bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Дек. 23, 2023
Abstract
The
planarian
Schmidtea
mediterranea
can
regenerate
its
entire
body
from
small
tissue
fragments
and
is
studied
as
regeneration
model
species.
assembly
functional
analysis
of
genomes
has
proven
challenging
due
high
A/T
content
(70%
A/T),
repetitive
nature,
limited
transferability
routine
laboratory
protocols
to
their
divergent
biochemistry.
Only
few
often
fragmented
genome
assemblies
are
currently
available,
open
challenges
include
the
provision
well-annotated
chromosome-scale
reference
species
other
planarians
for
a
comparative
evolution
perspective.
Here
we
report
haplotype-phased,
high-quality
gene
annotations
sexual
S2
strain
S.
provide
putative
regulatory
region
via
optimized
ATAC-seq
ChIP-seq
protocols.
To
additionally
leverage
sequence
conservation
element
annotations,
generated
chromatin
accessibility
data
three
closest
relatives
:
polychroa
,
nova
lugubris
.
We
find
substantial
divergence
in
protein-coding
sequences
regions,
yet
reveal
remarkable
ChIP-mark
bearing
regions
identified
promoters
enhancers
resulting
high-confidence
set
evolutionary
conserved
provides
valuable
resource
circuits
within
taxon.
In
addition,
our
four
first
perspective
on
evolution.
Our
analyses
frequent
retrotransposon-associated
chromosomal
inversions
inter-chromosomal
translocations
that
lead
degradation
synteny
across
genus.
Interestingly,
further
independent
near-complete
losses
ancestral
metazoan
two
flatworm
groups,
indicating
platyhelminth
largely
evolve
without
syntenic
constraints.
work
resources
research
community
sets
foundation
genomics
planarians.
contrast
between
fast
structural
elements,
suggesting
unique
flatworms
where
positioning
may
not
be
essential.
Nature Ecology & Evolution,
Год журнала:
2023,
Номер
7(12), С. 2108 - 2124
Опубликована: Окт. 19, 2023
Regenerative
abilities
vary
dramatically
across
animals.
Even
amongst
planarian
flatworms,
well-known
for
complete
regeneration
from
tiny
body
fragments,
some
species
have
restricted
while
others
are
almost
entirely
incompetent.
Here,
we
assemble
a
diverse
live
collection
of
40
to
probe
the
evolution
head
in
group.
Combining
quantification
species-specific
head-regeneration
with
comprehensive
transcriptome-based
phylogeny
reconstruction,
show
multiple
independent
transitions
between
robust
whole-body
and
freshwater
species.
RNA-mediated
genetic
interference
inhibition
canonical
Wnt
signalling
interference-sensitive
bypassed
all
defects,
suggesting
that
pathway
is
linked
emergence
defects.
Our
finding
has
roles
reproductive
system
model
Schmidtea
mediterranea
raises
possibility
trade-off
egg-laying,
asexual
reproduction
by
fission/regeneration
drives
regenerative
trait
evolution.
Although
quantitative
comparisons
levels,
yolk
content
strategy
our
remained
inconclusive,
they
revealed
divergent
planarians.
Altogether,
study
establishes
planarians
as
taxon
comparative
research
presents
framework
mechanistic
abilities.
ABSTRACT
In
order
to
contribute
the
appropriate
tissues
during
development,
cells
need
know
their
position
within
embryo.
This
positional
information
is
conveyed
by
gradients
of
signaling
molecules,
termed
morphogens,
that
are
produced
in
specific
regions
embryo
and
induce
concentration-dependent
responses
target
tissues.
Positional
remarkably
robust,
embryos
often
develop
with
correct
proportions
even
if
large
parts
removed.
this
Review,
we
discuss
classical
embryological
experiments
modern
quantitative
analyses
have
led
mechanistic
insights
into
how
morphogen
adapt,
scale
properly
pattern
differently
sized
domains.
We
analyze
these
experimental
findings
context
mathematical
models
synthesize
general
principles
apply
multiple
systems
across
species
developmental
stages.
Genes,
Год журнала:
2021,
Номер
12(4), С. 506 - 506
Опубликована: Март 29, 2021
While
virtually
all
animals
show
certain
abilities
for
regeneration
after
an
injury,
these
vary
greatly
among
metazoans.
Porifera
(Sponges)
is
basal
metazoans
characterized
by
a
wide
variety
of
different
regenerative
processes,
including
whole-body
(WBR).
Considering
phylogenetic
position
and
unique
body
organization,
sponges
are
highly
promising
models,
as
they
can
shed
light
on
the
origin
early
evolution
in
general
WBR
particular.
The
present
review
summarizes
available
data
morphogenetic
cellular
mechanisms
accompanying
types
sponges.
Sponges
high
diversity
WBR,
which
principally
could
be
divided
into
(1)
from
fragment
(2)
aggregation
dissociated
cells.
belonging
to
clades
even
species
and/or
differing
anatomical
structure
undergo
morphogeneses
similar
operations.
A
common
characteristic
feature
instability
main
axis:
change
organism
polarity
described
during
WBR.
across
sponge
classes,
while
cell
dedifferentiations
transdifferentiations
involved
processes
Data
considering
molecular
regulation
extremely
scarce.
However,
possibility
achieve
various
ensured
basis
single
makes
accessible
future
comprehensive
physiological,
biochemical,
studies
processes.
In
biology,
regeneration
is
a
mysterious
phenomenon
that
has
inspired
self-repairing
systems,
robots,
and
biobots.
It
collective
computational
process
whereby
cells
communicate
to
achieve
an
anatomical
set
point
restore
original
function
in
regenerated
tissue
or
the
whole
organism.
Despite
decades
of
research,
mechanisms
involved
this
are
still
poorly
understood.
Likewise,
current
algorithms
insufficient
overcome
knowledge
barrier
enable
advances
regenerative
medicine,
synthetic
living
machines/biobots.
We
propose
comprehensive
conceptual
framework
for
engine
with
hypotheses
stem
cell-mediated
enables
system
like
planarian
flatworm
fully
(form)
bioelectric
(function)
homeostasis
from
any
small-
large-scale
damage.
The
extends
available
novel
intelligent
self-repair
machines
multi-level
feedback
neural
control
systems
driven
by
somatic
cells.
computationally
implemented
demonstrate
robust
recovery
both
form
(anatomical
homeostasis)
silico
worm
that,
simple
way,
resembles
planarian.
absence
complete
knowledge,
contributes
understanding
generating
cell
mediated
regeneration,
which
may
help
advance
medicine
biology.
Further,
as
our
bio-inspired
bio-computing
machine,
it
be
useful
building
robots/biobots
artificial
systems.
Biological reviews/Biological reviews of the Cambridge Philosophical Society,
Год журнала:
2023,
Номер
99(1), С. 131 - 176
Опубликована: Сен. 12, 2023
ABSTRACT
Aquatic
invertebrates
play
a
pivotal
role
in
(eco)toxicological
assessments
because
they
offer
ethical,
cost‐effective
and
repeatable
testing
options.
Additionally,
their
significance
the
food
chain
ability
to
represent
diverse
aquatic
ecosystems
make
them
valuable
subjects
for
studies.
To
ensure
consistency
comparability
across
studies,
international
(eco)toxicology
guidelines
have
been
used
establish
standardised
methods
protocols
data
collection,
analysis
interpretation.
However,
current
primarily
focus
on
limited
number
of
invertebrate
species,
mainly
from
Arthropoda,
Mollusca
Annelida.
These
are
suitable
basic
toxicity
screening,
effectively
assessing
immediate
severe
effects
toxic
substances
organisms.
For
more
comprehensive
ecologically
relevant
assessments,
particularly
those
addressing
long‐term
ecosystem‐wide
impacts,
we
recommended
use
broader
diversity
since
present
choice
taxa
exacerbates
scope
ecotoxicological
This
review
provides
overview
focusing
major
how
assess
impact
chemicals
environments.
The
work
supports
broad‐taxa
approach
environmental
as
it
better
represents
natural
populations
inhabiting
various
ecosystems.
Advances
omics
other
biochemical
computational
techniques
feasible,
enabling
mechanistic
studies
non‐model
By
combining
these
approaches
with
vitro
together
approach,
researchers
can
gain
insights
into
less‐explored
impacts
pollution,
such
changes
population
diversity,
development
tolerance
transgenerational
inheritance
pollution
responses,
organism
phenotypic
plasticity,
biological
invasion
outcomes,
social
behaviour
changes,
metabolome
regeneration
phenomena,
disease
susceptibility
tissue
pathologies.
also
emphasises
need
harmonised
data‐reporting
standards
minimum
annotation
checklists
that
research
results
findable,
accessible,
interoperable
reusable
(FAIR),
maximising
reusability
data.
ultimate
goal
is
encourage
integrated
holistic
problem‐focused
collaboration
between
scientific
disciplines,
standardisation
organisations
decision‐making
bodies,
transdisciplinary
knowledge
co‐production
One‐Health
approach.
Angewandte Chemie International Edition,
Год журнала:
2023,
Номер
62(47)
Опубликована: Июль 11, 2023
Abstract
The
growth
of
living
systems
is
ubiquitous.
Living
organisms
can
continually
update
their
sizes,
shapes,
and
properties
to
meet
various
environmental
challenges.
Such
a
capability
also
demonstrated
by
emerging
self‐growing
materials
that
incorporate
externally
provided
compounds
grow
as
organisms.
In
this
Minireview,
we
summarize
these
in
terms
six
aspects.
First,
discuss
essential
characteristics,
then
describe
the
strategies
for
enabling
crosslinked
organic
self‐grow
from
nutrient
solutions
containing
polymerizable
compounds.
developed
examples
are
grouped
into
five
categories
based
on
molecular
mechanisms.
We
explain
mechanism
mass
transport
within
polymer
networks
during
growth,
which
critical
controlling
shape
morphology
grown
products.
Afterwards,
simulation
models
built
interesting
phenomena
observed
discussed.
development
accompanied
applications,
including
tuning
bulk
properties,
creating
textured
surfaces,
growth‐induced
self‐healing,
4D
printing,
implants,
actuation,
structural
coloration,
others.
These
summed
up.
Finally,
opportunities
brought
facing