Research highlights
Neuroscience
In situ generation of electrodes
Zebrafish tail with
in situ-fabricated electrodes
(dark blue).
Electrodes for recording or
stimulation of neural tissue are
typically rigid and can therefore
cause damage to the surround-
ing tissue. Efforts to reduce this
mechanical mismatch between
electrodes and tissue have been
reported, but such electrodes
require advanced fabrication
methods. Xenofon Strakosas,
Magnus Berggren and their
colleagues from Linköping Uni-
versity in Sweden have pursued
a different approach. They har-
ness endogenous metabolites
to catalyze polymerization of
small compounds into a soft yet
conductive material.
“There is a class of materials
that are organic in nature and
that are softer than the
traditional metals or
silicone-based electronics,” says
Strakosas. These conducting
polymers have previously been
used as coatings on metal elec-
trodes to improve the interface
between electrodes and tissues.
For their project, Strakosas and
his colleagues wanted to develop
a minimally invasive electrode
that would self-assemble within
tissue. This process mainly
requires the precursors and
fuel for the polymerization
reaction. The precursor is a
trithiophene-based monomer
called ETE-COONa, while the fuel
nature methods
is hydrogen peroxide. To induce
polymerization locally, the team
generated hydrogen peroxide
from endogenous metabolites
such as glucose or lactate with
the help of oxidase enzymes that
they co-injected with the precur-
sor molecules.
Strakosas and his colleagues
have demonstrated the
in situ formation of conducting
polymer-based electrodes in
proof-of-principle applications.
For instance, they injected their
precursor mixture into zebrafish
brain, tail and heart and could
produce conductive polymers
in situ. In addition, the research-
ers generated conductive poly-
mers at the interface between
metal electrodes and nervous
tissue in a leech preparation.
Here, they demonstrated that
impedance was lowered during
stimulation of the nervous
tissue.
Now that the concept of
metabolite-induced in situ
fabrication of electrodes is
established, Strakosas is hopeful
that further optimizations and
parameter tuning will enable a
wealth of future applications.
Aside from using this material
as stand-alone electrodes, Stra-
kosas also envisions harnessing
the enzymes being injected as
part of the precursor cocktail for
another purpose. “I want to uti-
lize them post-polymerization
to maybe record concentrations
of metabolites that exist in the
brain,” says Strakosas.
Nina Vogt
Nature Methods
Original reference: Science 379, 795–802
(2023).
Sequencing
Combined sequencing of genomes
and epigenomes
The chemical identities of dNA
bases in cells are not just A, T, C
and G. A number of modifica-
tions add epigenetic complex-
ity to dNA molecules. These
modifications regulate and are
regulated by various cellular
activities, and they bear impor-
tance in areas ranging from cell
biology to disease research.
High-throughput sequencing
technology has been widely
employed for reading either
genetic or epigenetic base
identities, but often in separate
experiments. To combine the
two into a single assay, Joanna
Holbrook from Cambridge
Epigenetix, Shankar Balasubra-
manian from the University of
Cambridge, and their colleagues
developed five- and six-letter
sequencing.
The main innovation of this
elegant method lies in using
a two-base coding strategy
for the four canonical bases
plus 5-methylcytosine (5mC)
and 5-hydroxymethylcytosine
(5hmC). In the five-letter
sequencing workflow, after
hairpin addition and splitting,
another copy of the dNA strand
is synthesized in which modified
cytosine is protected through
oxidation and glycosylation
while unmodified cytosine is
deaminated to uracil. Follow-
ing PCr and sequencing of the
resulting constructs, the bases
and status of cytosine modifica-
tion can be efficiently decoded.
“Our technology combined with
Illumina sequencing is more
accurate at identifying specific
bases in the genetic sequence
than Illumina sequencing
alone,” says Holbrook; “it took
a significant amount of time to
do the comparisons, as we had
to run multiple other workflows
to compare against our single
Volume 20 | April 2023 | 482–483 | 482
workflow.” The team further
expanded the technology to
six-letter sequencing, which
allows 5mC and 5hmC to be
distinguished. Much effort was
spent to make sure there is no
drop-off in performance of the
usual properties of sequencing
technologies — for instance, uni-
formity of read coverage and/
or recovery of material through
the process. Holbrook notes “we
optimized the original protocol
until we could show it was com-
petitive in all these aspects.”
The advantages of the five-
and six-letter sequencing are
manifold. For example, linking
dNA variants and epigenetic
modifications in the same
molecules facilitates interrogat-
ing the regulatory relationships
between the two. Furthermore,
when samples are precious or
low in quantity, such as cell-free
dNA from the blood of patients
with cancer, this new combined
sequencing strategy can achieve
sensitive analysis from as little
cell-free dNA as 2 ng. In ongoing
collaborations with researchers
working in multiple areas, the
team expects to see exciting
applications enabled by this
technology.
The team is planning to add
in other regulation signals that
will lead to a better understand-
ing of this multidimensional
problem, notes Holbrook. “In
particular, we are already tailor-
ing our approach to allow for
even lower amounts of input
dNA, ultimately down to a level
that would be compatible with
measurements on single cells.”
CrEdIT: XENOFON STrAkOSAS
Lin Tang
Nature Methods
Original reference: Nat. Biotechnol. https://
doi.org/10.1038/s41587-022-01652-0
(2023).