889 research outputs found
PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping
Many DNA hypermethylated and epigenetically silenced genes in adult cancers are Polycomb group (PcG) marked in embryonic stem (ES) cells. We show that a large region upstream (∼30 kb) of and extending ∼60 kb around one such gene, GATA-4, is organized—in Tera-2 undifferentiated embryonic carcinoma (EC) cells—in a topologically complex multi-loop conformation that is formed by multiple internal long-range contact regions near areas enriched for EZH2, other PcG proteins, and the signature PcG histone mark, H3K27me3. Small interfering RNA (siRNA)–mediated depletion of EZH2 in undifferentiated Tera-2 cells leads to a significant reduction in the frequency of long-range associations at the GATA-4 locus, seemingly dependent on affecting the H3K27me3 enrichments around those chromatin regions, accompanied by a modest increase in GATA-4 transcription. The chromatin loops completely dissolve, accompanied by loss of PcG proteins and H3K27me3 marks, when Tera-2 cells receive differentiation signals which induce a ∼60-fold increase in GATA-4 expression. In colon cancer cells, however, the frequency of the long-range interactions are increased in a setting where GATA-4 has no basal transcription and the loops encompass multiple, abnormally DNA hypermethylated CpG islands, and the methyl-cytosine binding protein MBD2 is localized to these CpG islands, including ones near the gene promoter. Removing DNA methylation through genetic disruption of DNA methyltransferases (DKO cells) leads to loss of MBD2 occupancy and to a decrease in the frequency of long-range contacts, such that these now more resemble those in undifferentiated Tera-2 cells. Our findings reveal unexpected similarities in higher order chromatin conformation between stem/precursor cells and adult cancers. We also provide novel insight that PcG-occupied and H3K27me3-enriched regions can form chromatin loops and physically interact in cis around a single gene in mammalian cells. The loops associate with a poised, low transcription state in EC cells and, with the addition of DNA methylation, completely repressed transcription in adult cancer cells
Three-dimensional femtosecond laser nanolithography of crystals
Nanostructuring hard optical crystals has so far been exclusively feasible at
their surface, as stress induced crack formation and propagation has rendered
high precision volume processes ineffective. We show that the inner chemical
etching reactivity of a crystal can be enhanced at the nanoscale by more than
five orders of magnitude by means of direct laser writing. The process allows
to produce cm-scale arbitrary three-dimensional nanostructures with 100 nm
feature sizes inside large crystals in absence of brittle fracture. To showcase
the unique potential of the technique, we fabricate photonic structures such as
sub-wavelength diffraction gratings and nanostructured optical waveguides
capable of sustaining sub-wavelength propagating modes inside yttrium aluminum
garnet crystals. This technique could enable the transfer of concepts from
nanophotonics to the fields of solid state lasers and crystal optics.Comment: Submitted Manuscript and Supplementary Informatio
A tagging SNP in INSIG2 is associated with obesity-related phenotypes among Samoans
<p>Abstract</p> <p>Background</p> <p>A genome wide association study found significant association of a sequence variant, rs7566605, in the insulin-induced gene 2 (<it>INSIG2</it>) with obesity. However, the association remained inconclusive in follow-up studies. We tested for association of four tagging SNPs (tagSNPs) including this variant with body mass index (BMI) and abdominal circumference (ABDCIR) in the Samoans of the Western Pacific, a population with high levels of obesity.</p> <p>Methods</p> <p>We studied 907 adult Samoan participants from a longitudinal study of adiposity and cardiovascular disease risk in two polities, American Samoa and Samoa. Four tagSNPs were identified from the Chinese HapMap database based on pairwise <it>r</it><sup><it>2 </it></sup>of ≥0.8 and minor allele frequency of ≥0.05. Genotyping was performed using the TaqMan assay. Tests of association with BMI and ABDCIR were performed under the additive model.</p> <p>Results</p> <p>We did not find association of rs7566605 with either BMI or ABDCIR in any group of the Samoans. However, the most distally located tagSNPs in Intron 3 of the gene, rs9308762, showed significant association with both BMI (p-value 0.024) and ABDCIR (p-value 0.009) in the combined sample and with BMI (p-value 0.038) in the sample from Samoa.</p> <p>Conclusion</p> <p>Although rs7566605 was not significantly associated with obesity in our study population, we can not rule out the involvement of <it>INSIG2 </it>in obesity related traits as we found significant association of another tagSNP in <it>INSIG2 </it>with both BMI and ABDCIR. This study suggests the importance of comprehensive assessment of sequence variants within a gene in association studies.</p
The P2X3 receptor antagonist filapixant in patients with refractory chronic cough: a randomized controlled trial
BACKGROUND: P2X3 receptor antagonists seem to have a promising potential for treating patients with refractory chronic cough. In this double-blind, randomized, placebo-controlled study, we investigated the efficacy, safety, and tolerability of the novel selective P2X3 receptor antagonist filapixant (BAY1902607) in patients with refractory chronic cough. METHODS: Following a crossover design, 23 patients with refractory chronic cough (age: 60.4 ± 9.1 years) received ascending doses of filapixant in one period (20, 80, 150, and 250 mg, twice daily, 4-days-on/3-days-off) and placebo in the other. The primary efficacy endpoint was the 24-h cough frequency on Day 4 of each dosing step. Further, subjective cough severity and health-related quality of life were assessed. RESULTS: Filapixant at doses ≥ 80 mg significantly reduced cough frequency and severity and improved cough health-related quality of life. Reductions in 24-h cough frequency over placebo ranged from 17% (80 mg dose) to 37% (250 mg dose), reductions over baseline from 23% (80 mg) to 41% (250 mg) (placebo: 6%). Reductions in cough severity ratings on a 100-mm visual analog scale ranged from 8 mm (80 mg) to 21 mm (250 mg). No serious or severe adverse events or adverse events leading to discontinuation of treatment were reported. Taste-related adverse events occurred in 4%, 13%, 43%, and 57% of patients treated with filapixant 20, 80, 150, and 250 mg, respectively, and in 12% treated with placebo. CONCLUSIONS: Filapixant proved to be efficacious, safe, and-apart from the occurrence of taste disturbances, especially at higher dosages-well tolerated during the short therapeutic intervention. Clinical trial registration EudraCT, eudract.ema.europa.eu, 2018-000129-29; ClinicalTrials.gov, NCT03535168
The relationship between the perception of distributed leadership in secondary schools and teachers' and teacher leaders' job satisfaction and organizational commitment
This study investigates the relation between distributed leadership, the cohesion of the leadership team, participative decision-making, context variables, and the organizational commitment and job satisfaction of teachers and teacher leaders. A questionnaire was administered to teachers and teacher leaders (n=1770) from 46 large secondary schools. Multiple regression analyses and path analyses revealed that the study variables explained significant variance in organizational commitment. The degree of explained variance for job satisfaction was considerably lower compared to organizational commitment. Most striking was that the cohesion of the leadership team and the amount of leadership support was strongly related to organizational commitment, and indirectly to job satisfaction. Decentralization of leadership functions was weakly related to organizational commitment and job satisfaction
The Complexity of Computing Minimal Unidirectional Covering Sets
Given a binary dominance relation on a set of alternatives, a common thread
in the social sciences is to identify subsets of alternatives that satisfy
certain notions of stability. Examples can be found in areas as diverse as
voting theory, game theory, and argumentation theory. Brandt and Fischer [BF08]
proved that it is NP-hard to decide whether an alternative is contained in some
inclusion-minimal upward or downward covering set. For both problems, we raise
this lower bound to the Theta_{2}^{p} level of the polynomial hierarchy and
provide a Sigma_{2}^{p} upper bound. Relatedly, we show that a variety of other
natural problems regarding minimal or minimum-size covering sets are hard or
complete for either of NP, coNP, and Theta_{2}^{p}. An important consequence of
our results is that neither minimal upward nor minimal downward covering sets
(even when guaranteed to exist) can be computed in polynomial time unless P=NP.
This sharply contrasts with Brandt and Fischer's result that minimal
bidirectional covering sets (i.e., sets that are both minimal upward and
minimal downward covering sets) are polynomial-time computable.Comment: 27 pages, 7 figure
Statistical mechanics of voting
Decision procedures aggregating the preferences of multiple agents can
produce cycles and hence outcomes which have been described heuristically as
`chaotic'. We make this description precise by constructing an explicit
dynamical system from the agents' preferences and a voting rule. The dynamics
form a one dimensional statistical mechanics model; this suggests the use of
the topological entropy to quantify the complexity of the system. We formulate
natural political/social questions about the expected complexity of a voting
rule and degree of cohesion/diversity among agents in terms of random matrix
models---ensembles of statistical mechanics models---and compute quantitative
answers in some representative cases.Comment: 9 pages, plain TeX, 2 PostScript figures included with epsf.tex
(ignore the under/overfull \vbox error messages
Wnt signalling in adenomas of familial adenomatous polyposis patients
BACKGROUND: Epigenetic silencing of Wnt antagonists and expression changes in genes associated with Wnt response pathways occur
in early sporadic colorectal tumourigenesis, indicating that tumour cells are more sensitive to Wnt growth factors and respond
differently. In this study, we have investigated whether similar changes occur in key markers of the Wnt response pathways in the
genetic form of the disease, familial adenomatous polyposis (FAP).
METHODS: We investigated epigenetic and expression changes using pyrosequencing and real-time RT-PCR in samples from seven
patients without neoplasia, and matched normal and tumour tissues from 22 sporadic adenoma and 14 FAP patients.
RESULTS: We found that 17 out of 24 (71%) FAP adenomas were hypermethylated at sFRP1, compared with 20 out of 22 (91%) of
sporadic cases. This was reflected at the level of sFRP1 transcription, where 73% of FAP and 100% of sporadic cases were downregulated.
Increased expression levels of c-myc and FZD3 were less common in FAP (35 and 46% respectively) than sporadic tumours
(78 and 67% respectively).
CONCLUSION: Overall, the changes in expression and methylation were comparable, although the degree of change was generally
lower in the FAP adenomas. Molecular heterogeneity between multiple adenomas from individual FAP patients may reflect different
developmental fates for these premalignant tumours
Outer-Sphere Contributions to the Electronic Structure of Type Zero Copper Proteins
Bioinorganic canon states that active-site
thiolate coordination promotes rapid electron transfer (ET)
to and from type 1 copper proteins. In recent work, we have
found that copper ET sites in proteins also can be constructed
without thiolate ligation (called “type zero” sites). Here we
report multifrequency electron paramagnetic resonance
(EPR), magnetic circular dichroism (MCD), and nuclear
magnetic resonance (NMR) spectroscopic data together with
density functional theory (DFT) and spectroscopy-oriented
configuration interaction (SORCI) calculations for type zero Pseudomonas aeruginosa azurin variants. Wild-type (type 1) and type
zero copper centers experience virtually identical ligand fields. Moreover, O-donor covalency is enhanced in type zero centers
relative that in the C112D (type 2) protein. At the same time, N-donor covalency is reduced in a similar fashion to type 1
centers. QM/MM and SORCI calculations show that the electronic structures of type zero and type 2 are intimately linked to the
orientation and coordination mode of the carboxylate ligand, which in turn is influenced by outer-sphere hydrogen bonding
Increasing diterpene yield with a modular metabolic engineering system in E. coli: comparison of MEV and MEP isoprenoid precursor pathway engineering
Engineering biosynthetic pathways in heterologous microbial host organisms offers an elegant approach to pathway elucidation via the incorporation of putative biosynthetic enzymes and characterization of resulting novel metabolites. Our previous work in Escherichia coli demonstrated the feasibility of a facile modular approach to engineering the production of labdane-related diterpene (20 carbon) natural products. However, yield was limited (<0.1 mg/L), presumably due to reliance on endogenous production of the isoprenoid precursors dimethylallyl diphosphate and isopentenyl diphosphate. Here, we report incorporation of either a heterologous mevalonate pathway (MEV) or enhancement of the endogenous methyl erythritol phosphate pathway (MEP) with our modular metabolic engineering system. With MEP pathway enhancement, it was found that pyruvate supplementation of rich media and simultaneous overexpression of three genes (idi, dxs, and dxr) resulted in the greatest increase in diterpene yield, indicating distributed metabolic control within this pathway. Incorporation of a heterologous MEV pathway in bioreactor grown cultures resulted in significantly higher yields than MEP pathway enhancement. We have established suitable growth conditions for diterpene production levels ranging from 10 to >100 mg/L of E. coli culture. These amounts are sufficient for nuclear magnetic resonance analyses, enabling characterization of enzymatic products and hence, pathway elucidation. Furthermore, these results represent an up to >1,000-fold improvement in diterpene production from our facile, modular platform, with MEP pathway enhancement offering a cost effective alternative with reasonable yield. Finally, we reiterate here that this modular approach is expandable and should be easily adaptable to the production of any terpenoid natural product
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