A 'through-DNA' mechanism for co-regulation of metal uptake and efflux.

Transition metals like Zn are essential for all organisms including bacteria, but fluctuations of their concentrations in the cell can be lethal. Organisms have thus evolved complex mechanisms for cellular metal homeostasis. One mechanistic paradigm involves pairs of transcription regulators sensing intracellular metal concentrations to regulate metal uptake and efflux.

Harnessing network pharmacology in drug discovery: an integrated approach.

Traditional drug discovery approach is based on one drug-one target, that is associated with very lengthy timelines, high costs and very low success rates. Network pharmacology (NP) is a novel method of drug designing, that is based on a multiple-target approach. NP integrates systems such as biology, pharmacology and computational techniques to address the limitations of traditional methods of drug discovery.

A 'through-DNA' mechanism for metal uptake-vs.-efflux regulation.

Transition metals like Zn are essential for all organisms including bacteria, but fluctuations of their concentrations in the cell can be lethal. Organisms have thus evolved complex mechanisms for cellular metal homeostasis. One mechanistic paradigm involves pairs of transcription regulators sensing intracellular metal concentrations to regulate metal uptake and efflux.

Improved electromagnetic tracking for catheter path reconstruction with application in high-dose-rate brachytherapy.

Purpose: Electromagnetic (EM) catheter tracking has recently been introduced in order to enable prompt and uncomplicated reconstruction of catheter paths in various clinical interventions. However, EM tracking is prone to measurement errors which can compromise the outcome of the procedure. Minimizing catheter tracking errors is therefore paramount to improve the path reconstruction accuracy.

Probing for Binding Regions of the FtsZ Protein Surface through Site-Directed Insertions: Discovery of Fully Functional FtsZ-Fluorescent Proteins.

Unlabelled: FtsZ, a bacterial tubulin homologue, is a cytoskeletal protein that assembles into protofilaments that are one subunit thick. These protofilaments assemble further to form a "Z ring" at the center of prokaryotic cells. The Z ring generates a constriction force on the inner membrane and also serves as a scaffold to recruit cell wall remodeling proteins for complete cell division in vivo One model of the Z ring proposes that protofilaments associate via lateral bonds to form ribbons; however, lateral bonds are still only hypothetical.

Metalloregulator CueR biases RNA polymerase's kinetic sampling of dead-end or open complex to repress or activate transcription.

Metalloregulators respond to metal ions to regulate transcription of metal homeostasis genes. MerR-family metalloregulators act on σ(70)-dependent suboptimal promoters and operate via a unique DNA distortion mechanism in which both the apo and holo forms of the regulators bind tightly to their operator sequence, distorting DNA structure and leading to transcription repression or activation, respectively. It remains unclear how these metalloregulator-DNA interactions are coupled dynamically to RNA polymerase (RNAP) interactions with DNA for transcription regulation.

Single-molecule dynamics and mechanisms of metalloregulators and metallochaperones.

Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interface of chemistry and biology. This Current Topic reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein-DNA and protein-protein interactions offer efficient pathways via which MerR-family metalloregulators and copper chaperones can fulfill their functions.

Cobalt-60 tomotherapy: clinical treatment planning and phantom dose delivery studies.

Purpose: Investigations have shown that a Cobalt-60 (Co-60) radioactive source has the potential to play a role in intensity modulated radiation therapy (IMRT). In this paper, Co-60 tomotherapy's conformal dose delivery potential is evaluated by delivering conformal dose plans on a cylindrical homogeneous phantom containing clinical structures similar to those found in a typical head and neck (H&N) cancer. Also, the clinical potential of Co-60 tomotherapy is investigated by generating 2D clinical treatment plans for H&N and prostate anatomical regions.

Direct substitution and assisted dissociation pathways for turning off transcription by a MerR-family metalloregulator.

Metalloregulators regulate transcription in response to metal ions. Many studies have provided insights into how transcription is activated upon metal binding by MerR-family metalloregulators. In contrast, how transcription is turned off after activation is unclear.

Dosimetry of interface region near closed air cavities for Co-60, 6 MV and 15 MV photon beams using Monte Carlo simulations.

Underdosing of treatment targets can occur in radiation therapy due to electronic disequilibrium around air-tissue interfaces when tumors are situated near natural air cavities. These effects have been shown to increase with the beam energy and decrease with the field size. Intensity modulated radiation therapy (IMRT) and tomotherapy techniques employ combinations of multiple small radiation beamlets of varying intensities to deliver highly conformal radiation therapy.

Practical and clinical considerations in Cobalt-60 tomotherapy.

Cobalt-60 (Co-60) based radiation therapy continues to play a significant role in not only developing countries, where access to radiation therapy is extremely limited, but also in industrialized countries. Howver, technology has to be developed to accommodate modern techniques, including image guided and adaptive radiation therapy (IGART). In this paper we describe some of the practical and clinical considerations for Co-60 based tomotherapy by comparing Co-60 and 6 MV linac-based tomotherapy plans for a head and neck (HandN) cancer and a prostate cancer case.

The role of Cobalt-60 in modern radiation therapy: Dose delivery and image guidance.

The advances in modern radiation therapy with techniques such as intensity-modulated radiation therapy and image-guided radiation therapy (IMRT and IGRT) have been limited almost exclusively to linear accelerators. Investigations of modern Cobalt-60 (Co-60) radiation delivery in the context of IMRT and IGRT have been very sparse, and have been limited mainly to computer-modeling and treatment-planning exercises. In this paper, we report on the results of experiments using a tomotherapy benchtop apparatus attached to a conventional Co-60 unit.

Strong hydrogen bond between glutamic acid 46 and chromophore leads to the intermediate spectral form and excited state proton transfer in the Y42F mutant of the photoreceptor photoactive yellow protein.

In the Y42F mutant of photoactive yellow protein (PYP) the photoreceptor is in an equilibrium between two dark states, the yellow and intermediate spectral forms, absorbing at 457 and 390 nm, respectively. The nature of this equilibrium and the light-induced protonation and structural changes in the two spectral forms were characterized by transient absorption, fluorescence, FTIR, and pH indicator dye experiments. In the yellow form, the oxygen of the deprotonated p-hydroxycinnamoyl chromophore is linked by a strong low-barrier hydrogen bond to the protonated carboxyl group of Glu46 and by a weaker one to Thr50.

Investigation of an efficient source design for Cobalt-60-based tomotherapy using EGSnrc Monte Carlo simulations.

Recent investigations demonstrate a strong potential for Cobalt-60 (Co-60)-based tomotherapy. Reported work suggests that Co-60-based tomotherapy offers a clinically and commercially viable alternative to megavoltage x-ray-based tomotherapy. Tomotherapy applications use a combination of intensity-modulated fan beams to deliver highly conformal radiotherapy.

Role of a conserved salt bridge between the PAS core and the N-terminal domain in the activation of the photoreceptor photoactive yellow protein.

The effect of ionic strength on the conformational equilibrium between the I(2) intermediate and the signaling state I(2)' of the photoreceptor PYP and on the rate of recovery to the dark state were investigated by time-resolved absorption and fluorescence spectroscopy. With increasing salt concentration up to approximately 600 mM, the recovery rate k(3) decreases and the I(2)/I(2)' equilibrium (K) shifts in the direction of I(2)'. At higher ionic strength both effects reverse.

The transient accumulation of the signaling state of photoactive yellow protein is controlled by the external pH.

The signaling state of the photoreceptor photoactive yellow protein is the long-lived intermediate I(2)'. The pH dependence of the equilibrium between the transient photocycle intermediates I(2) and I(2)' was investigated. The formation of I(2)' from I(2) is accompanied by a major conformational change.

Photocycle and photoreversal of photoactive yellow protein at alkaline pH: kinetics, intermediates, and equilibria.

Since the habitat of Halorhodospira halophila is distinctly alkaline, we investigated the kinetics and intermediates of the photocycle and photoreversal of the photoreceptor photoactive yellow protein (PYP) from pH 8 to 11. SVD analysis of the transient absorption time traces in a broad wavelength range (330-510 nm) shows the presence of three spectrally distinct species (I1, I1', and I2') at pH 10. The spectrum of I1' was obtained in two different ways.

Evaluation of an automated seed loader for seed calibration in prostate brachytherapy.

Automated seed loaders for permanent prostate implants are now commercially available. Besides improved radiation safety, these systems offer seed assay capability and ease of needle loading, making preplanned as well as intra-operative implant procedures more time-efficient. The Isoloader (Mentor Corp.

Effect of salt and pH on the activation of photoactive yellow protein and gateway mutants Y98Q and Y98F.

We investigated the photocycle of mutants Y98Q and Y98F of the photoactive yellow protein (PYP) from Halorhodospira halophila. Y98 is located in the beta4-beta5 loop and is thought to interact with R52 in the alpha3-alpha4 loop thereby stabilizing this region. Y98 is conserved in all known PYP species, except in Ppr and Ppd where it is replaced by F.

Photoreversal kinetics of the I1 and I2 intermediates in the photocycle of photoactive yellow protein by double flash experiments with variable time delay.

We investigated the kinetics of photoreversal from the I(1) and I(2) intermediates of photoactive yellow protein (PYP) by time-resolved optical absorption spectroscopy with double flash excitation. A first flash, at 430 nm, initiated the photocycle. After a variable time delay, the I(1) intermediate was photoreversed by a second flash, at 500 nm, or a mixture of I(2) and I(2)' intermediates was photoreversed by a second flash, at 355 nm.

pH Dependence of the photocycle kinetics of the E46Q mutant of photoactive yellow protein: protonation equilibrium between I1 and I2 intermediates, chromophore deprotonation by hydroxyl uptake, and protonation relaxation of the dark state.

The kinetics of the photocycle of PYP and its mutants E46Q and E46A were investigated as a function of pH. E46 is the putative donor of the chromophore which becomes protonated in the I(2) intermediate. For E46Q we find that I(2) is in a pH-dependent equilibrium with its precursor I(1)' with a pK(a) of 8.