Necroptosis is a recently described Caspase 8-independent method of cell death that denotes organized cellular necrosis. The roles of RIP1 and RIP3 in mediating hepatocyte death from acute liver ...injury are incompletely defined. Effects of necroptosis blockade were studied by separately targeting RIP1 and RIP3 in diverse murine models of acute liver injury. Blockade of necroptosis had disparate effects on disease outcome depending on the precise etiology of liver injury and component of the necrosome targeted. In ConA-induced autoimmune hepatitis, RIP3 deletion was protective, whereas RIP1 inhibition exacerbated disease, accelerated animal death, and was associated with increased hepatocyte apoptosis. Conversely, in acetaminophen-mediated liver injury, blockade of either RIP1 or RIP3 was protective and was associated with lower NLRP3 inflammasome activation. Our work highlights the fact that diverse modes of acute liver injury have differing requirements for RIP1 and RIP3; moreover, within a single injury model, RIP1 and RIP3 blockade can have diametrically opposite effects on tissue damage, suggesting that interference with distinct components of the necrosome must be considered separately.
The programmes that direct an organism's development and maintenance are encoded in its genome. Decoding of this information begins with regulated transcription of genomic DNA into RNA. Although ...transcription and its control can be tracked indirectly by measuring stable RNAs, it is only by directly measuring nascent RNAs that the immediate regulatory changes in response to developmental, environmental, disease and metabolic signals are revealed. Multiple complementary methods have been developed to quantitatively track nascent transcription genome-wide at nucleotide resolution, all of which have contributed novel insights into the mechanisms of gene regulation and transcription-coupled RNA processing. Here we critically evaluate the array of strategies used for investigating nascent transcription and discuss the recent conceptual advances they have provided.
Eukaryotic RNA polymerase II (Pol II) has been found at both promoters and distal enhancers, suggesting additional functions beyond mRNA production. To understand this role, we sequenced nascent RNAs ...at single-molecule resolution to unravel the interplay between Pol II initiation, capping and pausing genome-wide. Our analyses identify two pause classes that are associated with different RNA capping profiles. More proximal pausing is associated with less complete capping, less elongation and a more enhancer-like complement of transcription factors than later pausing. Unexpectedly, transcription start sites (TSSs) are predominantly found in constellations composed of multiple divergent pairs. TSS clusters are intimately associated with precise arrays of nucleosomes and correspond with boundaries of transcription factor binding and chromatin modification at promoters and enhancers. TSS architecture is largely unchanged during the dramatic transcriptional changes induced by heat shock. Together, our results suggest that promoter- and enhancer-associated Pol II is a regulatory nexus for integrating information across TSS ensembles.
Mutation of highly conserved residues in transcription factors may affect protein-protein or protein-DNA interactions, leading to gene network dysregulation and human disease. Human mutations in ...GATA4, a cardiogenic transcription factor, cause cardiac septal defects and cardiomyopathy. Here, iPS-derived cardiomyocytes from subjects with a heterozygous GATA4-G296S missense mutation showed impaired contractility, calcium handling, and metabolic activity. In human cardiomyocytes, GATA4 broadly co-occupied cardiac enhancers with TBX5, another transcription factor that causes septal defects when mutated. The GATA4-G296S mutation disrupted TBX5 recruitment, particularly to cardiac super-enhancers, concomitant with dysregulation of genes related to the phenotypic abnormalities, including cardiac septation. Conversely, the GATA4-G296S mutation led to failure of GATA4 and TBX5-mediated repression at non-cardiac genes and enhanced open chromatin states at endothelial/endocardial promoters. These results reveal how disease-causing missense mutations can disrupt transcriptional cooperativity, leading to aberrant chromatin states and cellular dysfunction, including those related to morphogenetic defects.
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•Systems-level approach reveals GATA4 roles in human cardiac development and function•Heterozygous GATA4 missense mutation impairs cardiac gene program•GATA4 G296S mutation disrupts TBX5 genome occupancy at cardiac super-enhancers•PI3K signaling is a key “hub” in the GATA4 gene regulatory network
A human missense mutation that causes congenital heart defects disrupts the cooperation between transcription factors at cardiac super-enhancers and gives rise to aberrant gene expression.
Mincle Signaling Exacerbates Autoimmune Hepatitis Greco, Stephanie, MD; Torres-Hernandez, Alejandro, MD; Rokosh, S. Rae ...
Journal of the American College of Surgeons,
October 2015, Volume:
221, Issue:
4
Journal Article
Abstract
We present a public, open-source relational data base (we name kaepora) containing a sample of 4975 spectra of 777 Type Ia supernovae (SNe Ia). Since we draw from many sources, we ...significantly improve the spectra by inspecting these data for quality, removing galactic emission lines and cosmic rays, generating variance spectra, and correcting for the reddening caused by both MW and host-galaxy dust. With our data base, we organize this homogenized data set by 56 unique categories of SN-specific and spectrum-specific metadata. With kaepora, we produce composite spectra of subpopulations of SNe Ia and examine how spectral features correlate with various SN properties. These composite spectra reproduce known correlations with phase, light-curve shape, and host-galaxy morphology. With our large data set, we are also able to generate fine-grained composite spectra simultaneously over both phase and light-curve shape. The colour evolution of our composite spectra is consistent with other SN Ia template spectra, and the spectral properties of our composite spectra are in rough agreement with these template spectra with some subtle differences. We investigate the spectral differences of SNe Ia that occur in galaxies with varying morphologies. Controlling for light-curve shape, which is highly correlated with host-galaxy morphology, we find that SNe Ia residing in late-type and early-type galaxies have similar spectral properties at multiple epochs. However for SNe Ia in these different environments, their spectra appear to have Ca ii near-infrared triplet features that have slightly different strengths. Although this is apparent in the composite spectra and there is some difference in the populations as seen by individual spectra, this difference is not large enough to indicate differences in the underlying populations. All individual spectra and metadata are available in our open-source data base kaepora
along with the tools developed for this investigation to facilitate future investigations of SN Ia properties.
Molecular factors that define stem cell identity have recently emerged as oncogenic drivers. For instance, brachyury, a key developmental transcriptional factor, is also implicated in carcinogenesis, ...most notably of chordoma, through mechanisms that remain elusive. Here, we show that brachyury is a crucial regulator of stemness in chordoma and in more common aggressive cancers. Furthermore, this effect of brachyury is mediated by control of synthesis and stability of Yes-associated protein (YAP), a key regulator of tissue growth and homeostasis, providing an unexpected mechanism of control of YAP expression. We further demonstrate that the brachyury-YAP regulatory pathway is associated with tumor aggressiveness. These results elucidate a mechanism of controlling both tumor stemness and aggressiveness through regulatory coupling of two developmental factors.
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•Chordomas harbor a putative cancer stem cell population that is driven by brachyury•Brachyury-YAP regulatory axis: identification of a direct transcriptional regulator of YAP•Brachyury can enhance YAP activity through a post-transcriptional mechanism in carcinomas•Brachyury-YAP activity is tied to tumor aggressiveness in several types of cancers
Malignant neoplasms exhibit uninhibited and dysregulated growth coupled with acquisition of stem-like properties that are integral to the development and progression of disease. Shah et al. demonstrate a critical role of brachyury in regulating stemness and growth by activating YAP through direct transcriptional and post-transcriptional mechanisms in various cancers.
The ability to control translation of endogenous or exogenous RNAs in eukaryotic cells would facilitate a variety of biotechnological applications. Current strategies are limited by low fold changes ...in transgene output and the size of trigger RNAs (trRNAs). Here we introduce eukaryotic toehold switches (eToeholds) as modular riboregulators. eToeholds contain internal ribosome entry site sequences and form inhibitory loops in the absence of a specific trRNA. When the trRNA is present, eToeholds anneal to it, disrupting the inhibitory loops and allowing translation. Through optimization of RNA annealing, we achieved up to 16-fold induction of transgene expression in mammalian cells. We demonstrate that eToeholds can discriminate among viral infection status, presence or absence of gene expression and cell types based on the presence of exogenous or endogenous RNA transcripts.
Oxidative stress and muscle damage occur during exhaustive bouts of exercise, and many runners report pain and soreness as major influences on changes or breaks in training regimens, creating a ...barrier to training persistence. Methylsulfonylmethane (MSM) is a sulfur-based nutritional supplement that is purported to have pain and inflammation-reducing effects. To investigate the effects of MSM in attenuating damage associated with physical exertion, this randomized, double-blind, placebo-controlled study evaluated the effects of MSM supplementation on exercise-induced pain, oxidative stress and muscle damage.
Twenty-two healthy females (
= 17) and males (
= 5) (age 33.7 ± 6.9 yrs.) were recruited from the 2014 Portland Half-Marathon registrant pool. Participants were randomized to take either MSM (OptiMSM®) (
= 11), or a placebo (
= 11) at 3 g/day for 21 days prior to the race and for two days after (23 total). Participants provided blood samples for measurement of markers of oxidative stress, and completed VAS surveys for pain approximately one month prior to the race (T
), and at 15 min (T
), 90 min (T
), 1 Day (T
), and 2 days (T
) after race finish. The primary outcome measure 8-hydroxy-2-deoxyguanine (8-OHdG) measured oxidative stress. Secondary outcomes included malondialdehyde (MDA) for oxidative stress, creatine kinase (CK) and lactate dehydrogenase (LDH) as measures of muscle damage, and muscle (MP) and joint pain (JP) recorded using a 100 mm Visual Analogue Scale (VAS). Data were analyzed using repeated and multivariate ANOVAs, and simple contrasts compared post-race time points to baseline, presented as mean (SD) or mean change (95% CI) where appropriate.
Running a half-marathon induced significant increases in all outcome measures (
< 0.001). From baseline, 8-OHdG increased significantly at T
by 1.53 ng/mL (0.86-2.20 ng/mL CI,
< 0.001) and T
by 1.19 ng/mL (0.37-2.01 ng/mL CI,
< 0.01), and fell below baseline levels at T
by -0.46 ng/mL (-1.18-0.26 CI,
> 0.05) and T
by -0.57 ng/mL (-1.27-0.13 CI,
> 0.05). MDA increased significantly at T
by 7.3 μM (3.9-10.7 CI,
< 0.001). Muscle damage markers CK and LDH saw significant increases from baseline at all time-points (
< 0.01). Muscle and joint pain increased significantly from baseline at T
, T
, and T
(
< 0.01) and returned to baseline levels at T
. Time-by-treatment results did not reach statistical significance for any outcome measure, however, the MSM group saw clinically significant (Δ > 10 mm) reductions in both muscle and joint pain.
Participation in a half-marathon was associated with increased markers of oxidative stress, muscle damage, and pain. MSM supplementation was not associated with a decrease from pre-training levels of oxidative stress or muscle damage associated with an acute bout of exercise. MSM supplementation attenuated post-exercise muscle and joint pain at clinically, but not statistically significant levels.
Test of charge conjugation invariance Nefkens, B M K; Prakhov, S; Gårdestig, A ...
Physical review letters,
02/2005, Volume:
94, Issue:
4
Journal Article
Peer reviewed
We report on the first determination of upper limits on the branching ratio (BR) of eta decay to pi0pi0gamma and to pi0pi0pi0gamma. Both decay modes are strictly forbidden by charge conjugation (C) ...invariance. Using the Crystal Ball multiphoton detector, we obtained BR(eta-->pi0pi0gamma)<5 x 10(-4) at the 90% confidence level, in support of C invariance of isoscalar electromagnetic interactions of the light quarks. We have also measured BR(eta-->pi0pi0pi0gamma)<6 x 10(-5) at the 90% confidence level, in support of C invariance of isovector electromagnetic interactions.
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