29 research outputs found
Investigating the Regulation of Distinct Epigenetic States in Human Embryonic Stem Cells
Accumulating
evidence
suggest
that
pluripotency
–
the
ability
to
generate
all
somatic
cell
types
–
is
not
a
fixed
state.
Pluripotent
cell
populations
encompass
a
heterogeneous
group
of
cells
with
different
phenotypic
and
functional
properties
in
equilibrium.
At
least
two
phases
of
pluripotency,
immature
and
primed
for
differentiation,
have
been
identified
during
early
mouse
development,
and
these
are
typified
by
the
two
distinct
stem
cell
populations
–
mouse
embryonic
(mES)
and
epiblast-‐derived
(mEpiS)
stem
cells
–
isolated
from
epiblast
layers
of
pre-‐
and
post-‐implantation
embryo,
respectively.
Many
lines
of
human
ES
(hES)
cells
have
also
been
established
in
vitro
from
the
inner
cell
mass
of
pre-‐
implantation
blastocysts
yet
the
precise
in
vivo
lineage
affiliation
of
these
cells
remains
largely
unresolved.
Profiling
chromatin
in
a
particular
cell
line
has
proven
to
be
a
valuable
signature
for
cell
identity
and
developmental
stage.
One
approach
has
been
to
assay
the
timing
of
DNA
replication
during
S-‐phase
of
the
cell
cycle
across
a
panel
of
loci,
as
an
indicator
of
chromatin
accessibility.
This
replication
timing
profiling
was
notably
capable
of
discriminating
pluripotent
mES
cells
from
cells
with
a
more
restricted
differentiation
capacity.
This
study
sought
to
address
whether
distinct
pluripotent
states
could
be
reliably
discriminated
at
the
chromatin
level.
In
particular,
the
replication
timing
profiles
of
a
number
of
hES
cell
lines
were
characterised
and
compared
to
those
of
mES
and
mEpiS
cell
lines
derived
from
different
genetic
backgrounds.
Profiles
of
undifferentiated
H1,
H7
and
H9
hES
cell
lines
typically
harboured
an
increased
proportion
of
late-‐replicating
loci
during
S-‐
phase
when
compared
to
mES
cells,
which
were
confirmed
to
have
a
steady
and
mostly
early-‐replicating
profile
regardless
of
their
genetic
background.
Moreover,
hES
cell
replication
profile
greatly
varied
between
cultures
and
cell
lines;
a
level
of
replication
timing
variability
also
observed
among
mEpiS
cells,
as
opposed
to
mES
cells.
These
results
highlight
that
hES
and
mEpiS
cells
most
likely
share
a
common
unstable
epigenetic
state
or
transitional
state
primed
on
the
verge
of
differentiation.
The
epigenetic
state
of
hES
cell
lines
was
further
interrogated
by
analysing
cells
grown
under
two
different
culture
conditions,
both
however
similarly
relying
on
TGF-‐β/Activin
signalling.
Results
demonstrated
that
hES
cells
could
adopt
distinct
yet
reversible
epigenetic
signatures
while
retaining
their
pluripotency.
In
particular,
extensive
and
dynamic
shifts
of
replication
timing,
from
late-‐to-‐early,
were
consistently
observed
at
many
target
loci
in
hES
cells
as
well
as
in
human
induced
pluripotent
cells
(iPS)
cells,
upon
increased
SMAD2/3-‐associated P300/CBP
histone
acetyltransferase
(HAT)
activity.
This
was
accompanied
by
fluctuations
in
the
expression
of
NANOG
and
REX1
(also
known
as
ZFP42),
and
a
change
in
hES
cell’s
functional
properties,
as
judged
by
their
responsiveness
to
differentiation-‐inducing
signals.
Interestingly,
inhibiting
P300/CBP
HAT
activity
by
curcumin
treatment
in
undifferentiated
hES
cells
was
sufficient
to
revert
back
to
a
late-‐replicating
profile
associated
with
a
histone
hypoacetylated
state.
Stable
knockdown
of
P300
in
hES
cell
cultures,
however,
resulted
in
a
gradual
loss
of
the
pluripotent
identity
through
differentiation
or
apoptosis,
preventing
further
analysis
of
effects
on
replication
timing.
Collectively,
these
data
strongly
support
the
view
that
different
but
interchangeable
pluripotent
states
exist
within
hES
cell
cultures
and
suggest
a
role
for
P300/CBP
HAT
activity
in
determining
distinct
epigenetic
states
in
hES
cells.
As
mentioned
above,
REX1
was
also
significantly
upregulated
in
H1
hES
cells
upon
culture
condition
change.
REX1
is
a
developmental
stage-‐specific
marker
that
is
expressed
in
the
ICM
of
both
mouse
and
human
embryos,
as
well
as
in
pluripotent
mES,
hES
and
iPS
cells.
However,
its
function
in
hES
cells
remains
largely
unclear.
Human
ES
cells
overexpressing
REX1
were
here
generated
to
investigate
the
role
of
REX1
in
regulating
hES
cell
pluripotent
identity.
These
cells
expressed
similar
levels
of
key
pluripotency
markers
than
their
normal
counterparts
and
remained
capable
of
self-‐renewing
and
differentiating
into
the
three
germ
layers
in
vitro.
Interestingly,
however,
upon
withdrawal
of
exogenous
Activin
A,
REX1
overexpressing
hES
cells
in
contrast
to
control
cells
retained
a
comparatively
high
level
of
OCT4
and
stained
positive
for
alkaline
phosphatase,
a
known
marker
of
undifferentiated
hES
cells.
Taken
together,
these
results
point
to
a
possible
role
for
REX1
in
sustaining
hES
cell
self-‐renewal
ability
Bannerituotannon työnkulku
Bannerimainonta on edelleen laajasti käytetty digitaalisen mainonnan muoto huolimatta sosiaalisen median valtavasta noususta viimeisen kymmenen vuoden aikana. Eri laitealustat ja ohjelmistoympäristöt luovat tilanteen, jonka vaatimukset poikkeavat merkittävästi bannerimainonnan alkuaikojen kuvabannereiden yksinkertaisuudesta.
Insinöörityössä oli tavoitteena tehdä optimoitu työnkulku internetin bannerimainosten tuotantoon. Työ toteutettiin digitaalista markkinointia tekevälle yritykselle. Tavoitteena oli löytää työprosessia helpottavia ja tehostavia työtapoja ja kartoittaa, millaisia mahdollisuuksia HTML5-pohjaisten bannereiden luontiin on olemassa. Osana insinöörityötä tehtiin myös dynaamista sisältöä käyttävää bannerimainontaa asiakasyritykselle.
Insinöörityössä kartoitettiin erilaisia työkaluja bannerien toteuttamiseen ja animointiin ja listattiin kunkin toteutustavan hyviä ja huonoja puolia. Myös bannereissa käytettävien kuvaformaattien käyttötarkoituksia ja laadun optimointiin käytettäviä työkaluja vertailtiin. Työnkulkua pohdittiin myös arkistoinnin ja luotujen materiaalien jatkokäyttömahdollisuuksien pohjalta. Tutkimuskirjallisuutta läpikäymällä pyrittiin löytämään tietoa siitä, minkälaiset bannerit toimivat parhaiten internetissä ja perehdyttiin bannerimainonnan markkinatilanteeseen vertailemalla sitä sosiaalisen median mainoskanaviin.
Työn tuloksena syntyi ehdotus siitä, millaisia optimointeja työnkulkuun voi tehdä päivittäisessä työssä, ja toisaalta, miten työnkulun hallintaa parannetaan pidemmällä aikajänteellä esimerkiksi banneripohjien ja -arkiston avulla. Bannerisokeutta voisi torjua muun muassa vaihtelemalla mainosten sijoittelua verkkosivulla ja animaation keinoin. Bannereiden animointiin ja toteutukseen ehdotettiin eri tekniikoiden tai ohjelmistojen käyttämistä käyttötapauksesta riippuen, eikä yhtä, kaikkiin projekteihin soveltuvaa menetelmää löydetty. Työnkulun automatisointiin löydettiin ratkaisuja, joilla usein samanlaisena toistuvaa työtä saataisiin vähennettyä.
Insinöörityössä kuvatut työnkulun menetelmät mietittiin tilaajayrityksen näkökulmasta ja sen ympäristöön sopiviksi, mutta niitä voidaan soveltaa yleisemminkin verkkokäyttöön tarkoitetun grafiikan ja animaation tuottamiseen. Työ tarjoaa pohjan siinä kuvattujen menetelmien käyttöönottoon tuotantoympäristössä.Banner advertising is still a widely-used method in digital advertising despite the immense rise of social media during the last ten years. Creating advertisements for different types of devices and environments is a process, which reaches far beyond in complexity the relatively simple era of still image banners. The goal of this thesis is to create an optimized workflow for producing modern HTML5 banner advertisements for the web and seek out the possibilities and technologies currently available. As part of the thesis banner advertisements using dynamic content were created for a client.
Different tools for creating and animating banners were evaluated and their pros and cons listed. The usage cases and quality optimization tools for image formats commonly used in banners were compared to find out the best quality / file size ratio for images. Workflow was considered also for archival and future usage of created materials. Existing research literature and statistics were used as a reference for assessing the effectiveness of banner advertising: what works and what does not.
As a result, suggestions for improving the workflow were created. Some of the suggestions are usable in day-to-day work while others lean more towards improving the overall functionality of the banner production with regards to archiving and re-usage of the produced materials. For banner creation, there was not one method or program that would fit all possible cases, but it was proposed that different tools would be used based on the individual requirements of the project. Banner workflow was found to include many repetitive tasks, which could be automated with solutions such as JavaScript build tools.
The methods described in the thesis for improving the workflow in banner creation were considered from the client company's point of view, and requirements may vary for other companies, but they are still applicable as general guidelines on how to create graphics and animation for use on the internet. This thesis acts as a basis for applying the described methods for actual production environment
Clinical Impact of Tumor-Associated Macrophage and T-Cell Contents in Diffuse Large B-Cell Lymphoma
Peer reviewe
Laitteita vai kokonaisuuksia:eheyttävä mediakasvatus varhaiskasvatuksessa
Tiivistelmä. Tutkielma perehtyy varhaiskasvatuksessa toteutettavaan mediakasvatukseen. Sen tavoitteena on selvittää, millaisena eheyttäminen näyttäytyy varhaiskasvatuksen mediakasvatuksessa, kuvailevan kirjallisuuskatsauksen kautta. Aihe on varhaiskasvatuksen kentällä ajankohtainen, sillä sekä eheyttäminen että mediakasvatus ovat osa varhaiskasvatusta ohjaavaa Varhaiskasvatussuunnitelman perusteita. Tutkielma on toteutettu kuvailevana kirjallisuuskatsauksena, jonka tutkimusmateriaalina on käytetty ajankohtaisia koti- ja ulkomaisia lähteitä sekä Varhaiskasvatussuunnitelman perusteita. Opetuksen eheyttämisen pitkät juuret huomioon ottaen, lähdekirjallisuus ulottuu eheyttämisen määrittelyn osalta pitkälle historiaan. Mediakasvatuksen osalta tutkimuskirjallisuus painottuu mahdollisimman tuoreisiin lähteisiin. Käytettäväksi tutkimusaineistoksi on valittu tieteellisiä artikkeleita, väitöskirjoja ja tutkimusaiheeseen sopivia perusteoksia.
Tutkimustulosten mukaan eheyttäminen näyttäytyi varhaiskasvatuksen mediakasvatuksessa kokonaisuuksien, lapsilähtöisyyden ja mielekkään työskentelyn kautta. Tulosten mukaan kokonaisuudet sitoutuivat vahvasti kasvattajan omiin näkemyksiin, tietoihin ja taitoihin mediakasvatuksesta. Kasvattajan teknologisen identiteetin nähtiin vaikuttavan siihen, millaista mediakasvatusta kasvattaja toteuttaa. Kasvattajilla havaittiin olevan eheyttävää ja kokonaisvaltaista pedagogiikkaa, mutta sen ei nähty ulottuvan mediakasvatukseen saakka. Eheyttävyyden lapsilähtöisyys näkyi mediakulttuurin asemassa varhaiskasvatuksessa. Tutkimustulosten perusteella lasten omia mielenkiinnon kohteita — kuten medialeikkejä — rajoitettiin monin tavoin, eikä varhaiskasvatusta nähty mediakulttuurisena paikkana. Eheyttävyyden mielekäs työskentely näyttäytyi laitekeskeisyyden kautta. Tulosten perusteella kasvattajat näkivät mediakasvatuksen usein rajoittuneesti, lähinnä laitteiden kautta
Clinical Impact of Immune Cells and Their Spatial Interactions in Diffuse Large B-Cell Lymphoma Microenvironment
Purpose: Tumor-infiltrating immune cells have prognostic sig-nificance and are attractive therapeutic targets. Yet, the clinical significance of their spatial organization and phenotype in diffuse large B-cell lymphoma (DLBCL) is unclear. Experimental Design: We characterized T cells, macrophages, and their spatial interactions by multiplex IHC (mIHC) in 178 patients with DLBCL and correlated the data with patient demo-graphics and survival. We validated the findings on gene expression data from two external DLBCL cohorts comprising 633 patients. Results: Macrophage and T-cell contents divided the samples into T cell-inflamed (60%) and noninflamed (40%) subgroups. The T cell-inflamed lymphoma microenvironment (LME) was also rich in other immune cells, defining immune hot phenotype, which did not as such correlate with outcome. However, when we divided the patients according to T-cell and macrophage contents, LME char-acterized by high T-cell/low macrophage content or a correspond-ing gene signature was associated with superior survival [5-year overall survival (OS): 92.3% vs. 74.4%, P = 0.036; 5-year progres-sion-free survival (PFS): 92.6% vs. 69.8%, P = 0.012]. High pro-portion of PD -L1-and TIM3-expressing CD163- macrophages in the T cell-inflamed LME defined a group of patients with poor outcome [OS: HR = 3.22, 95% confidence interval (CI), 1.63-6.37, P-adj = 0.011; PFS: HR = 2.76, 95% CI, 1.44-5.28, P-adj = 0.016]. Furthermore, PD-L1 and PD-1 were enriched on macrophages interacting with T cells. Conclusions: Our data demonstrate that the interplay between macrophages and T cells in the DLBCL LME is immune checkpoint dependent and clinically meaningful.Peer reviewe
T-cell inflamed tumor microenvironment predicts favorable prognosis in primary testicular lymphoma
Primary testicular lymphoma is a rare lymphoid malignancy, most often, histologically, representing diffuse large B-cell lymphoma. The tumor rnicroenvi.ro.nrnent and limited immune surveillance have a major impact on diffuse large B-cell lymphoma pathogenesis and. survival, but the impact on primary testicular lymphoma is unknown. Here, the purpose of the study was to characterize the tumor microenvironme.nt in primary testicular lymphoma, and associate the findings with outcome. We profiled the expression of 730 immune response enes in 60 primary testicular lymphomas utilizing the Nanostring platorm, and used multiplex imrnunohistochemistry to characterize the immune cell phenotypes in the tumor tissue. We identified a gene signature enriched for T-lymphocyte markers differentially expressed. between the patients. Low expression of the signature predicted poor outcome independently of the International Prognostic Index (progression -free survival: HR=2.810, 95%CI: 1.228-6.431, P=0.014; overall survival: HR=3.267, 95`)/0' CI: 1.406-7.590, P=0.006). The T-lymphocyte signature was associated with outcome also in an independent diffuse large B-cell lymphoma cohort (n=96). Multiplex immunohistochemistry revealed that poor survival of primary testicular lymphoma patients correlated with low percentage of CD3'CD4' and CD3+CD8' tumor-infiltrating lymphocytes (PPeer reviewe
What conditions favor the influence of seasonally frozen ground on hydrological partitioning? : a systematic review
The influence of seasonally frozen ground (SFG) on water, energy, and solute fluxes is important in cold climate regions. The hydrological role of permafrost is now being actively researched, but the influence of SFG has received less attention. Intuitively, SFG restricts (snowmelt) infiltration, thereby enhancing surface runoff and decreasing soil water replenishment and groundwater recharge. However, the reported hydrological effects of SFG remain contradictory and appear to be highly site- and event-specific. There is a clear knowledge gap concerning under what physiographical and climate conditions SFG is more likely to influence hydrological fluxes. We addressed this knowledge gap by systematically reviewing published work examining the role of SFG in hydrological partitioning. We collected data on environmental variables influencing the SFG regime across different climates, land covers, and measurement scales, along with the main conclusion about the SFG influence on the studied hydrological flux. The compiled dataset allowed us to draw conclusions that extended beyond individual site investigations. Our key findings were: (a) an obvious hydrological influence of SFG at small-scale, but a more variable hydrological response with increasing scale of measurement, and (b) indication that cold climate with deep snow and forest land cover may be related to reduced importance of SFG in hydrological partitioning. It is thus increasingly important to understand the hydrological repercussions of SFG in a warming climate, where permafrost is transitioning to seasonally frozen conditions
Immune cell constitution in the tumor microenvironment predicts the outcome in diffuse large B-cell lymphoma
Tumor microenvironment (TME) and limited immune surveillance play important roles in lymphoma pathogenesis. Here, we aimed to characterize immunological profiles of diffuse large B-cell lymphoma (DLBCL) and predict the outcome in response to immunochemotherapy. We profiled the expression of 730 immune-related genes in tumor tissues of DLBCL patients (n=81) utilizing the Nanostring platform, and used multiplex immunohistochemistry to characterize T-cell phenotypes, including cytotoxic T-cells (CD8, Granzyme B, OX40, Ki67), T-cell immune checkpoint (CD3, CD4, CD8, PD1, TIM3, LAG3), as well as regulatory T-cells and Th1 effector cells (CD3, CD4, FOXP3, TBET) in 188 patients. We observed a high degree of heterogeneity at the transcriptome level. Correlation matrix analysis identified gene expression signatures with highly correlating genes - the main cluster containing genes for cytolytic factors, immune checkpoint molecules, T-cells and macrophages, together entitled as a TME immune cell signature. Immunophenotyping of the distinct cell subsets revealed that a high proportion of immune checkpoint positive T-cells translated to unfavorable survival. Together, our results demonstrate that the immunological profile of DLBCL TME is heterogeneous and clinically meaningful. This highlights the potential impact of T-cell immune checkpoint in regulating survival and resistance to immunochemotherapy