Computer simulation of pulsed field gel runs allows the quantitation of radiation-induced double-strand breaks in yeast

A procedure for the quantification of double-strand breaks in yeast is presented that utilizes pulsed field gel electrophoresis (PFGE) and a comparison of the observed DNA mass distribution in the gel lanes with calculated distributions. Calculation of profiles is performed as follows. If double-strand breaks are produced by sparsely ionizing radiation, one can assume that they are distributed randomly in the genome, and the resulting DNA mass distribution in molecular length can be predicted by means of a random breakage model. The input data for the computation of molecular length profiles are the breakage frequency per unit length, , as adjustable parameter, and the molecular lengths of the intact chromosomes. The obtained DNA mass distributions in molecular length must then be transformed into distributions of DNA mass in migration distance. This requires a calibration of molecular length vs. migration distance that is specific for the gel lane in question. The computed profiles are then folded with a Lorentz distribution with adjusted spread parameter to account for and broadening. The DNA profiles are calculated for different breakage frequencies and for different values of , and the parameters resulting in the best fit of the calculated to the observed profile are determined

A transfer matrix method for the analysis of fractal quantum potentials

The scattering properties of quantum particles on fractal potentials at different stages of fractal growth are obtained by means of the transfer matrix method. This approach can be easily adopted for project assignments in introductory quantum mechanics for undergraduates. The reflection coefficients for both the fractal potential and the finite periodic potential are calculated and compared. It is shown that the reflection coefficient for the fractal has a self-similar structure associated with the fractal distribution of the potential

Tunable Multifunctional Topological Insulators in Ternary Heusler Compounds

Recently the Quantum Spin Hall effect (QSH) was theoretically predicted and experimentally realized in a quantum wells based on binary semiconductor HgTe[1-3]. QSH state and topological insulators are the new states of quantum matter interesting both for fundamental condensed matter physics and material science[1-11]. Many of Heusler compounds with C1b structure are ternary semiconductors which are structurally and electronically related to the binary semiconductors. The diversity of Heusler materials opens wide possibilities for tuning the band gap and setting the desired band inversion by choosing compounds with appropriate hybridization strength (by lattice parameter) and the magnitude of spin-orbit coupling (by the atomic charge). Based on the first-principle calculations we demonstrate that around fifty Heusler compounds show the band inversion similar to HgTe. The topological state in these zero-gap semiconductors can be created by applying strain or by designing an appropriate quantum well structure, similar to the case of HgTe. Many of these ternary zero-gap semiconductors (LnAuPb, LnPdBi, LnPtSb and LnPtBi) contain the rare earth element Ln which can realize additional properties ranging from superconductivity (e. g. LaPtBi[12]) to magnetism (e. g. GdPtBi[13]) and heavy-fermion behavior (e. g. YbPtBi[14]). These properties can open new research directions in realizing the quantized anomalous Hall effect and topological superconductors.Comment: 20 pages, 5 figure

The NR4A subgroup: immediate early response genes with pleiotropic physiological roles

The nuclear hormone receptor (NR) superfamily includes the orphan NR4A subgroup, comprised of Nur77 (NR4A1), Nurr1 (NR4A2) and NOR-1 (NR4A3). These NRs are classified as early response genes, are induced by a diverse range of signals, including fatty acids, stress, growth factors, cytokines, peptide hormones, phorbol esters, neurotransmitters, and physical stimuli (for example magnetic fields, shear stress). The ability to sense and rapidly respond to changes in the cellular environment thus appears to be a hallmark of this subfamily. The members of the NR4A subgroup are well conserved in the DNA binding domain (~91-95%) and the C-terminal ligand-binding domain (~60%), but are divergent in the N-terminal AB region. These receptors bind as monomers, homodimers and heterodimers with RXRs (to mediate retinoid signaling) to different permutations of the canonical NR binding motif. The NR4A subgroup activates gene expression in a constitutive ligand-independent manner. NR4A-mediated trans-activation (LBD) involves unusually active N-terminal AF-1 domains that mediate coactivator recruitment. Moreover, the NR4A receptors encode atypical LBDs and AF-2 domains. For example, the LBDs contain no cavity due to bulky hydrophobic residue side chains, and lack the classical coactivator-binding cleft constituted by helices 3, 4 and 12. However, a hydrophobic patch exists between helices 11 and 12, that encodes a novel cofactor interface that modulates transcriptional activity. In line with the pleiotropic physiological stimuli that induce the NR4A subgroup, these orphan NRs have been implicated in cell cycle regulation (and apoptosis), neurological disease, steroidogenesis, inflammation, carcinogenesis and atherogenesis

Roles of TRPV1 and neuropeptidergic receptors in dorsal root reflex-mediated neurogenic inflammation induced by intradermal injection of capsaicin

<p>Abstract</p> <p>Background</p> <p>Acute cutaneous neurogenic inflammation initiated by activation of transient receptor potential vanilloid-1 (TRPV₁) receptors following intradermal injection of capsaicin is mediated mainly by dorsal root reflexes (DRRs). Inflammatory neuropeptides are suggested to be released from primary afferent nociceptors participating in inflammation. However, no direct evidence demonstrates that the release of inflammatory substances is due to the triggering of DRRs and how activation of TRPV₁receptors initiates neurogenic inflammation via triggering DRRs.</p> <p>Results</p> <p>Here we used pharmacological manipulations to analyze the roles of TRPV₁and neuropeptidergic receptors in the DRR-mediated neurogenic inflammation induced by intradermal injection of capsaicin. The degree of cutaneous inflammation in the hindpaw that followed capsaicin injection was assessed by measurements of local blood flow (vasodilation) and paw-thickness (edema) of the foot skin in anesthetized rats. Local injection of capsaicin, calcitonin gene-related peptide (CGRP) or substance P (SP) resulted in cutaneous vasodilation and edema. Removal of DRRs by either spinal dorsal rhizotomy or intrathecal administration of the GABA_Areceptor antagonist, bicuculline, reduced dramatically the capsaicin-induced vasodilation and edema. In contrast, CGRP- or SP-induced inflammation was not significantly affected after DRR removal. Dose-response analysis of the antagonistic effect of the TRPV₁receptor antagonist, capsazepine administered peripherally, shows that the capsaicin-evoked inflammation was inhibited in a dose-dependent manner, and nearly completely abolished by capsazepine at doses between 30–150 μg. In contrast, pretreatment of the periphery with different doses of CGRP_8–37(a CGRP receptor antagonist) or spantide I (a neurokinin 1 receptor antagonist) only reduced the inflammation. If both CGRP and NK₁receptors were blocked by co-administration of CGRP_8–37and spantide I, a stronger reduction in the capsaicin-initiated inflammation was produced.</p> <p>Conclusion</p> <p>Our data suggest that 1) the generation of DRRs is critical for driving the release of neuropeptides antidromically from primary afferent nociceptors; 2) activation of TRPV₁receptors in primary afferent nociceptors following intradermal capsaicin injection initiates this process; 3) the released CGRP and SP participate in neurogenic inflammation.</p

Low frequency of somatic mutations in the FH/multiple cutaneous leiomyomatosis gene in sporadic leiomyosarcomas and uterine leiomyomas

Germline mutations in the fumarate hydratase gene at 1q43 predispose to dominantly inherited skin and uterine leiomyomata and leiomyosarcomas. The enzyme, which is a component of the tricarboxylic acid cycle, acts as a tumour suppressor. To evaluate fumarate hydratase in respective sporadic tumours, we analysed a series of 26 leiomyosarcomas and 129 uterine leiomyomas (from 21 patients) for somatic mutations in fumarate hydratase and allelic imbalance around 1q43. None of the 26 leiomyosarcomas harboured somatic mutations in fumarate hydratase. Fifty per cent of leiomysarcomas tested showed evidence of allelic imbalance at 1q, but this was not confined to the vicinity of fumarate hydratase. Only 5% (seven out of 129) of the leiomyomas showed allele imbalance at 1q42-q43 and no somatic mutations in fumarate hydratase were observed. Our findings indicate that mutations in fumarate hydratase do not play a major role in the development of sporadic leiomyosarcomas or uterine leiomyomas

Adult Intussusception Caused by an Inverted Meckel Diverticulum

Adult intussusception caused by an inverted Meckel diverticulum is rare. We report a 55-year-old Japanese man with intussusception. He was admitted to our hospital with vomiting and abdominal pain. The abdomen was hard with tenderness and muscle guarding. Computed tomography scanning demonstrated a typical inhomogeneous target-shaped mass in the right abdomen. We diagnosed intussusception and performed emergency surgery. At laparotomy, ileocolic intussusception was observed and the ileocecal segment was resected. The surgical specimen comprised an 84 cm segment of resected ileocecum with an elongated polypoid lesion measuring 11 × 2 cm within the ileal lumen. Histopathological examination demonstrated that the polypoid lesion was an inverted Meckel diverticulum. Postoperatively, the patient made an uneventful recovery

Quantitative cerebral blood flow with optical coherence tomography

Absolute measurements of cerebral blood flow (CBF) are an important endpoint in studies of cerebral pathophysiology. Currently no accepted method exists for in vivo longitudinal monitoring of CBF with high resolution in rats and mice. Using three-dimensional Doppler Optical Coherence Tomography and cranial window preparations, we present methods and algorithms for regional CBF measurements in the rat cortex. Towards this end, we develop and validate a quantitative statistical model to describe the effect of static tissue on velocity sensitivity. This model is used to design scanning protocols and algorithms for sensitive 3D flow measurements and angiography of the cortex. We also introduce a method of absolute flow calculation that does not require explicit knowledge of vessel angles. We show that OCT estimates of absolute CBF values in rats agree with prior measures by autoradiography, suggesting that Doppler OCT can perform absolute flow measurements in animal models.National Institutes of Health (U.S.) (Grant number R01-NS057476)National Institutes of Health (U.S.) (Grant number P01NS055104)National Institutes of Health (U.S.) (Grant number P50NS010828)ational Institutes of Health (U.S.) (Grant number K99NS067050)National Institutes of Health (U.S.) (Grant number R01-CA075289-13)United States. Air Force Office of Scientific Research (FA9550-07-1-0014)United States. Dept. of Defense. Medical Free Electron Laser Program (FA9550-07-1-0101