bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loop anchor modification causes the population of an alternative native state in an SH3‐like domain
Authors: Knappenberger Jane A. , Lecomte Juliette T.J. 
Published: April 2007

AbstractMany stably folded proteins are proposed to contain long, unstructured loops. A series of hybrid proteins (EbE1–4) containing the folded scaffold of photosystem I accessory protein E (PsaE), an SH3‐like protein, and the 40‐residue heme‐binding loop of cytochrome b5 was created to inspect the dependence of thermodynamic and kinetic parameters on the residues at the interface of folded and flexible regions. Compared to the simplest hybrid (EbE1), the chimeras differed by Gly insertions (EbE2, EbE3) or an asymmetric four‐residue restructuring of loop termini (EbE4). NMR spectroscopy indicated that the chimeras retained the PsaE topology; native and unfolded state solubilities, however, were affected to varying degrees. Thermal and chemical denaturation experiments revealed that the EbE2 and EbE1 constructs resulted in a modest destabilization of the PsaE core, whereas apparent stability was increased by >5 kJ/mol in EbE4. EbE3 aggregated at μM concentrations and was not studied in detail. EbE4 populated two native states (N1 and N2), which differed by hydrophobic core packing and C‐terminal interactions. At room temperature, the population ratio (∼3–4:1) favored the state whose spectroscopic properties most resembled those of PsaE (N1). EbE4 also demonstrated altered folding kinetics, displaying multiple slow phases related to the population of intermediates and possibly N2. It was concluded that loop anchors can affect protein properties, including stability, via short‐range effects on local structure and long‐range communication with the packed hydrophobic core. Modification of the attachment points appears to be a possible stepping stone in the transition from one three‐dimensional structure to another.
Expression of proteins with dimethylarginines in Escherichia coli for protein–protein interaction studies
Authors: Hsieh Cheng‐Hsilin , Huang San‐Yuan , Wu Yu‐Ching , Liu Li‐Fan , Han Chau‐Chung , Liu Yi‐Chen , Tam Ming F. 
Published: April 2007

AbstractProtein arginine methylation often modulates protein–protein interactions. To isolate a sufficient quantity of proteins enriched in methyl arginine(s) from natural sources for biochemical studies is laborious and difficult. We describe here an expression system that produces recombinant proteins that are enriched in ω‐NG,NG‐asymmetry dimethylarginines. A yeast type I arginine methyltransferase gene (HMT1) is put on a plasmid under the control of the Escherichia coli methionine aminopeptidase promoter for constitutive expression. The protein targeted for post‐translational modification is put on the same plasmid behind a T7 promoter for inducible expression of His6‐tagged proteins. Sbp1p and Stm1p were used as model proteins to examine this expression system. The 13 arginines within the arginine‐glycine‐rich motif of Sbp1p and the RGG sequence near the C terminus of Stm1p were methylated. Unexpectedly, the arginine residue on the thrombin cleavage site (LVPRGS) of the fusion proteins can also be methylated by Hmt1p. Sbp1p and Sbp1p/hmt1 were covalently attached to solid supports for the isolation of interacting proteins. The results indicate that arginine methylation on Sbp1p exerts both positive and negative effects on protein–protein interaction.
Molecular architecture of DesV from Streptomyces venezuelae: A PLP‐dependent transaminase involved in the biosynthesis of the unusual sugar desosamine
Authors: Burgie E. Sethe , Thoden James B. , Holden Hazel M. 
Published: April 2007

AbstractDesosamine is a 3‐(dimethylamino)‐3,4,6‐trideoxyhexose found in certain macrolide antibiotics such as the commonly prescribed erythromycin. Six enzymes are required for its biosynthesis in Streptomyces venezuelae. The focus of this article is DesV, which catalyzes the PLP‐dependent replacement of a 3‐keto group with an amino functionality in the fifth step of the pathway. For this study the three‐dimensional structures of both the internal aldimine and the ketimine intermediate with glutamate were determined to 2.05 Å resolution. DesV is a homodimer with each subunit containing 12 α‐helical regions and 12 β‐strands that together form three layers of sheet. The structure of the internal aldimine demonstrates that the PLP‐cofactor is held in place by residues contributed from both subunits (Asp 164 and Gln 167 from Subunit I and Tyr 221 and Asn 235 from Subunit II). When the ketimine intermediate is present in the active site, the loop defined by Gln 225 to Ser 228 from Subunit II closes down upon the active site. The structure of DesV is similar to another sugar‐modifying enzyme referred to as PseC. This enzyme is involved in the biosynthesis of pseudaminic acid, which is a sialic acid‐like nonulosonate found in the flagellin of Helicobacter pylori. In the case of PseC, however, the amino group is transferred to the C‐4 rather than the C‐3 position. Details concerning the structural analysis of DesV and a comparison of its molecular architecture to that of PseC are presented.
The 2.0 Å crystal structure of the ERα ligand‐binding domain complexed with lasofoxifene
Authors: Vajdos Felix F. , Hoth Lise R. , Geoghegan Kieran F. , Simons Samuel P. , LeMotte Peter K. , Danley Dennis E. , Ammirati Mark J. , Pandit Jayvardhan 
Published: April 2007

AbstractLasofoxifene is a new and potent selective estrogen receptor modulator (SERM). The structural basis of its interaction with the estrogen receptor has been investigated by crystallographic analysis of its complex with the ligand‐binding domain of estrogen receptor α at a resolution of 2.0 Å. As with other SERMs, lasofoxifene diverts the receptor from its agonist‐bound conformation by displacing the C‐terminal AF‐2 helix into the site at which the LXXLL motif of coactivator proteins would otherwise be able to bind. Lasofoxifene achieves this effect by occupying the space normally filled by residue Leu 540, as well as by modulating the conformation of residues of helix 11 (His 524, Leu 525). A well‐defined salt bridge between lasofoxifene and Asp 351 suggests that charge neutralization in this region of the receptor may explain the some of the antiestrogenic effects of lasofoxifene. The results suggest general features of ERα/SERM recognition, and add a new dimension to efforts to rationalize differences between the biological activity profiles exhibited by these important pharmacological agents.
Behavioural responses of larval container mosquitoes to a size‐selective predator
Authors: KESAVARAJU BANUGOPAN , ALTO BARRY W. , LOUNIBOS L. PHILIP , JULIANO STEVEN A. 
Published: April 2007

Abstract1. The hypothesis that size‐selective predation and species‐specific prey behaviours facilitate the coexistence between larvae of invasiveAedes albopictus(Skuse) and U.S.A.‐nativeOchlerotatus triseriatus(Say) was tested experimentally with the predatorCorethrella appendiculata(Grabham).2. Larval behaviours associated with a higher risk of predation were identified, and prey behavioural responses were tested in either the physical presence of predators or in water containing predation cues. Larvae that thrashed on container bottoms had a higher risk of being captured by fourth instarC. appendiculatathan did larvae resting on the water surface.Ochlerotatus triseriatus, but notA. albopictus, adopted low‐risk behaviours in response to water‐borne cues to predation. Both prey species reduced risky behaviours in the physical presence of the predator, butO. triseriatusshowed a stronger response.3. The vulnerability of 2nd and 3rd instar prey to predation was compared, and behavioural responses were correlated with prey vulnerability. Second instars of both species were more vulnerable to predation byC. appendiculatathan were 3rd instars, and the 3rd instarA. albopictuswas more vulnerable thanO. triseriatusof the same stage. All instars ofO. triseriatusshowed a similar reduction of risky behaviours in response to the presence ofC. appendiculatadespite 4th instar prey being relatively invulnerable to size‐selective predation.4. Weaker predator avoidance, coupled with superior competitive ability, of invasiveA. albopictusis likely to contribute to its coexistence withO. triseriatusin containers of the south‐eastern U.S.A., whereC. appendiculatacan be abundant.
Polygyny and polyandry in small ant societies
Authors: KELLNER K. , TRINDL A. , HEINZE J. , D’ETTORRE P. 
Published: April 2007

AbstractSocial insects, ants in particular, show considerable variation in queen number and mating frequency resulting in a wide range of social structures. The dynamics of reproductive conflicts in insect societies are directly connected to the colony kin structure, thus, the study of relatedness patterns is essential in order to understand the evolutionary resolution of these conflicts. We studied colony kin structure and mating frequencies in two closely related Neotropical ant species Pachycondyla inversa and Pachycondyla villosa. These represent interesting model systems because queens found new colonies cooperatively but, unlike many other ant species, they may still co‐exist when the colony becomes mature (primary polygyny). By using five specific and highly variable microsatellite markers, we show that in both species queens usually mate with two or more males and that cofounding queens are always unrelated. Polygynous and polyandrous colonies are characterized by a high genetic diversity, with a mean relatedness coefficient among worker nestmates of 0.27 (± 0.03 SE) for P. inversa and 0.31 (± 0.05 SE) for P. villosa. However, relatedness among workers of the same matriline is high (0.60 ± 0.03 in P. inversa, 0.62 ± 0.08 in P. villosa) since males that mated with the same queen are on average closely related. Hence, we have found a new taxon in social Hymenoptera with high queen‐mating frequencies and with intriguing mating and dispersal patterns of the sexuals.
Case studies and mathematical models of ecological speciation. 2. Palms on an oceanic island
Authors: GAVRILETS SERGEY , VOSE AARON 
Published: April 2007

AbstractA recent study of a pair of sympatric species of palms on the Lord Howe Island is viewed as providing probably one of the most convincing examples of sympatric speciation to date. Here we describe and study a stochastic, individual‐based, explicit genetic model tailored for this palms system. Overall, our results show that relatively rapid (< 50 000 generations) colonization of a new ecological niche, and sympatric or parapatric speciation via local adaptation and divergence in flowering periods are theoretically plausible if (i) the number of loci controlling the ecological and flowering period traits is small; (ii) the strength of selection for local adaptation is intermediate; and (iii) an acceleration of flowering by a direct environmental effect associated with the new ecological niche is present. We discuss patterns and time‐scales of ecological speciation identified by our model, and we highlight important parameters and features that need to be studied empirically in order to provide information that can be used to improve the biological realism and power of mathematical models of ecological speciation.
Population structure and genetic diversity in tristylousNarcissus triandrus: insights from microsatellite and chloroplast DNA variation
Authors: HODGINS KATHRYN A. , BARRETT SPENCER C. H. 
Published: April 2007

AbstractWe investigated cpDNA sequence and nuclear microsatellite variation among populations of the wild daffodilNarcissus triandrusto examine the role of historical vs. contemporary forces in shaping population structure, morphological differentiation and sexual‐system evolution. This wide‐ranging heterostylous species of the Iberian Peninsula is largely composed of two allopatric varieties (vars.cernuusandtriandrus), and populations with either stylar trimorphism or dimorphism. Dimorphic populations only occur in var.triandrus, are mainly restricted to the northwestern portion of the species range, and uniformly lack the mid‐styled morph (M‐morph). Chloroplast DNA (cpDNA) sequence variation revealed strong geographical structuring and evidence for a fragmentation event associated with differentiation of the two varieties. In var.triandrus,population fragmentation, restricted gene flow and isolation‐by‐distance were also inferred. Significant differences in genetic diversity and population structure between the two varieties likely reflect historical and contemporary differences in demography and gene flow among populations. Discordance between cpDNA markers and both microsatellite and morphological variation indicate that hybridization has occurred between the two varieties at contact zones. There were no differences in genetic diversity or population structure between dimorphic and trimorphic populations, and chloroplast haplotypes were not associated with either sexual system, indicating transitions in morph structure within each maternal lineage. M‐morph frequencies were positively correlated with differentiation at microsatellite loci, indicating that the evolutionary processes influencing these neutral markers also influence alleles controlling the style morphs.
Glacial survival and local adaptation in an alpine leaf beetle
Authors: MARGRAF NICOLAS , VERDON ALINE , RAHIER MARTINE , NAISBIT RUSSELL E. 
Published: April 2007

AbstractThe challenge in defining conservation units so that they represent evolutionary entities has been to combine both genetic properties and ecological significance. Here we make use of the complexity of the European Alps, with their genetic landscape shaped by geographical barriers and postglacial colonization, to examine the correlation between ecological and genetic divergence. Montane species, because of the fragmentation of their present habitat, constitute extreme cases in which to test if genetically distinct subgroups based on neutral markers are also ecologically differentiated and show local adaptation. In the leaf beetle Oreina elongata, populations show variation in host plant use and a patchy distribution throughout the Alps and Apennines. We demonstrate that despite very strong genetic isolation (FST = 0.381), variation in host plant use has led to differences in larval life‐history traits between populations only as a secondary effect of host defence chemistry, and not through physiological adaptation to plant nutritional value. We also establish that populations that are more ecologically different in terms of larval performance are also more genetically divergent. In addition, morphological variation used to define subspecies appears to be mirrored in the population genetics of this species, resulting in almost perfect clustering based on microsatellite data. Finally, we argue from their strong genetic structure and congruent distribution that the subspecies of O. elongata were divided among the same glacial refugia within the Alps that have been proposed for alpine plants.
Egg production and individual genetic diversity in lesser kestrels
Authors: ORTEGO JOAQUÍN , CALABUIG GUSTAU , CORDERO PEDRO J. , APARICIO JOSÉ MIGUEL 
Published: April 2007

AbstractFecundity is an important component of individual fitness and has major consequences on population dynamics. Despite this, the influence of individual genetic variability on egg production traits is poorly known. Here, we use two microsatellite‐based measures, homozygosity by loci and internal relatedness, to analyse the influence of female genotypic variation at 11 highly variable microsatellite loci on both clutch size and egg volume in a wild population of lesser kestrels (Falco naumanni). Genetic diversity was associated with clutch size, with more heterozygous females laying larger clutches, and this effect was statistically independent of other nongenetic variables such as female age and laying date, which were also associated with fecundity in this species. However, egg volume was not affected by female heterozygosity, confirming previous studies from pedigree‐based breeding experiments which suggest that this trait is scarcely subjected to inbreeding depression. Finally, we explored whether the association between heterozygosity and clutch size was due to a genome‐wide effect (general effect) or to single locus heterozygosity (local effect). Two loci showed a stronger influence but the correlation was not fully explained by these two loci alone, suggesting that a main general effect underlies the association observed. Overall, our results underscore the importance of individual genetic variation for egg production in wild bird populations, a fact that could have important implications for conservation research and provides insights into the study of clutch size evolution and genetic variability maintenance in natural populations.
The maize (Zea mays L.) RTCS gene encodes a LOB domain protein that is a key regulator of embryonic seminal and post‐embryonic shoot‐borne root initiation
Authors: Taramino Graziana , Sauer Michaela , Stauffer Jay L. , Multani Dilbag , Niu Xiaomu , Sakai Hajime , Hochholdinger Frank 
Published: April 2007

SummaryMaize has a complex root system composed of different root types formed during different stages of development. The rtcs (rootless concerning crown and seminal roots) mutant is impaired in the initiation of the embryonic seminal roots and the post‐embryonic shoot‐borne root system. The primary root of the mutant shows a reduced gravitropic response, while its elongation, lateral root density and reaction to exogenously applied auxin is not affected. We report here the map‐based cloning of the RTCS gene which encodes a 25.5 kDa LOB domain protein located on chromosome 1S. The RTCS gene has been duplicated during evolution. The RTCS‐LIKE (RTCL) gene displays 72% sequence identity on the protein level. Both genes are preferentially expressed in roots. Expression of RTCS in coleoptilar nodes is confined to emerging shoot‐borne root primordia. Sequence analyses of the RTCS and RTCL upstream genomic regions identified auxin response elements. Reverse transcriptase‐PCR revealed that both genes are auxin induced. Microsynteny analyses between maize and rice genomes revealed co‐linearity of 14 genes in the RTCS region. We conclude from our data that RTCS and RTCL are auxin‐responsive genes involved in the early events that lead to the initiation and maintenance of seminal and shoot‐borne root primordia formation.
Convergent evolution in the BAHD family of acyl transferases: identification and characterization of anthocyanin acyl transferases from Arabidopsis thaliana
Authors: Luo Jie , Nishiyama Yasutaka , Fuell Christine , Taguchi Goro , Elliott Katherine , Hill Lionel , Tanaka Yoshikazu , Kitayama Masahiko , Yamazaki Mami , Bailey Paul , Parr Adrian , Michael Anthony J. , Saito Kazuki , Martin Cathie 
Published: April 2007

SummaryMembers of the BAHD family of plant acyl transferases are very versatile catalytically, and are thought to be able to evolve new substrate specificities rapidly. Acylation of anthocyanins occurs in many plant species and affects anthocyanin stability and light absorption in solution. The versatility of BAHD acyl transferases makes it difficult to identify genes encoding enzymes with defined substrate specificities on the basis of structural homology to genes of known catalytic function alone. Consequently, we have used a modification to standard functional genomics strategies, incorporating co‐expression profiling with anthocyanin accumulation, to identify genes encoding three anthocyanin acyl transferases from Arabidopsis thaliana. We show that the activities of these enzymes influence the stability of anthocyanins at neutral pH, and some acylations also affect the anthocyanin absorption maxima. These properties make the BAHD acyl transferases suitable tools for engineering anthocyanins for an improved range of biotechnological applications.
Elastic plasma protein film blended with platelet releasate accelerates healing of diabetic mouse skin wounds
Authors: Tanaka R. , Ichioka S. , Sekiya N. , Ohura N. , Uchino S. , Ojima A. , Itoh Y. , Ishihara O. , Nakatsuka T. , Ikebuchi K. 
Published: April 2007

Background and Objectives  The growth factors derived from platelets and plasma proteins mediate the wound‐healing process that is characterized by the sequential migration and differentiation of several cell populations that give rise to angiogenesis, collagen synthesis, wound contraction, and re‐epithelialization. To evaluate the efficacy of the blood‐derived factors in wound healing, we examined a novel wound dressing consisting of concentrated human plasma proteins and platelet releasate (CPPP).Materials and Methods  To generate CPPP, plasma proteins and platelets in the peripheral blood (n = 5) were concentrated with the cold ethanol precipitation method. The thrombin obtained from the same blood unit and calcium chloride (CaCl2) were mixed to a concentrate. The CPPP has enough strength to dress cutaneous wounds and contains large amounts of cytokines and fibronectin. We applied the CPPP to excisional skin wounds in genetically healing‐impaired model mice (n= 5) and the wounds were evaluated 10 days after the operation.Results  The area of CPPP‐treated wounds decreased significantly compared with that of the control wounds (65% vs. 94% of the original size, respectively, P= 0·032). The immunostained section revealed a striking effect of CPPP on vascularization compared with the control wounds (13·2 vs. 2·7 vessels per mm2 as mean vascular density observed in the sections, respectively, P= 0·013).Conclusions  Our results suggest that CPPP is a promising biologically active dressing for full‐thickness skin wounds. CPPP can be an entirely autologous biological dressing, suggesting that it is free from the risk of transmission of pathogens through blood products.
The Evolution of Exploitation in Humans: ‘Surrounded by Strangers I Thought Were My Friends’1
Authors: Jones Clara B. 
Published: April 2007

AbstractEarly humans were obligately social, living in nested kin groups or close associations of related individuals. Theoretical and empirical research has demonstrated that group life is characterized by both costs (e.g. increased likelihood of disease transmission) and benefits (e.g. enhanced predator defense). This paper addresses the evolution of exploitation in humans (e.g. slavery, infanticide) as a response to within‐group competition for limiting resources (e.g. food, mates), a potential cost of living in groups. Exploitation is defined as one individual's use of another for selfish ends, in particular, the acquisition and/or use of another's resources for the optimization of inclusive fitness. It is argued that exploitation is most likely to occur in relationships characterized by asymmetries such as dependence, intimacy, and/or differential access to resources. A simple mathematical treatment assesses exploitation as a facultative response to local competition among relatives, providing insights into the conditions favorable and adverse to exploitation of conspecifics. Possible applications of the formulations are discussed, including the conditions under which intraspecific exploitation may be beneficial to both actor and recipient(s). Constraints on the evolution of exploitation in humans are identified, and suggestions are made for testing hypotheses related to the differential costs and benefits of exploitation to conspecifics. Future studies may promote the mitigation of exploitation's deleterious effects inHomo sapiens, a body of research which may apply, as well, to other social mammals.