bluuebunny/crossref_metadata_2025 huggingface dataset:
Design and Synthesis of Lipopeptide - Carbohydrate Assembled Multivalent Vaccine Candidates Using Native Chemical Ligation
Authors: Zhong Wei , Skwarczynski Mariusz , Fujita Yoshio , Simerska Pavla , Good Michael F. , Toth Istvan
Published: September 2009

Development of a synthetic vaccine against group A streptococcal infection is increasingly paramount due to the induction of autoimmunity by the main virulent factor – M protein. Peptide vaccines, however, are generally poorly immunogenic, necessitating administration with carriers and adjuvants. One of the promising approaches to deliver antigenic peptides is to assemble peptides on a suitable template which directs the attached peptides to form a well defined tertiary structure. For self-adjuvanting human vaccines, the conjugation of immunostimulatory lipids has been demonstrated as a potentially safe method. This study describes the design and optimized synthesis of two lipopeptide conjugated carbohydrate templates and the assembling of peptide antigens. These lipopeptide–carbohydrate assembled multivalent vaccine candidates were obtained in high yield and purity when native chemical ligation was applied. Circular dichroism studies indicated that the template-assembled peptides form four α-helix bundles. The developed technique extends the use of carbohydrate templates and lipopeptide conjugates for producing self-adjuvanting and topology-controlled vaccine candidates.
Spin Crossover and Paramagnetic Behaviour in Two-Dimensional Iron(II) Coordination Polymers with Stilbazole Push–Pull Ligands
Authors: Agustí Gloria , Gaspar Ana Belén , Muñoz M. Carmen , Lacroix Pascal G. , Real José Antonio
Published: September 2009

The suitability of the stilbazole push–pull ligands, 4′-dimethylaminostilbazole (DMAS) and 4′-diethylaminostilbazole (DEAS), for the construction of bimetallic FeII–AgI/AuI cyanide-based coordination polymers that exhibit spin crossover properties is investigated. The structural and physical characterization of four novel two-dimensional FeII polymers formulated as {Fe(DMAS)2[Ag(DMAS)(CN)2]2} (1) and {Fe(L)2[M(CN)2]2} (L = DMAS, M = Au (2); DEAS, Ag (3); DEAS, Au (4)) is reported. Polymers 1 and 4 are paramagnetic over the whole range of temperatures studied (5–300 K), whereas 2 and 3 exhibit spin crossover properties.
Hydrogenation of Glucose over Ru Nanoparticles Embedded in Templated Porous Carbon
Authors: Liu Jiajia , Tian Xiao Ning , Zhao Xiu Song
Published: September 2009

Ruthenium (Ru) nanoparticles incorporated into the pore walls of porous carbon was used as a catalyst in glucose hydrogenation to produce sorbitol. In comparison with other catalysts, including commercial catalysts and catalysts prepared using other methods, the Ru-C nanostructured catalyst displayed higher catalytic activity and stability. These effects were associated with the enhanced contact between the Ru nanoparticles and carbon matrix, as well as the unblocked pores of the catalyst.
Synthesis and Structural Characterization of Palladium Dicarbene Complexes Bearing Labile Co-Ligands
Authors: Huynh Han Vinh , Seow Hui Xian
Published: September 2009

Dicarbene complexes [Pd(OAc)2(diNHC)] (2), [Pd(O2CCF3)2(diNHC)] (3), and [Pd(CNCH3)2(diNHC)](SO3CF3)2 (4) bearing labile acetato, fluoroacetato, and acetonitrile co-ligands have been synthesized via metathesis reaction of the respective precursor [PdBr2(diNHC)] (1) with Ag-salts. All complexes are stable towards air and moisture and have been fully characterized by spectroscopic and spectrometric methods. Notably and in comparison to diphosphine analogues, they resist ligand disproportionation in solution. Their molecular structures have also been determined by single crystal X-ray diffraction. A preliminary catalytic study showed low activity in the hydroamination reaction, but revealed an interesting co-ligand influence.
Novel Orthogonal Synthesis of a Tagged Combinatorial Triazine Library via Grignard Reaction
Authors: Lee Jae Wook , Bork Jacqueline T. , Ha Hyung-Ho , Samanta Animesh , Chang Young-Tae
Published: September 2009

To expand the diversity of 1,3,5-triazine libraries to aryl and alkyl functionalities through the C–C bond, we employed a novel orthogonal synthesis via Grignard monoalkylation or monoarylation of cyanuric chloride in solution to prepare aryl- or alkyl-substituted triazine building blocks. These aryl- or alkyl-substituted triazine building blocks were captured by a resin-bound amine, followed by amination and acidic cleavage with high purity. Herein, we demonstrate a novel orthogonal synthesis of a tagged aryl- and alkyl-triazine library on solid support, utilizing building blocks prepared via Grignard reaction in solution. Through incorporation of a triethylene glycol linker at one of the alternate sites on the triazine scaffold we explored an intrinsic tagged library approach.
A Three-Dimensional Hydrogen-Bonded Network of Triiron(III) and Dilanthanum(III) Pivalate Complexes
Authors: Isilak Süreyya , Mereacre Valeriu , Lan Yanhua , Anson Christopher E. , Powell Annie K.
Published: September 2009

A cationic tri-nuclear iron(iii) complex and an anionic di-nuclear lanthanum(iii) complex assemble to form a three-dimensional hydrogen-bonded supramolecular 3d-4f network [Fe3(μ3-O)(μ-O2CtBu)6(im)3]2[La2(μ-O2CtBu)4(η-O2CtBu)4]·2C2H5OH (im = imidazole).
Fischer Indole Synthesis over Hydrous Zirconia-Supported Niobium Oxide
Authors: Zhong Liang , Chuah Gaik-Khuan
Published: September 2009

Supported niobium oxides are investigated as green catalysts for Fischer indole reaction. By means of wet impregnation, 10–40 wt-% Nb2O5 were loaded onto hydrous zirconia as a support. Pore size distribution curves showed that the niobium oxide overlayer was uniformly dispersed onto the mesoporous support. Samples with close to a monolayer coverage of niobium oxide had the highest activity in the Fischer indole reaction of phenylhydrazine with both 3-heptanone and cyclohexanone. A coverage higher than a monolayer led to lower activity. In comparison, the supported catalysts were more active than bulk niobium oxide or a sample prepared by co-precipitation of hydrous zirconia and niobium oxide.
Copper(I) Templated Synthesis of a 2,2´-Bipyridine Derived 2-Catenane: Synthetic, Modelling, and X-ray Studies
Authors: Price Jason R. , Clegg Jack K. , Fenton Ronald R. , Lindoy Leonard F. , McMurtrie John C. , Meehan George V. , Parkin Andrew , Perkins David , Turner Peter
Published: September 2009

Following molecular modelling employing molecular mechanics and semi-empirical (PM3) calculations as an aid to ligand design, a new copper(i)-containing [2]-catenane has been prepared by the reaction of 6,6′-bis[(4″-formylphenoxy)methyl]-2,2′-bipyridyl with 1,6-hexanediamine in the presence of a copper(i) template, followed by in situ sodium borohydride reduction of the tetra-imine species generated. The corresponding [2]-catenane was obtained as a deep orange crystalline solid. The X-ray structure of this product along with that of the corresponding bis-dialdehyde precursor copper(i) complex have been determined. In the latter case, the structure is pre-organized for catenane formation. The new catenane appears to be the first example of a tetrahedral metal template product incorporating a bis-bipyridyl derivative core. Isolation of the metal-free [2]-catenane has also been achieved following treatment of the copper(i) catenane complex in dimethylsulfoxide with tetrabutylammonium cyanide.
Recent Advances in Molecular Magnetic Materials
Authors: Murray Keith S.
Published: September 2009

This review describes advances made in three areas of molecular magnetic materials of the types A: extended frameworks (coordination polymers) showing long-range magnetic order, B: spin-coupled clusters with emphasis on single molecule magnets and (n × n) grid species, C: polynuclear spin-switching (spin crossover) compounds of FeII with emphasis on dinuclear compounds and one-dimensional (1D) and three-dimensional (3D) (framework) materials, including porous ‘hybrid’ systems. The work of the author and his group is largely used to provide examples, together with results from other groups and collaborators that are included for comparison and completeness. Supramolecular aspects such as cluster–cluster and chain–chain interactions are discussed where relevant. A brief discussion is also given of the recent studies, carried out elsewhere, dealing with aspects of spintronics and the possible future relevance to molecular computers (type B materials) and with memory and other device possibilities (type C materials)
Diphenoxo-Bridged Copper(II) Complexes of Reduced Schiff Base Ligands as Functional Models for Catechol Oxidase
Authors: Sreenivasulu Bellam
Published: September 2009

The design and development of synthetic analogues for the active dicopper(ii) sites of catechol oxidase, with the help of binucleating ligands in particular, is an attractive strategy to generate relevant information on structure–function relationships. Dicopper(ii) complexes of different yet closely related series of reduced Schiff base ligands (N-(2-hydroxybenzyl)-amino acids; N-(2-hydroxybenzyl)-amino amides, N-(2-hydroxybenzyl)-aminomethane or ethanesulfonic acids, and N-(2-hydroxy-5-substituted-benzyl)-cyclopentane or hexanecarboxylic acids) derived from various substituted salicylaldehydes and natural or unnatural amino acids or amides explored as functional models for the Type 3 copper enzyme catecholase oxidase are reviewed in the present paper. The catalytic activity of different series of dicopper(ii) complexes to oxidize the model substrate 3,5-di-tert-butylcatechol to the corresponding 3,5-di-tert-butylquinone is discussed with respect to the various ligand properties such as the length and chelating ability of the amino acid side-arm of the ligands, conformation of the ligand, nature of the donor groups on the amino acid backbone and role of different para-substituents. This article provides a short review summarizing the trend observed in the catecholase activity of different series of dicopper(ii) complexes investigated in our laboratory.
Total Synthesis of (±)-Vibsanin E
Authors: Schwartz Brett D. , Denton Justin R. , Davies Huw M. L. , Williams Craig M.
Published: September 2009

Vibsanin E (1), a structurally rare complex diterpene, consisting of a compact 3-oxatricyclo[6.3.2.05,10] tridecane core and an unprecedented 3,3-dimethylacroyl enol ester functional group, formulate a considerable synthetic challenge. Williams and Davies failed to independently synthesize this nemesis, however, a ‘two heads are better than one’ approach delivered the first total synthesis of the molecule, since its diamond aniversary isolation.
IGFBP2 is a candidate biomarker for
Ink4a-Arf
status and a therapeutic target for high-grade gliomas
Authors: Moore Lynette M. , Holmes Kristen M. , Smith Sarah M. , Wu Ying , Tchougounova Elena , Uhrbom Lene , Sawaya Raymond , Bruner Janet M. , Fuller Gregory N. , Zhang Wei
Published: September 2009

The levels of insulin-like growth factor-binding protein 2 (IGFBP2) are elevated during progression of many human cancers. By using a glial-specific transgenic mouse system (RCAS/Ntv-a), we reported previously that IGFBP2 is an oncogenic factor for glioma progression in combination with platelet-derived growth factor-β (PDGFB). Because the
INK4a-ARF
locus is often deleted in high-grade gliomas (anaplastic oligodendroglioma and glioblastoma), we investigated the effect of the
Ink4a-Arf
-null background on IGFBP2-mediated progression of PDGFB-initiated oligodendroglioma. We demonstrate here that homozygous deletion of
Ink4a-Arf
bypasses the requirement of exogenously introduced IGFBP2 for glioma progression. Instead, absence of
Ink4a-Arf
resulted in elevated endogenous tumor cell IGFBP2. An inverse relationship between p16
INK4a
and IGFBP2 expression was also observed in human glioma tissue samples and in 90 different cancer cell lines by using Western blotting and reverse-phase protein lysate arrays. When endogenous IGFBP2 expression was attenuated by an RCAS vector expressing antisense IGFBP2 in our mouse model, a decreased incidence of anaplastic oligodendroglioma as well as prolonged survival was observed. Thus, p16
INK4a
is a negative regulator of the IGFBP2 oncogene. Loss of
Ink4a-Arf
results in increased IGFBP2, which contributes to glioma progression, thereby implicating IGFBP2 as a marker and potential therapeutic target for
Ink4a-Arf
-deleted gliomas.
HIF-2α maintains an undifferentiated state in neural crest-like human neuroblastoma tumor-initiating cells
Authors: Pietras Alexander , Hansford Loen M. , Johnsson A. Sofie , Bridges Esther , Sjölund Jonas , Gisselsson David , Rehn Matilda , Beckman Siv , Noguera Rosa , Navarro Samuel , Cammenga Jörg , Fredlund Erik , Kaplan David R. , Påhlman Sven
Published: September 2009

High hypoxia-inducible factor-2α (HIF-2α) protein levels predict poor outcome in neuroblastoma, and hypoxia dedifferentiates cultured neuroblastoma cells toward a neural crest-like phenotype. Here, we identify HIF-2α as a marker of normoxic neural crest-like neuroblastoma tumor-initiating/stem cells (TICs) isolated from patient bone marrows. Knockdown of HIF-2α reduced
VEGF
expression and induced partial sympathetic neuronal differentiation when these TICs were grown in vitro under stem cell-promoting conditions. Xenograft tumors of HIF-2α-silenced cells were widely necrotic, poorly vascularized, and resembled the bulk of tumor cells in clinical neuroblastomas by expressing additional sympathetic neuronal markers, whereas control tumors were immature, well-vascularized, and stroma-rich. Thus, HIF-2α maintains an undifferentiated state of neuroblastoma TICs. Because low differentiation is associated with poor outcome and angiogenesis is crucial for tumor growth, HIF-2α is an attractive target for neuroblastoma therapy.
Between “I” and “We”
Authors: Postoutenko Kirill
Published: September 2009

Starting with Rene Descartes and Albrecht Dürer, Europeans obsessively contemplated, registered and expressed their being-in-the-worldandassigned those self-expressions a universal cognitive value. Such generalized personal accounts as Cartesiancogito ergo sumor John Locke’s memory- based theory of personal identity formed the basis of sweeping statements about nations and epochs. For instance, the turn-of-the-century decadent deconstruction of subjectivity brought to life the myth of a smooth transition from the 19th century individuated (‘I’-based) Self to the 20th century shared (‘We’-based) Self. To correct this uninformative and factually inaccurate social description of personal identity, I suggest searching for social identities beyond the realm of self-reflection. In this light, a cursory survey of first-person statements found in books, journals and newspapers published in major European languages between the First and the Second World Wars, is subjected to various kinds of discursive analysis in the light of the chosen topic. As a result, a few politically and aesthetically privileged self-identifications of Europeans give way to a diverse social hierarchy, providing a possible strategy for linguistic description of social identity beyond the European terrain.
Blair speeches in a polyphonic perspective
Authors: Fløttum Kjersti , Stenvoll Dag
Published: September 2009

In this article we examine some linguistic characteristics of two speeches made by Tony Blair, in the British (2004) and the European (2005) parliaments. These speeches can be characterised as visionary speeches on Europe and European integration. By introducing a polyphonic perspective, we will point to specific linguistic features, such as polemic negation by ‘not’ and contrastive-concessive constructions by ‘but’, revealing different types of hidden interaction in which explicit and implicit voices are interwoven. Combined with the identification of pronominal references (to self and others), this perspective helps to spell out the complex relationship between text and context, in particular how to define a relevant context in a text analysis, and how the text itself constitutes its context. The theoretical framework used for analysing the speeches will be linguistic polyphony, as developed in the ScaPoLine theory.
Coping with collective responsibilities
Authors: Leone Giovanna , Curigliano Graziana
Published: September 2009

Our study deals with the meaning of history in the process of construction of one’s self, particularly focusing on the role of historical identity, defined as the psychological awareness of family and cultural inheritance, received by the group in which individuals happen to be born. Since it is determined by the time and place of birth, historical identity may not be chosen, it may only be recognised as more or less meaningful. A psychological confrontation with one’s historical identity — no matter whether it is accepted or refused — is always a specific feature of the construction of one’s self. Starting from these assumptions, we conducted a number of focus group discussions among Italian participants. In order to highlight the evaluative dimensions of discourses, texts were submitted to the APPRAISAL system. All focus group discussions confirmed the difficulties in facing Italy’s collective responsibilities during WWII, suggesting that the protective function of historical identity is still at work down the generations; but they also show a less frequent use of affective resources by the younger generation, indicating a slow progress towards mature in-group reconciliation.
The iconization of Dominican Spanish in Pedro Henríquez Ureña’s linguistic texts
Authors: Valdez Juan R.
Published: September 2009

This study approaches Pedro Henríquez Ureña’s linguistic work on Dominican Spanish by situating it in the political context in which it emerged. Henríquez Ureña’s travels, work and publications encompass many parts of the Spanish-speaking world on both sides of the Atlantic. Linguists have generally tended to descriptively review Henríquez Ureña’s contributions to Spanish American dialectology and have avoided any critical examination of the conditions of production of his linguistic work. My study attempts to fill this gap by conducting a critical examination of these works against the relevant political, cultural and intellectual historical currents of the period. Specifically, I apply the semiotic concepts of ‘iconization’ and ‘erasure’ which are instrumental in the analysis of ideological phenomena. Iconization and erasure are language ideological processes that link language to social behavior and linguistic forms to social images, while eliminating or omitting sociolinguistic complexity. After a discussion of the ways in which these semiotic strategies have been employed and interpreted by scholars, I demonstrate Henríquez Ureña’s own implementation of them. I show how his linguistic work is a discursive site where race and identity in the Dominican Republic are both constructed and debated.
Power and place
Authors: Achugar Mariana , Pessoa Silvia
Published: September 2009

This paper explores the role of Spanish in an academic community in Southwest Texas in order to demonstrate how power, history and place affect linguistic attitudes. The changing status of Spanish from being an index of low wage paying jobs to being a marker of membership in an exclusive academic community serves as a case to investigate how power relations and history interact to shape linguistic attitudes of individuals and groups. Members of the Bilingual Creative Writing Graduate Program at the University of Texas, El Paso, were interviewed to identify the prevalent attitudes towards bilingualism, Spanish in the community and Spanish language users. A discourse analysis of the interviews revealed that participants in this community value Spanish use and bilingualism in the academic context, but have mostly negative attitudes towards local varieties of Spanish and monolingual speakers. This study demonstrates the importance of history, power and place in understanding language attitudes as shared evaluations of language users and uses.
Aspectos sociolectales del léxico dialectal
Authors: Muñoz Natividad Hernández
Published: September 2009

Este artículo analiza el léxico dialectal recogido en el diccionario de léxico disponible de Castilla-La Mancha desde un punto de vista sociolingüístico siguiendo modelos de trabajos anteriores y realizando nuevas aportaciones, como la inclusión en el análisis de un conjunto amplio de variables sociales (nivel sociocultural, sexo, tipo de centro educativo y ubicación), la ampliación de la consideración del fenómeno dialectal a través de los conceptos de amplitud y vitalidad de los términos y, finalmente, a través de la aplicación de análisis estadísticos para validar los resultados cuantitativos (t-Student y ANOVA).
EXTREME MAGNIFICATION MICROLENSING EVENT OGLE-2008-BLG-279: STRONG LIMITS ON PLANETARY COMPANIONS TO THE LENS STAR
Authors: Yee J. C. , Udalski A. , Sumi T. , Dong Subo , Kozłowski S. , Bird J. C. , Cole A. , Higgins D. , McCormick J. , Monard L. A. G. , Polishook D. , Shporer A. , Spector O. , Szymański M. K. , Kubiak M. , Pietrzyński G. , Soszyński I. , Szewczyk O. , Ulaczyk K. , Wyrzykowski Ł. , Poleski R. , Allen W. , Bos M. , Christie G. W. , DePoy D. L. , Eastman J. D. , Gaudi B. S. , Gould A. , Han C. , Kaspi S. , Lee C. -U. , Mallia F. , Maury A. , Maoz D. , Natusch T. , Park B. -G. , Pogge R. W. , Santallo R. , Abe F. , Bond I. A. , Fukui A. , Furusawa K. , Hearnshaw J. B. , Hosaka S. , Itow Y. , Kamiya K. , Korpela A. V. , Kilmartin P. M. , Lin W. , Ling C. H. , Makita S. , Masuda K. , Matsubara Y. , Miyake N. , Muraki Y. , Nagaya M. , Nishimoto K. , Ohnishi K. , Perrott Y. C. , Rattenbury N. J. , Sako T. , Saito To. , Skuljan L. , Sullivan D. J. , Sweatman W. L. , Tristram P. J. , Yock P. C. M. , Albrow M. D. , Batista V. , Fouqué P. , Beaulieu J. -P. , Bennett D. P. , Cassan A. , Comparat J. , Coutures C. , Dieters S. , Greenhill J. , Horne K. , Kains N. , Kubas D. , Martin R. , Menzies J. , Wambsganss J. , Williams A. , Zub M.
Published: September 2009

We analyze the extreme high-magnification microlensing event OGLE-2008-BLG-279, which peaked at a maximum magnification of A ∼ 1600 on 2008 May 30. The peak of this event exhibits both finite-source effects and terrestrial parallax, from which we determine the mass of the lens, Ml
= 0.64 ±  0.10 M
☉, and its distance, Dl
= 4.0 ±  0.6 kpc. We rule out Jupiter-mass planetary companions to the lens star for projected separations in the range 0.5–20 AU. More generally, we find that this event was sensitive to planets with masses as small as

with projected separations near the Einstein ring (∼3 AU).
Filamin A Regulates Caveolae Internalization and Trafficking in Endothelial Cells
Authors: Sverdlov Maria , Shinin Vasily , Place Aaron T. , Castellon Maricela , Minshall Richard D.
Published: September 2009

Transcytosis via caveolae is critical for maintaining vascular homeostasis by regulating the tissue delivery of macromolecules, hormones, and lipids. In the present study, we test the hypothesis that interactions between F-actin cross-linking protein filamin A and caveolin-1 facilitate the internalization and trafficking of caveolae. Small interfering RNA-mediated knockdown of filamin A, but not filamin B, reduced the uptake and transcytosis of albumin by ∼35 and 60%, respectively, without altering the actin cytoskeletal structure or cell–cell adherens junctions. Mobility of both intracellular caveolin-1–green fluorescent protein (GFP)-labeled vesicles measured by fluorescence recovery after photobleaching and membrane-associated vesicles measured by total internal reflection-fluorescence microscopy was decreased in cells with reduced filamin A expression. In addition, in melanoma cells that lack filamin A (M2 cells), the majority of caveolin-1-GFP was localized on the plasma membrane, whereas in cells in which filamin A expression was reconstituted (A7 cells and M2 cells transfected with filamin A-RFP), caveolin-1-GFP was concentrated in intracellular vesicles. Filamin A association with caveolin-1 in endothelial cells was confirmed by cofractionation of these proteins in density gradients, as well as by coimmunoprecipitation. Moreover, this interaction was enhanced by Src activation, associated with increased caveolin-1 phosphorylation, and blocked by Src inhibition. Taken together, these data suggest that filamin A association with caveolin-1 promotes caveolae-mediated transport by regulating vesicle internalization, clustering, and trafficking.
Rabex-5 Is a Rab22 Effector and Mediates a Rab22-Rab5 Signaling Cascade in Endocytosis
Authors: Zhu Huaiping , Liang Zhimin , Li Guangpu
Published: September 2009

Rabex-5 targets to early endosomes and functions as a guanine nucleotide exchange factor for Rab5. Membrane targeting is critical for Rabex-5 to activate Rab5 on early endosomes in the cell. Here, we report the identification of Rab22 as a binding site on early endosomes for direct recruitment of Rabex-5 and activation of Rab5, establishing a Rab22-Rab5 signaling relay to promote early endosome fusion. Rab22 in guanosine 5′-O-(3-thio)triphosphate-loaded form, but not guanosine diphosphate-loaded form, binds to the early endosomal targeting domain (residues 81-230) of Rabex-5 in pull-down assays. Rabex-5 targets to Rab22-containing early endosomes, and Rab22 knockdown by short hairpin RNA abrogates the membrane targeting of Rabex-5 in the cell. In addition, coexpression of Rab22 and Rab5 shows synergistic enlargement of early endosomes, and this synergy is dependent on Rabex-5, providing further support for the collaboration of the two Rab GTPases in regulation of endosome dynamics. This novel Rab22–Rabex-5–Rab5 cascade is functionally important for the endocytosis and degradation of epidermal growth factor.
Streamlined Architecture and Glycosylphosphatidylinositol-dependent Trafficking in the Early Secretory Pathway of African Trypanosomes
Authors: Sevova Elitza S. , Bangs James D.
Published: September 2009

The variant surface glycoprotein (VSG) of bloodstream form Trypanosoma brucei (Tb) is a critical virulence factor. The VSG glycosylphosphatidylinositol (GPI)-anchor strongly influences passage through the early secretory pathway. Using a dominant-negative mutation of TbSar1, we show that endoplasmic reticulum (ER) exit of secretory cargo in trypanosomes is dependent on the coat protein complex II (COPII) machinery. Trypanosomes have two orthologues each of the Sec23 and Sec24 COPII subunits, which form specific heterodimeric pairs: TbSec23.1/TbSec24.2 and TbSec23.2/TbSec24.1. RNA interference silencing of each subunit is lethal but has minimal effects on trafficking of soluble and transmembrane proteins. However, silencing of the TbSec23.2/TbSec24.1 pair selectively impairs ER exit of GPI-anchored cargo. All four subunits colocalize to one or two ER exit sites (ERES), in close alignment with the postnuclear flagellar adherence zone (FAZ), and closely juxtaposed to corresponding Golgi clusters. These ERES are nucleated on the FAZ-associated ER. The Golgi matrix protein Tb Golgi reassembly stacking protein defines a region between the ERES and Golgi, suggesting a possible structural role in the ERES:Golgi junction. Our results confirm a selective mechanism for GPI-anchored cargo loading into COPII vesicles and a remarkable degree of streamlining in the early secretory pathway. This unusual architecture probably maximizes efficiency of VSG transport and fidelity in organellar segregation during cytokinesis.
Characterization of 1H NMR spectroscopic data and the generation of synthetic validation sets
Authors: Anderson Paul E. , Raymer Michael L. , Kelly Benjamin J. , Reo Nicholas V. , DelRaso Nicholas J. , Doom T. E.
Published: September 2009

Motivation: Common contemporary practice within the nuclear magnetic resonance (NMR) metabolomics community is to evaluate and validate novel algorithms on empirical data or simplified simulated data. Empirical data captures the complex characteristics of experimental data, but the optimal or most correct analysis is unknown a priori; therefore, researchers are forced to rely on indirect performance metrics, which are of limited value. In order to achieve fair and complete analysis of competing techniques more exacting metrics are required. Thus, metabolomics researchers often evaluate their algorithms on simplified simulated data with a known answer. Unfortunately, the conclusions obtained on simulated data are only of value if the data sets are complex enough for results to generalize to true experimental data. Ideally, synthetic data should be indistinguishable from empirical data, yet retain a known best analysis.

Results: We have developed a technique for creating realistic synthetic metabolomics validation sets based on NMR spectroscopic data. The validation sets are developed by characterizing the salient distributions in sets of empirical spectroscopic data. Using this technique, several validation sets are constructed with a variety of characteristics present in ‘real’ data. A case study is then presented to compare the relative accuracy of several alignment algorithms using the increased precision afforded by these synthetic data sets.

Availability: These data sets are available for download at http://birg.cs.wright.edu/nmr_synthetic_data_sets.

Contact:  travis.doom@wright.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Phenolic Content, Antioxidant Activity, and Consumer Acceptability of Sorghum Cookies
Authors: Chiremba Constance , Taylor John R. N. , Duodu Kwaku G.
Published: September 2009

Cookies were produced from different sorghum flours to determine their potential as vectors of antioxidants. Different sorghum cultivars and their flour extraction rates were evaluated for their effects on phenolic content and antioxidant activity of the cookies. Consumer acceptance of the sorghum cookies was compared with that of wheat flour cookies. For each sorghum cultivar, cookies of 100% extraction rate flours had two to three times more total phenolics compared with those of 70% extraction rate flours, while antioxidant activity was 22–90% higher. Cookies of the condensed tannin sorghum had two to five times more phenolics compared with those of condensed tannin‐free sorghum. Antioxidant activity was 145–227 μMol Trolox equivalents (TE)/g in cookies of condensed tannin sorghum compared with 10–102 μMol TE/g in those of condensed tannin‐free sorghum. The sorghum flours had slightly higher phenolic content and antioxidant activity values than their corresponding cookies. Cookies of the red tannin‐free sorghum flours (PAN 8564/8446) were equally liked as wheat flour cookies, except for texture. However, cookies of condensed tannin sorghum were least accepted compared with wheat flour cookies despite their high antioxidant activity.
Starch Synthesis in Arabidopsis Is Achieved by Spatial Cotranscription of Core Starch Metabolism Genes
Authors: Tsai Huang-Lung , Lue Wei-Ling , Lu Kuan-Jen , Hsieh Ming-Hsiun , Wang Shue-Mei , Chen Jychian
Published: September 2009

Starch synthesis and degradation require the participation of many enzymes, occur in both photosynthetic and nonphotosynthetic tissues, and are subject to environmental and developmental regulation. We examine the distribution of starch in vegetative tissues of Arabidopsis (Arabidopsis thaliana) and the expression of genes encoding core enzymes for starch synthesis. Starch is accumulated in plastids of epidermal, mesophyll, vascular, and root cap cells but not in root proper cells. We also identify cells that can synthesize starch heterotrophically in albino mutants. Starch synthesis in leaves is regulated by developmental stage and light. Expression of gene promoter-β-glucuronidase fusion constructs in transgenic seedlings shows that starch synthesis genes are transcriptionally active in cells with starch synthesis and are inactive in root proper cells except the plastidial phosphoglucose isomerase. In addition, ADG2 (for ADPG PYROPHOSPHORYLASE2) is not required for starch synthesis in root cap cells. Expression profile analysis reveals that starch metabolism genes can be clustered into two sets based on their tissue-specific expression patterns. Starch distribution and expression pattern of core starch synthesis genes are common in Arabidopsis and rice (Oryza sativa), suggesting that the regulatory mechanism for starch metabolism genes may be conserved evolutionarily. We conclude that starch synthesis in Arabidopsis is achieved by spatial coexpression of core starch metabolism genes regulated by their promoter activities and is fine-tuned by cell-specific endogenous and environmental controls.
Functional Analysis ofα-DOX2, an Activeα-Dioxygenase Critical for Normal Development in Tomato Plants
Authors: Bannenberg Gerard , Martínez Marta , Rodríguez María José , López Miguel Angel , Ponce de León Inés , Hamberg Mats , Castresana Carmen
Published: September 2009

Plant α-dioxygenases initiate the synthesis of oxylipins by catalyzing the incorporation of molecular oxygen at the α-methylene carbon atom of fatty acids. Previously, α-DOX1 has been shown to display α-dioxygenase activity and to be implicated in plant defense. In this study, we investigated the function of a second α-dioxygenase isoform, α-DOX2, in tomato (Solanum lycopersicum) and Arabidopsis (Arabidopsis thaliana). Recombinant Slα-DOX2 and Atα-DOX2 proteins catalyzed the conversion of a wide range of fatty acids into 2(R)-hydroperoxy derivatives. Expression of Slα-DOX2 and Atα-DOX2 was found in seedlings and increased during senescence induced by detachment of leaves. In contrast, microbial infection, earlier known to increase the expression of α-DOX1, did not alter the expression of Slα-DOX2 or Atα-DOX2. The tomato mutant divaricata, characterized by early dwarfing and anthocyanin accumulation, carries a mutation at the Slα-DOX2 locus and was chosen for functional studies of α-DOX2. Transcriptional changes in such mutants showed the up-regulation of genes playing roles in lipid and phenylpropanoid metabolism, the latter being in consonance with the anthocyanin accumulation. Transgenic expression of Atα-DOX2 and Slα-DOX2 in divaricata partially complemented the compromised phenotype in mature plants and fully complemented it in seedlings, thus indicating the functional exchangeability between α-DOX2 from tomato and Arabidopsis. However, deletion of Atα-DOX2 in Arabidopsis plants did not provoke any visible phenotypic alteration indicating that the relative importance of α-DOX2 in plant physiology is species specific.
Characterization of the Entire Cystatin Gene Family in Barley and Their Target Cathepsin L-Like Cysteine-Proteases, Partners in the Hordein Mobilization during Seed Germination
Authors: Martinez Manuel , Cambra Ines , Carrillo Laura , Diaz-Mendoza Mercedes , Diaz Isabel
Published: September 2009

Plant cystatins are inhibitors of cysteine-proteases of the papain C1A and legumain C13 families. Cystatin data from multiple plant species have suggested that these inhibitors act as defense proteins against pests and pathogens and as regulators of protein turnover. In this study, we characterize the entire cystatin gene family from barley (Hordeum vulgare), which contain 13 nonredundant genes, and identify and characterize their target enzymes, the barley cathepsin L-like proteases. Cystatins and proteases were expressed and purified from Escherichia coli cultures. Each cystatin was found to have different inhibitory capability against barley cysteine-proteases in in vitro inhibitory assays using specific substrates. Real-time reverse transcription-polymerase chain reaction revealed that inhibitors and enzymes present a wide variation in their messenger RNA expression patterns. Their transcripts were mainly detected in developing and germinating seeds, and some of them were also expressed in leaves and roots. Subcellular localization of cystatins and cathepsin L-like proteases fused to green fluorescent protein demonstrated the presence of both protein families throughout the endoplasmic reticulum and the Golgi complex. Proteases and cystatins not only colocalized but also interacted in vivo in the plant cell, as revealed by bimolecular fluorescence complementation. The functional relationship between cystatins and cathepsin L-like proteases was inferred from their common implication as counterparts of mobilization of storage proteins upon barley seed germination. The opposite pattern of transcription expression in gibberellin-treated aleurones presented by inhibitors and enzymes allowed proteases to specifically degrade B, C, and D hordeins stored in the endosperm of barley seeds.
Effects of water dependence on the utilization pattern of woody vegetation by elephants in the Tembe Elephant Park, Maputaland, South Africa
Authors: Gaugris Jerome Y. , Van Rooyen Margaretha W.
Published: September 2009

The utilization of vegetation and particularly trees in enclosed small reserves where elephant populations are confined is a contentious conservation issue. In Tembe Elephant Park in Maputaland, the diverse Sand Forest is considered the most valuable feature to conserve; yet it is considered at risk from increasing elephant utilization of the park’s vegetation in general. The mean canopy removal by elephants across the park was studied over two periods: a recent period including the twelve months before the study and an older period >12 months earlier. Age of utilization was determined from the degree of decay observed on woody fibres. The relationships between intensity of utilization, vegetation unit selection and distance to water were evaluated. Results show that utilization patterns have shifted in the recent drier period, during which elephants used vegetation communities closer to permanent water. Concurringly, a significant decrease in utilization intensity was correlated to an increasing distance from water points in the park during that period, while this effect was not observed during the wetter old period. We debate that active water availability management may be a way to limit elephant utilization in small fenced reserves.
Factors affecting the distribution patterns of zebra and wildebeest in a resource‐stressed environment
Authors: Groom Rosemary , Harris Stephen
Published: September 2009

Understanding the spatial dynamics of landscape use by free‐ranging herbivores is integral for successful ecosystem management. We used binary logistic regression analyses to determine the relative importance of biotic, abiotic and human factors in influencing the distribution (presence/absence) of wild grazers on two Maasai ranches in Kenya’s Amboseli‐Tsavo ecosystem. Both ranches had low grass biomass and suffered from regular droughts. We found that grazers consistently located themselves where grass biomass was highest, usually irrespective of grass quality, suggesting that forage quantity may be the limiting factor where grass biomass is generally low. The availability of surface water had no significant effect on the likelihood of grazers being present, even in the dry season.
Hunting differentially affects mixed‐sex and bachelor‐herds in a gregarious ungulate, the impala (Aepyceros melampus: Bovidae)
Authors: Averbeck Christiane , Apio Ann , Plath Martin , Wronski Torsten
Published: September 2009

We investigated herd‐sizes and herd‐compositions of Impala (Aepyceros melampus) inside a protected area [Lake Mburo National Park (LMNP) in western Uganda] and the unprotected adjacent ranchland [the Ankole Ranching Scheme (ARS)]. Impala experience intense hunting and poaching in the study area, and poaching is especially strong on the ARS. We found evidence for changes in overall group‐sizes in both mixed‐sex and pure bachelor herds between areas in and outside LMNP. Mixed‐sex herds strongly decreased in size outside the National Park, but bachelor herds even slightly increased in size. While the group‐composition of mixed‐sex herds was very similar in areas in and outside LMNP, bachelor herds comprised more yearlings and subadult males on the ARS. Our study suggests that effects of hunting and other human nuisance may differ between herd types: mixed herds probably decrease in size because females are more strongly hunted. Around LMNP, impala are usually hunted using nets and spears, thereby increasing the hunters’ chance of being injured. Poachers therefore prefer hornless females (and their calves), as it is less dangerous to handle net‐caught females than males. As a result, males are less hunted, but increased vigilance and, therefore, reduced aggression among the members of a bachelor herd, may account for the observed increase in herd sizes and changes in group‐compositions.
Spider family composition and species richness patterns in two savannah habitats along the eastern coastal plain of Africa
Authors: Haddad Charles R. , Russell‐Smith Anthony
Published: September 2009

The spider faunas of two savannah reserves along the eastern coastal plain of Africa are compared. Species richness was higher in the tropical area, with 493 species (54 families) from Mkomazi Game Reserve, Tanzania. Species richness was also high in the subtropics, with a total of 431 species (46 families) recorded from Ndumo Game Reserve, South Africa. Spider community structure was remarkably similar in the two reserves, with Salticidae, Gnaphosidae, Thomisidae, Theridiidae and Araneidae the most species‐rich families in both reserves. Eleven of the fourteen most species rich families were the same. A similar proportion of families were represented by singleton and doubleton species. A genus‐ and species‐level comparison of ten spider families indicates that while there is considerable overlap in the generic composition of the reserves (Sorensen’s Quotient of similarity: all >0.650 except Linyphiidae, 0.166; Corinnidae, 0.500) there is little overlap between the species occurring in the two sites (0.000–0.571), which was particularly evident in the more species‐rich families. A comparison of diversity of 57 families in each reserve with the spider biodiversity in the two sub‐regions suggests that local biodiversity is largely determined by regional biogeographical influences rather than local ecological factors.
Seasonal variation in forages utilized by the African buffalo (Syncerus caffer) in the succulent thicket of South Africa
Authors: Tshabalala Thulani , Dube Sikhalazo , Lent Peter C.
Published: September 2009

The succulent thicket of the Eastern Cape, South Africa, is characterized by densely wooded vegetation that is dominated by succulents with little understory of ephemeral and weakly perennial grasses and forbs. Studies have developed around the question: how do bulk grazers such as the African buffalo (Syncerus caffer) survive in the succulent thicket? In this study, the diet of the African buffalo at the Great Fish River Reserve (GFRR) was studied in two seasons (wet and dry). The diet profile was assessed from faecal matter, using the micro‐histological analysis method. During the wet season, grass species contributed 72% to the diet while 28% was contributed by browse species. In the dry season there was a significant increase in the intake of browse by 5% (χ2 = 19.94, df = 11, P < 0.05). There were species that were neglected in the wet season but became principal dietary items in the dry season, these included Setaria neglecta, Cymbopogon plurinodis, Capparis sepiaria and Portulacaria afra. Diet quality, as estimated from faecal samples, suggested that the buffalo were nutritionally stable; however, the presence of sarcoptic mange in the buffalo suggests nutritional stress.
Inbreeding and inbreeding depression in a threatened endemic plant, the African violet (Saintpaulia ionantha ssp. grotei), of the East Usambara Mountains, Tanzania
Authors: Kolehmainen Johanna , Korpelainen Helena , Mutikainen Pia
Published: September 2009

Mating among closely‐related individuals in small and isolated plant populations may result in reduced vigour of the inbred offspring, i.e. inbreeding depression, especially in naturally outbreeding plants. Occurrence of inbreeding and inbreeding depression was studied in Saintpaulia ionantha ssp. grotei, a threatened endemic plant species with a narrow ecological amplitude from the East Usambara Mountains. The level of inbreeding (measured as the fixation index, F) was investigated in twelve populations by analyzing variation at one microsatellite marker locus. The effect of one generation of selfing and outcrossing on the progeny fitness was studied by controlled crosses in two small patches that differ in the level isolation. The fixation index (F) across the populations was on the average 0.21 and varied among the populations from substantial inbreeding (F = 0.58) to surplus heterozygosity (F = −0.29). High inbreeding depression (δ) was observed at early and late stages of the life‐cycle. The isolated patch exhibited lower inbreeding depression than did the non‐isolated patch. The results of this study suggest that inbreeding and subsequent inbreeding depression are potential threats to the survival of Saintpaulia populations.
Phantom testis syndrome: prevalence, phenomenology and putative mechanisms
Authors: Pühse Gerald , Wachsmuth Julia Urte , Kemper Sebastian , Husstedt Ingo W. , Kliesch Sabine , Evers Stefan
Published: September 2009

Chronic phantom pain has been found in up to 78% of limb amputees and is a major complication of limb amputation. Less is known about phantom phenomena after the amputation of other, i.e. visceral, parts of the body. In a retrospective design, we identified 539 patients in whom one testis was removed between 1995 and 2005. The operative technique was a unilateral standard radical inguinal orchiectomy. The underlying pathology in all cases was a testicular germ cell tumour. All patients received a detailed questionnaire asking about the occurrence of phantom testis pain (pain felt in the removed testis), phantom testis sensations (non‐painful sensations as if the removed testis was still intact) and hallucinations (illusionary perceptions on the removed testis). Furthermore, we asked about the occurrence and clinical presentation of pain before and after surgery and about pre‐operative testicular pain. Out of 238 respondents, 125 patients (53%) reported any kind of phantom experience. The prevalence of phantom testis pain was 25% (60/238), non‐painful phantom sensations 16% (37/238) and male gonad hallucinations 12% (28/238). Patients with phantom symptoms reported pre‐operative pain in the removed testis more often than patients without phantom symptoms. This study presents first data on the clinical characteristics and possible mechanisms of the phantom testis syndrome after surgical removal of one testis.
Changes in physical and sensory characteristics of marinated broiler drumsticks, treated with nisin and lactoperoxidase system
Authors: Tan Fa‐Jui , Ockerman Herbert W.
Published: September 2009

The lactoperoxidase system (LPS) and nisin have been shown to inactivate some micro‐organisms in foods. However, further studies were needed to evaluate whether these treatments had any influence on the physical and sensory characteristics of broiler drumsticks. In this study, a solution that contained 1% acetic acid and 3% salt with pH adjusted to 4 was developed as a standard marinade. The LPS consisted of 1‐μg mL−1 lactoperoxidase, 5.9‐mm potassium thiocyanate (KSCN), and 2.5‐mm H2O2 was added to the marinade, followed by nisin at 100 IU mL−1. The results showed that the physical characteristics, including raw and cooked drumstick pH, percentage incorporation of marinade solution, cooking loss, skin and muscle L*, a*, b* values, and sensory characteristics, including skin and muscle sensory colour, aroma and flavour, off aroma, off flavour, juiciness and tenderness of the broiler drumsticks, treated with 100‐IU mL−1 nisin and LPS were not impaired.