Abstract
Foxi1
is
a
master
regulator
of
ionocytes
(ISCs
/
INCs)
across
species
and
organs.
Two
subtypes
ISCs
exist,
both
α-
β-ISCs
regulate
pH-
ion-homeostasis
in
epithelia.
Gain
loss
FOXI1
function
are
associated
with
human
diseases,
including
Pendred
syndrome,
male
infertility,
renal
acidosis
cancers.
functions
were
predominantly
studied
the
context
ISC
specification,
however,
reports
indicate
additional
early
ectodermal
development.
Here,
we
re-investigated
Xenopus
laevis
embryonic
mucociliary
epidermis
development
found
novel
for
generation
Notch-ligand
expressing
multipotent
progenitors
(MPPs).
We
demonstrate
that
has
multiple
concentration-dependent
functions:
At
low
levels,
confers
competence
through
transcriptional
epigenetic
mechanisms,
while
at
high
induces
multi-step
process
specification
differentiation.
further
describe
how
foxi1
expression
affected
auto-
Notch-regulation,
Ubp1
Dmrt2
subtype
differentiation,
this
developmental
program
affects
Notch
signaling
as
well
patterning.
Together,
reveal
formation,
relevant
to
our
understanding
vertebrate
disease.
Abstract
The
Alliance
of
Genome
Resources
(Alliance)
is
an
extensible
coalition
knowledgebases
focused
on
the
genetics
and
genomics
intensively
studied
model
organisms.
organized
as
individual
knowledge
centers
with
strong
connections
to
their
research
communities
a
centralized
software
infrastructure,
discussed
here.
Model
organisms
currently
represented
in
are
budding
yeast,
Caenorhabditis
elegans,
Drosophila,
zebrafish,
frog,
laboratory
mouse,
rat,
Gene
Ontology
Consortium.
project
rapid
development
phase
harmonize
knowledge,
store
it,
analyze
present
it
community
through
web
portal,
direct
downloads,
application
programming
interfaces
(APIs).
Here,
we
focus
developments
over
last
2
years.
Specifically,
added
enhanced
tools
for
browsing
genome
(JBrowse),
downloading
sequences,
mining
complex
data
(AllianceMine),
visualizing
pathways,
full-text
searching
literature
(Textpresso),
sequence
similarity
(SequenceServer).
We
existing
interactive
tables
table
paralogs
complement
our
representation
orthology.
To
support
organism
communities,
implemented
species-specific
“landing
pages”
will
add
disease-specific
portals
soon;
addition,
common
forum
Discourse
software.
describe
progress
toward
central
persistent
database
curation,
modeling
that
underpins
harmonization,
state-of-the-art
curation
system
integrated
artificial
intelligence
machine
learning
(AI/ML).
Abstract
Echinobase
(www.echinobase.org)
is
a
model
organism
knowledgebase
serving
as
resource
for
the
community
that
studies
echinoderms,
phylum
of
marine
invertebrates
includes
sea
urchins
and
stars.
Echinoderms
have
been
important
experimental
models
over
100
years
continue
to
make
contributions
environmental,
evolutionary,
developmental
studies,
including
research
on
gene
regulatory
networks.
As
centralized
resource,
hosts
genomes
collects
functional
genomic
data,
reagents,
literature,
other
information
community.
This
third-generation
site
based
Xenbase
design
utilizes
gene-centric
pages
minimize
time
effort
required
access
information.
Summary
display
symbols
names,
links
JBrowse
genome
browser,
orthology
organisms
tabs
from
page
contain
more
detailed
concerning
mRNAs,
proteins,
diseases,
protein–protein
interactions.
The
also
1:1
orthologs
between
fully
supported
species
Strongylocentrotus
purpuratus
(purple
urchin),
Lytechinus
variegatus
(green
Patiria
miniata
(bat
star),
Acanthaster
planci
(crown-of-thorns
star).
tracks
are
available
visualization
data
both
partially
Anneissia
japonica
(feather
Asterias
rubens
(sugar
L.
pictus
(painted
urchin).
serves
vital
role
by
providing
researchers
with
annotated
orthology,
aligned
genomes,
curated
reagents
data.
Echinoderm
Anatomical
Ontology
provides
framework
standardizing
across
phylum,
content
formatted
be
findable,
accessible,
interoperable,
reusable
Nucleic Acids Research,
Год журнала:
2024,
Номер
53(D1), С. D1516 - D1525
Опубликована: Ноя. 18, 2024
Abstract
PubChem
(https://pubchem.ncbi.nlm.nih.gov)
is
a
large
and
highly-integrated
public
chemical
database
resource
at
NIH.
In
the
past
two
years,
significant
updates
were
made
to
PubChem.
With
additions
from
over
130
new
sources,
contains
>1000
data
119
million
compounds,
322
substances
295
bioactivities.
New
interfaces,
such
as
consolidated
literature
panel
patent
knowledge
panel,
developed.
The
combines
all
references
about
compound
into
single
list,
allowing
users
easily
find,
sort,
export
relevant
articles
for
in
one
place.
panels
given
query
or
gene
display
chemicals,
genes,
diseases
co-mentioned
with
documents,
helping
explore
relationships
between
co-occurring
entities
within
documents.
PubChemRDF
was
expanded
include
co-occurrence
underlying
enabling
exploit
semantic
web
technologies
entity
based
on
co-occurrences
scientific
literature.
usability
accessibility
of
information
chemicals
non-discrete
structures
(e.g.
biologics,
minerals,
polymers,
UVCBs
glycans)
greatly
improved
dedicated
pages
that
provide
comprehensive
view
available
these
chemicals.
Mammalian Genome,
Год журнала:
2023,
Номер
34(4), С. 531 - 544
Опубликована: Сен. 4, 2023
Abstract
Comparing
genomic
and
biological
characteristics
across
multiple
species
is
essential
to
using
model
systems
investigate
the
molecular
cellular
mechanisms
underlying
human
biology
disease
translate
mechanistic
insights
from
studies
in
organisms
for
clinical
applications.
Building
a
scalable
knowledge
commons
platform
that
supports
cross-species
comparison
of
rich,
expertly
curated
regarding
gene
function,
phenotype,
associations
available
humans
primary
mission
Alliance
Genome
Resources
(the
Alliance).
The
consortium
seven
organism
knowledgebases
(mouse,
rat,
yeast,
nematode,
zebrafish,
frog,
fruit
fly)
Gene
Ontology
resource.
uses
common
set
ortholog
assertions
as
basis
comparing
annotations
represented
Alliance.
major
types
associated
with
genes
are
database
currently
include
phenotypic
alleles
variants,
associations,
pathways,
expression,
both
protein–protein
genetic
interactions.
has
enhanced
ability
researchers
easily
compare
data
through
implementation
shared
programmatic
access
mechanisms,
data-specific
web
pages
unified
“look
feel”,
interactive
user
interfaces
specifically
designed
support
comparative
biology.
modular
infrastructure
developed
by
allows
resource
serve
an
extensible
“knowledge
commons”
capable
expanding
accommodate
additional
organisms.
Nucleic Acids Research,
Год журнала:
2023,
Номер
52(D1), С. D938 - D949
Опубликована: Ноя. 24, 2023
Bridging
the
gap
between
genetic
variations,
environmental
determinants,
and
phenotypic
outcomes
is
critical
for
supporting
clinical
diagnosis
understanding
mechanisms
of
diseases.
It
requires
integrating
open
data
at
a
global
scale.
The
Monarch
Initiative
advances
these
goals
by
developing
ontologies,
semantic
models,
knowledge
graphs
translational
research.
App
an
integrated
platform
combining
about
genes,
phenotypes,
diseases
across
species.
Monarch's
APIs
enable
access
to
carefully
curated
datasets
advanced
analysis
tools
that
support
disease
diverse
applications
such
as
variant
prioritization,
deep
phenotyping,
patient
profile-matching.
We
have
migrated
our
system
into
scalable,
cloud-based
infrastructure;
simplified
ingestion
graph
integration
systems;
enhanced
mapping
standards;
developed
new
user
interface
with
novel
search
navigation
features.
Furthermore,
we
analytic
customized
plugin
OpenAI's
ChatGPT
increase
reliability
its
responses
data,
allowing
us
interrogate
in
using
state-of-the-art
Large
Language
Models.
resources
can
be
found
monarchinitiative.org
corresponding
code
repository
github.com/monarch-initiative/monarch-app.
Molecular Biology and Evolution,
Год журнала:
2024,
Номер
41(4)
Опубликована: Апрель 1, 2024
Abstract
Visual
systems
adapt
to
different
light
environments
through
several
avenues
including
optical
changes
the
eye
and
neurological
in
how
signals
are
processed
interpreted.
Spectral
sensitivity
can
evolve
via
visual
pigments
housed
retinal
photoreceptors
gene
duplication
loss,
differential
coexpression,
sequence
evolution.
Frogs
provide
an
excellent,
yet
understudied,
system
for
evolution
research
due
their
diversity
of
ecologies
(including
biphasic
aquatic-terrestrial
life
cycles)
that
we
hypothesize
imposed
selective
pressures
leading
adaptive
system,
notably
opsins
encode
protein
component
responsible
first
step
perception.
Here,
analyze
opsin
genes
from
93
new
transcriptomes
plus
published
data
a
combined
dataset
spanning
122
frog
species
34
families.
We
find
most
express
four
previously
identified
frogs
but
show
evidence
loss
two
lineages.
Further,
present
positive
selection
three
shifts
associated
with
differences
habitat
history,
not
activity
pattern.
identify
substantial
novel
variation
and,
using
microspectrophotometry,
highly
variable
spectral
sensitivities,
expanding
known
ranges
all
pigments.
Mutations
at
spectral-tuning
sites
only
partially
account
this
variation,
suggesting
have
used
tuning
pathways
unique
among
vertebrates.
These
results
support
hypothesis
photoreceptor
physiology
across
tree
response
varying
environmental
ecological
factors
further
our
growing
understanding
vertebrate
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Март 6, 2025
The
co-occurrence
of
autism
and
gastrointestinal
distress
is
well-established,
yet
the
molecular
underpinnings
remain
unknown.
identification
high-confidence,
large-effect
genes
offers
opportunity
to
identify
convergent,
underlying
biology
by
studying
these
in
context
system.
Here
we
show
that
expression
enriched
human
prenatal
gut
neurons
their
migratory
progenitors,
suggesting
development
and/or
function
may
be
disrupted
autism-associated
genetic
variants,
leading
dysfunction.
document
prevalence
issues
patients
with
variants
sixteen
genes,
highlighting
dysmotility,
consistent
potential
enteric
neuron
Using
Xenopus
tropicalis,
individually
target
five
(SYNGAP1,
CHD8,
SCN2A,
CHD2,
DYRK1A)
observe
neuronal
progenitor
migration
for
each.
Further
analysis
DYRK1A
reveals
perturbation
causes
dysmotility
vivo,
which
can
ameliorated
treatment
either
two
serotonin
signaling
modulators,
identified
vivo
drug
screening.
This
work
suggests
atypical
contributes
commonly
seen
individuals
a
productive
therapeutic
pathway.
Nucleic Acids Research,
Год журнала:
2024,
Номер
53(D1), С. D243 - D257
Опубликована: Ноя. 11, 2024
Reference
sequences
and
annotations
serve
as
the
foundation
for
many
lines
of
research
today,
from
organism
sequence
identification
to
providing
a
core
description
genes,
transcripts
proteins
found
in
an
organism's
genome.
Interpretation
data
including
transcriptomics,
proteomics,
variation
comparative
analyses
based
on
reference
gene
informs
our
understanding
function
possible
disease
mechanisms,
leading
new
biomedical
discoveries.
The
Sequence
(RefSeq)
resource
created
at
National
Center
Biotechnology
Information
(NCBI)
leverages
both
automatic
processes
expert
curation
create
robust
set
genomic,
transcript
protein
spanning
tree
life.
RefSeq
continues
refine
its
annotation
quality
control
utilize
better
genomes
resulting
advances
sequencing
technologies
well
RNA-Seq
produce
high-quality
annotated
genomes,
ortholog
predictions
across
more
organisms
other
products
that
are
easily
accessible
through
multiple
NCBI
resources.
This
report
summarizes
current
status
eukaryotic,
prokaryotic
viral
resources,
with
focus
eukaryotic
annotation,
increase
taxonomic
representation
effect
it
will
have
genomics.
is
publicly
https://www.ncbi.nlm.nih.gov/refseq.
