International Journal of Molecular Sciences,
Journal Year:
2022,
Volume and Issue:
23(17), P. 9834 - 9834
Published: Aug. 30, 2022
Whole
genome
sequencing
(WGS)
provides
the
highest
resolution
for
genome-based
species
identification
and
can
provide
insight
into
antimicrobial
resistance
virulence
potential
of
a
single
microbiological
isolate
during
diagnostic
process.
In
contrast,
metagenomic
allows
analysis
DNA
segments
from
multiple
microorganisms
within
community,
either
using
an
amplicon-
or
shotgun-based
approach.
However,
WGS
shotgun
data
are
rarely
combined,
although
such
approach
may
generate
additive
synergistic
information,
critical
for,
e.g.,
patient
management,
infection
control,
pathogen
surveillance.
To
produce
combined
workflow
with
actionable
outputs,
we
need
to
understand
pre-to-post
analytical
process
both
technologies.
This
will
require
specific
databases
storing
interlinked
metadata,
also
involves
customized
bioinformatic
pipelines.
review
article
overview
steps
clinical
application
combining
metagenomics
together
diagnosis.
Bioinformatics,
Journal Year:
2021,
Volume and Issue:
38(1), P. 1 - 8
Published: Aug. 16, 2021
The
COVID-19
pandemic
has
ignited
a
broad
scientific
interest
in
viral
research
general
and
coronavirus
particular.
identification
characterization
of
species
natural
reservoirs
typically
involves
de
novo
assembly.
However,
existing
genome,
metagenome
transcriptome
assemblers
often
are
not
able
to
assemble
many
viruses
(including
coronaviruses)
into
single
contig.
Coverage
variation
between
datasets
within
dataset,
presence
close
strains,
splice
variants
contamination
set
high
bar
for
process
with
diverse
properties.We
developed
coronaSPAdes,
novel
assembler
RNA
recovery
coronaviruses
coronaSPAdes
leverages
the
knowledge
about
genome
structures
improve
assembly
extending
ideas
initially
implemented
biosyntheticSPAdes.
We
have
shown
that
outperforms
SPAdes
modes
other
popular
short-read
full-length
genomes.coronaSPAdes
version
used
this
article
is
part
3.15
release
freely
available
at
http://cab.spbu.ru/software/spades.Supplementary
data
Bioinformatics
online.
PeerJ,
Journal Year:
2022,
Volume and Issue:
10, P. e14055 - e14055
Published: Oct. 13, 2022
RNA
viruses
encoding
a
polymerase
gene
(riboviruses)
dominate
the
known
eukaryotic
virome.
High-throughput
sequencing
is
revealing
wealth
of
new
riboviruses
only
from
sequence,
precluding
classification
by
traditional
taxonomic
methods.
Sequence
often
based
on
sequences,
but
standardised
methods
to
support
this
approach
are
currently
lacking.
To
address
need,
we
describe
palmprint,
segment
palm
sub-domain
robustly
delineated
well-conserved
catalytic
motifs.
We
present
an
algorithm,
Palmscan,
which
identifies
palmprints
in
nucleotide
and
amino
acid
sequences;
PALMdb,
collection
derived
public
sequence
databases;
palmID,
website
implementing
palmprint
identification,
search,
annotation.
Together,
these
demonstrate
proof-of-concept
workflow
for
high-throughput
characterisation
viruses,
paving
path
continued
rapid
growth
virus
discovery
anticipated
coming
decade.
Environmental Microbiology,
Journal Year:
2022,
Volume and Issue:
25(1), P. 40 - 44
Published: Sept. 13, 2022
Abstract
Viruses
are
considered
to
be
the
most
abundant
biological
entities
on
earth.
They
also
display
striking
genetic
diversity
as
emphatically
demonstrated
by
recent
advances
of
metagenomics
and
metatranscriptomics.
But
what
limits
this
diversity,
that
is,
how
many
virus
species
in
earth
virome?
By
combining
available
estimates
number
prokaryote
with
those
virome
size,
we
obtain
back‐of‐the‐envelope
total
distinct
species,
which
come
out
astronomically
large,
from
about
10
7
9
.
The
route
origins
apparently
involved
non‐viral
replicators
capturing
exapting
various
cellular
proteins
become
capsid
subunits.
How
times
history
life
has
happened?
In
other
words,
realms
viruses,
highest
rank
taxa
supposed
monophyletic,
comprise
global
We
argue
viruses
emerged
a
(even
if
far
astronomical)
independent
occasions,
so
will
considerably
increase
current
6,
splitting
some
realms,
giving
realm
status
currently
unclassified
groups
discovery
new
groups.
Archives of Toxicology,
Journal Year:
2022,
Volume and Issue:
96(6), P. 1521 - 1539
Published: March 25, 2022
Abstract
Tetanus
and
botulinum
neurotoxins
cause
the
neuroparalytic
syndromes
of
tetanus
botulism,
respectively,
by
delivering
inside
different
types
neurons,
metalloproteases
specifically
cleaving
SNARE
proteins
that
are
essential
for
release
neurotransmitters.
Research
on
their
mechanism
action
is
intensively
carried
out
in
order
to
devise
improved
therapies
based
antibodies
chemical
drugs.
Recently,
major
results
have
been
obtained
with
human
monoclonal
single
chain
allowed
one
neutralize
metalloprotease
activity
neurotoxin
type
A1
neurons.
In
addition,
a
method
has
devised
induce
rapid
molecular
evolution
domain
followed
selection
driven
re-target
versus
novel
targets
respect
proteins.
At
same
time,
an
intense
wide
spectrum
clinical
research
therapeutics
out,
which
also
reviewed
here.
International Journal of Molecular Sciences,
Journal Year:
2022,
Volume and Issue:
23(17), P. 9834 - 9834
Published: Aug. 30, 2022
Whole
genome
sequencing
(WGS)
provides
the
highest
resolution
for
genome-based
species
identification
and
can
provide
insight
into
antimicrobial
resistance
virulence
potential
of
a
single
microbiological
isolate
during
diagnostic
process.
In
contrast,
metagenomic
allows
analysis
DNA
segments
from
multiple
microorganisms
within
community,
either
using
an
amplicon-
or
shotgun-based
approach.
However,
WGS
shotgun
data
are
rarely
combined,
although
such
approach
may
generate
additive
synergistic
information,
critical
for,
e.g.,
patient
management,
infection
control,
pathogen
surveillance.
To
produce
combined
workflow
with
actionable
outputs,
we
need
to
understand
pre-to-post
analytical
process
both
technologies.
This
will
require
specific
databases
storing
interlinked
metadata,
also
involves
customized
bioinformatic
pipelines.
review
article
overview
steps
clinical
application
combining
metagenomics
together
diagnosis.
