Critical Role of Glu175 on Stability and Folding of Bacterial Luciferase: Stopped-flow Fluorescence Study

Shirazy, Najmeh Hadizadeh,Ranjbar, Bijan,Hosseinkhani, Saman,Khalifeh, Khosrow,Madvar, Ali Riahi,Naderi-Manesh, Hossein Korean Society for Biochemistry and Molecular Biol 2007 Journal of biochemistry and molecular biology Vol.40 No.4

Bacterial luciferase is a heterodimeric enzyme, which catalyzes the light emission reaction, utilizing reduced FMN (FMNH2), a long chain aliphatic aldehyde and $O_2$, to produce green-blue light. This enzyme can be readily classed as slow or fast decay based on their rate of luminescence decay in a single turnover. Mutation of Glu175 in $\alpha$ subunit to Gly converted slow decay Xenorhabdus Luminescence luciferase to fast decay one. The following studies revealed that changing the luciferase flexibility and lake of Glu-flavin interactions are responsible for the unusual kinetic properties of mutant enzyme. Optical and thermodynamics studies have caused a decrease in free energy and anisotropy of mutant enzyme. Moreover, the role of Glu175 in transition state of folding pathway by use of stopped-flow fluorescence technique has been studied which suggesting that Glu175 is not involved in transition state of folding and appears as surface residue of the nucleus or as a member of one of a few alternative folding nuclei. These results suggest that mutation of Glu175 to Gly extended the structure of Xenorhabdus Luminescence luciferase, locally.

Pyramidal reaction wheel arrangement optimization of satellite attitude control subsystem for minimizing power consumption

Shirazi, Abolfazl,Mirshams, Mehran The Korean Society for Aeronautical and Space Scie 2014 International Journal of Aeronautical and Space Sc Vol.15 No.2

The pyramidal reaction wheel arrangement is one of the configurations that can be used in attitude control simulators for evaluation of attitude control performance in satellites. In this arrangement, the wheels are oriented in a pyramidal configuration with a tilt angle. In this paper, a study of pyramidal reaction wheel arrangement is carried out in order to find the optimum tilt angle that minimizes total power consumption of the system. The attitude control system is analyzed and the pyramidal configuration is implemented in numerical simulation. Optimization is carried out by using an iterative process and the optimum tilt angle that provides minimum system power consumption is obtained. Simulation results show that the system requires the least power by using optimum tilt angle in reaction wheels arrangement.

Quality assessment of the optical thin films using line field spectral domain optical coherence tomography

Shirazi, Muhammad Faizan,Wijesinghe, Ruchire Eranga,Ravichandran, Naresh Kumar,Kim, Pilun,Jeon, Mansik,Kim, Jeehyun Elsevier 2018 Optics and lasers in engineering Vol.110 No.-

<P>In this study, the industrial inspection of optical thin film on touch screen panels was demonstrated using line field spectral domain optical coherence tomography. The conventional Fourier domain optical coherence tomography system requires a single scanner for two-dimensional cross-sectional images and two scanners for volumetric images. Our developed line field spectral domain optical coherence tomography has the advantage of needing only a single scanner for volumetric images, while two-dimensional cross-sectional images are obtained by the parallel acquisition of an illuminated line on a sample using an area camera. Further, the image acquisition speed was enhanced by implementing a high speed camera (340 frames per seconds) with improved quantum efficiency at near infrared region enabling two-fold frame rate. Cross-sectional and volumetric images were acquired to detect the internal sublayer defects in the optical thin films, which are difficult to observe using visual or machine vision-based inspection methods. The developed pseudo code for defect identification in optical thin films was well-utilized here for the defect inspection. The system characterization is demonstrated using United State Air Force (USAF) resolution target. The results indicate the possible application of the proposed system in touch screen panel inspection for the quality assurance of products at the consumer end.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Quality assessment of the optical thin films used for touch screen panel. </LI> <LI> Line illumination is utilized to get the cross-sectional information without scanner. </LI> <LI> The sublayer defects are detected using line field optical coherence tomography. </LI> <LI> A defect detection algorithm is developed for the quality assurance of optical thin films. </LI> <LI> Cross-sectional and three-dimensional images show the effectiveness of the system. </LI> </UL> </P>

Free space broad-bandwidth tunable laser diode based on Littman configuration for 3D profile measurement

Shirazi, Muhammad Faizan,Kim, Pilun,Jeon, Mansik,Kim, Chang-Seok,Kim, Jeehyun Elsevier 2018 Optics and laser technology Vol.101 No.-

<P><B>Abstract</B></P> <P>We developed a tunable laser diode for an optical coherence tomography system that can perform three-dimensional profile measurement using an area scanning technique. The tunable laser diode is designed using an Eagleyard tunable laser diode with a galvano filter. The Littman free space configuration is used to demonstrate laser operation. The line- and bandwidths of this source are 0.27 nm (∼110 GHz) and 43 nm, respectively, at the center wavelength of 860 nm. The output power is 20 mW at an operating current of 150 mA. A step height target is imaged using a wide-area scanning system to show the measurement accuracy of the proposed tunable laser diode. A TEM grid is also imaged to measure the topography and thickness of the sample by proposed tunable laser diode.</P> <P><B>Highlights</B></P> <P> <UL> <LI> High power free space broad-bandwidth tunable laser diode is developed. </LI> <LI> A simple Littman free space cavity is utilized with galvano-mirror scanner. </LI> <LI> Large field-of-view with no mechanical scanning can be imaged using the laser diode. </LI> <LI> A VLSI standard height target is imaged using the proposed tunable laser diode. </LI> <LI> Cross-sectional and three-dimensional images show the effectiveness of the system. </LI> </UL> </P>

Diagnostic Accuracy of Magnetic Resonance Imaging versus Clinical Staging in Cervical Cancer

Shirazi, Ahmad Soltani,Razi, Taghi,Cheraghi, Fatemeh,Rahim, Fakher,Ehsani, Sara,Davoodi, Mohammad Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.14

Background: Cervical cancer is the third most common gynecological cancer and a widespread malignancy in women, accounting for a large proportion of the cancer burden in developing countries. We compared accuracy of MRI staging with clinical staging and also concordance between the two methods for newly diagnosed patients with cervical cancer, using clinical staging as the reference. Materials and Methods: This prospective study was conducted on 27 newly diagnosed patients with cervical cancer from Imam Khomeini hospital from June 2012 to Feb 2014. New cases of cervical cancer with positive PAP test were staged separately with a clinical exam based on the FIGO system by a gynecologist, oncologist and also with MRI by an expert radiologist. Then we compared the predicted stage for each patient with the two methods. Results: Based on clinical staging 9 patients (33%) were observed at stage 1. MRI staging was in coordination with clinical staging in eight of them and for one patient MRI accorded stage 2B (88% concordance). Conclusions: MRI is a reliable noninvasive method with high accuracy for cervical cancer staging. Also presently it is easily obtainable, so we recommend using this technique along with clinical examination for staging cervical cancer patients. We also recommend to radiologists and residents of radiology to get experience with this method of staging.

Structural Evolution of Environmentally Responsive Cationic Liposome–DNA Complexes with a Reducible Lipid Linker

Shirazi, Rahau S.,Ewert, Kai K.,Silva, Bruno F. B.,Leal, Cecilia,Li, Youli,Safinya, Cyrus R. American Chemical Society 2012 Langmuir Vol.28 No.28

<P>Environmentally responsive materials (i.e., materials that respond to changes in their environment with a change in their properties or structure) are attracting increasing amounts of interest. We recently designed and synthesized a series of cleavable multivalent lipids (CMVLn, with <I>n</I> = 2–5 being the number of positive headgroup charges at full protonation) with a disulfide bond in the linker between their cationic headgroup and hydrophobic tails. The self-assembled complexes of the CMVLs and DNA are a prototypical environmentally responsive material, undergoing extensive structural rearrangement when exposed to reducing agents. We investigated the structural evolution of CMVL–DNA complexes at varied complex composition, temperature, and incubation time using small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS). A related lipid with a stable linker, TMVL4, was used as a control. In a nonreducing environment, CMVL–DNA complexes form the lamellar (L<SUB>α</SUB><SUP>C</SUP>) phase, with DNA rods sandwiched between lipid bilayers. However, new self-assembled phases form when the disulfide linker is cleaved by dithiothreitol or the biologically relevant reducing agent glutathione. The released DNA and cleaved CMVL headgroups form a loosely organized phase, giving rise to a characteristic broad SAXS correlation profile. CMVLs with high headgroup charge also form condensed DNA bundles. Intriguingly, the cleaved hydrophobic tails of the CMVLs reassemble into tilted chain-ordered L<SUB>β′</SUB> phases upon incubation at physiological temperature (37 °C), as indicated by characteristic WAXS peaks. X-ray scattering further reveals that two of the three phases (L<SUB>βF</SUB>, L<SUB>βL</SUB>, and L<SUB>βI</SUB>) constituting the L<SUB>β′</SUB> phase coexist in these samples. The described system may have applications in lipid-based nanotechnologies.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/langd5/2012/langd5.2012.28.issue-28/la301181b/production/images/medium/la-2012-01181b_0001.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/la301181b'>ACS Electronic Supporting Info</A></P>

Multiview registration-based handheld 3D profiling system using visual navigation and structured light

Ayaz, Shirazi Muhammad,Kim, Min Young Informa UK (TaylorFrancis) 2017 International journal of optomechatronics Vol.11 No.1

<P>This article describes the 3D handheld profiling system composed of a stereo camera and an illumination projector to collect high-resolution data for close range of applications. Visual navigation approach is either based on feature matching or on accurate target, and the target-based approach was found to be more accurate if the 3D object has less texture on its surface. Block matching algorithm was used to render the single-view 3D reconstruction. For multiview 3D modeling, coarse registration and final refinement of the point clouds using iterative closest point algorithm were utilized. The proposed approach yields good accuracy for multiview registration as demonstrated in the results of this research.</P>

Stereological Comparison of the Effects of Pentoxifylline, Captopril, Simvastatin, and Tamoxifen on Kidney and Bladder Structure After Partial Urethral Obstruction in Rats

Mehdi Shirazi,Mohammad-Reza Soltani,Zahra Jahanabadi,Mohammad Amin Abdollahifar,Nader Tanideh,Ali Noorafshan 대한비뇨의학회 2014 Investigative and Clinical Urology Vol.55 No.11

Purpose: Limited studies have shown antifibrotic effects of pentoxifylline, captopril,simvastatin, and tamoxifen. No comparisons are available of the effects of these drugson prevention of renal and bladder changes in partial urethral obstruction (PUO). Materials and Methods: The rats were divided into six groups (n=7). The sham-operatedrats (group I) only underwent laparotomy and did not receive any treatments. The PUOgroups (group II–VI) received normal saline (PUO+NS), pentoxifylline (100 mg/kg/d;PUO+PEN), captopril (35 mg/kg/d; PUO+CAP), simvastatin (15 mg/kg/d; PUO+SIM),or tamoxifen (10 mg/kg/d; PUO+TAM) by gavage for 28 days. Then, the volume and/orlength of the kidney components (tubules, vessels, and fibrous tissue) and the bladdercomponents (epithelial and muscular layers, fibrous tissue, fibroblast and fibrocytenumber) were quantitatively evaluated on the microscopic sections by use of stereologicaltechniques. Results: The volume of renal and bladder fibrosis was significantly ameliorated in thePUO+PEN group, followed by the PUO+CAP, PUO+SIM, and PUO+TAM groups. Also,the volume and length of the renal tubules and vessels and bladder layers were moresignificantly protected in the PUO+PEN group, followed by the PUO+CAP, PUO+SIM,and PUO+TAM groups. Conclusions: Treatment of PUO with PEN was more effective in the prevention of renaland bladder fibrosis and in the preservation of renal and bladder structures.

Which Patients Are at Higher Risk for Residual Valves After Posterior Urethral Valve Ablation?

Mehdi Shirazi,Mohamadreza Farsiani,Mohammad Natami,Kiomars Izadpanah,Amir Malekahmadi,Abbasali Khakbaz 대한비뇨의학회 2014 Investigative and Clinical Urology Vol.55 No.1

Purpose: To find patients at high risk of obstructive remnant leaflets after valve ablationamong boys with posterior urethral valve (PUV), we evaluated any possible relationshipbetween preoperative findings in our patients and residual obstructive leafletsafter valve ablation. Materials and Methods: We retrospectively reviewed the medical records of 55 patientswith PUV that was treated by the same surgeon between 2008 and 2012. Of these, 37patients (67.3%) had no obstructive remnant leaflets (group A) and 18 patients (32.7%)had obstructive remnant leaflets (group B) in follow-up cystoscopy. Preoperative clinicaland radiological findings were evaluated and compared between the groups. Results: Among all the preoperative data we examined, the analysis revealed that ageat the time of surgery (median age: group A, 15 months; group B, 7 months; p=0.017),echogenicity of kidneys (p<0.05), presence of vesicoureteral reflux (p<0.05), and gradeof reflux (p<0.05) were significantly different between the groups. Method of valveablation, anterior-posterior diameters of the renal pelvis, renal cortical thickness, bladderwall thickening, and scarring on the dimercaptosuccinic acid scan showed no significantdifferences between the two groups. Conclusions: In our patients, younger age at surgery time, hyperechogenicity of renalparenchyma, presence of vesicoureteral reflux, and grade 4 or 5 reflux before surgeryhad a significant relationship with residual valves. More studies may result in enhancedmanagement of patients at high risk of residual valves after PUV ablation, becausethe sooner the obstruction is resolved entirely, the better the outcome.

Wavelet based estimation for the derivative of a density by block thresholding under random censorship

Esmaeil Shirazi,Yogendra P. Chaubey,Hassan Doosti,Hossein Ali Nirumand 한국통계학회 2012 Journal of the Korean Statistical Society Vol.41 No.2

We consider wavelet based method for estimating derivatives of a density via block thresholding when the data obtained are randomly right censored. The proposed method is analogous to that of Hall and Patil (1995) for density estimation in the complete data case that has been extended recently by Li (2003, 2008). We find bounds for the L2-loss over a large range of Besov function classes for the resulting estimators. The results of Hall and Patil (1995), Prakasa Rao (1996) and Li (2003, 2008) are obtained as special cases and the performance of the proposed estimator is investigated by a numerical study.