Light scattering and optical diffusion from willemite spherulites

Willemite is a zinc silicate mineral used in modern day pottery as a decorative feature within glazes. It is produced by controlled heat treatment of zinc oxide-containing ceramic glazes. The heat-treated glazes devitrify, producing thin nanoscale needle-like willemite crystals growing in spherulitic morphologies through branching of the needles. We show here that this resulting morphology of willemite crystals in an inorganic glass matrix has a previously unreported strong interaction with light, displaying remarkable optical diffraction patterns. Thin sections of such spherulites act as optical diffusers, enabling light beams to be spread up to 160° in width. Analysis of the interaction between the willemite spherulites and light suggests that the high density of willemite crystals in the spherulites and the length scales associated with both the thickness of the needles and the spacings between branches are together responsible for this optical diffusion behaviour.This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.optmat.2015.12.02

Molecular weight effects on chain pull-out fracture of reinforced polymeric interfaces

Using Brownian dynamics, we simulate the fracture of polymer interfaces reinforced by diblock connector chains. We find that for short chains the interface fracture toughness depends linearly on the degree of polymerization $N$ of the connector chains, while for longer chains the dependence becomes $N^{3/2}$. Based on the geometry of initial chain configuration, we propose a scaling argument that accounts for both short and long chain limits and crossover between them.Comment: 5 pages, 3 figure

The Goldbeter-Koshland switch in the first-order region and its response to dynamic disorder

In their classical work (Proc. Natl. Acad. Sci. USA, 1981, 78:6840-6844), Goldbeter and Koshland mathematically analyzed a reversible covalent modification system which is highly sensitive to the concentration of effectors. Its signal-response curve appears sigmoidal, constituting a biochemical switch. However, the switch behavior only emerges in the "zero-order region", i.e. when the signal molecule concentration is much lower than that of the substrate it modifies. In this work we showed that the switching behavior can also occur under comparable concentrations of signals and substrates, provided that the signal molecules catalyze the modification reaction in cooperation. We also studied the effect of dynamic disorders on the proposed biochemical switch, in which the enzymatic reaction rates, instead of constant, appear as stochastic functions of time. We showed that the system is robust to dynamic disorder at bulk concentration. But if the dynamic disorder is quasi-static, large fluctuations of the switch response behavior may be observed at low concentrations. Such fluctuation is relevant to many biological functions. It can be reduced by either increasing the conformation interconversion rate of the protein, or correlating the enzymatic reaction rates in the network.Comment: 23 pages, 4 figures, accepted by PLOS ON

Pressure dependent electronic properties of MgO polymorphs: A first-principles study of Compton profiles and autocorrelation functions

The first-principles periodic linear combination of atomic orbitals method within the framework of density functional theory implemented in the CRYSTAL06 code has been applied to explore effect of pressure on the Compton profiles and autocorrelation functions of MgO. Calculations are performed for the B1, B2, B3, B4, B8_1 and h-MgO polymorphs of MgO to compute lattice constants and bulk moduli. The isothermal enthalpy calculations predict that B4 to B8_1, h-MgO to B8_1, B3 to B2, B4 to B2 and h-MgO to B2 transitions take place at 2, 9, 37, 42 and 64 GPa respectively. The high pressure transitions B8_1 to B2 and B1 to B2 are found to occur at 340 and 410 GPa respectively. The pressure dependent changes are observed largely in the valence electrons Compton profiles whereas core profiles are almost independent of the pressure in all MgO polymorphs. Increase in pressure results in broadening of the valence Compton profiles. The principal maxima in the second derivative of Compton profiles shifts towards high momentum side in all structures. Reorganization of momentum density in the B1 to B2 structural phase transition is seen in the first and second derivatives before and after the transition pressure. Features of the autocorrelation functions shift towards lower r side with increment in pressure.Comment: 19 pages, 8 figures, accepted for publication in Journal of Materials Scienc

Pennsylvanian-Early Triassic stratigraphy in the Alborz Mountains (Iran)

New fieldwork was carried out in the central and eastern Alborz, addressing the sedimentary succession from the Pennsylvanian to the Early Triassic. A regional synthesis is proposed, based on sedimentary analysis and a wide collection of new palaeontological data. The Moscovian Qezelqaleh Formation, deposited in a mixed coastal marine and alluvial setting, is present in a restricted area of the eastern Alborz, transgressing on the Lower Carboniferous Mobarak and Dozdehband formations. The late Gzhelian–early Sakmarian Dorud Group is instead distributed over most of the studied area, being absent only in a narrow belt to the SE. The Dorud Group is typically tripartite, with a terrigenous unit in the lower part (Toyeh Formation), a carbonate intermediate part (Emarat and Ghosnavi formations, the former particularly rich in fusulinids), and a terrigenous upper unit (Shah Zeid Formation), which however seems to be confined to the central Alborz. A major gap in sedimentation occurred before the deposition of the overlying Ruteh Limestone, a thick package of packstone–wackestone interpreted as a carbonate ramp of Middle Permian age (Wordian–Capitanian). The Ruteh Limestone is absent in the eastern part of the range, and everywhere ends with an emersion surface, that may be karstified or covered by a lateritic soil. The Late Permian transgression was directed southwards in the central Alborz, where marine facies (Nesen Formation) are more common. Time-equivalent alluvial fans with marsh intercalations and lateritic soils (Qeshlaq Formation) are present in the east. Towards the end of the Permian most of the Alborz emerged, the marine facies being restricted to a small area on the Caspian side of the central Alborz. There, the Permo-Triassic boundary interval is somewhat similar to the Abadeh–Shahreza belt in central Iran, and contains oolites, flat microbialites and domal stromatolites, forming the base of the Elikah Formation. The P–T boundary is established on the basis of conodonts, small foraminifera and stable isotope data. The development of the lower and middle part of the Elikah Formation, still Early Triassic in age, contains vermicular bioturbated mudstone/wackestone, and anachronostic-facies-like gastropod oolites and flat pebble conglomerates. Three major factors control the sedimentary evolution. The succession is in phase with global sea-level curve in the Moscovian and from the Middle Permian upwards. It is out of phase around the Carboniferous–Permian boundary, when the Dorud Group was deposited during a global lowstand of sealevel. When the global deglaciation started in the Sakmarian, sedimentation stopped in the Alborz and the area emerged. Therefore, there is a consistent geodynamic control. From the Middle Permian upwards, passive margin conditions control the sedimentary evolution of the basin, which had its depocentre(s) to the north. Climate also had a significant role, as the Alborz drifted quickly northwards with other central Iran blocks towards the Turan active margin. It passed from a southern latitude through the aridity belt in the Middle Permian, across the equatorial humid belt in the Late Permian and reached the northern arid tropical belt in the Triassic

Cell-cycle-dependent transcriptional and translational DNA-damage response of 2 ribonucleotide reductase genes in S. cerevisiae

The ribonucleotide reductase (RNR) enzyme catalyzes an essential step in the production of deoxyribonucleotide triphosphates (dNTPs) in cells. Bulk biochemical measurements in synchronized Saccharomyces cerevisiae cells suggest that RNR mRNA production is maximal in late G1 and S phases; however, damaged DNA induces RNR transcription throughout the cell cycle. But such en masse measurements reveal neither cell-to-cell heterogeneity in responses nor direct correlations between transcript and protein expression or localization in single cells which may be central to function. We overcame these limitations by simultaneous detection of single RNR transcripts and also Rnr proteins in the same individual asynchronous S. cerevisiae cells, with and without DNA damage by methyl methanesulfonate (MMS). Surprisingly, RNR subunit mRNA levels were comparably low in both damaged and undamaged G1 cells and highly induced in damaged S/G2 cells. Transcript numbers became correlated with both protein levels and localization only upon DNA damage in a cell cycle-dependent manner. Further, we showed that the differential RNR response to DNA damage correlated with variable Mec1 kinase activity in the cell cycle in single cells. The transcription of RNR genes was found to be noisy and non-Poissonian in nature. Our results provide vital insight into cell cycle-dependent RNR regulation under conditions of genotoxic stress.Massachusetts Institute of Technology. Center for Environmental Health Sciences (deriving from NIH P30-ES002109)National Institutes of Health (U.S.) (grant R01-CA055042)National Institutes of Health (U.S.) (grant DP1-OD006422)Massachusetts Institute of Technology (CSBi Merck-MIT Fellowship

Coxsackie-adenovirus receptor expression is enhanced in pancreas from patients with type 1 diabetes

Objectives: One of the theories connecting enterovirus (EV) infection of human islets with type 1 diabetes (T1D) is the development of a fertile field in the islets. This implies induction of appropriate proteins for the viral replication such as the coxsackie–adenovirus receptor (CAR). The aim of this study was to investigate to what extent CAR is expressed in human islets of Langerhans, and what conditions that would change the expression. Design: Immunohistochemistry for CAR was performed on paraffin-embedded pancreatic tissue from patients with T1D (n=9 recent onset T1D, n=4 long-standing T1D), islet autoantibody-positive individuals (n=14) and non-diabetic controls (n=24) individuals. The expression of CAR was also examined by reverse transcription PCR on microdissected islets (n=5), exocrine tissue (n=5) and on explanted islets infected with EV or exposed to chemokines produced by EV-infected islet cells. Results: An increased frequency of patients with T1D and autoantibody-positive individuals expressed CAR in the pancreas (p<0.039). CAR staining was detected more frequently in pancreatic islets from patients with T1D and autoantibody-positive subjects (15/27) compared with (6/24) non-diabetic controls (p<0.033). Also in explanted islets cultured in UV-treated culture medium from coxsackievirus B (CBV)-1-infected islets, the expression of the CAR gene was increased compared with controls. Laser microdissection of pancreatic tissue revealed that CAR expression was 10-fold higher in endocrine compared with exocrine cells of the pancreas. CAR was also expressed in explanted islets and the expression level decreased with time in culture. CBV-1 infection of explanted islets clearly decreased the expression of CAR (p<0.05). In contrast, infection with echovirus 6 did not affect the expression of CAR. Conclusions: CAR is expressed in pancreatic islets of patients with T1D and the expression level of CAR is increased in explanted islets exposed to proinflammatory cytokines/chemokines produced by infected islets. T1D is associated with increased levels of certain chemokines/cytokines in the islets and this might be the mechanism behind the increased expression of CAR in TID islets

Nanosecond pulsed laser texturing of optical diffusers

High-quality optical glass diffusers have applications in aerospace, displays, imaging systems, medical devices, and optical sensors. The development of rapid and accurate fabrication techniques is highly desirable for their production. Here, a micropatterning method for the fast fabrication of optical diffusers by means of nanosecond pulsed laser ablation is demonstrated (λ=1064 nm, power=7.02, 9.36 and 11.7 W and scanning speed=200 and 800 mm s-1). The experiments were carried out by point-to-point texturing of a glass surface in spiral shape. The laser machining parameters, the number of pulses and their power had significant effect on surface features. The optical characteristics of the diffusers were characterized at different scattering angles. The features of the microscale structures influenced average roughness from 0.8 μm to 1.97 μm. The glass diffusers scattered light at angles up to 20° and their transmission efficiency were measured up to ∼97% across the visible spectrum. The produced optical devices diffuse light less but do so with less scattering and energy losses as compared to opal diffusing glass. The presented fabrication method can be applied to any other transparent material to create optical diffusers. It is anticipated that the optical diffusers presented in this work will have applications in the production of LED spotlights and imaging devices

G-quadruplex structures mark human regulatory chromatin

G-quadruplex (G4) structural motifs have been linked to transcription, replication and genome instability and are implicated in cancer and other diseases. However, it is crucial to demonstrate the bona fide formation of G4 structures within an endogenous chromatin context. Herein we address this through the development of G4 ChIP-seq, an antibody-based G4 chromatin immunoprecipitation and high-throughput sequencing approach. We find ∼10,000 G4 structures in human chromatin, predominantly in regulatory, nucleosome-depleted regions. G4 structures are enriched in the promoters and 5' UTRs of highly transcribed genes, particularly in genes related to cancer and in somatic copy number amplifications, such as $\textit{MYC}$. Strikingly, $\textit{de novo}$ and enhanced G4 formation are associated with increased transcriptional activity, as shown by HDAC inhibitor-induced chromatin relaxation and observed in immortalized as compared to normal cellular states. Our findings show that regulatory, nucleosome-depleted chromatin and elevated transcription shape the endogenous human G4 DNA landscape.European Molecular Biology Organization (EMBO Long-Term Fellowship), University of Cambridge, Cancer Research UK (Grant ID: C14303/A17197), Wellcome Trust (Grant ID: 099232/z/12/z

Evaluation of Iranian Scientists Productions in Biotechnology and Applied Microbiology based on ISI through 2000 to 2008

In most countries, internationally indexed scientific publications provide the possibility for the scientometric experts to study their scientific progress. In Iran, the number of scientific productions indexed in ISI was 323 in 1993 and rose to 14832 in 2008 showing about 46 manifolds. The main aim of this research is to illustrate the dynamic structure of scientific productions of Iranian biotechnologists and applied microbiologists in WOS database during 2000–2008. The data was gathered through searching WOS database of ISI. The field of search was country (CU=IRAN). 681 scientific products were reported to be indexed in ISI. Iranians' international collaboration has been mainly with Canadian, Swedish and Australian coauthors. Compared to other Iranian universities, University of Tehran, Tarbiat Modares University and Tehran University of Medical Sciences have contributed mostly to ISI. Iranian biotechnologists’ and microbiologists’ intercontinental collaboration is generally in Biochemistry and Molecular Biology, Engineering and chemical and Biochemical research. There has been an increase in the fundamental research activities in Biotechnology and Applied Microbiology research projects which have triggered motivation for higher contribution to ISI