathological
activities
regulation
microtubule
network
promotion
SYN
aggregation.
role
TPPP
often
neglected
research,
we
here
attempt
to
remedy.
In
normal
brain,
are
expressed
endogenously
neurons
oligodendrocytes,
respectively,
whilst,
an
early
stage
Parkinsonism,
soluble
hetero-associations
these
proteins
found
both
cell
types.
cell-to-cell
transmission
proteins,
central
disease
progression,
provides
unique
situation
for
specific
drug
targeting.
Different
strategies
intervention
discovery
biomarkers
include
(i)
interface
targeting
SYN-TPPP
hetero-complex;
(ii)
proteolytic
degradation
and/or
using
PROTAC
technology;
(iii)
depletion
by
miRNA
technology.
also
discuss
potential
roles
phenotype
stabilization
oligodendrocytes.
Language: Английский
Recognizing the Beauty of Myelination through Identifying Sites of Phospholipid, Protein, and RNA Syntheses and Characterizing Their Movements in Myelin Internodes
Published: May 10, 2024
We
used
light,
electron
microscope
and
teased
fiber
autoradiography
to
show
that
myelinating
Schwann
cells
synthesize
phospholipids
proteins
in
perinuclear
cytoplasm
superficial
cytoplasmic
channels
or
Cajal
bands
(SCC/CB).
Neither
phospholipid
nor
protein
syntheses
occur
paranodal
loops,
Schmidt-Lanterman
incisures
adaxonal
cytoplasm.
Autoradiographic
studies
also
support
of
local
synthesis,
RNAs
move
from
the
nucleus
into
out
along
SCC/CB.
Unlike
other
phospholipids,
phosphatidylinositol
synthesis
occurs
extensively
axons.
This
finding
indicates
differences
distributions
synthesizing
enzymes
smooth
endoplasmic
reticulum
cell
processes
axoplasm.Autoradiographs
nerves
at
longer
survival
times
tritiated
phosphatidylcholine
fucose-labeled
glycoproteins
synthetic
sites
outermost
myelin
lamellae.
From
there,
spreads
inward
reaching
innermost
lamellae
thicker
sheaths
days.
Coupled
with
retention
fucose
outer
is
presence
glycoprotein
synthesized
during
early
myelination
inner
sheaths,
a
result
consistent
growth
out.
In
this
review,
we
revisit
these
because
they
provide
temporal
spatial
perspectives
needed
understanding
dynamic
aspects
myelinogenesis
how
respond
injury
altered
gene
expression.
Language: Английский