bluuebunny/crossref_metadata_2025 huggingface dataset:
Relaxation of packaging-induced strains in AlGaAs-based high-power diode laser arrays
Authors: Tien Tran Quoc , Gerhardt Axel , Schwirzke-Schaaf Sandy , Tomm Jens W. , Müntz Holger , Biesenbach Jens , Oudart Myriam , Nagle Julien , Biermann Mark L.
Published: March 2005

We monitor the mechanical strain evolution with typical use in the quantum well of AlGaAs∕GaAs-based high-power diode laser arrays (cm bars) by spectroscopic means. We show experimentally that pristine devices are essentially uniaxially compressed along the 110-direction with a strain maximum of −0.16% at the center of the device. At the device edges, almost no packaging-induced strain is detectable. After 500h of continuous wave operation at a current of I=80A, the strain is reduced by 50%. Furthermore, we observe the growth of a localized region of compressive strain, of hydrostatic symmetry, in one emitter of a particular cm-bar. A compression of about −0.017% is observed, and is most likely caused by point defect accumulation. Our results demonstrate information about absolute strain values and, at least in part, about strain symmetry as well can be obtained by spectroscopic means even within packaged complex optoelectronic devices.
Covalently linked deoxyribonucleic acid with multiwall carbon nanotubes: Synthesis and characterization
Authors: Chen Weiwei , Tzang Chi Hung , Tang Jianxin , Yang Mengsu , Lee Shuit Tong
Published: March 2005

We have developed a multistep method to covalently link functionalized multiwall carbon nanotubes (MWNT) to deoxyribonucleic acid (DNA) oligonucleotides. X-ray photoelectron spectroscopy was used to characterize the initial chemical modification to form amine-terminated MWNTs, which were then covalently combined with DNA. The morphology recorded by atomic force microscopy gave direct and explicit imaging of the resulting DNA-MWNT adducts, showing that chemical functionalization occurred at the ends and sidewalls of MWNTs. The present methodology is an important first step in realizing a DNA-guided self-assembly process for carbon nanotubes.
Critical thickness of ultrathin ferroelectric BaTiO3 films
Authors: Kim Y. S. , Kim D. H. , Kim J. D. , Chang Y. J. , Noh T. W. , Kong J. H. , Char K. , Park Y. D. , Bu S. D. , Yoon J.-G. , Chung J.-S.
Published: March 2005

To investigate the critical thickness of ferroelectric BaTiO3 (BTO) films, we fabricated fully strained SrRuO3∕BTO∕SrRuO3 heterostructures on SrTiO3 substrates by pulsed laser deposition with in situ reflection high-energy electron diffraction. We varied the BTO layer thickness from 3to30nm. By fabricating 10×10μm2 capacitors, we could observe polarization versus electric-field hysteresis loops, which demonstrate the existence of ferroelectricity in BTO layers thicker than 5nm. This observation provides an experimental upper bound of 5nm for the critical thickness. The BTO thickness-dependent scaling of the remanent polarization agrees with the predictions of recent first-principle simulations [J. Junquera and P. Ghosez, Nature 422, 506 (2003)].
A prototype protein field-effect transistor
Authors: Yau Siu-Tung , Qian Guoguang
Published: March 2005

Electrical conduction in a macroscopic assembly of apoferritin, a non-redox protein, has been characterized using a three-terminal prototype device. Our result shows an ohmic conduction near zero bias. The ohmic conduction can be controlled using an electric field applied to the protein assembly via the gate terminal of the device. The transconductance of the protein device shows a highly nonlinear dependence on the gate voltage. The transconductance curve indicates that the device has the attributes of an n-channel metal-oxide-semiconductor field-effect transistor with electrons as charge carriers. The input/output dynamic response of the device has been demonstrated.
Luminescence studies of Ti-doped Al2O3 using vacuum ultraviolet synchrotron radiation
Authors: Mikhailik V. B. , Kraus H. , Wahl D. , Mykhaylyk M. S.
Published: March 2005

In this study, we examined the luminescence response of Ti-doped Al2O3 crystals to high-energy vacuum ultraviolet (UV) excitation. In addition to the thoroughly studied emission band of Ti3+ in the near-infrared region and blue emission at 420nm, we detected a UV emission band at 290nm. The excitation spectra of all emission bands were measured over the 4–20eV spectral range. Our results indicate that intrinsic anion defects are involved in the process of the excitation of the 420nm emission assigned to the charge transfer transitions 2pO2−→3dTi4+. Analysis of the spectral and decay characteristics of the UV emission enables us to suggest that this band is associated with radiative decay of excitons localized at Ti ions.
Ultrasensitive displacement sensing using photonic crystal waveguides
Authors: Levy O. , Steinberg B. Z. , Nathan M. , Boag A.
Published: March 2005

We present an ultrasensitive displacement sensor and sensing technique based on photonic crystal waveguides (PCWG), useful for integration with microelectromechanical system (MEMS) structures. The sensor consists of two PCWGs aligned along a common axis, one mounted on a moving part and the other fixed to a stationary substrate. A gap between the fixed and moving PCWGs creates an intersection with a third, perpendicular PCWG, which has two branches. The intensity exiting each PCWG changes when the suspended PCWG moves in plane relative to the fixed one. The difference in intensities exiting the two perpendicular PCWG branches can be correlated with the relative displacement between the fixed and moving PCWGs. Numerical simulations predict a sensitivity of ∼1[μm−1] using a light source of 9.02μm.
Nickel nanocrystal formation on HfO2 dielectric for nonvolatile memory device applications
Authors: Lee Jong Jin , Harada Yoshinao , Pyun Jung Woo , Kwong Dim-Lee
Published: March 2005

This letter presents the formation of nickel nanocrystal on HfO2 high-k dielectric and its application to the nonvolatile memory devices. The effects of the initial nickel layer thickness and annealing temperature on nickel nanocrystal formation are investigated. The n-metal-oxide-semiconductor field-effect transistor with nickel nanocrystals and HfO2 tunneling dielectrics is fabricated and its programming, data retention, and endurance properties are characterized to demonstrate its advantages for nonvolatile memory device applications.
Effect of doping on the magnetic properties of GaMnN: Fermi level engineering
Authors: Reed M. J. , Arkun F. E. , Berkman E. A. , Elmasry N. A. , Zavada J. , Luen M. O. , Reed M. L. , Bedair S. M.
Published: March 2005

GaMnN dilute magnetic semiconductor samples, prepared by metalorganic chemical vapor deposition, are shown to exhibit ferromagnetism or even paramagnetism depending upon the type and concentration of extrinsic impurity present in the film. In addition, GaMnN deposited using growth parameters normally yielding a nonferromagnetic film becomes strongly ferromagnetic with the addition of magnesium, an acceptor dopant. Based upon these observations, it seems that ferromagnetism in this material system depends on the relative position of the Mn energy band and the Fermi level within the GaMnN band gap. Only when the Fermi level closely coincides with the Mn-energy level is ferromagnetism achieved. By actively engineering the Fermi energy to be within or near the Mn energy band, room temperature ferromagnetism is realized.
First-principles study of Ti-doped sodium alanate surfaces
Authors: Íñiguez Jorge , Yildirim Taner
Published: March 2005

We have performed first-principles calculations of thick slabs of Ti-doped sodium alanate (NaAlH4), which allows one to study the system energetics as the dopant progresses from the surface to the bulk. Our calculations predict that Ti stays on the surface, substitutes for Na, and attracts a large number of H atoms to its vicinity. Molecular dynamics simulations suggest that the most likely product of the Ti doping is the formation of H-rich TiAln(n>1) compounds on the surface, and hint at the mechanism by which Ti enhances the reaction kinetics of NaAlH4.
Measurements of energy fluctuations of a saturated 46.9nm Ar laser produced in Z-pinch capillary discharges
Authors: Ritucci A. , Tomassetti G. , Reale A. , Reale L. , Flora F. , Mezi L.
Published: March 2005

We report on the achievement of significant energy stability in a 46.9nm soft x-ray laser pumped by fast Z-pinch capillary discharges. The energy stability, investigated over, hundreds of shots, is optimized by operating the laser in the highly saturated regime using capillary discharges with length up to 45cm. We demonstrate standard deviation on the energy fluctuations smaller than ±5% and an energy∕pulse of 300μJ at 0.2Hz. These results demonstrate the reliability of this soft x-ray laser for its widespread use for the development of applications.
Effect of inductively coupled plasma damage on performance of GaN–InGaN multiquantum-well light-emitting diodes
Authors: Yang Hyuck Soo , Han Sang Youn , Baik K. H. , Pearton S. J. , Ren F.
Published: March 2005

InGaN multiquantum-well light-emitting diodes (LEDs) in the form of unpackaged die with emission wavelengths from 420to505nm were exposed to either Ar or H2 inductively coupled plasmas as a function of both rf chuck power (controlling incident ion energy) and source power (controlling ion flux). The forward turn-on voltage is increased by both types of plasma exposure and is a function of both the incident ion energy and flux. The reverse bias current in the LEDs is much larger in the case of H2 plasma exposure, indicating that preferential loss of nitrogen leads to increased surface leakage. The current transport in the LEDs is dominated by generation-recombination (ideality factor ∼2) both before and after the plasma exposures.
Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling
Authors: Zhou Yi , Mishra Bud
Published: March 2005

A large number of the segmental duplications in mammalian genomes have been cataloged by genome-wide sequence analyses. The molecular mechanisms involved in these duplications mostly remain a matter of speculation. To uncover, test, and further quantify the hypotheses on the mechanisms for the recent duplications in the mammalian genomes, we have performed a series of statistical analyses on the sequences flanking the duplicated segments and proposed a dynamic model for the duplication process. The model, when applied to the human duplication data, indicates that ≈30% of the recent human segmental duplications were caused by a recombination-like mechanism, among which 12% were mediated by the most recently active repeat, Alu. But a significant proportion of the duplications are caused by some mechanism independent of the repeat distribution. A less sure but similar picture is found in the rodent genomes. A further analysis on the physical features of the flanking sequences suggests that one of the uncharacterized duplication mechanisms shared by the mammalian genomes is surprisingly well correlated with the physical instability in the DNA sequences.
Rotavirus nonstructural protein 1 subverts innate immune response by inducing degradation of IFN regulatory factor 3
Authors: Barro Mario , Patton John T.
Published: March 2005

IFN regulatory factor 3 (IRF3), a constitutively expressed protein localizing largely to the cytoplasm, is a primary effector of the innate immune response. Infection can trigger the phosphorylation, dimerization, and nuclear translocation of IRF3, where the factor stimulates the expression and release of IFN. In this study, we determined that the rotavirus gene 5 product, nonstructural protein 1 (NSP1), interacts with IRF3 in the infected cell. To understand the importance of the interaction, we compared IRF3 activation by rotaviruses expressing wild-type and C-truncated forms of NSP1. The analysis showed that IRF3 underwent dimerization and nuclear translocation and stimulated IFN promoter activity in infected cells expressing truncated NSP1. In contrast, infected cells expressing wild-type NSP1 were characterized by the rapid degradation of IRF3 during the replication cycle, severe decreases in IRF3 dimerization and nuclear translocation, and lack of IFN promoter activity. The implication of these results, that wild-type NSP1 is an antagonist of the IFN-signaling pathway, was confirmed in transient expression assays, which showed that wild-type NSP1, but not the C-truncated protein, induced the degradation of IRF3 fusion proteins. Related experiments indicated that NSP1 mediates IRF3 degradation through a proteasome-dependent pathway. The critical role of NSP1 in promoting cell-to-cell spread of rotavirus was demonstrated by using gene 5-specific short interfering RNAs in plaque assays. Although several viruses have been described that subvert the innate immune response by preventing IRF3 activation, rotavirus is identified as one that accomplishes this task by inducing the degradation of IRF3.
Helminth regulation of host IL-4Rα/Stat6 signaling: Mechanism underlying NOS-2 inhibition byTrichinella spiralis
Authors: Bian Ka , Zhong Meng , Harari Yael , Lai Mildred , Weisbrodt Norman , Murad Ferid
Published: March 2005

Gastrointestinal nematode infection is known to alter host T cell activation and has been used to study immune and inflammatory reactions in which nitric oxide (NO) is a versatile player. We previously demonstrated thatTrichinella spiralisinfection inhibits host inducible NO synthase (NOS-2) expression. We now demonstrate that (i) an IL-4 receptor α-subunit (IL-4Rα)/Stat6-dependent but T cell-independent pathway is the key for the nematode-induced host NOS-2 inhibition; (ii) endogenous IL-4 and IL-13, the only known IL-4Rα ligands, are not required for activating the pathway; and (iii) treatment of RAW264.7 cells with parasite-cultured medium inhibits NOS-2 expression but not cyclooxygenase 2 expression. We propose that a yet-unidentified substance is released by the nematode during the host–parasite interaction.
Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS
Authors: Steen Hanno , Jebanathirajah Judith A. , Springer Michael , Kirschner Marc W.
Published: March 2005

Qualitative and quantitative information are crucial to a detailed understanding of the function of protein phosphorylation. MS is now becoming a quantitative approach to analyze protein phosphorylation. All methods that have been described either require the elaborate/expensive use of stable isotopes to compare a limited number of samples or do not provide phosphorylation stoichiometries. Here, we present stable isotope-free MS strategies that allow relative and absolute quantitation of phosphorylation stoichiometries. By using the developed methods, we can normalize to robustly account for run-to-run variations and variations in amounts of starting material. This procedure monitors the unmodified proteolytic peptides derived from the protein of interest and identifies peptides that are suitable for normalization purposes. Also, we can determine changes in phosphorylation stoichiometry by monitoring the changes in the normalized ion currents of the phosphopeptide(s) of interest. Absolute phosphorylation stoichiometry are measured by monitoring the ion currents of a phosphopeptide and its unmodified cognate as the signal intensity changes of both peptide species are correlated. The method is applicable to multiply phosphorylated species (for which one more sample with varying phosphorylation stoichiometry than number of phosphorylation sites is required to correct for the differences in the ionization/detection efficiencies of the phosphopeptide, its partially phosphorylated and unphosphorylated cognates). Last, we can quantitate species with ragged ends resulting from incomplete proteolysis and measure phosphorylation stoichiometries of single samples by controlled dephosphorylation. These approaches were validated and subsequently applied to the phosphorylation of the yeast transcription factor Pho4.
Evolutionary profiles from the QR factorization of multiple sequence alignments
Authors: Sethi Anurag , O'Donoghue Patrick , Luthey-Schulten Zaida
Published: March 2005

We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. We observe a general trend that these smaller, more evolutionarily balanced profiles have comparable and, in many cases, better performance in database searches than conventional profiles containing hundreds of sequences, constructed in an iterative and computationally intensive procedure. For more diverse families or superfamilies, with sequence identity <30%, structural alignments, based purely on the geometry of the protein structures, provide better alignments than pure sequence-based methods. Merging the structure and sequence information allows the construction of accurate profiles for distantly related groups. These structure-based profiles outperformed other sequence-based methods for finding distant homologs and were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. Phylogenetic analysis showed the putative class II CysRSs to be a monophyletic group and homology modeling revealed a constellation of active site residues similar to that in the known class I CysRS.
Anti‐stress and Adaptogenic Activity of l‐Arginine Supplementation
Authors: Gupta Vanita , Gupta Asheesh , Saggu Shalini , Divekar Harish M. , Grover K. , Kumar Ratan
Published: March 2005

In the present study, oral supplementation of l‐arginine in rats was evaluated for its anti‐stress and adaptogenic activity using the cold (5°C)–hypoxia (428 mmHg)–restraint (C‐H‐R) animal model. A dose‐dependent study of l‐arginine was carried out at doses of 12.5, 25.0, 50.0, 100.0, 200.0 and 500.0 mg/kg body weight, administered orally 30 min prior to C‐H‐R exposure. The time taken by the rat to attain a rectal temperature of 23°C (Trec 23°C) during C‐H‐R exposure and its recovery to Trec 37°C at normal atmospheric pressure and 32 ± 1°C were used as biomarkers of anti‐stress and adaptogenic activity. Biochemical parameters related to lipid peroxidation, anti‐oxidants, cell membrane permeability, nitric oxide and stress, with and without administration of the least effective l‐arginine dose, were measured in rats on attaining Trec 23°C and Trec 37°C. The least effective adaptogenic dose of l‐arginine was 100.0 mg/kg body weight. The C‐H‐R exposure of control rats, on attaining Trec 23°C, resulted in a significant increase in plasma malondialdehyde (MDA), blood lactate dehydrogenase (LDH) and a decrease in blood catalase (CAT) and plasma testosterone levels. On recovery (Trec 37°C) of control rats, there was a further decrease in CAT and plasma testosterone, and an increase in LDH. l‐Arginine supplementation resulted in a significant decrease in plasma MDA, an increase in blood superoxide dismutase (SOD), CAT levels maintained at control values and a lower increase in LDH compared with controls (45.3 versus 58.5% and 21.5 versus 105.2%) on attaining Trec 23°C during C‐H‐R exposure and on recovery to Trec 37°C. The results suggested that l‐arginine possesses potent anti‐stress activity during C‐H‐R exposure and recovery from C‐H‐R‐induced hypothermia.
Recent trends and important developments in propolis research
Authors: Bankova Vassya
Published: March 2005

The newest developments in propolis pharmacological research are summarized. The problem regarding biological studies, caused by the chemical variability of propolis, is discussed. The most important trends and developments in recent propolis research are outlined: biological studies performed with chemically characterized samples, bioassay‐guided studies of active principles and comparative biological studies of propolis of different origin and chemical composition. These types of studies are extremely valuable with respect to propolis standardization and practical applications in therapy. They will allow scientists to connect a particular chemical propolis type to a specific type of biological activity and formulate recommendations for practitioners.
Snake Venom: Any Clue for Antibiotics and CAM?
Authors: de Lima Deivy Clementino , Alvarez Abreu Paula , de Freitas Cícero Carlos , Santos Dilvani Oliveira , Borges Rodrigo Oliveira , dos Santos Tereza Cristina , Mendes Cabral Lúcio , Rodrigues Carlos R. , Castro Helena Carla
Published: March 2005

Lately several naturally occurring peptides presenting antimicrobial activity have been described in the literature. However, snake venoms, which are an enormous source of peptides, have not been fully explored for searching such molecules. The aim of this work is to review the basis of antimicrobial mechanisms revealing snake venom as a feasible source for searching an antibiotic prototype. Therefore, it includes (i) a description of the constituents of the snake venoms involved in their main biological effects during the envenomation process; (ii) examples of snake venom molecules of commercial use; (iii) mechanisms of action of known antibiotics; and (iv) how the microorganisms can be resistant to antibiotics. This review also shows that snake venoms are not totally unexplored sources for antibiotics and complementary and alternative medicine (CAM).
An Overview of Bee Venom Acupuncture in the Treatment of Arthritis
Authors: Lee Jae-Dong , Park Hi-Joon , Chae Younbyoung , Lim Sabina
Published: March 2005

Bee venom acupuncture (BVA), as a kind of herbal acupuncture, exerts not only pharmacological actions from the bioactive compounds isolated from bee venom but also a mechanical function from acupuncture stimulation. BVA is growing in popularity, especially in Korea, and is used primarily for pain relief in many kinds of diseases. We aimed to summarize and evaluate the available evidence of BVA for rheumatoid arthritis and osteoarthritis. Computerized literature searches for experimental studies and clinical trials of BVA for arthritis were performed on the databases from PUBMED, EMBASE and the Cochrane Library. In addition, two leading Korean journals (The Journal of Korean Society for Acupuncture and Moxibustion and The Journal of Korean Oriental Medicine) were searched for relevant studies. The search revealed 67 studies, 15 of which met our criteria. The anti‐inflammation and analgesic actions of BVA were proved in various kinds of animal arthritic models. Two randomized controlled trials and three uncontrolled clinical trials showed that BVA was effective in the treatment of arthritis. It is highly likely that the effectiveness of BVA for arthritis is a promising area of future research. However, there is limited evidence demonstrating the efficacy of BVA in arthritis. Rigorous trials with large sample size and adequate design are needed to define the role of BVA for these indications. In addition, studies on the optimal dosage and concentration of BVA are recommended for future trials.
The Advantages of Traditional Chumash Healing
Authors: Adams James D. , Garcia Cecilia
Published: March 2005

Chumash healing has been practiced in California for ∼13 000 years. Chumash healers treat their patients with prayer, laughter, dreaming, phytotherapy, aromatherapy, healing ceremonies and other techniques. Healing involves first healing the spirit, then healing the body. Chumash people still maintain their unique identity. Chumash Healers still practice the ancient healing arts in California. This lecture is a brief introduction to Chumash Healing.
CAM Modalities Can Stimulate Advances in Theoretical Biology
Authors: Hankey Alex
Published: March 2005

Most complementary medicine is distinguished by not being supported by underlying theory accepted by Western science. However, for those who accept their validity, complementary and alternative medicine (CAM) modalities offer clues to understanding physiology and medicine more deeply. Ayurveda and vibrational medicine are stimulating new approaches to biological regulation. The new biophysics can be integrated to yield a single consistent theory, which may well underly much of CAM—a true ‘physics of physick’. The resulting theory seems to be a new, fundamental theory of health and etiology. It suggests that many CAM approaches to health care are scientifically in advance of those based on current Western biology. Such theories may well constitute the next steps in our scientific understanding of biology itself. If successfully developed, these ideas could result in a major paradigm shift in both biology and medicine, which will benefit all interested parties—consumers, health professionals, scientists, institutions and governments.
Parties in Elections, Parties in Government, and Partisan Bias
Authors: Krehbiel Keith , Meirowitz Adam , Romer Thomas
Published: March 2005

Political parties are active when citizens choose among candidates inelectionsand when winning candidates choose among policy alternatives ingovernment. But the inextricably linked institutions, incentives, and behavior that determine these multistage choices are substantively complex and analytically unwieldy, particularly if modeled explicitly and considered in total, from citizen preferences through government outcomes. To strike a balance between complexity and tractability, we modify standard spatial models of electoral competition and governmental policy-making to study how components of partisanship—such as candidate platform separation in elections, party ID-based voting, national partisan tides, and party-disciplined behavior in the legislature—are related to policy outcomes. We definepartisan biasas the distance between the following two points in a conventional choice space: the ideal point of the median voter in the median legislative district and the policy outcome selected by the elected legislature. The study reveals that none of the party-in-electorate conditions is capable of producing partisan bias independently. Specified combinations of conditions, however, can significantly increase the bias and/or the variance of policy outcomes, sometimes in subtle ways.
Macro Measures and Mechanics of Social Capital
Authors: Keele Luke
Published: March 2005

Interest in social capital has grown as it has become apparent that it is an important predictor of collective well-being. Recently, attention has shifted to how levels of social capital have changed over time. But better measures are required to test even basic hypotheses such as establishing the direction of causality between the two components of social capital. In the following analysis, I develop macro measures of social capital through the development of longitudinal measures of civic engagement and interpersonal trust. I use these measures to test basic assumptions about social capital. The result is not only the first over time measures of social capital, but also an increase in our understanding of social capital as a macro process with complex causes and effects.
A Solution to Separation in Binary Response Models
Authors: Zorn Christopher
Published: March 2005

A common problem in models for dichotomous dependent variables is “separation,” which occurs when one or more of a model's covariates perfectly predict some binary outcome. Separation raises a particularly difficult set of issues, often forcing researchers to choose between omitting clearly important covariates and undertaking post—hoc data or estimation corrections. In this article I present a method for solving the separation problem, based on a penalized likelihood correction to the standard binomial GLM score function. I then apply this method to data from an important study on the postwar fate of leaders.
Practical Issues in Implementing and Understanding Bayesian Ideal Point Estimation
Authors: Bafumi Joseph , Gelman Andrew , Park David K. , Kaplan Noah
Published: March 2005

Logistic regression models have been used in political science for estimating ideal points of legislators and Supreme Court justices. These models present estimation and identifiability challenges, such as improper variance estimates, scale and translation invariance, reflection invariance, and issues with outliers. We address these issues using Bayesian hierarchical modeling, linear transformations, informative regression predictors, and explicit modeling for outliers. In addition, we explore new ways to usefully display inferences and check model fit.
Transcriptional silencing of a transgene by RNAi in the soma ofC. elegans
Authors: Grishok Alla , Sinskey Jina L. , Sharp Phillip A.
Published: March 2005

The silencing of transgene expression at the level of transcription in the soma ofCaenorhabditis elegansthrough an RNAi-dependent pathway has not been previously characterized. Most gene silencing due to RNAi inC. elegansoccurs at the post-transcriptional level. We observed transcriptional silencing when worms containing theelt-2::gfp/LacZtransgene were fed RNA produced from the commonly used L4440 vector. The transgene and the vector share plasmid backbone sequences. This transgene silencing depends on multiple RNAi pathway genes, includingdcr-1,rde-1,rde-4, andrrf-1. Unlike post-transcriptional gene silencing in worms,elt-2::gfp/LacZsilencing is dependent on the PAZ-PIWI protein Alg-1 and on the HP1 homolog Hpl-2. The latter is a chromatin silencing factor, and expression of the transgene is inhibited at the level of intron-containing precursor mRNA. This inhibition is accompanied by a decrease in the acetylation of histones associated with the transgene. This transcriptional silencing in the soma can be distinguished from transgene silencing in the germline by its inability to be transmitted across generations and its dependence on therde-1gene. We therefore define this type of silencing as RNAi-induced Transcriptional Gene Silencing (RNAi-TGS). Additional chromatin-modifying components affecting RNAi-TGS were identified in a candidate RNAi screen.
Arginine methylation of MRE11 by PRMT1 is required for DNA damage checkpoint control
Authors: Boisvert François-Michel , Déry Ugo , Masson Jean-Yves , Richard Stéphane
Published: March 2005

The role of protein arginine methylation in the DNA damage checkpoint response and DNA repair is largely unknown. Herein we show that the MRE11 checkpoint protein is arginine methylated by PRMT1. Mutation of the arginines within MRE11 severely impaired the exonuclease activity of MRE11 but did not influence its ability to form complexes with RAD50 and NBS1. Cells containing hypomethylated MRE11 displayed intra-S-phase DNA damage checkpoint defects that were significantly rescued with the MRE11-RAD50-NBS1 complex. Our results suggest that arginine methylation regulates the activity of MRE11-RAD50-NBS1 complex during the intra-S-phase DNA damage checkpoint response.
The Legal Approach to EEC Dairy Policy
Authors: Harmsworth Geoffrey N.
Published: March 2005

The Common Agricultural Policy governing the dairy sector may on
first sight give the impression of consisting of a mass of bureaucratic
rules creating a system which is the antithesis of the free market.
However, although the skeleton of the policy may be bureaucratic its
life‐blood is the operation of competitive forces. Actual management of
the market is limited to the minimum strictly necessary to achieve
current policy aims. Community law itself recognises a number of
guarantees to which resort can be made in the case of interference by
member states or commercial enterprises with the operation of
competitive forces in the dairy sector. Even the Community Council of
Ministers has certain legal constraints on its legislative powers such
as the requirement to satisfy the principle of proportionality which has
been held by the Community Court as being relevant, for example in
determining to what extent it is legitimate to affect the competitive
position of another agricultural sector by a measure designed to
encourage the disposal of surplus milk products. Remaining impediments
to free movement of dairy products mean that the single market envisaged
by the creation of the common dairy regime more than 20 years ago has
not been completely achieved. 1992 is therefore a significant date for
the dairy trade. The abolition of the remaining restrictions in
Intra‐Community trade and the increasing concentration of the dairy
industry are likely to increase the relevance of the Articles of the EEC
Treaty dealing with anti‐competitive conduct of enterprises to this
sector.
Sugar and the Modern Food System
Authors: Heasman Michael
Published: March 2005

The development of individual and national dietary goals and
guidelines has mainly concentrated on modifying fat consumption.
However, a reduction in sugar intake has also been an important feature
of much dietary advice. Whilst considering cutting back on sugar
consumption or to what extent it is “bad for you” it is
possible to lose sight of the place and role of sugar in the modern food
system, and the social, cultural and economic reasons why sugar had
become an everyday taken‐for‐granted food commodity. This article
explores these issues in more detail.
Listeriosis – The Unsolved Food Poisoning Disease
Authors: Lacey Richard W.
Published: March 2005

Food has only recently been implicated as the major culprit in
human acquisition of listeriosis. Procedures need to be developed for
its control, notably cleanliness, and the specific problems associated
with this bacterium – for instance the incubation period of
between five days and six weeks – are discussed.
The Official Inspection of Foodstuffs
Authors: Allen Paul
Published: March 2005

An overview of proposals for an EC Directive on the official
inspection of foodstuffs is presented, an important step towards 1992.
The Quality of Minced Meat on Sale: A Case Study from Somerset
Authors: Cassidy W. , Fryer J.
Published: March 2005

A survey of the composition of minced meat – fat, protein,
gristle – was carried out in Somerset. Its findings are described
and it is concluded that the recommendation of the Food Standard
Committee for the control of the fat content of mince should be
implemented.
Marketing of Ginger in the United Kingdom: An Overview
Authors: Satney Andrew O.
Published: March 2005

A discussion of ginger in the UK market (the largest market for
ginger in Europe) with some details of its history and geography is
presented.
Mangoes: An Exotic Choice
Authors: Jabati Miranda
Published: March 2005

Mangoes have shown a large increase in sales in the UK over the
past few years. The reasons for this are given and various problems
associated with this particular market are discussed.
“What′s Sauce for the Goose?”
Authors: Williams Tony
Published: March 2005

A comic little saga on the intricacies of food and food labelling
law is provided.
Rapid formation of amyloid from α‐monomeric recombinant human PrP in vitro
Authors: Tahiri‐Alaoui Abdessamad , James William
Published: March 2005

The infectious agent of prion diseases is identified with PrPSc, a β‐rich, amyloidogenic and partially protease resistant isoform of the cellular glycoprotein, PrPC. To understand the process of prion formation in vivo, we and others have studied defined misfolding pathways of recombinant PrP in vitro. The low‐level infectivity of the in vitro misfolded murine PrP amyloid has recently been reported. Here we analyze the in vitro kinetics of amyloid formation from recombinant human PrP90–231 in vitro in the context of two common allelic forms of PrP found in human populations that are associated with differences in prion disease susceptibility and pathological phenotype. We show that human PrP amyloid forms readily from its PrPC‐like state in vitro, that the lag time of the reaction can be further shortened by the presence of a “seed” of pre‐formed PrP amyloid, and that amyloid propagation is more complex than a simple crystallization process. We further show that the kinetics of amyloid formation do not differ between the Met129 and Val129 allelomorphs of human PrP, and that amyloid from each functions as an equally effective seed in heterologous, as in homologous amyloid reactions. The results could illuminate the process of amyloid formation in vivo as well as help understanding prion pathogenesis.
Extraordinarily stable disulfide‐linked homodimer of human growth hormone
Authors: Grigorian Alexei L. , Bustamante Juan J. , Hernandez Peter , Martinez Andrew O. , Haro Luis S.
Published: March 2005

Although a 22‐kDa human growth hormone (hGH) is the predicted protein product of the hGH‐Ngene, a pleiotropic collection of uncharacterized molecular weight and charge isoforms is also produced. Using chromatography and preparative SDS‐PAGE under reducing conditions we isolated an unusually stable mercaptoethanol‐resistant (MER) 45‐kDa hGH. A 5‐h incubation at 100°C in the presence of 2‐mercaptoethanol was required to convert approximately 90% of MER‐45‐kDa hGH into a 22‐kDa hGH. Other reductants were not as effective in splitting MER‐45‐kDa hGH. After fracturing MER‐45‐kDa hGH, the 22‐kDa hGH fragments would spontaneously reassociate if the reductant was removed; however, alkylation of cysteine residues prevented their reassociation. Identical amino acid sequences for the first six N‐terminal residues were obtained for MER‐45‐kDa hGH and its 22‐kDa hGH cleavage product. Structural identity of MER‐45‐kDa hGH and 22‐kDa hGH was demonstrated by MALDI‐TOF mass spectrometry of tryptic digests. MER‐45‐kDa hGH did not break up upon incubation with EDTA and EGTA. The significance of this work to our understanding of the structure of hGH isoforms is that it demonstrates that MER‐45‐kDa hGH is not a single chain polypeptide but is instead a homodimer of 22‐kDa hGH monomers. The MER‐45‐kDa hGH dimer is held together by interchain disulfide bonds and not by divalent metal cation bridges. Additionally, MER‐45‐kDa hGH's interchain disulfide links are exceptionally resistant to reducing agents and thus confer extreme stability to the homodimer.
ATP specifically drives refolding of non‐native conformations of cytochrome c
Authors: Sinibaldi Federica , Mei Giampiero , Polticelli Fabio , Piro M. Cristina , Howes Barry D. , Smulevich Giulietta , Santucci Roberto , Ascoli Franca , Fiorucci Laura
Published: March 2005

An increasing body of evidence ascribes to misfolded forms of cytochrome c (cyt c) a role in pathophysiological events such as apoptosis and disease. Here, we examine the conformational changes induced by lipid binding to horse heart cyt c at pH 7 and study the ability of ATP (and other nucleotides) to refold several forms of unfolded cyt c such as oleic acid‐bound cyt c, nicked cyt c, and acid denatured cyt c. The CD and fluorescence spectra demonstrate that cyt c unfolded by oleic acid has an intact secondary structure, and a disrupted tertiary structure and heme environment. Furthermore, evidence from the Soret CD, electronic absorption, and resonance Raman spectra indicates the presence of an equilibrium of at least two low‐spin species having distinct heme‐iron(III) coordination. As a whole, the data indicate that binding of cyt c to oleic acid leads to a partially unfolded conformation of the protein, resembling that typical of the molten globule state. Interestingly, the native conformation is almost fully recovered in the presence of ATP or dATP, while other nucleotides, such as GTP, are ineffective. Molecular modeling of ATP binding to cyt c and mutagenesis experiments show the interactions of phosphate groups with Lys88 and Arg91, with adenosine ring interaction with Glu62 explaining the unfavorable binding of GTP. The finding that ATP and dATP are unique among the nucleotides in being able to turn non‐native states of cyt c back to native conformation is discussed in the light of cyt c involvement in cell apoptosis.
l‐Arginine increases the solubility of unfolded species of hen egg white lysozyme
Authors: Reddy K. Ravi Charan , Lilie Hauke , Rudolph Rainer , Lange Christian
Published: March 2005

l‐Arginine (l‐Arg) has been widely used as an enhancer of protein renaturation. The mechanism behind its action is still not fully understood. Using hen egg white lysozyme as a model protein, we present data that clearly demonstrate the suppression of the aggregation of denatured protein by l‐Arg. By chemical modification of free cysteines, a series of unfolded lysozyme species were obtained that served as models for unfolded and intermediate states during the process of oxidative refolding. An increased equilibrium solubility of unfolded species and intermediates in the presence of l‐Arg seems to be its major mechanism of action.
Rotational orientation of monomers within a designed homo‐oligomer transmembrane helical bundle
Authors: Howard Kathleen P. , Liu Wei , Crocker Evan , Nanda Vikas , Lear James , Degrado William F. , Smith Steven O.
Published: March 2005

A peptide designed to form a homo‐oligomeric transmembrane helical bundle was reconstituted into lipid bilayers and studied by using 2H NMR (nuclear magnetic resonance) with magic angle spinning to confirm that the helical interface corresponds to the interface intended in the design. The peptide belongs to a family of model peptides derived from a membrane‐solubilized version of the water‐soluble coiled‐coil GCN4‐P1. The variant studied here contains two asparagines thought to engage in interhelical hydrogen bonding critical to the formation of a stable trimer. For the NMR studies, three different peptides were synthesized, each with one of three consecutive leucines in the transmembrane region deuterium labeled. Prior to NMR data collection, polarized infrared spectroscopy was used to establish that the peptides were reconstituted in lipid bilayers in a transmembrane helical conformation. The 2H NMR line shapes of the three different peptides are consistent with a trimer structure formed by the designed peptide that is stabilized by inter‐helical hydrogen bonding of asparagines at positions 7 and 14.
Cryoelectron microscopy reveals new features in the three‐dimensional structure of phosphorylase kinase
Authors: Nadeau Owen W. , Gogol Edward P. , Carlson Gerald M.
Published: March 2005

Phosphorylase kinase (PhK), a regulatory enzyme in the cascade activation of glycogenolysis, is a 1.3‐MDa hexadecameric complex, (αβγδ)4. PhK comprises two arched octameric (αβγδ)2 lobes that are oriented back‐to‐back with overall D2 symmetry and connected by small bridges. These interlobal bridges, arguably the most questionable structural component of PhK, are one of several structural features that potentially are artifactually generated or altered by conventional sample preparation techniques for electron microscopy (EM). To minimize such artifacts, we have solved by cryoEM the first three‐dimensional (3D) structure of nonactivated PhK from images of frozen hydrated molecules of the kinase. Minimal dose electron micrographs of PhK in vitreous ice revealed particles in a multitude of orientations. A simple model was used to orient the individual images for 3D reconstruction, followed by multiple rounds of refinement. Three‐dimensional reconstruction of nonactivated PhK from approximately 5000 particles revealed a bridged, bilobal molecule with a resolution estimated by Fourier shell correlation analysis at 25 Å. This new structure suggests that several prominent features observed in the structure of PhK derived from negatively stained particles arise as artifacts of specimen preparation. In comparison to the structure from negative staining, the cryoEM structure shows three important differences: (1) a dihedral angle between the two lobes of approximately 90° instead of 68°, (2) a compact rather than extended structure for the lobes, and (3) the presence of four, rather than two, connecting bridges, which provides the first direct evidence for these components as authentic elements of the kinase solution structure.
Ca2+‐induced structural changes in phosphorylase kinase detected by small‐angle X‐ray scattering
Authors: Priddy Timothy S. , Macdonald Brian A. , Heller William T. , Nadeau Owen W. , Trewhella Jill , Carlson Gerald M.
Published: March 2005

Phosphorylase kinase (PhK), a 1.3‐MDa (αβγδ)4 hexadecameric complex, is a Ca2+‐dependent regulatory enzyme in the cascade activation of glycogenolysis. PhK comprises two arched (αβγδ)2 octameric lobes that are oriented back‐to‐back with overall D2 symmetry and joined by connecting bridges. From chemical cross‐linking and electron microscopy, it is known that the binding of Ca2+ by PhK perturbs the structure of all its subunits and promotes redistribution of density throughout both its lobes and bridges; however, little is known concerning the interrelationship of these effects. To measure structural changes induced by Ca2+ in the PhK complex in solution, small‐angle X‐ray scattering was performed on nonactivated and Ca2+‐activated PhK. Although the overall dimensions of the complex were not affected by Ca2+, the cation did promote a shift in the distribution of the scattering density within the hydrated volume occupied by the PhK molecule, indicating a Ca2+‐induced conformational change. Computer‐generated models, based on elements of the known structure of PhK from electron microscopy, were constructed to aid in the interpretation of the scattering data. Models containing two ellipsoids and four cylinders to represent, respectively, the lobes and bridges of the PhK complex provided theoretical scattering profiles that accurately fit the experimental data. Structural differences between the models representing the nonactivated and Ca2+‐activated conformers of PhK are consistent with Ca2+‐induced conformational changes in both the lobes and the interlobal bridges.
Self‐cleavage of fusion protein in vivo using TEV protease to yield native protein
Authors: Shih Yan‐Ping , Wu Hui‐Chung , Hu Su‐Ming , Wang Ting‐Fang , Wang Andrew H.‐J.
Published: March 2005

Overproduction of proteins from cloned genes using fusion protein expression vectors in Escherichia coli and eukaryotic cells has increased the quantity of protein produced. This approach has been widely used in producing soluble recombinant proteins for structural and functional analysis. One major disadvantage, however, of applying this approach for clinical or bioindustrial uses is that proteolytic removal of the fusion carrier is tedious, expensive, and often results in products with additional amino acid residues than the native proteins. Here we describe a new method for productions of native proteins with original amino termini in vivo via intracellular self‐cleavage of the fusion protein using tobacco etch virus (TEV) protease. Our design allows one to simultaneously clone any gene into multiple fusion protein vectors using two unique cloning sites (i.e., SnaBI and XhoI) without restriction digestion, and then rapidly identifies those constructs producing soluble native proteins. This method will make the fusion protein approach more feasible for protein drug research.