bluuebunny/crossref_metadata_2025 huggingface dataset:
Towards an optimal search strategy of optical and gravitational wave emissions from binary neutron star coalescence
Authors: Coward D. M. , Gendre B. , Sutton P. J. , Howell E. J. , Regimbau T. , Laas-Bourez M. , Klotz A. , Boër M. , Branchesi M.
Published: June 2011

Observations of an optical source coincident with gravitational wave emission detected from a binary neutron star coalescence will improve the confidence of detection, provide host galaxy localization and test models for the progenitors of short gamma-ray bursts. We employ optical observations of three short gamma-ray bursts, 050724, 050709 and 051221, to estimate the detection rate of a coordinated optical and gravitational wave search of neutron star mergers. Model R-band optical afterglow light curves of these bursts that include a jet-break are extrapolated for these sources at the sensitivity horizon of an Advanced LIGO/Virgo network. Using optical sensitivity limits of three telescopes, namely TAROT (m = 18), Zadko (m = 21) and an 8–10 m class telescope (m = 26), we approximate detection rates and cadence times for imaging. We find a median coincident detection rate of 4 yr-1 for the three bursts. GRB 050724 like bursts, with wide opening jet angles, offer the most optimistic rate of 13 coincident detections per year, and would be detectable by Zadko up to 5 d after the trigger. Late-time imaging to m = 26 could detect off-axis afterglows for GRB 051221 like bursts several months after the trigger. For a broad distribution of beaming angles, the optimal strategy for identifying the optical emissions triggered by gravitational wave detectors is rapid response searches with robotic telescopes followed by deeper imaging at later times if an afterglow is not detected within several days of the trigger.
Too big to fail? The puzzling darkness of massive Milky Way subhaloes
Authors: Boylan-Kolchin Michael , Bullock James S. , Kaplinghat Manoj
Published: June 2011

We show that dissipationless Λ cold dark matter simulations predict that the majority of the most massive subhaloes of the Milky Way are too dense to host any of its bright satellites (LV > 105 L⊙). These dark subhaloes have peak circular velocities at infall of Vinfall= 30–70 km s-1 and infall masses of (0.2–4) × 1010 M⊙. Unless the Milky Way is a statistical anomaly, this implies that galaxy formation becomes effectively stochastic at these masses. This is in marked contrast to the well-established monotonic relation between galaxy luminosity and halo circular velocity (or halo mass) for more massive haloes. We show that at least two (and typically four) of these massive dark subhaloes are expected to produce a larger dark matter annihilation flux than Draco. It may be possible to circumvent these conclusions if baryonic feedback in dwarf satellites or different dark matter physics can reduce the central densities of massive subhaloes by order unity on a scale of 0.3–1 kpc.
The optimal weighting function for cosmic magnification measurements through the foreground galaxy—background galaxy (quasar) cross-correlation
Authors: Yang Xiaofeng , Zhang Pengjie
Published: June 2011

Cosmic magnification has been detected through the cross-correlation between foreground and background populations (galaxies or quasars). It has been shown that weighting each background object by its α− 1 can significantly improve the cosmic magnification measurement. Here α is the logarithmic slope of the luminosity function of background populations. However, we find that this weighting function is optimal only for sparse background populations in which intrinsic clustering is negligible with respect to shot noise. We derive the optimal weighting function for a general case, including scale-independent and scale-dependent weights. The optimal weighting function improves the signal-to-noise ratio by ∼20 per cent for a BigBOSS-like survey and the improvement can reach a factor of ∼2 for surveys with much denser background populations.
Why Do We Need Networking for European Rural Development Policies?  The implementation of LEADER and the National Network for Rural Development in Romania Pourquoi avons‐nous besoin de réseaux pour les politiques de développement rural ?  La mise en œuvre de LEADER et le réseau national pour le développement rural en Roumanie Warum ist Vernetzung wichtig für die europäischen Politikmaßnahmen zur Entwicklung des ländlichen Raums? Die Umsetzung von LEADER und des Nationalen Netzwerks für den ländlichen Raum in Rumänien
Authors: Marquardt Doris , Möllers Judith , Buchenrieder Gertrud
Published: June 2011

summary

Why Do We Need Networking for European Rural Development Policies? The implementation of LEADER and the National Network for Rural Development in Romania

Networking is a political instrument intrinsically tied to social capital. Although the effects are difficult to measure, it is financially supported under the European Agricultural Fund for Rural Development (EAFRD) in the current programming period 2007–13. This article presents the most recent, partly unpublished, data on the EAFRD budget foreseen for networking. EAFRD networking measures include the establishment of the European and National Networks for Rural Development and networking activities within the well‐known LEADER programme. Potential effects of networking activities are presented on the basis of findings of surveys conducted among agencies in Romania and (potential) LEADER beneficiaries in Romania, Hungary and Germany in 2008. We also discuss the importance of European‐wide networking and draw conclusions on whether networking should be funded or not. Based on our findings, we conclude that: 1) cost‐efficient informal networking can have a considerable impact on the implementation of policy measures for rural development; 2) financial support is important if networks need to be stimulated and channelled, and to guarantee continuity; and 3) networking is particularly important for the new member states of the European Union, where, moreover, additional attention should be paid to administrative networking.
Representational neglect for words as revealed by bisection tasks
Authors: Arduino Lisa S. , Marinelli Chiara Valeria , Pasotti Fabrizio , Ferrè Elisa Raffaella , Bottini Gabriella
Published: June 2011

In the present study, we showed that a representational disorder for words can dissociate from both representational neglect for objects and neglect dyslexia. This study involved 14 brain‐damaged patients with left unilateral spatial neglect and a group of normal subjects. Patients were divided into four groups based on presence of left neglect dyslexia and representational neglect for non‐verbal material, as evaluated by the Clock Drawing test. The patients were presented with bisection tasks for words and lines. The word bisection tasks (with words of five and seven letters) comprised the following: (1) representational bisection: the experimenter pronounced a word and then asked the patient to name the letter in the middle position; (2) visual bisection: same as (1) with stimuli presented visually; and (3) motor bisection: the patient was asked to cross out the letter in the middle position. The standard line bisection task was presented using lines of different length. Consistent with the literature, long lines were bisected to the right and short lines, rendered comparable in length to the words of the word bisection test, deviated to the left (crossover effect). Both patients and controls showed the same leftward bias on words in the visual and motor bisection conditions. A significant difference emerged between the groups only in the case of the representational bisection task, whereas the group exhibiting neglect dyslexia associated with representational neglect for objects showed a significant rightward bias, while the other three patient groups and the controls showed a leftward bisection bias. Neither the presence of neglect alone nor the presence of visual neglect dyslexia was sufficient to produce a specific disorder in mental imagery. These results demonstrate a specific representational neglect for words independent of both representational neglect and neglect dyslexia.
The New York Stem Cell Foundation: Fifth Annual Translational Stem Cell Research Conference
Authors: Marshall Caroline , Kai Wang George , Cimetta Elisa , Talchai Chutima , Egli Dieter , Shim Jae‐won , Martin Ian , Ahmad Faizzan , Sproul Andrew , Chen Ting , Fossati Valentina , McKeon David , Smith Kristin , Solomon Susan L.
Published: June 2011

The New York Stem Cell Foundation's “Fifth Annual Translational Stem Cell Research Conference” convened on October 12–13, 2010 at the Rockefeller University in New York City. The conference attracted over 400 scientists, patient advocates, and stem cell research supporters from 16 countries. In addition to poster and platform presentations, the conference featured panels entitled “Road to the Clinic” and “Regulatory Roadblocks.”
G protein–coupled receptor modulation with pepducins: moving closer to the clinic
Authors: Dimond Patricia , Carlson Kenneth , Bouvier Michel , Gerard Craig , Xu Lei , Covic Lidija , Agarwal Anika , Ernst Oliver P. , Janz Jay M. , Schwartz Thue W. , Gardella Thomas J. , Milligan Graeme , Kuliopulos Athan , Sakmar Thomas P. , Hunt III Stephen W.
Published: June 2011

At the 2nd Pepducin Science Symposium held in Cambridge, Massachusetts, on November 4–5, 2010, investigators working in G protein–coupled receptor (GPCR) research convened to discuss progress since last year's inaugural conference. This year's symposium focused on increasing knowledge of the structure and function of this ubiquitous superfamily of membrane receptors and their potential modulation for disease treatment. Presentations also focused on how GPCR mechanisms might be exploited to treat diseases with pepducins, novel synthetic lipopeptide pharmacophores that modulate heptahelical GPCR activity. While the multiple roles of GPCRs in physiological and pathophysiological processes offer significant opportunities for novel drug development, the global nature of their activity challenges drug‐specific and validated target identification. This year's conference highlighted advances in understanding of GPCR agonist and antagonist ligand‐binding motifs, their ligand‐independent functions, structure‐activity relationships (SARs), and evolving unique methods to probe GPCR structure and function. Study results summarized at the meeting also provided evidence for evolving views of how signaling mechanisms work through these receptors.
Mechanism of PrP‐Amyloid Formation in Mice Without Transmissible Spongiform Encephalopathy
Authors: Jeffrey Martin , McGovern Gillian , Chambers Emily V. , King Declan , González Lorenzo , Manson Jean C. , Ghetti Bernardino , Piccardo Pedro , Barron Rona M.
Published: June 2011

Gerstmann–Sträussler–Scheinker (GSS) P102L disease is a familial form of a transmissible spongiform encephalopathy (TSE) that can present with or without vacuolation of neuropil. Inefficient disease transmission into 101LL transgenic mice was previously observed from GSS P102L without vacuolation. However, several aged, healthy mice had large plaques composed of abnormal prion protein (PrPd). Here we perform the ultrastructural characterization of such plaques and compare them with PrPd aggregates found in TSE caused by an infectious mechanism. PrPd plaques in 101LL mice varied in maturity, with some being composed of deposits without visible amyloid fibrils. PrPd was present on cell membranes in the vicinity of all types of plaques. In contrast to the unicentric plaques seen in infectious murine scrapie, the plaques seen in the current model were multicentric and were initiated by protofibrillar forms of PrPd situated on oligodendroglia, astrocytes and neuritic cell membranes. We speculate that the initial conversion process leading to plaque formation begins with membrane‐bound PrPC but that subsequent fibrillization does not require membrane attachment. We also observed that the membrane alterations consistently seen in murine scrapie and other infectious TSEs were not present in 101LL mice with plaques, suggesting differences in the pathogenesis of these conditions.
Determination of Reference Values for NIST SRM 610–617 Glasses Following ISO Guidelines
Authors: Jochum Klaus Peter , Weis Ulrike , Stoll Brigitte , Kuzmin Dmitry , Yang Qichao , Raczek Ingrid , Jacob Dorrit E. , Stracke Andreas , Birbaum Karin , Frick Daniel A. , Günther Detlef , Enzweiler Jacinta
Published: June 2011

We present new reference values for the NIST SRM 610–617 glasses following ISO guidelines and the International Association of Geoanalysts’ protocol. Uncertainties at the 95% confidence level (CL) have been determined for bulk‐ and micro‐analytical purposes. In contrast to former compilation procedures, this approach delivers data that consider present‐day requirements of data quality. New analytical data and the nearly complete data set of the GeoReM database were used for this study. Data quality was checked by the application of the Horwitz function and by a careful investigation of analytical procedures. We have determined quantitatively possible element inhomogeneities using different test portion masses of 1, 0.1 and 0.02 μg. Although avoiding the rim region of the glass wafers, we found moderate inhomogeneities of several chalcophile/siderophile elements and gross inhomogeneities of Ni, Se, Pd and Pt at small test portion masses. The extent of inhomogeneity was included in the determination of uncertainties. While the new reference values agree with the NIST certified values with the one exception of Mn in SRM 610, they typically differ by as much as 10% from the Pearce et al. (1997) values in current use. In a few cases (P, S, Cl, Ta, Re) the discrepancies are even higher.
Evaluation of hyaluronan gel (Gengigel®) as a topical applicant in the treatment of gingivitis
Authors: Sapna Nadiger , Vandana Kharidi Laxman
Published: June 2011

Aim:  To clinically and histopathologically evaluate the anti‐inflammatory effect of 0.2% hyaluronan gel alone and with mechanical therapy on gingivitis. The argyrophilic nucleolar organizer region staining technique was attempted to routinely determine its diagnostic and prognostic dependability for periodontal lesions.

Methods:  In each of the 28 gingivitis patients, the four quadrants were subjected to different treatments: scaling, scaling + topical hyaluronan gel, only topical hyaluronan gel, and topical + intrasulcular hyaluronan gel. Clinical parameters were recorded at baseline, and on days 7, 14, and 21. Biopsies were taken from each quadrant, inflammatory infiltrates were graded, and the argyrophilic nucleolar organizer region count was measured before and after treatment.

Results:  A significant reduction was seen in clinical parameters, inflammatory infiltrates, and the argyrophilic nucleolar organizer region count within the groups. The effect of topical + intrasulcular gel was equivalent to scaling (P > 0.05). Topical + intrasulcular hyaluronan gel application demonstrated a better reduction than topical hyaluronan gel alone.

Conclusions:  Hyaluronan gel is an effective topical agent for treating gingivitis, along with scaling and intrasulcular application. The argyrophilic nucleolar organizer region count can be used as a histopathological indicator in cases of non‐responsive gingivitis to assess the severity of gingival inflammation.
Congenital double upper lip: review of literature and report of a case
Authors: Ariyawardana Anura
Published: June 2011

Congenital maxillary double lip is a rare anomaly in which a fold of redundant labial tissue becomes apparent at rest or while smiling. This might pose cosmetic or functional problems, as well as serious impact on psychological well‐being, especially when it affects young children or adolescents. The treatment of choice is surgical excision. This paper presents a successfully managed case of maxillary double lip using elliptical incision under local anesthesia in a 15‐year‐old female patient.
Distance‐based multivariate analyses confound location and dispersion effects
Authors: Warton David I. , Wright Stephen T. , Wang Yi
Published: June 2011

1. A critical property of count data is its mean–variance relationship, yet this is rarely considered in multivariate analysis in ecology.

2. This study considers what is being implicitly assumed about the mean–variance relationship in distance‐based analyses – multivariate analyses based on a matrix of pairwise distances – and what the effect is of any misspecification of the mean–variance relationship.

3. It is shown that distance‐based analyses make implicit assumptions that are typically out‐of‐step with what is observed in real data, which has major consequences.

4. Potential consequences of this mean–variance misspecification are: confounding location and dispersion effects in ordinations; misleading results when trying to identify taxa in which an effect is expressed; failure to detect a multivariate effect unless it is expressed in high‐variance taxa.

5. Data transformation does not solve the problem.

6. A solution is to use generalised linear models and their recent multivariate generalisations, which is shown here to have desirable properties.
Gender‐specific contribution of a visual cognition network to reading abilities
Authors: Huestegge Lynn , Heim Stefan , Zettelmeyer Elena , Lange‐Küttner Christiane
Published: June 2011

Based on the assumption that boys are more likely to tackle reading based on the visual modality, we assessed reading skills, visual short‐term memory (VSTM), visual long‐term memory for details (VLTM‐D), and general non‐verbal cognitive ability in primary school children. Reading was within the normal range in both accuracy and understanding. There was no reading performance gap in favour of girls, on the contrary, in this sample boys read better. An entire array of visual, non‐verbal processes was associated directly or indirectly with reading in boys, whereas this pattern was not observed for the girls.
Admitting evidence of a defendant's previous conviction (PCE) and its impact on juror deliberation in relation to both juror‐processing style and juror concerns over the fairness of introducing PCE
Authors: Honess T. M. , Mathews G. A.
Published: June 2011

Purpose. To examine the impact of admitting previous conviction evidence (PCE) on juror and jury deliberation. Major questions are: (1) Is there is an association between the inclusion of PCE and confidence in a defendant's guilt using a relatively rich trial simulation? (2) Does PCE invoke jurors’ considerations of fairness to the defendant? (3) Is heuristic processing (HP) associated with a prejudicial interpretation of evidence?

Methods. In experiment 1 (n= 82), individual jurors were asked to recall evidence, express opinion, and justify verdicts on the two counts of Affray and Grievous Bodily Harm (GBH). In experiment 2 (new n= 121), PCE information was emphasized and a jury deliberation condition was included.

Results. There was no simple association between admitting PCE and judgements of guilt. However, both interviews and jury deliberations indicated careful consideration of evidence. In particular, juror arguments showed that some were troubled by PCE, which they saw as unwarranted and therefore unfair to the defendant. Finally, HP was associated with both a prejudicial focus on the defendant's character and a higher confidence in guilt.

Conclusions. A simple link between PCE and judgements of guilt may only hold in relatively circumscribed experimental simulations. Results also indicate that the introduction of PCE is unlikely to aid evidence‐based deliberation without careful testing of different forms of judges’ explanation concerning PCE.
Validation and Adjustment of Prior and Data for Bayesian Reliability Analysis in Engineering Design
Authors: Huang Zhaofeng , Jin Yan
Published: June 2011

Bayesian reliability analysis (BRA) technique has been actively used in reliability assessment for engineered systems. However, there are two key controversies surrounding the BRA: the reasonableness of the prior and the consistency among all data sets. These issues have been debated in Bayesian analysis for many years. As we observed, they have not been resolved satisfactorily. These controversies have seriously hindered the applications of BRA as a useful reliability analysis tool to support engineering design. In this paper, a Bayesian reliability analysis methodology with a prior and data validation and adjustment scheme (PDVAS) is developed to address these issues. As the part of the PDVAS development, a consistency measure is first defined that judges the level of consistency among all data sets including the prior. The consistency measure is then used to adjust either the prior or the data or both to the extent that the prior and the data are statistically consistent. This prior and data validation and adjustment scheme is developed for Binomial sampling with Beta prior, called Beta-Binomial Bayesian model. The properties of the scheme are presented and discussed that provides some insights of PDVAS. Various forms of the adjustment formulas are shown, and a selection framework of a specific formula, based on engineering design and analysis knowledge, is established. Several illustrative examples are presented, which show the reasonableness, effectiveness, and usefulness of PDVAS. General discussion of the scheme is offered to enhance the Bayesian reliability analysis in engineering design for reliability assessment.
Kinematic Effect of the Compliant Cup in Harmonic Drives
Authors: Dong Huimin , Wang Delun , Ting Kwun-Lon
Published: June 2011

The paper and its companion [Dong et al., 2011, “Kinematic Fundamentals of Planar Harmonic Drives,” ASME J. Mech. Des., 133(1), p. 011007], which treats a harmonic drive without a cup, present the geometry-relevant operation of harmonic drives under an ideal little or no-load condition. This paper shows that the cup is essentially a compliant mechanism with the unique feature of transforming a set of different tooth rotations into a single rigid body rotation and demonstrates how the cup affects tooth conjugation and the conjugate tooth profiles. It proves and demonstrates that the conjugating tooth profile should be a three-dimensional surface because of the cup deformation. The use of spur gears on both flexspline and circular spline will cause excessive interference and excessive deformation will become necessary to overcome the interference. Since no-load geometry is clearly identified, excessive deformation and errors due to incorrect geometry can be removed or filtered and the loading effects can be identified. Contact ratio of a harmonic drive is also obtained through the range of conjugate positions. Although loading is not considered, the geometric error is. Eliminating or reducing geometric error will improve the performance.
An Alternative Formulation of Collaborative Optimization Based on Geometric Analysis
Authors: Li Xiang , Liu Changan , Li Weiji , Long Teng
Published: June 2011

Collaborative optimization (CO) is a multidisciplinary design optimization (MDO) method with bilevel computational structure, which decomposes the original optimization problem into one system-level problem and several subsystem problems. The strategy of decomposition in CO is a useful way for solving large engineering design problems. However, the computational difficulties caused by the system-level consistency equality constraints hinder the development of CO. In this paper, an alternative formulation of CO called CO with combination of linear approximations (CLA-CO) is presented based on the geometric analysis of CO, which is more intuitive and direct than the previous algebraic analysis. In CLA-CO, the consistency equality constraints in CO are replaced by linear approximations to the subsystem responses. As the iterative process goes on, more linear approximations are added into the system level. Consequently, the combination of these linear approximations makes the system-level problem gradually approximate the original problem. In CLA-CO, the advantages of the decomposition strategy are maintained while the computational difficulties of the conventional CO are avoided. However, there are still difficulties in applying the presented CLA-CO to problems with nonconvex constraints. The application of CLA-CO to three optimization problems, a numerical test problem, a composite beam design problem, and a gear reducer design problem, illustrates the capabilities and limitations of CLA-CO.
On the Design of Interference-Fitted and Adhesively Bonded Joints for Lightweight Structures
Authors: Croccolo Dario , Vincenzi Nicolò
Published: June 2011

Interference-fitted and adhesively bonded joints are hybrid fastening systems that involve a hub (cylindrical or asymmetric) and a shaft (solid or hollow) locked together by both a frictional force (based on the radial pressure and the Coulomb friction law) and an adhesive strength generated at their coupling surfaces. Total interface forces allow the transmission of a high torque moment and/or a high axial force with respect to the joint dimension so that hybrid joints are demonstrated to be a smart solution for lightweight structures. This paper investigates the optimal combinations of geometrical parameters (ratios between internal and external diameters of the shaft and the hub) in order to maximize the axial load transmitted by the joint as well as to save the weight of the structure. Some design formulae, based on the maximum shear (Tresca) yield criterion, are proposed as a function of different materials for both the shaft and the hub (steel, aluminum, magnesium, and titanium).
Numerical ellipsometry: n-k plane analysis of transparent conducting films
Authors: Barton D. , Urban F. K.
Published: June 2011

It is well known that across the optical spectrum, indium tin oxide (ITO) has a window of transparency and that it is optically opaque (has a high extinction coefficient, k) at energies outside of the window. Such a material presents a particular challenge to ellipsometry data analysis arising from these different optical behaviors. The purpose of this work is to apply n-k plane data analysis to such an ITO film. An ITO film grown on a silicon substrate was measured at 293 wavelengths, every 5 nm from 210 to 1700 nm, and at each of three incidence angles of 55°, 65°, and 75°. Thus at each wavelength, there are three measurements which result in a set of three solution curves. If measurements had no experimental uncertainty and if the film were “perfect,” the three curves would intersect at a point at the value of film n, k, and d. In actual fact, they come close to intersecting and have a region of closest approach. The key result is that the mathematics supports different approximating film models across wavelength, considering measurement error. In the transparent region from approximately 300–980 nm, the ITO matches a single layer film ideal model while additional layers do not result in improved modeling due to measurement error. On the other hand, due to the underlying mathematics, from 980 to 1000 nm a two-layer ideal model provides two well defined intersections and so there are six real number unknowns which may be determined. At longer wavelengths, the film corresponds to an absorbing layer which appears vertically inhomogeneous but which cannot be well characterized due to the different light interaction depths at the three incidence angles. Lorenz, Cauchy, Drude, generalized oscillator, and other models of optical properties as a function of light wavelength were not used. Additional measurements, for example during film growth, are needed to further refine the modeling.
Improved oxidation resistance of Ru/Si capping layer for extreme ultraviolet lithography reflector
Authors: Park Jeong Y. , Belau Leonid , Seo Hyungtak , Somorjai Gabor A.
Published: June 2011

The authors report on the chemical durability and oxidation resistance of Ru/Si, Ru/B, Ru/C, and Ru capping layers on the extreme ultraviolet (EUV) reflector surface. Surface etching and changes in the oxidation state were probed with x-ray photoelectron spectroscopy. The changes in surface morphology and roughness are characterized using scanning electron microscopy and atomic force microscopy. Out of four different capping layers, Ru/Si layers exhibited the least surface oxidation after oxygen plasma and UV/ozone treatment, indicating a superior oxidation resistance. The authors found that the reflectivity of the Ru/Si capped reflector is similar to that of a bare Ru capped reflector. This study suggests that a Ru/Si layer can be an excellent capping layer for the EUV reflector.
Deep electron and hole traps in neutron transmutation doped n-GaN
Authors: Lee In-Hwan , Polyakov A. Y. , Smirnov N. B. , Govorkov A. V. , Kozhukhova E. A. , Kolin N. G. , Boiko V. M. , Korulin A. V. , Pearton S. J.
Published: June 2011

In neutron transmutation doped n-GaN, the electrical properties are found to be dominated not by shallow Ge donors produced by interaction of thermal neutrons with Ga, but by electron traps at 0.45 or 0.2 eV. The traps switch from the former to the latter when the anneal temperature increased from 800 to 1000 °C. The concentrations of both traps rose linearly with neutron fluence and were close to the concentration of Ge donors, suggesting they are Ge complexed with different radiation defects. The authors note the similarity of the properties of these traps to the properties of the dominant electron traps in as-irradiated n-GaN. They also observed prominent hole traps with a level near Ev+1.2 eV. These traps were not detected in virgin or as-irradiated samples. The concentration of the 1.2 eV hole traps increased linearly with neutron fluence, and these traps were assigned to Ga vacancy complexes with oxygen.
Genetic Control of Biosynthesis and Transport of Riboflavin and Flavin Nucleotides and Construction of Robust Biotechnological Producers
Authors: Abbas Charles A. , Sibirny Andriy A.
Published: June 2011

Riboflavin [7,8-dimethyl-10-(1′-d-ribityl)isoalloxazine, vitamin B2] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded bySEF1is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains ofBacillus subtilis,Ashbya gossypii, andCandida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.
cis-Antisense RNA, Another Level of Gene Regulation in Bacteria
Authors: Georg Jens , Hess Wolfgang R.
Published: June 2011

A substantial amount of antisense transcription is a hallmark of gene expression in eukaryotes. However, antisense transcription was first demonstrated in bacteria almost 50 years ago. The transcriptomes of bacteria as different asHelicobacter pylori,Bacillus subtilis,Escherichia coli,Synechocystissp. strain PCC6803,Mycoplasma pneumoniae,Sinorhizobium meliloti,Geobacter sulfurreducens,Vibrio cholerae,Chlamydia trachomatis,Pseudomonas syringae, andStaphylococcus aureushave now been reported to contain antisense RNA (asRNA) transcripts for a high percentage of genes. Bacterial asRNAs share functional similarities withtrans-acting regulatory RNAs, but in addition, they use their own distinct mechanisms. Among their confirmed functional roles are transcription termination, codegradation, control of translation, transcriptional interference, and enhanced stability of their respective target transcripts. Here, we review recent publications indicating that asRNAs occur as frequently in simple unicellular bacteria as they do in higher organisms, and we provide a comprehensive overview of the experimentally confirmed characteristics of asRNA actions and intimately linked quantitative aspects. Emerging functional data suggest that asRNAs in bacteria mediate a plethora of effects and are involved in far more processes than were previously anticipated. Thus, the functional impact of asRNAs should be considered when developing new strategies against pathogenic bacteria and when optimizing bacterial strains for biotechnology.
Atomic Force Microscopy in Imaging of Viruses and Virus-Infected Cells
Authors: Kuznetsov Yurii G. , McPherson Alexander
Published: June 2011

Atomic force microscopy (AFM) can visualize almost everything pertinent to structural virology and at resolutions that approach those for electron microscopy (EM). Membranes have been identified, RNA and DNA have been visualized, and large protein assemblies have been resolved into component substructures. Capsids of icosahedral viruses and the icosahedral capsids of enveloped viruses have been seen at high resolution, in some cases sufficiently high to deduce the arrangement of proteins in the capsomeres as well as the triangulation number (
T
). Viruses have been recorded budding from infected cells and suffering the consequences of a variety of stresses. Mutant viruses have been examined and phenotypes described. Unusual structural features have appeared, and the unexpectedly great amount of structural nonconformity within populations of particles has been documented. Samples may be imaged in air or in fluids (including culture medium or buffer),
in situ
on cell surfaces, or after histological procedures. AFM is nonintrusive and nondestructive, and it can be applied to soft biological samples, particularly when the tapping mode is employed. In principle, only a single cell or virion need be imaged to learn of its structure, though normally images of as many as is practical are collected. While lateral resolution, limited by the width of the cantilever tip, is a few nanometers, height resolution is exceptional, at approximately 0.5 nm. AFM produces three-dimensional, topological images that accurately depict the surface features of the virus or cell under study. The images resemble common light photographic images and require little interpretation. The structures of viruses observed by AFM are consistent with models derived by X-ray crystallography and cryo-EM.
Regulatory Circuitry Governing Fungal Development, Drug Resistance, and Disease
Authors: Shapiro Rebecca S. , Robbins Nicole , Cowen Leah E.
Published: June 2011

Pathogenic fungi have become a leading cause of human mortality due to the increasing frequency of fungal infections in immunocompromised populations and the limited armamentarium of clinically useful antifungal drugs.
Candida albicans
,
Cryptococcus neoformans
, and
Aspergillus fumigatus
are the leading causes of opportunistic fungal infections. In these diverse pathogenic fungi, complex signal transduction cascades are critical for sensing environmental changes and mediating appropriate cellular responses. For
C. albicans
, several environmental cues regulate a morphogenetic switch from yeast to filamentous growth, a reversible transition important for virulence. Many of the signaling cascades regulating morphogenesis are also required for cells to adapt and survive the cellular stresses imposed by antifungal drugs. Many of these signaling networks are conserved in
C. neoformans
and
A. fumigatus
, which undergo distinct morphogenetic programs during specific phases of their life cycles. Furthermore, the key mechanisms of fungal drug resistance, including alterations of the drug target, overexpression of drug efflux transporters, and alteration of cellular stress responses, are conserved between these species. This review focuses on the circuitry regulating fungal morphogenesis and drug resistance and the impact of these pathways on virulence. Although the three human-pathogenic fungi highlighted in this review are those most frequently encountered in the clinic, they represent a minute fraction of fungal diversity. Exploration of the conservation and divergence of core signal transduction pathways across
C. albicans
,
C. neoformans
, and
A. fumigatus
provides a foundation for the study of a broader diversity of pathogenic fungi and a platform for the development of new therapeutic strategies for fungal disease.
Nucleosome Positioning in Saccharomyces cerevisiae
Authors: Jansen An , Verstrepen Kevin J.
Published: June 2011

The DNA of eukaryotic cells is spooled around large histone protein complexes, forming nucleosomes that make up the basis for a high-order packaging structure called chromatin. Compared to naked DNA, nucleosomal DNA is less accessible to regulatory proteins and regulatory processes. The exact positions of nucleosomes therefore influence several cellular processes, including gene expression, chromosome segregation, recombination, replication, and DNA repair. Here, we review recent technological advances enabling the genome-wide mapping of nucleosome positions in the model eukaryote
Saccharomyces cerevisiae
. We discuss the various parameters that determine nucleosome positioning
in vivo
, including
cis
factors like AT content, variable tandem repeats, and poly(dA:dT) tracts that function as chromatin barriers and
trans
factors such as chromatin remodeling complexes, transcription factors, histone-modifying enzymes, and RNA polymerases. In the last section, we review the biological role of chromatin in gene transcription, the evolution of gene regulation, and epigenetic phenomena.
Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch
Authors: Zhang Guoyu , Cheng Zhijun , Zhang Xin , Guo Xiuping , Su Ning , Jiang Ling , Mao Long , Wan Jianmin
Published: June 2011

Soluble starch synthases (SSs) are major enzymes involved in starch biosynthesis in developing rice ( Oryza sativa L.) endosperm. Despite extensive studies of SSs in various plant species including rice, the functional modes of action among multiple SS genes are still not clear. Here, we generated transgenic RNA interference (RNAi) repressed lines for seven of the eight members of the rice SS gene family and studied their effects on starch synthesis and grain formation. Consistent with their expression domains, RNAi repression of genes that encode isozymes SSI, SSIIa, and SSIIIa had strong effects on grain development, whereas no obvious phenotypic changes were observed in transgenic plants with the other SS genes being RNAi repressed, indicating functional redundancies among the genes. To study the potential functional interactions of SS genes, we generated SSIIa/SSIIIa double repression lines whose kernels displayed a chalky kernel appearance and had increased amylose levels, increased pasting temperatures, and decreased viscosities. The double mutation also reduced short (degree of polymerization (DP) 5–6) and long (DP 12–23) amylopectin chain contents in the grain and increased the medium long types (DP 7–11). The nonadditive nature of the double mutation line suggests that SSIIa and SSIIIa interact with each other during starch synthesis. Such interaction may be physical via starch phophorylase as indicated by our pair-wise yeast two-hybrid assays on major starch synthesis enzymes. Collectively, the data showed that SSIIa and SSIIIa play distinctive, but partially overlapping, roles during rice grain starch synthesis. The possibility of extensive redundancy or complementarity among SS isozymes is discussed.
Characterization of a plant-transformation-ready large-insert BIBAC library ofArabidopsisand bombardment transformation of a large-insert BIBAC of the library into tobacco
Authors: Chang Yueh-Long , Chuang Huey-Wen , Meksem Khalid , Wu Fang-Chun , Chang Chang-Yee , Zhang Meiping , Zhang Hong-Bin
Published: June 2011

Plant-transformation-ready, large-insert binary bacterial artificial chromosome (BIBAC) libraries are of significance for functional and network analysis of large genomic regions, gene clusters, large-spanning genes, and complex loci in the post-genome era. Here, we report the characterization of a plant-transformation-ready BIBAC library of the sequenced Arabidopsis genome for which such a library is not available to the public, the transformation of a large-insert BIBAC of the library into tobacco by biolistic bombardment, and the expression analysis of its containing genes in transgenic plants. The BIBAC library was constructed from nuclear DNA partially digested with BamHI in the BIBAC vector pCLD04541. It contains 6144 clones and has a mean insert size of 108 kb, representing 5.2× equivalents of the Arabidopsis genome or a probability of greater than 99% of obtaining at least one positive clone from the library using a single-copy sequence as a probe. The transformation of the large-insert BIBAC and analyses of the transgenic plants showed that not only did transgenic plants have intact BIBAC DNA, but also could the BIBAC be transmitted stably into progenies and its containing genes be expressed actively. These results suggest that the large-insert BIBAC library, combined with the biolistic bombardment transformation method, could provide a useful tool for large-scale functional analysis of the Arabidopsis genome sequence and applications in plant-molecular breeding.
Transcript profiling and gene characterization of three fatty acid desaturase genes in high, moderate, and low linolenic acid genotypes of flax (Linum usitatissimumL.) and their role in linolenic acid accumulation
Authors: Banik Mitali , Duguid Scott , Cloutier Sylvie
Published: June 2011

Three genes encoding fatty acid desaturase 3 (fad3a, fad3b, and a novel fad3c) were cloned from four flax genotypes varying in linolenic acid content. Real-time PCR was used to quantify expression levels of the three fad3 genes during seed development. High amounts of both fad3a and fad3b transcripts were observed and reached their peak levels at 20 days after anthesis, except for fad3a from SP2047 where only low level expression was observed throughout seed development. Transcript accumulation of the novel fad3c gene was at similar background levels. The fatty acid composition was analysed for all genotypes and stages of development and compared with the fad3 gene expression patterns. α-Linolenic acid gradually accumulated during seed development, while linoleic acid was transient and decreased in M5791, UGG5-5, and AC McDuff. In contrast, the linolenic acid present in the early stages of development nearly completely disappeared in SP2047, while linoleic acid steadily accumulated. fad3a of the low linolenic acid line SP2047 encoded a truncated protein caused by a premature stop codon resulting from a single point mutation, and the low level of transcript accumulation in this genotype is likely due to nonsense-mediated mRNA decay caused by the premature termination of translation as a result of this early stop codon. Although substantial amounts of transcript accumulation occurred with fad3b of SP2047 genotype, cloning of the gene revealed a mutation in the first histidine box causing an amino acid change. Heterologous expression in yeast of the SP2047 and UGG5-5 fad3b genes showed that the mutation in the histidine box in SP2047 caused the enzyme inactivity. Taken together, these results showed that fad3a and fad3b are responsible for linolenic acid accumulation in flax seeds but did not support a major role for the novel fad3c. These observations were further supported by phenotypic and genotypic assessment of a doubled haploid population. Expression patterns of fad3a and fad3b were highly correlated with linolenic acid accumulation during seed development, with the exception of fad3b in SP2047 whose lack of activity was caused by the histidine box mutation despite its transcript accumulation being similar to that of the fad3b of the other genotypes.
Genetic association of crown rust resistance genePc68, storage protein loci, and resistance gene analogues in oats
Authors: Satheeskumar Sivakala , Sharp Peter J. , Lagudah Evans S. , McIntosh Robert A. , Molnar Stephen J.
Published: June 2011

Segregating F3families, derived from a cross between oat cultivar Swan and the putative single gene line PC68, were used to determine the association of seed storage protein loci and resistance gene analogues (RGAs) with the crown rust resistance gene Pc68. SDS–PAGE analysis detected three avenin loci, AveX, AveY, and AveZ, closely linked to Pc68. Their diagnostic alleles are linked in coupling to Pc68 and were also detected in three additional lines carrying Pc68. Another protein locus was linked in repulsion to Pc68. In complementary studies, three wheat RGA clones (W2, W4, and W10) detected restriction fragment length polymorphisms (RFLPs) between homozygous resistant and homozygous susceptible F3DNA bulks. Four oat homologues of W2 were cloned and sequenced. RFLPs detected with two of them were mapped using F3and F4populations. Clone 18 detected a locus, Orga2, linked in repulsion to Pc68. Clone 22 detected several RFLPs including Orga1 (the closest locus to Pc68) and three RGA loci (Orga22-2, Orga22-3, and Orga22-4) loosely linked to Pc68. The diagnostic RFLPs linked in coupling to Pc68 were detected by clone 22 in three additional oat lines carrying Pc68 and have potential utility in investigating and improving crown rust resistance of oat.
Genetic structure of landraces in foxtail millet (Setaria italica(L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet
Authors: Hirano Ryoko , Naito Ken , Fukunaga Kenji , Watanabe Kazuo N. , Ohsawa Ryo , Kawase Makoto
Published: June 2011

Although the origin and domestication process of foxtail millet (Setaria italica subsp. italica (L.) P. Beauv.) has been studied by several groups, the issue is still ambiguous. It is essential to resolve this issue by studying a large number of accessions with sufficient markers covering the entire genome. Genetic structures were analyzed by transposon display (TD) using 425 accessions of foxtail millet and 12 of the wild ancestor green foxtail (Setaria italica subsp. viridis (L.) P. Beauv.). We used three recently active transposons (TSI-1, TSI-7, and TSI-10) as genome-wide markers and succeeded in demonstrating geographical structures of the foxtail millet. A neighbor-joining dendrogram based on TD grouped the foxtail millet accessions into eight major clusters, each of which consisted of accessions collected from adjacent geographical areas. Eleven out of 12 green foxtail accessions were grouped separately from the clusters of foxtail millet. These results indicated strong regional differentiations and a long history of cultivation in each region. Furthermore, we discuss the relationship between foxtail millet and green foxtail and suggest a monophyletic origin of foxtail millet domestication.