Transcription termination at intrinsic terminators: the role of the RNA hairpin.

Intrinsic termination of transcription in Escherichia coli involves the formation of an RNA hairpin in the nascent RNA. This hairpin plays a central role in the release of the transcript and polymerase at intrinsic termination sites on the DNA template. We have created variants of the lambda tR2 terminator hairpin and examined the relationship between the structure and stability of this hairpin and the template positions and efficiencies of termination. The results were used to test the simple nucleic acid destabilization model of Yager and von Hippel and showed that this model must be modified to provide a distinct role for the rU-rich sequence in the nascent RNA, since a perfect palindromic sequence that is sufficiently long to form an RNA hairpin that could destabilize the entire putative 12-bp RNA-DNA hybrid does not trigger termination at the expected positions. Rather, our results show that both a stable terminator hairpin and the run of 6-8 rU residues that immediately follows are required for effective intrinsic termination and that termination occurs at specific and invariant template positions relative to these two components. Possible structural or kinetic modifications of the simple model are proposed in the light of these findings and of recent results implicating "inchworming" and possible conformational heterogeneity of transcription complexes in intrinsic termination. Thus, these findings argue that the structure and dimensions of the hairpin are important determinants of the termination-elongation decision and suggest that a complete mechanism is likely to involve specific interactions of the polymerase, the RNA terminator hairpin, and, perhaps, the dT-rich template sequence that codes for the run of rU residues at the 3' end of the nascent transcript.

Intrinsic changes in developing retinal neurons result in regenerative failure of their axons.

The failure of mature mammalian central nervous system axons to regenerate after transection is usually attributed to influences of the extraneuronal milieu. Using explant cocultures of retina and midbrain tectum from hamsters, we have found evidence that these influences account for failure of regrowth of only a small minority of retinal axons. For most of the axons, there is a programmed loss of ability to elongate in the central nervous system. We show that there is a precipitous decline in the ability of retinal axons to reinnervate tectal targets when the retina is derived from pups on or after postnatal day 2, even when the target is embryonic. By contrast, embryonic retinal axons can regrow into tectum of any age, overcoming growth-inhibiting influences of glial factors.

Immunolocalization of the mercurial-insensitive water channel and glycerol intrinsic protein in epithelial cell plasma membranes.

Two water channel homologs were cloned recently from rat kidney, mercurial-insensitive water channel (MIWC) and glycerol intrinsic protein (GLIP). Polyclonal antibodies were raised against synthetic C-terminal peptides and purified by affinity chromatography. MIWC and GLIP antibodies recognized proteins in rat kidney with an apparent molecular mass of 30 and 27 kDa, respectively, and did not cross-react. By immunofluorescence, MIWC and GLIP were expressed together on the basolateral plasma membrane of collecting duct principal cells in kidney. By immunohistochemistry, MIWC and GLIP were expressed on tracheal epithelial cells with greater expression of GLIP on the basal plasma membrane and MIWC on the lateral membrane; only MIWC was expressed in bronchial epithelia. In eye, GLIP was expressed in conjunctival epithelium, whereas MIWC was found in iris, ciliary body, and neural cell layers in retina. MIWC and GLIP colocalized on the basolateral membrane of villus epithelial cells in colon and brain ependymal cells. Expression of MIWC and GLIP was not detected in small intestine, liver, spleen, endothelia, and cells that express water channels CHIP28 or WCH-CD. These studies suggest water/solute transporting roles for MIWC and GLIP in the urinary concentrating mechanism, cerebrospinal fluid absorption, ocular fluid balance, fecal dehydration, and airway humidification. The unexpected membrane colocalization of MIWC and GLIP in several tissues suggests an interaction at the molecular and/or functional levels.

Intrinsic transcript cleavage activity of RNA polymerase.

The GreA and GreB transcript cleavage factors of Escherichia coli suppress elongation arrest and may have a proofreading role in transcription. With the use of E. coli greA-greB- mutant, RNA polymerase is demonstrated to possess substantial intrinsic transcript cleavage activity. Mildly alkaline pH mimics the effect of the Gre proteins by inducing transcript cleavage in ternary complexes and antagonizing elongation arrest through a cleavage-and-restart reaction. Thus, transcript cleavage constitutes the second enzymological activity of RNA polymerase along with polymerization/pyrophosphorolysis of RNA, whereas the Gre proteins merely enhance this intrinsic property.

The First Child In A Chinese Family Who Could Read Prior To Entry Into Elementary School: A Qualitative Intrinsic Case Study

ABSTRACT This study is an account of the literacy-related human environment a Chinese girl experienced as the first person in the history of her family who was able to read prior to entry into elementary school. Temporally speaking, the study spanned more than a decade from the initial, tentative research question to the formal, primary research question. Spatially speaking, it crossed three cultures: the Chinese, Korean, and American cultures. The study was inspired by the Zero Project in China, known as the "Project of Quality Education and Implementation for Children Aged Zero (fetus) to Six." The significance of the content issue in a child's literacy curriculum was explored in an interdisciplinary way. Case study served as a holistic research approach and provided the researcher with free temporal and spatial distance to pursue the indefinably multi-dimensional intricacies of a child's early literacy acquisition among generations in the family. Interpretation of the case was based on the relevant concepts within the scope of the researcher's knowledge of Chinese culture. Major findings revealed that the child's literacy acquisition was inseparably related to her parents' background as well as their awareness of and attitudes towards literacy, and that the foundation of all this was the harmony of the family. Through the lens of generational attitudes towards literacy and especially the lens of the researcher's multicultural life experiences, this study contributes to the field of curriculum studies in general and early literacy curriculum in particular by stimulating people to reconsider what to read to children, besides how to read to them. It calls attention once again to the classic curriculum question, "What knowledge is of most worth?" as well as what is the most essential spiritual food human beings need besides physical needs. This study suggests that Chinese philosophy should be included in a child's early literacy curriculum in China and calls for dialogues on the content issue of curriculum to gain a deeper understanding of human nature so that humans might co-live peacefully with all beings in the universe.

Theory of ferromagnetism in planar heterostructures of (Mn,III)-V semiconductors

A density-functional theory of ferromagnetism in heterostructures of compound semiconductors doped with magnetic impurities is presented. The variable functions in the density-functional theory are the charge and spin densities of the itinerant carriers and the charge and localized spins of the impurities. The theory is applied to study the Curie temperature of planar heterostructures of III-V semiconductors doped with manganese atoms. The mean-field, virtual-crystal and effective-mass approximations are adopted to calculate the electronic structure, including the spin-orbit interaction, and the magnetic susceptibilities, leading to the Curie temperature. By means of these results, we attempt to understand the observed dependence of the Curie temperature of planar δ-doped ferromagnetic structures on variation of their properties. We predict a large increase of the Curie temperature by additional confinement of the holes in a δ-doped layer of Mn by a quantum well.

Ferromagnetism mediated by few electrons in a semimagnetic quantum dot

A (II,Mn)VI diluted magnetic semiconductor quantum dot with an integer number of electrons controlled with a gate voltage is considered. We show that a single electron is able to induce a collective spontaneous magnetization of the Mn spins, overcoming the short range antiferromagnetic interactions, at a temperature order of 1 K, 2 orders of magnitude above the ordering temperature in bulk. The magnetic behavior of the dot depends dramatically on the parity of the number of electrons in the dot.

Coherently photoinduced ferromagnetism in diluted magnetic semiconductors

Ferromagnetism is predicted in undoped diluted magnetic semiconductors illuminated by intense sub-band-gap laser radiation . The mechanism for photoinduced ferromagnetism is coherence between conduction and valence bands induced by the light which leads to an optical exchange interaction. The ferromagnetic critical temperature TC depends both on the properties of the material and on the frequency and intensity of the laser and could be above 1K.

Efficient intrinsic spin relaxation in graphene due to flexural distortions

We propose an intrinsic spin scattering mechanism in graphene originated by the interplay of atomic spin-orbit interaction and the local curvature induced by flexural distortions of the atomic lattice. Starting from a multiorbital tight-binding Hamiltonian with spin-orbit coupling considered non-perturbatively, we derive an effective Hamiltonian for the spin scattering of the Dirac electrons due to flexural distortions. We compute the spin lifetime due to both flexural phonons and ripples and we find values in the 1-10 ns range at room temperature. The proposed mechanism dominates the spin relaxation in high mobility graphene samples and should also apply to other planar aromatic compounds.

Anisotropic intrinsic spin relaxation in graphene due to flexural distortions

We propose an intrinsic spin scattering mechanism in graphene originated by the interplay of atomic spin-orbit interaction and the local curvature induced by flexural distortions of the atomic lattice. Starting from a multiorbital tight-binding Hamiltonian with spin-orbit coupling considered nonperturbatively, we derive an effective Hamiltonian for the spin scattering of the Dirac electrons due to flexural distortions. We compute the spin lifetime due to both flexural phonons and ripples and we find values in the microsecond range at room temperature. Interestingly, this mechanism is anisotropic on two counts. First, the relaxation rate is different for off-plane and in-plane spin quantization axis. Second, the spin relaxation rate depends on the angle formed by the crystal momentum with the carbon-carbon bond. In addition, the spin lifetime is also valley dependent. The proposed mechanism sets an upper limit for spin lifetimes in graphene and will be relevant when samples of high quality can be fabricated free of extrinsic sources of spin relaxation.

Intrinsic spin noise in MgO magnetic tunnel junctions

We consider two intrinsic sources of noise in ultra-sensitive magnetic field sensors based on MgO magnetic tunnel junctions, coming both from 25 Mg nuclear spins (I = 5/2, 10% natural abundance) and S = 1 Mg-vacancies. While nuclear spins induce noise peaked in the MHz frequency range, the vacancies noise peaks in the GHz range. We find that the nuclear noise in submicron devices has a similar magnitude than the 1/f noise, while the vacancy-induced noise dominates in the GHz range. Interestingly, the noise spectrum under a finite magnetic field gradient may provide spatial information about the spins in the MgO layer.

The Economics of Subsidies for R&D: The Intrinsic Difficulty of Determining Optimum Subsidies and Implications for Reform of EU State Aid Rules on R&D. Bruges European Economic Research (BEER) Papers 26/February 2013

The European Commission is reforming state aid rules. An important element of the reform is to prevent the granting of excessive subsidies. This paper shows that the determination of the optimum subsidy for research is difficult. What appears to be the socially optimum level of research effort depends on the benchmark of comparison and whether this benchmark is the situation before subsidies or the situation after subsidies. In the presence of asymmetric information, policy makers should induce firms to reveal their true costs and should grant subsidies to the relatively more efficient firms by allocating subsidies not on a first-come-first- serve basis but through a competitive process. However, competitive selection of subsidy recipients is not a panacea as it may not be possible to be effectively used in all cases and for all research programmes. This is because in principle public subsidies should support those programmes with the largest value for society, rather than with the lowest costs. Although this paper focuses on R&D, its findings are relevant to any subsidy whose aim is to remedy market failure caused by positive externalities.

Lung Structure and the Intrinsic Challenges of Gas Exchange

Structural and functional complexities of the mammalian lung evolved to meet a unique set of challenges, namely, the provision of efficient delivery of inspired air to all lung units within a confined thoracic space, to build a large gas exchange surface associated with minimal barrier thickness and a microvascular network to accommodate the entire right ventricular cardiac output while withstanding cyclic mechanical stresses that increase several folds from rest to exercise. Intricate regulatory mechanisms at every level ensure that the dynamic capacities of ventilation, perfusion, diffusion, and chemical binding to hemoglobin are commensurate with usual metabolic demands and periodic extreme needs for activity and survival. This article reviews the structural design of mammalian and human lung, its functional challenges, limitations, and potential for adaptation. We discuss (i) the evolutionary origin of alveolar lungs and its advantages and compromises, (ii) structural determinants of alveolar gas exchange, including architecture of conducting bronchovascular trees that converge in gas exchange units, (iii) the challenges of matching ventilation, perfusion, and diffusion and tissue-erythrocyte and thoracopulmonary interactions. The notion of erythrocytes as an integral component of the gas exchanger is emphasized. We further discuss the signals, sources, and limits of structural plasticity of the lung in alveolar hypoxia and following a loss of lung units, and the promise and caveats of interventions aimed at augmenting endogenous adaptive responses. Our objective is to understand how individual components are matched at multiple levels to optimize organ function in the face of physiological demands or pathological constraints. © 2016 American Physiological Society. Compr Physiol 6:827-895, 2016.

Notes on intrinsic calculus /

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