44 research outputs found
Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer
BACKGROUND: There is considerable interest in identifying target genes and chromatin binding sites for transcription factors in a genome-wide manner. Such information may become useful in diagnosis and treatment of disease, drug target identification, and for prognostication. In cancer diagnosis, patterns of transcription factor binding to specific regulatory chromatin elements are expected to complement and enhance current diagnostic predictions of tumor behavior based on protein and mRNA analyses. Signal transducer and activator of transcription-5 (Stat5) is a cytokine-activated transcription factor implicated in growth and progression of many malignancies, including hematopoietic, prostate, and breast cancer. We have explored immunoaffinity purification of Stat5-bound chromatin from breast cancer cells to identify Stat5 target sites in an unbiased, genome-wide manner. RESULTS: In this report, we evaluate the efficacy of a Stat5-bound chromatin library to identify valid Stat5 chromatin binding sites within the oncogenome of T-47D human breast cancer cells. A general problem with cloning of immunocaptured, transcription factor-bound chromatin fragments is contamination with non-specific chromatin. However, using an optimized strategy, five out of ten randomly selected clones could be experimentally verified to bind Stat5 both in vitro and in vivo as tested by electrophoretic mobility shift assay and chromatin immunoprecipitation, respectively. While there was no binding to fragments lacking a Stat5 consensus binding sequence, presence of a Stat5 binding sequence did not assure binding. CONCLUSION: A chromatin library coupled with experimental validation may productively identify novel in vivo Stat5 chromatin binding sites in cancer, including abnormal regulatory sites in tumor-specific neochromatin
STAT5 regulation of BCL10 parallels constitutive NFkappaB activation in lymphoid tumor cells.
BACKGROUND: Signal Transducer and Activator of Transcription 5 A and B (STAT5) are key survival factors in cells of the lymphoid lineage. Identification of novel, tissue-specific STAT5 regulated genes would advance the ability to combat diseases due to aberrant STAT5 signaling. In the present work a library of human STAT5 bound genomic elements was created and validated. RESULTS: Of several STAT5 responsive genomic regulatory elements identified, one was located within the first intron of the human BCL10 gene. Chromatin immuno-precipitation reactions confirmed constitutive in vivo STAT5 binding to this intronic fragment in various human lymphoid tumor cell lines. Interestingly, non-phosphorylated STAT5 was found in the nuclei of Kit225 and YT cells in the absence of cytokine stimulation that paralleled constitutive NFkappaB activation. Inhibition of the hyperactive JAK3/STAT5 pathway in MT-2 cells via the Mannich-base, NC1153, diminished the constitutive in vivo occupancy of BCL10-SBR by STAT5, reduced NFkappaB activity and BCL10 protein expression in a dose dependent manner. Moreover, depletion of STAT5 via selective antisense oligonucleotide treatment similarly resulted in decreased BCL10 mRNA and protein expression, cellular viability and impaired NFkappaB activity independent of IL-2. CONCLUSION: These results suggest that the NFkappaB regulator BCL10 is an IL-2-independent STAT5 target gene. These findings proffer a model in which un-activated STAT5 can regulate pathways critical for lymphoid cell survival and inhibitors that disrupt STAT5 function independent of tyrosine phosphorylation may be therapeutically effective in treating certain leukemias/lymphomas
STAT5 regulation of BCL10 parallels constitutive NFκB activation in lymphoid tumor cells
<p>Abstract</p> <p>Background</p> <p>Signal Transducer and Activator of Transcription 5 A and B (STAT5) are key survival factors in cells of the lymphoid lineage. Identification of novel, tissue-specific STAT5 regulated genes would advance the ability to combat diseases due to aberrant STAT5 signaling. In the present work a library of human STAT5 bound genomic elements was created and validated.</p> <p>Results</p> <p>Of several STAT5 responsive genomic regulatory elements identified, one was located within the first intron of the human <it>BCL10 </it>gene. Chromatin immuno-precipitation reactions confirmed constitutive <it>in vivo </it>STAT5 binding to this intronic fragment in various human lymphoid tumor cell lines. Interestingly, non-phosphorylated STAT5 was found in the nuclei of Kit225 and YT cells in the absence of cytokine stimulation that paralleled constitutive NFκB activation. Inhibition of the hyperactive JAK3/STAT5 pathway in MT-2 cells via the Mannich-base, NC1153, diminished the constitutive <it>in vivo </it>occupancy of BCL10-SBR by STAT5, reduced NFκB activity and BCL10 protein expression in a dose dependent manner. Moreover, depletion of STAT5 via selective antisense oligonucleotide treatment similarly resulted in decreased BCL10 mRNA and protein expression, cellular viability and impaired NFκB activity independent of IL-2.</p> <p>Conclusion</p> <p>These results suggest that the NFκB regulator BCL10 is an IL-2-independent STAT5 target gene. These findings proffer a model in which un-activated STAT5 can regulate pathways critical for lymphoid cell survival and inhibitors that disrupt STAT5 function independent of tyrosine phosphorylation may be therapeutically effective in treating certain leukemias/lymphomas.</p
Scary Barbie: An Extremely Energetic, Long-Duration Tidal Disruption Event Candidate Without a Detected Host Galaxy at z = 0.995
We report multi-wavelength observations and characterization of the
ultraluminous transient AT 2021lwx (ZTF20abrbeie; aka ``Barbie'') identified in
the alert stream of the Zwicky Transient Facility (ZTF) using a Recommender
Engine For Intelligent Transient Tracking (REFITT) filter on the ANTARES alert
broker. From a spectroscopically measured redshift of 0.995, we estimate a peak
observed pseudo-bolometric luminosity of log (L) = 45.7 from slowly fading ztf- and ztf-
light curves spanning over 1000 observer-frame days. The host galaxy is not
detected in archival Pan-STARRS observations ( mag), implying a lower
limit to the outburst amplitude of more than 5 mag relative to the quiescent
host galaxy. Optical spectra from Lick and Keck Observatories exhibit strong
emission lines with narrow cores from the H Balmer series and ultraviolet
semi-forbidden lines of Si III] 1892, C III] 1909, and C II]
2325. Typical nebular lines in AGN spectra from ions such as [O II]
and [O III] are not detected. These spectral features, along with the smooth
light curve that is unlike most AGN flaring activity, and the luminosity that
exceeds any observed or theorized supernova, lead us to conclude that AT
2021lwx is most likely an extreme tidal disruption event (TDE). Modeling of ZTF
photometry with MOSFiT suggests that the TDE was between a star and a supermassive black hole of mass
. Continued monitoring of the still-evolving light curve
along with deep imaging of the field once AT 2021lwx has faded can test this
hypothesis and potentially detect the host galaxy.Comment: 15 pages, 4 figures, 1 Table; Version as published in The
Astrophysical Journal Letters. Observations of AT 2021lwx published in the
paper can be found at https://bsubraya.github.io/research
Comparison of techniques used to count single-celled viable phytoplankton
Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Journal of Applied Phycology 24 (2012): 751-758, doi:10.1007/s10811-011-9694-z.Four methods commonly used to count phytoplankton were evaluated based upon the precision of concentration
estimates: Sedgewick Rafter and membrane filter direct counts, flow cytometry, and flow-based imaging cytometry
(FlowCAM). Counting methods were all able to estimate the cell concentrations, categorize cells into size classes,
and determine cell viability using fluorescent probes. These criteria are essential to determine whether discharged
ballast water complies with international standards that limit the concentration of viable planktonic organisms based
on size class. Samples containing unknown concentrations of live and UV-inactivated phytoflagellates (Tetraselmis
impellucida) were formulated to have low concentrations (<100 ml-1) of viable phytoplankton. All count methods
used chlorophyll a fluorescence to detect cells and SYTOX fluorescence to detect non-viable cells. With the
exception of one sample, the methods generated live and non-viable cell counts that were significantly different
from each other, although estimates were generally within 100% of the ensemble mean of all subsamples from all
methods. Overall, percent coefficient of variation (CV) among sample replicates was lowest in membrane filtration
sample replicates, and CVs for all four counting methods were usually lower than 30% (although instances of ~60%
were observed). Since all four methods were generally appropriate for monitoring discharged ballast water,
ancillary considerations (e.g., ease of analysis, sample processing rate, sample size, etc.) become critical factors for
choosing the optimal phytoplankton counting method.This study was supported by the U.S. Coast Guard Research and Development Center under contract HSCG32-07-
X-R00018. Partial research support to DMA and DMK was provided
through NSF International Contract 03/06/394, and Environmental Protection Agency Grant RD-83382801-0
Flight of the Bumblebee: the Early Excess Flux of Type Ia Supernova 2023bee revealed by , and Young Supernova Experiment Observations
We present high-cadence ultraviolet through near-infrared observations of the
Type Ia supernova (SN Ia) 2023bee in NGC~2708 ( Mpc), finding
excess flux in the first days after explosion relative to the expected
power-law rise from an expanding fireball. This deviation from typical behavior
for SNe Ia is particularly obvious in our 10-minute cadence light curve
and UV data. Compared to a few other normal SNe Ia with detected early
excess flux, the excess flux in SN 2023bee is redder in the UV and less
luminous. We present optical spectra of SN 2023bee, including two spectra
during the period where the flux excess is dominant. At this time, the spectra
are similar to those of other SNe Ia but with weaker Si II, C II and Ca II
absorption lines, perhaps because the excess flux creates a stronger continuum.
We compare the data to several theoretical models that have been proposed to
explain the early flux excess in SNe Ia. Interaction with either a nearby
companion star or close-in circumstellar material is expected to produce a
faster evolution than seen in the data. Radioactive material in the outer
layers of the ejecta, either from a double detonation explosion or simply an
explosion with a Ni clump near the surface, can not fully reproduce the
evolution either, likely due to the sensitivity of early UV observable to the
treatment of the outer part of ejecta in simulation. We conclude that no
current model can adequately explain the full set of observations. We find that
a relatively large fraction of nearby, bright SNe Ia with high-cadence
observations have some amount of excess flux within a few days of explosion.
Considering potential asymmetric emission, the physical cause of this excess
flux may be ubiquitous in normal SNe Ia.Comment: 21 pages, 12 figures. Accepted by the astrophysical journa
Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea
A seven-year oceanographic time series in NW Mediterranean surface waters was combined with pyrosequencing of ribosomal RNA (16S rRNA) and ribosomal RNA gene copies (16S rDNA) to examine the environmental controls on SAR11 ecotype dynamics and potential activity. SAR11 diversity exhibited pronounced seasonal cycles remarkably similar to total bacterial diversity. The timing of diversity maxima was similar across narrow and broad phylogenetic clades and strongly associated with deep winter mixing. Diversity minima were associated with periods of stratification that were low in nutrients and phytoplankton biomass and characterised by intense phosphate limitation (turnover time80%) by SAR11 Ia. A partial least squares (PLS) regression model was developed that could reliably predict sequence abundances of SAR11 ecotypes (Q2=0.70) from measured environmental variables, of which mixed layer depth was quantitatively the most important. Comparison of clade-level SAR11 rRNA:rDNA signals with leucine incorporation enabled us to partially validate the use of these ratios as an in-situ activity measure. However, temporal trends in the activity of SAR11 ecotypes and their relationship to environmental variables were unclear. The strong and predictable temporal patterns observed in SAR11 sequence abundance was not linked to metabolic activity of different ecotypes at the phylogenetic and temporal resolution of our study
Strong Carbon Features and a Red Early Color in the Underluminous Type Ia SN 2022xkq
We present optical, infrared, ultraviolet, and radio observations of SN
2022xkq, an underluminous fast-declining type Ia supernova (SN Ia) in NGC 1784
( Mpc), from to 180 days after explosion. The
high-cadence observations of SN 2022xkq, a photometrically transitional and
spectroscopically 91bg-like SN Ia, cover the first days and weeks following
explosion which are critical to distinguishing between explosion scenarios. The
early light curve of SN 2022xkq has a red early color and exhibits a flux
excess which is more prominent in redder bands; this is the first time such a
feature has been seen in a transitional/91bg-like SN Ia. We also present 92
optical and 19 near-infrared (NIR) spectra, beginning 0.4 days after explosion
in the optical and 2.6 days after explosion in the NIR. SN 2022xkq exhibits a
long-lived C I 1.0693 m feature which persists until 5 days post-maximum.
We also detect C II 6580 in the pre-maximum optical spectra. These
lines are evidence for unburnt carbon that is difficult to reconcile with the
double detonation of a sub-Chandrasekhar mass white dwarf. No existing
explosion model can fully explain the photometric and spectroscopic dataset of
SN 2022xkq, but the considerable breadth of the observations is ideal for
furthering our understanding of the processes which produce faint SNe Ia.Comment: 38 pages, 16 figures, accepted for publication in ApJ, the figure 15
input models and synthetic spectra are now available at
https://zenodo.org/record/837925
Flight of the bumblebee : the early excess flux of Type Ia supernova 2023bee revealed by TESS, Swift, and Young Supernova Experiment observations
We present high-cadence ultraviolet through near-infrared observations of the Type Ia supernova (SN Ia) 2023bee at D = 32 ± 3 Mpc, finding excess flux in the first days after explosion, particularly in our 10 minutes cadence TESS light curve and Swift UV data. Compared to a few other normal SNe Ia with early excess flux, the excess flux in SN 2023bee is redder in the UV and less luminous. We present optical spectra of SN 2023bee, including two spectra during the period where the flux excess is dominant. At this time, the spectra are similar to those of other SNe Ia but with weaker Si ii, C ii, and Ca ii absorption lines, perhaps because the excess flux creates a stronger continuum. We compare the data to several theoretical models on the origin of early excess flux in SNe Ia. Interaction with either the companion star or close-in circumstellar material is expected to produce a faster evolution than observed. Radioactive material in the outer layers of the ejecta, either from double detonation explosion or from a 56Ni clump near the surface, cannot fully reproduce the evolution either, likely due to the sensitivity of early UV observable to the treatment of the outer part of ejecta in simulation. We conclude that no current model can adequately explain the full set of observations. We find that a relatively large fraction of nearby, bright SNe Ia with high-cadence observations have some amount of excess flux within a few days of explosion. Considering potential asymmetric emission, the physical cause of this excess flux may be ubiquitous in normal SNe Ia