45 research outputs found
NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules
Similarities in the 3D patterns of RNA base interactions or arrangements can provide insights into their functions and roles in stabilization of the RNA 3D structure. Nucleic Acids Search for Substructures and Motifs (NASSAM) is a graph theoretical program that can search for 3D patterns of base arrangements by representing the bases as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. The input files for NASSAM are PDB formatted 3D coordinates. This web server can be used to identify matches of base arrangement patterns in a query structure to annotated patterns that have been reported in the literature or that have possible functional and structural stabilization implications. The NASSAM program is freely accessible without any login requirement at http://mfrlab.org/grafss/nassam/
Raman cooling and heating of two trapped Ba+ ions
We study cooling of the collective vibrational motion of two 138Ba+ ions
confined in an electrodynamic trap and irradiated with laser light close to the
resonances S_1/2-P_1/2 (493 nm) and P_1/2-D_3/2 (650 nm). The motional state of
the ions is monitored by a spatially resolving photo multiplier. Depending on
detuning and intensity of the cooling lasers, macroscopically different
motional states corresponding to different ion temperatures are observed. We
also derive the ions' temperature from detailed analytical calculations of
laser cooling taking into account the Zeeman structure of the energy levels
involved. The observed motional states perfectly match the calculated
temperatures. Significant heating is observed in the vicinity of the dark
resonances of the Zeeman-split S_1/2-D_3/2 Raman transitions. Here two-photon
processes dominate the interaction between lasers and ions. Parameter regimes
of laser light are identified that imply most efficient laser cooling.Comment: 8 pages, 5 figure
Motional sidebands and direct measurement of the cooling rate in the resonance fluorescence of a single trapped ion
Resonance fluorescence of a single trapped ion is spectrally analyzed using a
heterodyne technique. Motional sidebands due to the oscillation of the ion in
the harmonic trap potential are observed in the fluorescence spectrum. From the
width of the sidebands the cooling rate is obtained and found to be in
agreement with the theoretical prediction.Comment: 4 pages, 4 figures. Final version after minor changes, 1 figure
replaced; to be published in PRL, July 10, 200
Quantum jumps induced by the center-of-mass motion of a trapped atom
We theoretically study the occurrence of quantum jumps in the resonance
fluorescence of a trapped atom. Here, the atom is laser cooled in a
configuration of level such that the occurrence of a quantum jump is associated
to a change of the vibrational center-of-mass motion by one phonon. The
statistics of the occurrence of the dark fluorescence period is studied as a
function of the physical parameters and the corresponding features in the
spectrum of resonance fluorescence are identified. We discuss the information
which can be extracted on the atomic motion from the observation of a quantum
jump in the considered setup
Two Estrogen Response Element Sequences Near the PCNA Gene Are Not Responsible for Its Estrogen-Enhanced Expression in MCF7 Cells
The proliferating cell nuclear antigen (PCNA) is an essential component of DNA replication, cell cycle regulation, and epigenetic inheritance. High expression of PCNA is associated with poor prognosis in patients with breast cancer. The 5'-region of the PCNA gene contains two computationally-detected estrogen response element (ERE) sequences, one of which is evolutionarily conserved. Both of these sequences are of undocumented cis-regulatory function. We recently demonstrated that estradiol (E2) enhances PCNA mRNA expression in MCF7 breast cancer cells. MCF7 cells proliferate in response to E2.Here, we demonstrate that E2 rapidly enhanced PCNA mRNA and protein expression in a process that requires ERalpha as well as de novo protein synthesis. One of the two upstream ERE sequences was specifically bound by ERalpha-containing protein complexes, in vitro, in gel shift analysis. Yet, each ERE sequence, when cloned as a single copy, or when engineered as two tandem copies of the ERE-containing sequence, was not capable of activating a luciferase reporter construct in response to E2. In MCF7 cells, neither ERE-containing genomic region demonstrated E2-dependent recruitment of ERalpha by sensitive ChIP-PCR assays.We conclude that E2 enhances PCNA gene expression by an indirect process and that computational detection of EREs, even when evolutionarily conserved and when near E2-responsive genes, requires biochemical validation
Reactive oxygen species and male reproductive hormones
Reports of the increasing incidence of male infertility paired with decreasing semen quality have triggered studies
on the effects of lifestyle and environmental factors on the male reproductive potential. There are numerous exogenous
and endogenous factors that are able to induce excessive production of reactive oxygen species (ROS) beyond that of
cellular antioxidant capacity, thus causing oxidative stress. In turn, oxidative stress negatively affects male reproductive
functions and may induce infertility either directly or indirectly by affecting the hypothalamus-pituitary-gonadal (HPG)
axis and/or disrupting its crosstalk with other hormonal axes. This review discusses the important exogenous and
endogenous factors leading to the generation of ROS in different parts of the male reproductive tract. It also highlights
the negative impact of oxidative stress on the regulation and cross-talk between the reproductive hormones. It further
describes the mechanism of ROS-induced derangement of male reproductive hormonal profiles that could ultimately
lead to male infertility. An understanding of the disruptive effects of ROS on male reproductive hormones would
encourage further investigations directed towards the prevention of ROS-mediated hormonal imbalances, which in turn
could help in the management of male infertility