Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion
npj Biofilms and Microbiomes,
Год журнала:
2025,
Номер
11(1)
Опубликована: Фев. 2, 2025
Bacterial
biofilms
are
complex
cell
communities
within
a
self-produced
extracellular
matrix,
crucial
in
various
fields
but
challenging
to
analyze
3D.
We
developed
"biofilm-in-capillary"
growth
method
compatible
with
full-rotation
soft
X-ray
tomography,
enabling
high-resolution
3D
imaging
of
bacterial
cells
and
their
matrix
during
biofilm
formation.
This
approach
offers
50
nm
isotropic
spatial
resolution,
rapid
imaging,
quantitative
native
analysis
structure.
Using
Bacillus
subtilis
biofilms,
we
detected
coherent
alignment
chaining
wild-type
towards
the
oxygen-rich
capillary
tip.
In
contrast,
ΔtasA
genetic
knock-out
showed
loss
cellular
orientation
changes
matrix.
Adding
TasA
protein
strain
restored
density
led
assembly
compaction,
without
observed
biofilms.
scalable
transferable
opens
new
avenues
for
examining
structure
function
across
species,
including
mixed
response
environmental
factors.
Язык: Английский
Limited-angle artifacts removal and jitter correction in soft x-ray tomography via physical model-driven deep learning
Applied Physics Letters,
Год журнала:
2023,
Номер
123(19)
Опубликована: Ноя. 6, 2023
Soft
x-ray
nanoscale
tomography
provides
high-resolution
three-dimensional
visualization
of
the
imaged
objects
and
promotes
development
multiple
research
fields.
However,
current
challenges
lie
in
presence
limited-angle
artifacts
projection
jitter,
which
degrade
imaging
resolution
quality.
To
address
these
issues,
we
propose
a
physical
model-driven
deep
learning
including
forward
backward
CT
models.
Combing
with
iterative
algorithm,
proposed
method
simultaneously
suppresses
jitter
artifacts.
Furthermore,
model
generates
plenty
data
to
overcome
requirement
abundant
experimental
datasets.
Both
simulation
experiment
demonstrate
feasibility
validity
reconstruction
algorithm.
Язык: Английский
Subcellular Feature-Based Classification of α and β Cells Using Soft X-ray Tomography
Cells,
Год журнала:
2024,
Номер
13(10), С. 869 - 869
Опубликована: Май 18, 2024
The
dysfunction
of
α
and
β
cells
in
pancreatic
islets
can
lead
to
diabetes.
Many
questions
remain
on
the
subcellular
organization
islet
during
progression
disease.
Existing
three-dimensional
cellular
mapping
approaches
face
challenges
such
as
time-intensive
sample
sectioning
subjective
identification.
To
address
these
challenges,
we
have
developed
a
feature-based
classification
approach,
which
allows
us
identify
quantify
their
structural
characteristics
using
soft
X-ray
tomography
(SXT).
We
observed
significant
differences
whole-cell
morphological
organelle
statistics
between
two
cell
types.
Additionally,
characterize
subtle
biophysical
individual
insulin
glucagon
vesicles
by
analyzing
vesicle
size
molecular
density
distributions,
were
not
previously
possible
other
methods.
These
sub-vesicular
parameters
enable
predict
types
systematically
supervised
machine
learning.
also
visualize
distinct
subtypes
Uniform
Manifold
Approximation
Projection
(UMAP)
embeddings,
provides
with
an
innovative
approach
explore
heterogeneity
cells.
This
methodology
presents
for
tracking
biologically
meaningful
that
be
applied
any
system.
Язык: Английский
Optimization of Soft X-Ray Fresnel Zone Plate Fabrication Through Joint Electron Beam Lithography and Cryo-Etching Techniques
Nanomaterials,
Год журнала:
2024,
Номер
14(23), С. 1898 - 1898
Опубликована: Ноя. 26, 2024
The
ability
to
manufacture
complex
3D
structures
with
nanometer-scale
resolution,
such
as
Fresnel
Zone
Plates
(FZPs),
is
crucial
achieve
state-of-the-art
control
in
X-ray
sources
for
use
a
diverse
range
of
cutting-edge
applications.
This
study
demonstrates
novel
approach
combining
Electron
Beam
Lithography
(EBL)
and
cryoetching
produce
silicon-based
FZP
prototypes
test
bench
assess
the
strong
points
limitations
this
fabrication
method.
Through
method,
we
obtained
FZPs
100
zones,
diameter
20
µm,
an
outermost
zone
width
50
nm,
resulting
high
aspect
ratio
that
suitable
across
photon
energies.
process
incorporates
chromium
mask
EBL
stage,
enhancing
microstructure
precision
mitigating
pattern
collapse
challenges.
minimized
issues
under-
over-etching,
producing
well-defined
patterns
resolution
low
roughness.
refined
thus
holds
promise
achieving
improved
optical
efficiency
FZPs,
making
it
viable
high-performance,
devices.
Язык: Английский
Absorption‐coefficient calculation of short‐wavelength photoresist materials: From EUV to BEUV and water window X‐ray
Smart Molecules,
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 16, 2024
Abstract
In
photolithography,
shortening
the
exposure
wavelength
from
ultraviolet
to
extreme
(EUV,
13.5
nm)
and
soft
X‐ray
region
in
terms
of
beyond
EUV
(BEUV,
6.X
water
window
(WWX,
2.2–4.4
is
expected
further
miniaturize
technology
node
down
sub‐5
nm
level.
However,
absorption
ability
molecules
these
ranges,
especially
WWX
region,
unknown,
which
should
be
very
important
for
utilization
energy.
Herein,
molar
cross
sections
different
elements
at
2.4
were
firstly
calculated
compared
with
wavelengths
6.7
nm.
Based
on
ranges
density
estimation
results
density‐functional
theory
calculation,
linear
coefficients
typical
resist
materials,
including
metal‐oxy
clusters,
organic
small
molecules,
polymers,
photoacid
generators
(PAGs),
are
evaluated.
The
analysis
suggests
that
Zn
cluster
has
higher
BEUV,
whereas
Sn
WWX.
Doping
PAGs
high
atoms
improves
chemically
amplified
photoresist
(CAR)
polymer
performance.
WWX,
it
necessary
introduce
an
layer
containing
such
as
Zr,
Sn,
Hf
increase
absorption.
Язык: Английский
Dehydration as alternative sample preparation for soft X‐ray tomography
Journal of Microscopy,
Год журнала:
2023,
Номер
291(3), С. 248 - 255
Опубликована: Июль 12, 2023
Abstract
Soft
X‐ray
tomography
(SXT)
is
an
imaging
technique
to
visualise
whole
cells
without
fixation,
staining,
and
sectioning.
For
SXT
imaging,
are
cryopreserved
imaged
at
cryogenic
conditions.
Such
‘near‐to‐native’
state
in
high
demand
initiated
the
development
of
laboratory
table‐top
microscope.
As
many
laboratories
do
not
have
access
equipment,
we
asked
ourselves
whether
feasible
on
dry
specimens.
This
paper
shows
how
dehydration
can
be
used
as
alternative
sample
preparation
obtain
ultrastructure
information.
We
compare
different
processes
mouse
embryonic
fibroblasts
terms
ultrastructural
preservation
shrinkage.
Based
this
analysis,
chose
critical
point
(CPD)
dried
for
imaging.
In
comparison
air‐dried
cells,
CPD
dehydrated
show
structural
integrity
although
with
about
3–7
times
higher
absorption
cellular
organelles.
difference
values
between
organelles
preserved,
3D
anatomy
CPD‐dried
segmented
analysed,
demonstrating
applicability
LAY
DESCRIPTION
:
that
allows
see
internal
structures
need
special
treatments
like
fixation
or
staining.
Typically,
involves
freezing
very
low
temperatures.
However,
since
labs
lack
necessary
explored
could
done
samples
instead.
compared
methods
found
drying
was
most
promising
showed
integrity,
they
absorbed
more
X‐rays
than
hydrated
a
viable
Язык: Английский
Soft X-ray 3D Imaging: A Powerful Tool for Visualizing Virus Infections with Increased Resolution and Field of View
Microscopy and Microanalysis,
Год журнала:
2023,
Номер
29(Supplement_1), С. 1155 - 1156
Опубликована: Июль 22, 2023
Journal
Article
Soft
X-ray
3D
Imaging:
A
Powerful
Tool
for
Visualizing
Virus
Infections
with
Increased
Resolution
and
Field
of
View
Get
access
Jian-Hua
Chen,
Chen
Molecular
Biophysics
Integrated
Bioimaging
Division,
Lawrence
Berkeley
National
Laboratory,
Berkeley,
California,
United
States
AmericaDepartment
Anatomy,
University
California
San
Francisco,
America
Search
other
works
by
this
author
on:
Oxford
Academic
Google
Scholar
Bieke
Vanslembrouck,
Vanslembrouck
Axel
Ekman,
Ekman
Department
Valentina
Loconte,
Loconte
Venera
Weinhardt,
Weinhardt
Infectious
Diseases,
Virology
Heidelberg
University,
Heidelberg,
Germany
Mark
LeGros,
LeGros
Carolyn
Larabell
Microscopy
Microanalysis,
Volume
29,
Issue
Supplement_1,
1
August
2023,
Pages
1155–1156,
https://doi.org/10.1093/micmic/ozad067.590
Published:
22
July
2023
Язык: Английский