bluuebunny/crossref_metadata_2025 huggingface dataset:
Enzymatic characterization and molecular modeling of an evolutionarily interesting fungal β‐N‐acetylhexosaminidase
Authors: Ryšlavá Helena , Kalendová Alžběta , Doubnerová Veronika , Skočdopol Přemysl , Kumar Vinay , Kukačka Zdeněk , Pompach Petr , Vaněk Ondřej , Slámová Kristýna , Bojarová Pavla , Kulik Natallia , Ettrich Rudiger , Křen Vladimír , Bezouška Karel
Published: May 2011

Fungal β‐N‐acetylhexosaminidases are inducible extracellular enzymes with many biotechnological applications. The enzyme from Penicillium oxalicum has unique enzymatic properties despite its close evolutionary relationship with other fungal hexosaminidases. It has high GalNAcase activity, tolerates substrates with the modified N‐acyl group better and has some other unusual catalytic properties. In order to understand these features, we performed isolation, biochemical and enzymological characterization, molecular cloning and molecular modelling. The native enzyme is composed of two catalytic units (65 kDa each) and two propeptides (15 kDa each), yielding a molecular weight of 160 kDa. Enzyme deglycosylated by endoglycosidase H had comparable activity, but reduced stability. We have cloned and sequenced the gene coding for the entire hexosaminidase from P. oxalicum. Sufficient sequence identity of this hexosaminidase with the structurally solved enzymes from bacteria and humans with complete conservation of all catalytic residues allowed us to construct a molecular model of the enzyme. Results from molecular dynamics simulations and substrate docking supported the experimental kinetic and substrate specificity data and provided a molecular explanation for why the hexosaminidase from P. oxalicum is unique among the family of fungal hexosaminidases.

Enzymes

hexosaminidase, β‐N‐acetyl‐d‐hexosaminide N‐acetylhexosaminhydrolase, EC 3.2.1.52
Cassava Genetic Transformation and its Application in BreedingF
Authors: Liu Jia , Zheng Qijie , Ma Qiuxiang , Gadidasu Kranthi Kumar , Zhang Peng
Published: May 2011

Peng Zhang (Corresponding author)

As a major source of food, cassava (Manihot esculenta Crantz) is an important root crop in the tropics and subtropics of Africa and Latin America, and serves as raw material for the production of starches and bioethanol in tropical Asia. Cassava improvement through genetic engineering not only overcomes the high heterozygosity and serious trait separation that occurs in its traditional breeding, but also quickly achieves improved target traits. Since the first report on genetic transformation in cassava in 1996, the technology has gradually matured over almost 15 years of development and has overcome cassava genotype constraints, changing from mode cultivars to farmer‐preferred ones. Significant progress has been made in terms of an increased resistance to pests and diseases, biofortification, and improved starch quality, building on the fundamental knowledge and technologies related to planting, nutrition, and the processing of this important food crop that has often been neglected. Therefore, cassava has great potential in food security and bioenergy development worldwide.
The Dominant Glutamic Acid Metabolic Flux to Produce γ‐Amino Butyric Acid over Proline in Nicotiana tabacum Leaves under Water Stress Relates to its Significant Role in Antioxidant Activity
Authors: Liu Cuili , Zhao Li , Yu Guanghui
Published: May 2011

γ‐Amino butyric acid (GABA) and proline play a crucial role in protecting plants during various environmental stresses. Their synthesis is from the common precursor glutamic acid, which is catalyzed by glutamate decarboxylase and Δ1‐pyrroline‐5‐carboxylate synthetase respectively. However, the dominant pathway under water stress has not yet been established. To explore this, excised tobacco leaves were used to simulate a water‐stress condition. The results showed GABA content was much higher than that of proline in leaves under water‐deficit and non‐water‐deficit conditions. Specifically, the amount of GABA significantly increased compared to proline under continuous water loss for 16 h, indicating that GABA biosynthesis is the dominant pathway from glutamic acid metabolism under these conditions. Quantitative reverse transcription polymerase chain reaction and protein Western gel‐blot analysis further confirmed this. To explore the function of GABA accumulation, a system producing superoxide anion (O2−), peroxide hydrogen (H2O2), and singlet oxygen (1O2) was employed to investigate the scavenging role on free‐radical production. The results demonstrated that the scavenging ability of GABA for O2−, H2O2, and 1O2 was significantly higher than that of proline. This indicated that GABA acts as an effective osmolyte to reduce the production of reactive oxygen species under water stress.
Targeting Metalloproteins by Fragment‐Based Lead Discovery
Authors: Johnson Sherida , Barile Elisa , Farina Biancamaria , Purves Angela , Wei Jun , Chen Li‐Hsing , Shiryaev Sergey , Zhang Ziming , Rodionova Irina , Agrawal Arpita , Cohen Seth M. , Osterman Andrei , Strongin Alex , Pellecchia Maurizio
Published: May 2011

It has been estimated that nearly one‐third of functional proteins contain a metal ion. These constitute a wide variety of possible drug targets including metalloproteinases, dehydrogenases, oxidoreductases, hydrolases, deacetylases, or many others in which the metal ion is either of catalytic or of structural nature. Despite the predominant role of a metal ion in so many classes of drug targets, current high‐throughput screening techniques do not usually produce viable hits against these proteins, likely due to the lack of proper metal‐binding pharmacophores in the current screening libraries. Herein, we describe a novel fragment‐based drug discovery approach using a metal‐targeting fragment library that is based on a variety of distinct classes of metal‐binding groups designed to reliably anchor the fragments at the target’s metal ions. We show that the approach can effectively identify novel, potent and selective agents that can be readily developed into metalloprotein‐targeted therapeutics.
Comparison of pandemic and seasonal influenza A infections in pediatric patients: were they different?
Authors: Song Xiaoyan , DeBiasi Roberta L. , Campos Joseph M. , Fagbuyi Daniel B. , Jacobs Brian R. , Singh Nalini
Published: May 2011

Please cite this paper as: Song et al. (2012) Comparison of pandemic and seasonal influenza A infections in pediatric patients: were they different?. Influenza and Other Respiratory Viruses 6(1), 25–27.

This retrospective cohort study revealed that the presence of pandemic H1N1 influenza resulted in a 77.7% increase of patient visits in the emergency department for influenza like illnesses and a 67.2% increase of hospital days in our hospital by comparing to a regular influenza season (2008–2009 season). However, median length of hospital stay was no different in either period (pandemic: 3 days versus seasonal: 4 days, P = 0.06). Except for the patients hospitalized for pandemic H1N1 influenza (n = 111) were older (median age: 4.7 years versus 1.6 years, P = 0.04) and tended to have pre‐existing asthma (21.6% versus 9.0%, P = 0.07) than those hospitalized for seasonal influenza A infections (n = 44), this study found no significant difference between the two comparison groups with regards of other clinical and epidemiological features.
Current trends in microsatellite genotyping
Authors: GUICHOUX E. , LAGACHE L. , WAGNER S. , CHAUMEIL P. , LÉGER P. , LEPAIS O. , LEPOITTEVIN C. , MALAUSA T. , REVARDEL E. , SALIN F. , PETIT R.J.
Published: May 2011

Microsatellites have been popular molecular markers ever since their advent in the late eighties. Despite growing competition from new genotyping and sequencing techniques, the use of these versatile and cost‐effective markers continues to increase, boosted by successive technical advances. First, methods for multiplexing PCR have considerably improved over the last years, thereby decreasing genotyping costs and increasing throughput. Second, next‐generation sequencing technologies allow the identification of large numbers of microsatellite loci at reduced cost in non‐model species. As a consequence, more stringent selection of loci is possible, thereby further enhancing multiplex quality and efficiency. However, current practices are lagging behind. By surveying recently published population genetic studies relying on simple sequence repeats, we show that more than half of the studies lack appropriate quality controls and do not make use of multiplex PCR. To make the most of the latest technical developments, we outline the need for a well‐established strategy including standardized high‐throughput bench protocols and specific bioinformatic tools, from primer design to allele calling.
A mitochondrial species identification assay for Australian blacktip sharks (Carcharhinus tilstoni, C. limbatus and C. amblyrhynchoides) using real‐time PCR and high‐resolution melt analysis
Authors: MORGAN JESS A. T. , WELCH DAVID J. , HARRY ALISTAIR V. , STREET RAEWYN , BRODERICK DAMIEN , OVENDEN JENNIFER R.
Published: May 2011

Tropical Australian shark fisheries target two morphologically indistinguishable blacktip sharks, the Australian blacktip (Carcharhinus tilstoni) and the common blacktip (C. limbatus). Their relative contributions to northern and eastern Australian coastal fisheries are unclear because of species identification difficulties. The two species differ in their number of precaudal vertebrae, which is difficult and time consuming to obtain in the field. But, the two species can be distinguished genetically with diagnostic mutations in their mitochondrial DNA ND4 gene. A third closely related sister species, the graceful shark C. amblyrhynchoides, can also be distinguished by species‐specific mutations in this gene. DNA sequencing is an effective diagnostic tool, but is relatively expensive and time consuming. In contrast, real‐time high‐resolution melt (HRM) PCR assays are rapid and relatively inexpensive. These assays amplify regions of DNA with species‐specific genetic mutations that result in PCR products with unique melt profiles. A real‐time HRM PCR species‐diagnostic assay (RT‐HRM‐PCR) has been developed based on the mtDNA ND4 gene for rapid typing of C. tilstoni, C. limbatus and C. amblyrhynchoides. The assay was developed using ND4 sequences from 66 C. tilstoni, 33. C. limbatus and five C. amblyrhynchoides collected from Indonesia and Australian states and territories; Western Australia, the Northern Territory, Queensland and New South Wales. The assay was shown to be 100% accurate on 160 unknown blacktip shark tissue samples by full mtDNA ND4 sequencing.
Genetic and quantitative assessment of Vibrio vulnificus populations in oyster (Crassostrea virginica) tissues
Authors: Staley Christopher , Jones Melissa K. , Wright Anita C. , Harwood Valerie J.
Published: May 2011

Vibrio vulnificus is a leading cause of shellfish‐associated food‐borne illness. US regulations stipulate shellfish processing procedures to limit V. vulnificus densities; however, the effect of these procedures on V. vulnificus strain distribution and/or genetic diversity is unknown. Vibrio vulnificus concentrations and strain diversity were analysed in various oyster tissues stored overnight at 26°C that were subsequently divided into two treatment groups: one received post‐harvest processing (PHP) via individual quick freeze and one was stored on ice. Vibrio vulnificus densities were 10‐fold lower in all PHP‐treated tissues compared with untreated tissues. Genetic diversity of V. vulnificus was assessed by BOX‐PCR genotyping and was high in all oyster tissues, but was significantly lower in untreated compared with PHP‐treated oysters. BOX‐PCR discriminated strains into BOX‐C (clinical‐associated) and BOX‐E (environmental‐associated) types based on a 1.1 kb DNA band, which correlated well (83% agreement) with 16S rRNA (A/B) typing. A significantly higher proportion of BOX‐C isolates were recovered from PHP oysters compared with untreated oysters (24% of all isolates versus 12%) suggesting that BOX‐C strains may be more resistant to treatment. These results reveal highly diverse populations of V. vulnificus in oysters with different responses to PHP, emphasizing the need to better understand the organism's ecology and population genetics to optimize food safety practices.
Evaluation of Satraplatin in Dogs with Spontaneously Occurring Malignant Tumors
Authors: Selting K.A. , Wang X. , Gustafson D.L. , Henry C.J. , Villamil J.A. , McCaw D.L. , Tate D. , Beittenmiller M. , Garnett C. , Robertson J.D.
Published: May 2011

Background: Satraplatin is the 1st orally bioavailable platinum anticancer drug.

Objective: Our objectives were to evaluate efficacy in vitro against a canine cancer cell line, to determine the maximally tolerated dose (MTD) of satraplatin in tumor‐bearing dogs, to identify the dose‐limiting and other toxicities in dogs, and to record pharmacokinetics (PK).

Animals: Dogs with macro‐ or microscopic malignant neoplasia.

Methods: D17 canine osteosarcoma cells first were evaluated in a clonogenic survival assay. Then, dogs with a diagnosis of malignant neoplasia were prospectively entered in standard 3 + 3 cohorts. Additional patients were entered at the MTD to assess efficacy. Total and free platinum (by ultrafiltrate) concentrations were determined with inductively coupled plasma mass spectroscopy.

Results: Satraplatin inhibited clonogenic survival in vitro at clinically relevant and achievable concentrations. Twenty‐three dogs were treated, 14 with PK evaluation. The MTD was 35 mg/m2/d for 5 days, repeated every 3–4 weeks. Bioavailability was 41%. PK variables (mean ± SD) at the MTD included Tmax 1.8 (± 0.7) hours, Cmax 72 (± 26) ng/mL, area under concentration (AUC)0–24 h 316 (± 63) h × ng/mL, and MRT 7 (± 1.3) hours. Higher AUC after the 5th versus the 1st dose suggested drug accumulation. Interestingly, platelets consistently reached nadir sooner than did neutrophils (day 14 versus 19). Myelosuppression was dose‐limiting and gastrointestinal toxicity was mild.

Conclusions and Clinical Importance: Satraplatin was well tolerated in tumor‐bearing dogs, thus warranting further investigation in a phase II trial.
Serum Acute Phase Proteins as Clinical Phase Indicators and Outcome Predictors in Naturally Occurring Canine Monocytic Ehrlichiosis
Authors: Mylonakis M.E. , Ceron J.J. , Leontides L. , Siarkou V.I. , Martinez S. , Tvarijonaviciute A. , Koutinas A.F. , Harrus S.
Published: May 2011

Background: Canine monocytic ehrlichiosis (CME), caused by Ehrlichia canis, is an important tick‐borne disease of global importance. Currently, limited information is available on the diagnostic and prognostic value of acute phase proteins (APPs) in dogs naturally infected with E. canis.

Hypothesis: APPs may be useful indicators of the clinical phase of CME and predictive of the clinical outcome (death or survival).

Animals: Fifty‐six dogs naturally infected with E. canis and 7 clinically healthy control dogs.

Methods: C‐reactive protein (CRP), serum amyloid A (SAA), haptoglobin (Hp), and albumin concentrations determined on admission were retrospectively compared among 27 dogs with nonmyelosuppressive CME, 29 dogs with myelosuppressive CME and 7 healthy dogs. Diagnosis of CME was based on clinical and clinicopathological findings, seropositivity to E. canis, polymerase chain reaction amplification of E. canis‐specific 16S rDNA, microscopic observation of Ehrlichia sp. morulae in blood monocytes or some combination of these.

Results: Mean concentrations of CRP, SAA, and Hp were significantly higher in the myelosuppressed dogs compared with the other groups, but no significant differences were found in the concentration of albumin. Survival analysis of the affected animals indicated that APP concentrations were not associated with clinical outcome; the latter was strongly associated with pancytopenia (odds ratio for death 22.7) and neutropenia (odds ratio for death 7.7).

Conclusions and Clinical Importance: CRP, SAA, and Hp serum concentrations on admission are useful indicators of the clinical phase of CME, but are not useful predictors of clinical outcome.
Biological Variability of C‐Reactive Protein and Specific Canine Pancreatic Lipase Immunoreactivity in Apparently Healthy Dogs
Authors: Carney P.C. , Ruaux C.G. , Suchodolski J.S. , Steiner J.M.
Published: May 2011

Background: C‐reactive protein (CRP) and specific canine pancreatic lipase immunoreactivity (Spec cPL) are biomarkers of generalized or nonspecific inflammation and pancreatic inflammation in dogs, respectively. The extent of inter‐ and intraindividual variation over time of these analytes is not well defined in dogs. The minimal critical difference for sequential determinations of these markers (ie, the smallest change necessary to represent physiological change rather than biological variation), has not been defined.

Objectives: To determine the inter‐ and intraindividual variability (CVG and CVI) and minimal critical difference for sequential determinations of serum CRP and Spec cPL concentrations in apparently healthy dogs.

Animals: Eleven apparently healthy dogs owned by staff or students at a veterinary teaching hospital.

Methods: Blood was collected repeatedly at varying intervals over 12 weeks. CRP and Spec cPL concentrations were determined with commercially available assays. Indices of inter‐, intraindividual, and assay variability and 1‐sided minimal critical differences for sequential concentrations were calculated.

Results: For CRP, CVG was 90.8%, CVI was 115.5%, and the analytical variability (CVA) was 6.3%; the index of individuality was 0.74, and 1‐sided critical difference was 269.9%. For Spec cPL, CVG= 49.48%, CVI= 193.8%, CVA= 8.4%, index of individuality = 0.24, and 1‐sided critical difference was 452.6%.

Conclusions and Clinical Importance: A population‐based reference range is appropriate for Spec cPL, but questionable for CRP in dogs. Large changes in serial measurements of Spec cPL are necessary to infer clinical importance, more modest changes in CRP are likely to be meaningful.
Idiopathic Cystitis in Domestic Cats—Beyond the Lower Urinary Tract
Authors: Buffington C.A.T.
Published: May 2011

Signs of lower urinary tract (LUT) disease in domestic cats can be acute or chronic, and can result from variable combinations of abnormalities within the lumen of the LUT, the parenchyma of the LUT itself, or other organ system(s) that then lead to LUT dysfunction. In the majority of cats with chronic signs of LUT dysfunction, no specific underlying cause can be confirmed after standard clinical evaluation of the LUT, so these cats typically are classified as having idiopathic cystitis. A syndrome in human beings commonly known as interstitial cystitis (IC) shares many features in common with these cats, permitting comparisons between the two species. A wide range of similarities in abnormalities has been identified between these syndromes outside as well as inside the LUT. A variety of potential familial and developmental risk factors also have been identified. These results have permitted generation of the hypothesis that some of these people have a disorder affecting the LUT rather than a disorder of the LUT. This perspective has suggested alternative diagnostic strategies and novel approaches to treatment, at least in cats. The purpose of this review is to summarize research investigations into the various abnormalities present in cats, to compare some of these findings with those identified in human beings, and to discuss how they might modify perceptions about the etiopathogenesis, diagnosis, and treatment of cats with this disease.

Dedication: I dedicate this contribution to Professor Dennis J. Chew, whose collaboration, patience, and support made it all possible.
Tai chi/qigong improves selected indicators of metabolic syndrome, QoL, depression and perceived stress
Authors: Posadzki P
Published: May 2011

Liu X, Miller YD, Burton NW, Brown WJ.

A preliminary study of the effects of Tai Chi and Qigong medical exercise on indicators of metabolic syndrome, glycaemic control, health‐related quality of life, and psychological health in adults with elevated blood glucose.

Br J Sports Med 2010; 44: 704–9.
What do we know about needling sensation (de qi) and pain outcomes?
Authors: Lim DCE
Published: May 2011

White P, Prescott P, Lewith G.

Does needling sensation (de qi) affect treatment outcome in pain? Analysis of data from a larger single blind, randomised controlled trial.

Acupunct Med 2010; 28: 120–5.
Large trial finds acupuncture effective for chronic shoulder pain
Authors: Linde K
Published: May 2011

Molsberger AF, Schneider T, Gotthardt H, Drabik A.

German randomized acupuncture trial for chronic shoulder pain (GRASP) – a pragmatic, controlled, patient‐blinded, multi‐centre trial in an outpatient care environment.

Pain 2010; 151: 146–154.
Acupuncture for children with autism spectrum disorder
Authors: Lee H , Chun‐Nei VW
Published: May 2011

Wong VCN, Chen W‐X, Liu W‐L.

Randomized controlled trial of electro‐acupuncture for autism spectrum disorder.

Altern Med Rev 2010; 15: 136–46.
Does acupuncture improve pregnancy rate in sub‐fertile women undergoing frozen–thawed embryo transfer cycles?
Authors: Liu J , Ng EHY
Published: May 2011

So EWS, Ng EHY, Wong YY, Yeung WSB, Ho PC.

Acupuncture for frozen‐thawed embryo transfer cycles: a double‐blind randomized controlled trial.

Reprod Biomed Online 2010; 20: 814–21.
Complementary and alternative medicine's opposition to measles immunisation continues
Authors: Ernst Edzard
Published: May 2011

Complementary and alternative medicine has a long tradition of opposition against immunisation. The aim of this article is to determine whether chiropractors, homeopaths and naturopaths advise parents through websites not to immunise their children against measles. A search of the Internet was conducted employing the search engine Google. The contents of the first 12 websites for each of the three categories (i.e. chiropractic, homeopathy and naturopathy) were printed and analysed according to predefined criteria. Of the 36 websites identified, only two offered advice in favour of conventional immunisation; three sites presented information that was considered neutral. The remaining sites did not recommend immunisation and most promoted anti‐immunisation attitudes. It appears that the anti‐immunisation stance of these healthcare professionals does not seem to be abating. As this position is likely to affect immunisation‐rates, it is recommended that effective ways of dealing with this problem be found.
Multidimensional Modeling of Natural Gas Jet and Mixture Formation in Direct Injection Spark Ignition Engines—Development and Validation of a Virtual Injector Model
Authors: Baratta Mirko , Catania Andrea E. , Pesce Francesco C.
Published: May 2011

During the last few years, the integration of CFD tools in the internal combustion (IC) engine design process has continually increased, allowing time and cost savings as the need for experimental prototypes has diminished. Numerical analyses of IC engine flows are rather complex from both the conceptual and operational sides. In fact, these flows involve a variety of unsteady phenomena and the right balance between numerical solution accuracy and computational cost should always be reached. The present paper is focused on computational modeling of natural gas (NG) direct injection (DI) processes from a poppet-valve injector into a bowl-shaped combustion chamber. At high injection pressures, the gas efflux from the injector and the mixture formation processes include turbulent and compressible flow features, such as rarefaction waves and shock formation, which are difficult to accurately capture with numerical simulations, particularly when the combustion chamber geometry is complex and the piston and intake/exhaust valve grids are moving. In this paper, a three-dimensional moving grid model of the combustion engine chamber, originally developed by the authors to include simulation of the actual needle lift, has been enhanced by increasing the accuracy in the proximity of the sonic section of the critical valve-seat nozzle, in order to precisely capture the expansion dynamics the methane undergoes inside the injector and immediately downstream from it. The enhanced numerical model was then validated by comparing the numerical results to Schlieren experimental images for gas injection into a constant-volume bomb. Numerical studies were carried out in order to characterize the fuel-jet properties and the evolution of mixture formation for a centrally mounted injector configuration in the case of a pancake-shaped test chamber and the real engine chamber. Finally, the fluid properties calculated by the model in the throat section of the critical nozzle were taken as reference data for developing a new effective virtual injector model, which allows the designer to remove the whole computational domain upstream from the sonic section of the nozzle, keeping the flow properties virtually unchanged there. The virtual injector model outcomes were shown to be in very good agreement with the results of the enhanced complete injector model, substantiating the reliability of the proposed novel approach.
Integrated Motor/Propulsor Duct Optimization for Increased Vehicle and Propulsor Performance
Authors: Huyer Stephen A. , Dropkin Amanda
Published: May 2011

This paper presents a computational study to better understand the underlying fluid dynamics associated with various duct shapes and the resultant impact on both total vehicle drag and propulsor efficiency. A post-swirl propulsor configuration (downstream stator blade row) was selected with rotor and stator blade number kept constant. A generic undersea vehicle hull shape was chosen and the maximum shroud radius was required to lie within this body radius. A cylindrical rim-driven electric motor capable of generating a specific horsepower to achieve the design operational velocity required a set volume that established a design constraint limiting the shape of the duct. Individual duct shapes were designed to produce constant flow acceleration from upstream of the rotor blade row to downstream of the stator blade row. Ducts producing accelerating and decelerating flow were systematically examined. The axisymmetric Reynolds Averaged Navier–Stokes (RANS) version of fluent® was used to study the fluid dynamics associated with a range of accelerated and decelerated duct flow cases as well as provide the base total vehicle drag. For each given duct shape, the propeller blade design code, PBD 14.3, was used to generate an optimized rotor and stator. To provide fair comparisons, the maximum rotor radius was held constant with similar circulation distributions intended to generate equivalent amounts of thrust. Computations predicted that minimum vehicle drag was produced with a duct that produced zero mean flow acceleration. Ducted designs generating accelerating or decelerating flow increased drag. However, propulsive efficiency based exclusively on blade thrust and torque was significantly increased for accelerating flow through the duct and reduced for decelerating flow cases. Full 3D RANS flow simulations were then conducted for select test cases to quantify the specific blade, hull, and shroud forces and highlight the increased component drag produced by an operational propulsor, which reduced overall propulsive efficiency. From these results, a final optimized design was proposed.
Experimental Evidence Supports a Sex-Specific Selective Sieve in Mitochondrial Genome Evolution
Authors: Innocenti Paolo , Morrow Edward H. , Dowling Damian K.
Published: May 2011

Polymorphisms in the organelle genome have little effect in female flies but do alter gene expression in males.
Beating Crystallization in Glass-Forming Metals by Millisecond Heating and Processing
Authors: Johnson William L. , Kaltenboeck Georg , Demetriou Marios D. , Schramm Joseph P. , Liu Xiao , Samwer Konrad , Kim C. Paul , Hofmann Douglas C.
Published: May 2011

Resistive heating can be used to rapidly heat a bulk metallic glass without inducing crystallization.
Natural Microbe-Mediated Refractoriness to
Plasmodium
Infection in
Anopheles gambiae
Authors: Cirimotich Chris M. , Dong Yuemei , Clayton April M. , Sandiford Simone L. , Souza-Neto Jayme A. , Mulenga Musapa , Dimopoulos George
Published: May 2011

Insect midgut-dwelling bacteria generate reactive oxygen species that inhibit malaria parasite development.
Toward the Second Commitment Period of the Kyoto Protocol
Authors: Weaver Andrew J.
Published: May 2011

Black carbon should be included in the Kyoto framework, and treatment of short-lived gases like methane should change.
Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
Authors: Fleishman Sarel J. , Whitehead Timothy A. , Ekiert Damian C. , Dreyfus Cyrille , Corn Jacob E. , Strauch Eva-Maria , Wilson Ian A. , Baker David
Published: May 2011

Proteins can be designed that bind to specific patches on target proteins to alter their subsequent interactions.
Late Mousterian Persistence near the Arctic Circle
Authors: Slimak Ludovic , Svendsen John Inge , Mangerud Jan , Plisson Hugues , Heggen Herbjørn Presthus , Brugère Alexis , Pavlov Pavel Yurievich
Published: May 2011

Artefacts at a site in the northern Urals dating to about 33,000 years ago suggest a last northern refuge of Neandertals.
Role for piRNAs and Noncoding RNA in de Novo DNA Methylation of the Imprinted Mouse
Rasgrf1
Locus
Authors: Watanabe Toshiaki , Tomizawa Shin-ichi , Mitsuya Kohzoh , Totoki Yasushi , Yamamoto Yasuhiro , Kuramochi-Miyagawa Satomi , Iida Naoko , Hoki Yuko , Murphy Patrick J. , Toyoda Atsushi , Gotoh Kengo , Hiura Hitoshi , Arima Takahiro , Fujiyama Asao , Sado Takashi , Shibata Tatsuhiro , Nakano Toru , Lin Haifan , Ichiyanagi Kenji , Soloway Paul D. , Sasaki Hiroyuki
Published: May 2011

Small, noncoding PIWI-interacting RNAs regulate the imprinting of a mouse gene.
Planarian Pluripotency
Authors: Slack Jonathan M. W.
Published: May 2011

Cellular and molecular details underlying tissue regeneration are revealed in the flatworm.
Walter M. Fitch (1929–2011)
Authors: Atchley William R.
Published: May 2011

A meticulous biologist developed fundamental tools for the field of molecular evolution.
The Birth of the Operon
Authors: Jacob François
Published: May 2011

What is the operon, whose 50th anniversary is being celebrated this week? The word heralded the discovery of how genes are turned on and off, and it launched the now-immense field of gene regulation. The idea was born in André Lwoff's laboratory at the Institut Pasteur. At one end of a long corridor in the loft of a building devoted to research on bacteria were Lwoff, Elie Wollman, and myself. At the other end were Jacques Monod and his group. Lwoff studied lysogenic
Eschericia coli
bacteria capable of producing bacteriophage without infection. Monod was analyzing the properties of the β-galactosidase enzyme in the same bacterium: an enzyme required for the metabolism of lactose that was produced only when the culture medium contained galactosides. To all and sundry the two systems appeared mechanistically miles apart. But their juxtaposition would produce a critical breakthrough for our understanding of life, demonstrating that we cannot presume to know how new ideas will arise and where scientific research will lead.
Loosing the Louse on Europe's Largest Invasive Pest
Authors: Carpenter Jennifer
Published: May 2011

Last week, the United Kingdom approved the widespread release of a natural enemy of invasive Japanese knotweed, a plant louse, or psyllid, called
Aphalara itadori
.
Expression of CD25highRegulatory T Cells and PD-1 in Gastric Infiltrating CD4+T Lymphocytes in Patients with Helicobacter pylori Infection
Authors: Wu Yi-Ying , Chen Jiunn-Horng , Kao Jung-Ta , Liu Kuo-Ching , Lai Chih-Ho , Wang Yuan-Min , Hsieh Chin-Tung , Tzen Jason T. C. , Hsu Ping-Ning
Published: May 2011

We observed by flow cytometry that the frequency of both gastric infiltrating Tregs and PD-1-positive CD4 T cells is correlated with the density ofHelicobacter pylori, suggesting that cellular immunity against this pathogen is inhibited.
Performance of the BioPlex 2200 Multiplexing Immunoassay Platform for the Detection of Herpes Simplex Virus Type 2 Specific Antibodies in African Settings
Authors: LeGoff Jérôme , Grésenguet Gérard , Gody Chrysostome , Longo Jean De Dieu , Khonde Nzambi , Weiss Helen A. , Mayaud Philippe , Bélec Laurent ,   the ANRS 12-12 Study Group
Published: May 2011

The BioPlex platform was evaluated for the detection of herpes simplex virus 2 (HSV-2) antibodies in sub-Saharan Africa individuals in comparison to clinicovirological standards and compared to HerpeSelect. The sensitivities and specificities were, respectively, 88.9% and 93.5% for BioPlex and 89.9% and 92.7% for HerpeSelect. The agreement between both assays was 95.7%.
Development of a New Chlamydiales-Specific Real-Time PCR and Its Application to Respiratory Clinical Samples
Authors: Lienard Julia , Croxatto Antony , Aeby Sebastien , Jaton Katia , Posfay-Barbe Klara , Gervaix Alain , Greub Gilbert
Published: May 2011

Originally composed of the single family
Chlamydiaceae
, the
Chlamydiales
order has extended considerably over the last several decades.
Chlamydia
-related bacteria were added and classified into six different families and family-level lineages: the
Criblamydiaceae
,
Parachlamydiaceae
,
Piscichlamydiaceae
,
Rhabdochlamydiaceae
,
Simkaniaceae
, and
Waddliaceae
. While several members of the
Chlamydiaceae
family are known pathogens, recent studies showed diverse associations of
Chlamydia
-related bacteria with human and animal infections. Some of these latter bacteria might be of medical importance since, given their ability to replicate in free-living amoebae, they may also replicate efficiently in other phagocytic cells, including cells of the innate immune system. Thus, a new
Chlamydiales
-specific real-time PCR targeting the conserved 16S rRNA gene was developed. This new molecular tool can detect at least five DNA copies and show very high specificity without cross-amplification from other bacterial clade DNA. The new PCR was validated with 128 clinical samples positive or negative for
Chlamydia trachomatis
or
C. pneumoniae
. Of 65 positive samples, 61 (93.8%) were found to be positive with the new PCR. The four discordant samples, retested with the original test, were determined to be negative or below detection limits. Then, the new PCR was applied to 422 nasopharyngeal swabs taken from children with or without pneumonia; a total of 48 (11.4%) samples were determined to be positive, and 45 of these were successfully sequenced. The majority of the sequences corresponded to
Chlamydia
-related bacteria and especially to members of the
Parachlamydiaceae
family.
Finer Snapshot of Circulating Mycobacterium tuberculosis Genotypes in Guadeloupe, Martinique, and French Guiana
Authors: Millet Julie , Laurent William , Zozio Thierry , Rastogi Nalin
Published: May 2011

This study shows the benefit of spoligotyping coupled to mycobacterial interspersed repetitive-unit (MIRU) typing to pinpoint circulating
Mycobacterium tuberculosis
genotypes in Guadeloupe, Martinique, and French Guiana. We hereby propose reduced 4-locus and 6-locus subsets for LAM and Haarlem lineage strains that predominate in South America and the Caribbean, retaining 99.35% and 99.64% of the total discriminatory power of the 12-locus scheme, respectively.
Ultrasensitive Quantification of Hepatitis B Virus A1762T/G1764A Mutant by a SimpleProbe PCR Using a Wild-Type-Selective PCR Blocker and a Primer-Blocker-Probe Partial-Overlap Approach
Authors: Nie Hui , Evans Alison A. , London W. Thomas , Block Timothy M. , Ren Xiangdong David
Published: May 2011

Hepatitis B virus (HBV) carrying the A1762T/G1764A double mutation in the basal core promoter (BCP) region is associated with HBe antigen seroconversion and increased risk of liver cirrhosis and hepatocellular carcinoma (HCC). Quantification of the mutant viruses may help in predicting the risk of HCC. However, the viral genome tends to have nucleotide polymorphism, which makes it difficult to design hybridization-based assays including real-time PCR. Ultrasensitive quantification of the mutant viruses at the early developmental stage is even more challenging, as the mutant is masked by excessive amounts of the wild-type (WT) viruses. In this study, we developed a selective inhibitory PCR (siPCR) using a locked nucleic acid-based PCR blocker to selectively inhibit the amplification of the WT viral DNA but not the mutant DNA. At the end of siPCR, the proportion of the mutant could be increased by about 10,000-fold, making the mutant more readily detectable by downstream applications such as real-time PCR and DNA sequencing. We also describe a primer-probe partial overlap approach which significantly simplified the melting curve patterns and minimized the influence of viral genome polymorphism on assay accuracy. Analysis of 62 patient samples showed a complete match of the melting curve patterns with the sequencing results. More than 97% of HBV BCP sequences in the GenBank database can be correctly identified by the melting curve analysis. The combination of siPCR and the SimpleProbe real-time PCR enabled mutant quantification in the presence of a 100,000-fold excess of the WT DNA.
Apoptotic and Antiapoptotic Activity of L Protein of Theiler's Murine Encephalomyelitis Virus
Authors: Stavrou Spyridon , Ghadge Ghanashyam , Roos Raymond P.
Published: May 2011

Cellular apoptosis induced by viral genes can play a critical role in determining virulence as well as viral persistence. This form of cell death has been of interest with respect to Theiler's murine encephalomyelitis virus (TMEV) because the GDVII strain and members of the GDVII subgroup are highly neurovirulent, while the DA strain and members of the TO subgroup induce a chronic progressive inflammatory demyelination with persistence of the virus in the central nervous system. The TMEV L protein has been identified as important in the pathogenesis of Theiler's virus-induced demyelinating disease (TMEV-IDD). We now show that DA L is apoptotic following transfection of L expression constructs or following DA virus infection of HeLa cells; the apoptotic activity depends on the presence of the serine/threonine domain of L, especially a serine at amino acid 57. In contrast, GDVII L has little apoptotic activity following transfection of L expression constructs in HeLa cells and is antiapoptotic following GDVII infection of HeLa cells. Of note, both DA and GDVII L cleave caspase-3 in BHK-21 cells, although neither implements the full apoptotic machinery in this cell type as manifested by the induction of terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) staining. The differences in apoptotic activities of DA and GDVII L in varied cell types may play an important role in TMEV subgroup-specific disease phenotypes.
Activity of Broadly Neutralizing Antibodies, Including PG9, PG16, and VRC01, against Recently Transmitted Subtype B HIV-1 Variants from Early and Late in the Epidemic
Authors: Euler Zelda , Bunnik Evelien M. , Burger Judith A. , Boeser-Nunnink Brigitte D. M. , Grijsen Marlous L. , Prins Jan M. , Schuitemaker Hanneke
Published: May 2011

For the development of a neutralizing antibody-based human immunodeficiency virus type 1 (HIV-1) vaccine, it is important to characterize which antibody specificities are most effective against currently circulating HIV-1 variants. We recently reported that HIV-1 has become more resistant to antibody neutralization over the course of the epidemic, and we here explore whether this increased neutralization resistance is also observed for the newly identified broadly neutralizing antibodies (BrNAbs) PG9, PG16, and VRC01. Furthermore, we performed a comprehensive analysis of the neutralizing sensitivity of currently circulating recently transmitted subtype B viruses to the currently most known BrNAbs. Virus variants isolated less than 6 months after seroconversion from individuals who seroconverted between 2003 and 2006 (
n
= 21) were significantly more resistant to neutralization by VRC01 than viruses from individuals who seroconverted between 1985 and 1989 (
n
= 14). In addition, viruses from contemporary seroconverters tended to be more resistant to neutralization by PG16, which coincided with the presence of more mutations at positions in the viral envelope that may potentially influence neutralization by this antibody. Despite this increased neutralization resistance, all recently transmitted viruses from contemporary seroconverters were sensitive to at least one BrNAb at concentrations of ≤5 μg/ml, with PG9, PG16, and VRC01 showing the greatest breadth of neutralization at lower concentrations. These results suggest that a vaccine capable of eliciting multiple BrNAb specificities will be necessary for protection of the population against HIV-1 infection.
Herpes Simplex Virus 1 pUL34 Plays a Critical Role in Cell-to-Cell Spread of Virus in Addition to Its Role in Virus Replication
Authors: Haugo Alison C. , Szpara Moriah L. , Parsons Lance , Enquist Lynn W. , Roller Richard J.
Published: May 2011

Herpes simplex virus (HSV) pUL34 plays a critical role in virus replication by mediating egress of nucleocapsids from the infected cell nucleus. We have identified a mutation in pUL34 (Y68A) that produces a major defect in virus replication and impaired nuclear egress but also profoundly inhibits cell-to-cell spread and trafficking of gE. Virion release to the extracellular medium is not affected by the Y68A mutation, indicating that the mutation specifically inhibits cell-to-cell spread. We isolated extragenic suppressors of the Y68A plaque formation defect and mapped them by a combination of high-throughput Illumina sequencing and PCR-based screening. We found that suppression is highly correlated with a nonsense mutation in the US9 gene, which plays a critical role in cell-to-cell spread of HSV-1 in neurons. The US9 mutation alone is not sufficient to suppress the Y68A spread phenotype, indicating a likely role for multiple viral factors.
Single Amino Acid Changes in the Virus Capsid Permit Coxsackievirus B3 To Bind Decay-Accelerating Factor
Authors: Pan Jieyan , Narayanan Bhargavi , Shah Shardule , Yoder Joshua D. , Cifuente Javier O. , Hafenstein Susan , Bergelson Jeffrey M.
Published: May 2011

Many coxsackievirus B isolates bind to human decay-accelerating factor (DAF) as well as to the coxsackievirus and adenovirus receptor (CAR). The first-described DAF-binding isolate, coxsackievirus B3 (CB3)-RD, was obtained during passage of the prototype strain CB3-Nancy on RD cells, which express DAF but very little CAR. CB3-RD binds to human DAF, whereas CB3-Nancy does not. To determine the molecular basis for the specific interaction of CB3-RD with DAF, we produced cDNA clones encoding both CB3-RD and CB3-Nancy and mutated each of the sites at which the RD and Nancy sequences diverged. We found that a single amino acid change, the replacement of a glutamate within VP3 (VP3-234E) with a glutamine residue (Q), conferred upon CB3-Nancy the capacity to bind DAF and to infect RD cells. Readaptation of molecularly cloned CB3-Nancy to RD cells selected for a new virus with the same VP3-234Q residue. In experiments with CB3-H3, another virus isolate that does not bind measurably to DAF, adaptation to RD cells resulted in a DAF-binding isolate with a single amino acid change within VP2 (VP2-138 N to D). Both VP3-234Q and VP2-138D were required for binding of CB3-RD to DAF. In the structure of the CB3-RD-DAF complex determined by cryo-electron microscopy, both VP3-234Q and VP2-138D are located at the contact site between the virus and DAF.
PA Residues in the 2009 H1N1 Pandemic Influenza Virus Enhance Avian Influenza Virus Polymerase Activity in Mammalian Cells
Authors: Bussey Kendra A. , Desmet Emily A. , Mattiacio Jonelle L. , Hamilton Alice , Bradel-Tretheway Birgit , Bussey Howard E. , Kim Baek , Dewhurst Stephen , Takimoto Toru
Published: May 2011

The 2009 pandemic influenza virus (pH1N1) is a swine-origin reassortant containing human, avian, and swine influenza genes. We have previously shown that the polymerase complex of the pH1N1 strain A/California/04/2009 (Cal) is highly active in mammalian 293T cells, despite the avian origin of both its PA and PB2. In this study, we analyzed the polymerase residues that are responsible for high pH1N1 polymerase activity in the mammalian host. Characterization of polymerase complexes containing various combinations of Cal and avian influenza virus A/chicken/Nanchang/3-120/01 (H3N2) (Nan) by reporter gene assay indicates that Cal PA, but not PB2, is a major contributing factor to high Cal polymerase activity in 293T cells. In particular, Cal PA significantly activates the otherwise inactive Nan polymerase at 37 and 39°C but not at the lower temperature of 34°C. Further analysis using site-directed mutagenesis showed that the Cal PA residues 85I, 186S, and 336M contribute to enhanced activity of the Cal polymerase. Recombinant A/WSN/33 (H1N1) (WSN) viruses containing Nan NP and polymerase (PA, PB1, PB2) genes with individual mutations in PA at residues 85, 186, and 336 produced higher levels of viral protein than the virus containing wild-type (WT) Nan PA. Interestingly, compared to the WT, the virus containing the 85I mutation grew faster in human A549 cells and the 336M mutation most significantly enhanced pathogenicity in a mouse model, among the three PA mutations tested. Our results suggest that multiple mutations in PA, which were rarely present in previous influenza isolates, are involved in mammalian adaptation and pathogenicity of the 2009 pH1N1.
Gammaretroviral Integration into Nucleosomal Target DNA
In Vivo
Authors: Roth Shoshannah L. , Malani Nirav , Bushman Frederic D.
Published: May 2011

Some of the earliest studies of retroviral integration targeting reported that sites of gammaretroviral DNA integration were positively correlated with DNase I-hypersensitive sites in chromatin. This led to the suggestion that open chromatin was favorable for integration. More recent deep sequencing experiments confirmed that gammaretroviral integration sites and DNase I cleavage sites are associated in genome-wide surveys. Paradoxically,
in vitro
studies of integration show that nucleosomal DNA is actually favored over naked DNA, raising the question of whether integration target DNA in chromosomes is wrapped in nucleosomes or nucleosome free. In this study we examined gammaretroviral integration by infecting primary human CD4
+
T lymphocytes with a murine leukemia virus (MLV)-based retroviral vector or xenotropic murine leukemia virus-related virus (XMRV), and isolated 32,585 unique integration sites using ligation-mediated PCR and 454 pyrosequencing. CD4
+
T lymphocytes were chosen for study because of the particularly dense genome-wide mapping of chromatin features available for comparison. Analysis relative to predicted nucleosome positions showed that gammaretroviruses direct integration into outward-facing major grooves on nucleosome-wrapped DNA, similar to the integration pattern of HIV. Also, a suite of histone modifications correlated with gene activity are positively associated with integration by both MLV and XMRV. Thus, we conclude that favored integration near DNase I-hypersensitive sites does not imply that integration takes place exclusively in nucleosome-free regions.