4,934 research outputs found
Oligomerization of the E. coli Core RNA Polymerase: Formation of (α2ββ'ω)2–DNA Complexes and Regulation of the Oligomerization by Auxiliary Subunits
In this work, using multiple, dissimilar physico-chemical techniques, we demonstrate that the Escherichia coli RNA polymerase core enzyme obtained through a classic purification procedure forms stable (α2ββ'ω)2 complexes in the presence or absence of short DNA probes. Multiple control experiments indicate that this self-association is unlikely to be mediated by RNA polymerase-associated non-protein molecules. We show that the formation of (α2ββ'ω)2 complexes is subject to regulation by known RNA polymerase interactors, such as the auxiliary SWI/SNF subunit of RNA polymerase RapA, as well as NusA and σ70. We also demonstrate that the separation of the core RNA polymerase and RNA polymerase holoenzyme species during Mono Q chromatography is likely due to oligomerization of the core enzyme. We have analyzed the oligomeric state of the polymerase in the presence or absence of DNA, an aspect that was missing from previous studies. Importantly, our work demonstrates that RNA polymerase oligomerization is compatible with DNA binding. Through in vitro transcription and in vivo experiments (utilizing a RapAR599/Q602 mutant lacking transcription-stimulatory function), we demonstrate that the formation of tandem (α2ββ'ω)2–DNA complexes is likely functionally significant and beneficial for the transcriptional activity of the polymerase. Taken together, our findings suggest a novel structural aspect of the E. coli elongation complex. We hypothesize that transcription by tandem RNA polymerase complexes initiated at hypothetical bidirectional “origins of transcription” may explain recurring switches of the direction of transcription in bacterial genomes
Ray and wave chaos in asymmetric resonant optical cavities
Optical resonators are essential components of lasers and other
wavelength-sensitive optical devices. A resonator is characterized by a set of
modes, each with a resonant frequency omega and resonance width Delta
omega=1/tau, where tau is the lifetime of a photon in the mode. In a
cylindrical or spherical dielectric resonator, extremely long-lived resonances
are due to `whispering gallery' modes in which light circulates around the
perimeter trapped by total internal reflection. These resonators emit light
isotropically. Recently, a new category of asymmetric resonant cavities (ARCs)
has been proposed in which substantial shape deformation leads to partially
chaotic ray dynamics. This has been predicted to give rise to a universal,
frequency-independent broadening of the whispering-gallery resonances, and
highly anisotropic emission. Here we present solutions of the wave equation for
ARCs which confirm many aspects of the earlier ray-optics model, but also
reveal interesting frequency-dependent effects characteristic of quantum chaos.
For small deformations the lifetime is controlled by evanescent leakage, the
optical analogue of quantum tunneling. We find that the lifetime is much
shortened by a process known as `chaos-assisted tunneling'. In contrast, for
large deformations (~10%) some resonances are found to have longer lifetimes
than predicted by the ray chaos model due to `dynamical localization'.Comment: 4 pages RevTeX with 7 Postscript figure
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Parameter Reduction in Log-normal Chain-ladder Models
Multiplicative chain-ladder (CL) models are characterized by CL factors that explain the development of claims from one period to the next. In classical CL models every development period has its own CL factor. In the present paper we give a method describing how some of these CL factors can be modeled by a joint functional dependence. This joint functional form reduces the number of model parameters needed
Thermally induced rotation of 3d orbital stripes in Pr(Sr0.1Ca0.9)(2)Mn2O7
We have investigated orbital ordering in the bilayer manganite, Pr(Sr0.1Ca0.9)2Mn2O7, using synchrotron x-ray diffraction techniques, in particular resonant soft x-ray diffraction. Diffraction signals are observed at (0,12,0) above 300 K and (12,0,0) below 300 K, corresponding to orbital stripes along the a and b axes, respectively. The previously observed transition at 300 K is evidence of a rotation of the orientation of the 3d orbital stripes. Large resonances of the orbital signals are observed at the Mn L edges, with a complex dependence on incident photon energy indicative of a weakly Jahn-Teller distorted system. A structural transition observed at 92 K is found not to involve a further change in the orbital order
Disease-Associated Mutations in CEP120 Destabilize the Protein and Impair Ciliogenesis.
Ciliopathies are a group of genetic disorders caused by a failure to form functional cilia. Due to a lack of structural information, it is currently poorly understood how ciliopathic mutations affect protein functionality to give rise to the underlying disease. Using X-ray crystallography, we show that the ciliopathy-associated centriolar protein CEP120 contains three C2 domains. The point mutations V194A and A199P, which cause Joubert syndrome (JS) and Jeune asphyxiating thoracic dystrophy (JATD), respectively, both reduce the thermostability of the second C2 domain by targeting residues that point toward its hydrophobic core. Genome-engineered cells homozygous for these mutations have largely normal centriole numbers but show reduced CEP120 levels, compromised recruitment of distal centriole markers, and deficient cilia formation. Our results provide insight into the disease mechanism of two ciliopathic mutations in CEP120, identify putative binding partners of CEP120 C2B, and suggest a complex genotype-phenotype relation of the CEP120 ciliopathy alleles
Evaluating predictive pharmacogenetic signatures of adverse events in colorectal cancer patients treated with fluoropyrimidines
The potential clinical utility of genetic markers associated with response to fluoropyrimidine treatment in colorectal cancer patients remains controversial despite extensive study. Our aim was to test the clinical validity of both novel and previously identified markers of adverse events in a broad clinical setting. We have conducted an observational pharmacogenetic study of early adverse events in a cohort study of 254 colorectal cancer patients treated with 5-fluorouracil or capecitabine. Sixteen variants of nine key folate (pharmacodynamic) and drug metabolising (pharmacokinetic) enzymes have been analysed as individual markers and/or signatures of markers. We found a significant association between TYMP S471L (rs11479) and early dose modifications and/or severe adverse events (adjusted OR = 2.02 [1.03; 4.00], p = 0.042, adjusted OR = 2.70 [1.23; 5.92], p = 0.01 respectively). There was also a significant association between these phenotypes and a signature of DPYD mutations (Adjusted OR = 3.96 [1.17; 13.33], p = 0.03, adjusted OR = 6.76 [1.99; 22.96], p = 0.002 respectively). We did not identify any significant associations between the individual candidate pharmacodynamic markers and toxicity. If a predictive test for early adverse events analysed the TYMP and DPYD variants as a signature, the sensitivity would be 45.5 %, with a positive predictive value of just 33.9 % and thus poor clinical validity. Most studies to date have been under-powered to consider multiple pharmacokinetic and pharmacodynamic variants simultaneously but this and similar individualised data sets could be pooled in meta-analyses to resolve uncertainties about the potential clinical utility of these markers
Dynamics on expanding spaces: modeling the emergence of novelties
Novelties are part of our daily lives. We constantly adopt new technologies,
conceive new ideas, meet new people, experiment with new situations.
Occasionally, we as individuals, in a complicated cognitive and sometimes
fortuitous process, come up with something that is not only new to us, but to
our entire society so that what is a personal novelty can turn into an
innovation at a global level. Innovations occur throughout social, biological
and technological systems and, though we perceive them as a very natural
ingredient of our human experience, little is known about the processes
determining their emergence. Still the statistical occurrence of innovations
shows striking regularities that represent a starting point to get a deeper
insight in the whole phenomenology. This paper represents a small step in that
direction, focusing on reviewing the scientific attempts to effectively model
the emergence of the new and its regularities, with an emphasis on more recent
contributions: from the plain Simon's model tracing back to the 1950s, to the
newest model of Polya's urn with triggering of one novelty by another. What
seems to be key in the successful modelling schemes proposed so far is the idea
of looking at evolution as a path in a complex space, physical, conceptual,
biological, technological, whose structure and topology get continuously
reshaped and expanded by the occurrence of the new. Mathematically it is very
interesting to look at the consequences of the interplay between the "actual"
and the "possible" and this is the aim of this short review.Comment: 25 pages, 10 figure
De novo mutations in EIF2B1 affecting eIF2 signaling cause neonatal/early onset diabetes and transient hepatic dysfunction
This is the author accepted manuscript. The final version is available from the American Diabetes Association via the DOI in this recordData and resource availability. EIF2B1 mutation details have been deposited in the Decipher
database (https://decipher.sanger.ac.uk/). All other data sets generated and/or analysed for this study
are available from the corresponding author upon reasonable request.Permanent neonatal diabetes is caused by reduced β-cell number or impaired β-cell function.
Understanding the genetic basis of this disorder highlights fundamental β-cell mechanisms.
We performed trio genome sequencing for 44 permanent neonatal diabetes patients and their
unaffected parents to identify causative de novo variants. Replication studies were performed in 188
patients diagnosed with diabetes before 2 years of age without a genetic diagnosis.
EIF2B1 (encoding the eIF2B complex α subunit) was the only gene with novel de novo variants (all
missense) in at least three patients. Replication studies identified 2 further patients with de novo
EIF2B1 variants. In addition to diabetes, 4/5 patients had hepatitis-like episodes in childhood. The
EIF2B1 de novo mutations were found to map to the same protein surface. We propose that these
variants render the eIF2B complex insensitive to eIF2 phosphorylation which occurs under stress
conditions and triggers expression of stress-response genes. Failure of eIF2B to sense eIF2
phosphorylation likely leads to unregulated unfolded protein response and cell death.
Our results establish de novo EIF2B1 mutations as a novel cause of permanent diabetes and liver
dysfunction. These findings confirm the importance of cell stress regulation for β-cells and highlight
EIF2B1’s fundamental role within this pathway.European Foundation for the Study of DiabetesDiabetes UKDiabetes Research and Wellness FoundationWellcome TrustNational Institute for Health Research (NIHR)Royal Societ
Factors which modulate platelet reactivity as measured by five assay platforms in 3,429 individuals
Binocular summation and other forms of non-dominant eye contribution in individuals with strabismic amblyopia during habitual viewing
YesAdults with amblyopia ('lazy eye'), long-standing strabismus (ocular misalignment) or both typically do not experience visual symptoms because the signal from weaker eye is given less weight than the signal from its fellow. Here we examine the contribution of the weaker eye of individuals with strabismus and amblyopia with both eyes open and with the deviating eye in its anomalous motor position. The task consisted of a blue-on-yellow detection task along a horizontal line across the central 50 degrees of the visual field. We compare the results obtained in ten individuals with strabismic amblyopia with ten visual normals. At each field location in each participant, we examined how the sensitivity exhibited under binocular conditions compared with sensitivity from four predictions, (i) a model of binocular summation, (ii) the average of the monocular sensitivities, (iii) dominant-eye sensitivity or (iv) non-dominant-eye sensitivity. The proportion of field locations for which the binocular summation model provided the best description of binocular sensitivity was similar in normals (50.6%) and amblyopes (48.2%). Average monocular sensitivity matched binocular sensitivity in 14.1% of amblyopes' field locations compared to 8.8% of normals'. Dominant-eye sensitivity explained sensitivity at 27.1% of field locations in amblyopes but 21.2% in normals. Non-dominant-eye sensitivity explained sensitivity at 10.6% of field locations in amblyopes but 19.4% in normals. Binocular summation provided the best description of the sensitivity profile in 6/10 amblyopes compared to 7/10 of normals. In three amblyopes, dominant-eye sensitivity most closely reflected binocular sensitivity (compared to two normals) and in the remaining amblyope, binocular sensitivity approximated to an average of the monocular sensitivities. Our results suggest a strong positive contribution in habitual viewing from the non-dominant eye in strabismic amblyopes. This is consistent with evidence from other sources that binocular mechanisms are frequently intact in strabismic and amblyopic individuals
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