bluuebunny/crossref_metadata_2025 huggingface dataset:
Catch me if you can: Adaptation from standing genetic variation to a moving phenotypic optimum
Authors: Matuszewski Sebastian , Hermisson Joachim , Kopp Michael
Published: February 2015

Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Out of these, two complementary modelling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation ofde-novomutations only, quantitative genetic models assume that adaptation proceeds exclusively from pre-existing standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation fromde-novomutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect; (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow.
Extensivede novomutation rate variation between individuals and across the genome ofChlamydomonas reinhardtii
Authors: Ness Rob W. , Morgan Andrew D. , Vasanthakrishnan Radhakrishnan B. , Colegrave Nick , Keightley Peter D.
Published: February 2015

Describing the process of spontaneous mutation is fundamental for understanding the genetic basis of disease, the threat posed by declining population size in conservation biology, and in much evolutionary biology. However, directly studying spontaneous mutation is difficult because of the rarity of de novo mutations. Mutation accumulation (MA) experiments overcome this by allowing mutations to build up over many generations in the near absence of natural selection. In this study, we sequenced the genomes of 85 MA lines derived from six genetically diverse wild strains of the green algaChlamydomonas reinhardtii. We identified 6,843 spontaneous mutations, more than any other study of spontaneous mutation. We observed seven-fold variation in the mutation rate among strains and that mutator genotypes arose, increasing the mutation rate dramatically in some replicates. We also found evidence for fine-scale heterogeneity in the mutation rate, driven largely by the sequence flanking mutated sites, and by clusters of multiple mutations at closely linked sites. There was little evidence, however, for mutation rate heterogeneity between chromosomes or over large genomic regions of 200Kbp. Using logistic regression, we generated a predictive model of the mutability of sites based on their genomic properties, including local GC content, gene expression level and local sequence context. Our model accurately predicted the average mutation rate and natural levels of genetic diversity of sites across the genome. Notably, trinucleotides vary 17-fold in rate between the most mutable and least mutable sites. Our results uncover a rich heterogeneity in the process of spontaneous mutation both among individuals and across the genome.
The structure of bradyzoite-specific enolase fromToxoplasma gondiireveals insights into its dual cytoplasmic and nuclear functions
Authors: Ruan Jiapeng , Mouveaux Thomas , Light Samuel H. , Minasov George , Anderson Wayne F. , Tomavo Stanislas , Ngô Huân M.
Published: February 2015

In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasiteToxoplasma gondiidifferentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2) in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein inToxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops. The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstratedin vivousing chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal thatT. gondiienolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Enolase 1 provides a potential lead in the design of drugs againstToxoplasmabrain cysts.
Structural insights intoAspergillus fumigatuslectin specificity: AFL binding sites are functionally non-equivalent
Authors: Houser Josef , Komarek Jan , Cioci Gianluca , Varrot Annabelle , Imberty Anne , Wimmerova Michaela
Published: February 2015

TheAspergillus fumigatuslectin AFL was recently described as a new member of the AAL lectin family. As a lectin from an opportunistic pathogen, it might play an important role in the interaction of the pathogen with the human host. A detailed study of structures of AFL complexed with several monosaccharides and oligosaccharides, including blood-group epitopes, was combined with affinity data from SPR and discussed in the context of previous findings. Its six binding sites are non-equivalent, and owing to minor differences in amino-acid composition they exhibit a marked difference in specific ligand recognition. AFL displays a high affinity in the micromolar range towards oligosaccharides which were detected in plants and also those bound on the human epithelia. All of these results indicate AFL to be a complex member of the lectin family and a challenging target for future medical research and, owing to its binding properties, a potentially useful tool in specific biotechnological applications.
Genuine open form of the pentameric ligand-gated ion channel GLIC
Authors: Fourati Zaineb , Sauguet Ludovic , Delarue Marc
Published: February 2015

Pentameric ligand-gated ion channels (pLGICs) mediate fast chemical neurotransmission of nerve signalling in the central and peripheral nervous systems. GLIC is a bacterial homologue of eukaryotic pLGIC, the X-ray structure of which has been determined in three different conformations. GLIC is thus widely used as a model to study the activation and the allosteric transition of this family of receptors. The recently solved high-resolution structure of GLIC (2.4 Å resolution) in the active state revealed two bound acetate molecules in the extracellular domain (ECD). Here, it is shown that these two acetates exactly overlap with known sites of pharmacological importance in pLGICs, and their potential influence on the structure of the open state is studied in detail. Firstly, experimental evidence is presented for the correct assignment of these acetate molecules by using the anomalous dispersion signal of bromoacetate. Secondly, the crystal structure of GLIC in the absence of acetate was solved and it is shown that acetate binding induces local conformational changes that occur in strategic sites of the ECD. It is expected that this acetate-free structure will be useful in future computational studies of the gating transition in GLIC and other pLGICs.
X-ray, spectroscopic and normal-mode dynamics of calexcitin: structure–function studies of a neuronal calcium-signalling protein
Authors: Erskine P. T. , Fokas A. , Muriithi C. , Rehman H. , Yates L. A. , Bowyer A. , Findlow I. S. , Hagan R. , Werner J. M. , Miles A. J. , Wallace B. A. , Wells S. A. , Wood S. P. , Cooper J. B.
Published: February 2015

The protein calexcitin was originally identified in molluscan photoreceptor neurons as a 20 kDa molecule which was up-regulated and phosphorylated following a Pavlovian conditioning protocol. Subsequent studies showed that calexcitin regulates the voltage-dependent potassium channel and the calcium-dependent potassium channel as well as causing the release of calcium ions from the endoplasmic reticulum (ER) by binding to the ryanodine receptor. A crystal structure of calexcitin from the squidLoligo pealeishowed that the fold is similar to that of another signalling protein, calmodulin, the N- and C-terminal domains of which are known to separate upon calcium binding, allowing interactions with the target protein. Phosphorylation of calexcitin causes it to translocate to the cell membrane, where its effects on membrane excitability are exerted and, accordingly,L. pealeicalexcitin contains two protein kinase C phosphorylation sites (Thr61 and Thr188). Thr-to-Asp mutations which mimic phosphorylation of the protein were introduced and crystal structures of the corresponding single and double mutants were determined, which suggest that the C-terminal phosphorylation site (Thr188) exerts the greatest effects on the protein structure. Extensive NMR studies were also conducted, which demonstrate that the wild-type protein predominantly adopts a more open conformation in solution than the crystallographic studies have indicated and, accordingly, normal-mode dynamic simulations suggest that it has considerably greater capacity for flexible motion than the X-ray studies had suggested. Like calmodulin, calexcitin consists of four EF-hand motifs, although only the first three EF-hands of calexcitin are involved in binding calcium ions; the C-terminal EF-hand lacks the appropriate amino acids. Hence, calexcitin possesses two functional EF-hands in close proximity in its N-terminal domain and one functional calcium site in its C-terminal domain. There is evidence that the protein has two markedly different affinities for calcium ions, the weaker of which is most likely to be associated with binding of calcium ions to the protein during neuronal excitation. In the current study, site-directed mutagenesis has been used to abolish each of the three calcium-binding sites of calexcitin, and these experiments suggest that it is the single calcium-binding site in the C-terminal domain of the protein which is likely to have a sensory role in the neuron.
Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality
Authors: Menyhárd Dóra Karancsiné , Orgován Zoltán , Szeltner Zoltán , Szamosi Ilona , Harmat Veronika
Published: February 2015

Acylaminoacyl peptidase (AAP) is an oligopeptidase that only cleaves short peptides or protein segments. In the case of AAP fromAeropyrum pernix(ApAAP), previous studies have led to a model in which the clamshell-like opening and closing of the enzyme provides the means of substrate-size selection. The closed form of the enzyme is catalytically active, while opening deactivates the catalytic triad. The crystallographic results presented here show that the open form of ApAAP is indeed functionally disabled. The obtained crystal structures also reveal that the closed form is penetrable to small ligands: inhibitor added to the pre-formed crystal was able to reach the active site of the rigidified protein, which is only possible through the narrow channel of the propeller domain. Molecular-dynamics simulations investigating the structure of the complexes formed with longer peptide substrates showed that their binding within the large crevice of the closed form of ApAAP leaves the enzyme structure unperturbed; however, their accessing the binding site seems more probable when assisted by opening of the enzyme. Thus, the open form of ApAAP corresponds to a scavenger of possible substrates, the actual cleavage of which only takes place if the enzyme is able to re-close.
Structural and functional analysis of Hikeshi, a new nuclear transport receptor of Hsp70s
Authors: Song Jinsue , Kose Shingo , Watanabe Ai , Son Se-Young , Choi Saehae , Hong Hyerim , Yamashita Eiki , Park Il Yeong , Imamoto Naoko , Lee Soo Jae
Published: February 2015

Hikeshi is a nuclear transport receptor required for cell survival after stress. It mediates heat-shock-induced nuclear import of 70 kDa heat-shock proteins (Hsp70s) through interactions with FG-nucleoporins (FG-Nups), which are proteins in nuclear pore complexes (NPCs). Here, the crystal structure of human Hikeshi is presented at 1.8 Å resolution. Hikeshi forms an asymmetric homodimer that is responsible for the interaction with Hsp70s. The asymmetry of Hikeshi arises from the distinct conformation of the C-terminal domain (CTD) and the flexibility of the linker regions of each monomer. Structure-guided mutational analyses showed that both the flexible linker region and the CTD are important for nuclear import of Hsp70. Pull-down assays revealed that only full-length Hsp70s can interact with Hikeshi. The N-terminal domain (NTD) consists of a jelly-roll/β-sandwich fold structure which contains hydrophobic pockets involved in FG-Nup recognition. A unique extended loop (E-loop) in the NTD is likely to regulate the interactions of Hikeshi with FG-Nups. The crystal structure of Hikeshi explains how Hikeshi participates in the regulation of nuclear import through the recognition of FG-Nups and which part of Hikeshi affects its binding to Hsp70. This study is the first to yield structural insight into this highly unique import receptor.
Interaction of the amyloid precursor protein-like protein 1 (APLP1) E2 domain with heparan sulfate involves two distinct binding modes
Authors: Dahms Sven O. , Mayer Magnus C. , Roeser Dirk , Multhaup Gerd , Than Manuel E.
Published: February 2015

Beyond the pathology of Alzheimer's disease, the members of the amyloid precursor protein (APP) family are essential for neuronal development and cell homeostasis in mammals. APP and its paralogues APP-like protein 1 (APLP1) and APP-like protein 2 (APLP2) contain the highly conserved heparan sulfate (HS) binding domain E2, which effects various (patho)physiological functions. Here, two crystal structures of the E2 domain of APLP1 are presented in the apo form and in complex with a heparin dodecasaccharide at 2.5 Å resolution. The apo structure of APLP1 E2 revealed an unfolded and hence flexible N-terminal helix αA. The (APLP1 E2)2–(heparin)2complex structure revealed two distinct binding modes, with APLP1 E2 explicitly recognizing the heparin terminus but also interacting with a continuous heparin chain. The latter only requires a certain register of the sugar moieties that fits to a positively charged surface patch and contributes to the general heparin-binding capability of APP-family proteins. Terminal binding of APLP1 E2 to heparin specifically involves a structure of the nonreducing end that is very similar to heparanase-processed HS chains. These data reveal a conserved mechanism for the binding of APP-family proteins to HS and imply a specific regulatory role of HS modifications in the biology of APP and APP-like proteins.
The 1.65 Å resolution structure of the complex of AZD4547 with the kinase domain of FGFR1 displays exquisite molecular recognition
Authors: Yosaatmadja Yuliana , Patterson Adam Vorn , Smaill Jeff Bruce , Squire Christopher John
Published: February 2015

The fibroblast growth factor receptor (FGFR) family are expressed widely in normal tissues and play a role in tissue repair, inflammation, angiogenesis and development. However, aberrant signalling through this family can lead to cellular proliferation, evasion of apoptosis and induction of angiogenesis, which is implicated in the development of many cancers and also in drug resistance. The high frequency of FGFR amplification or mutation in multiple cancer types is such that this family has been targeted for the discovery of novel, selective drug compounds, with one of the most recently discovered being AZD4547, a subnanomolar (IC50) FGFR1 inhibitor developed by AstraZeneca and currently in clinical trials. The 1.65 Å resolution crystal structure of AZD4547 bound to the kinase domain of FGFR1 has been determined and reveals extensive drug–protein interactions, an integral network of water molecules and the tight closure of the FGFR1 P-loop to form a long, narrow crevice in which the AZD4547 molecule binds.
A disulfide-bond cascade mechanism for arsenic(III)S-adenosylmethionine methyltransferase
Authors: Marapakala Kavitha , Packianathan Charles , Ajees A. Abdul , Dheeman Dharmendra S. , Sankaran Banumathi , Kandavelu Palani , Rosen Barry P.
Published: February 2015

Methylation of the toxic metalloid arsenic is widespread in nature. Members of every kingdom have arsenic(III)S-adenosylmethionine (SAM) methyltransferase enzymes, which are termed ArsM in microbes and AS3MT in animals, including humans. Trivalent arsenic(III) is methylated up to three times to form methylarsenite [MAs(III)], dimethylarsenite [DMAs(III)] and the volatile trimethylarsine [TMAs(III)]. In microbes, arsenic methylation is a detoxification process. In humans, MAs(III) and DMAs(III) are more toxic and carcinogenic than either inorganic arsenate or arsenite. Here, new crystal structures are reported of ArsM from the thermophilic eukaryotic algaCyanidioschyzonsp. 5508 (CmArsM) with the bound aromatic arsenicals phenylarsenite [PhAs(III)] at 1.80 Å resolution and reduced roxarsone [Rox(III)] at 2.25 Å resolution. These organoarsenicals are bound to two of four conserved cysteine residues: Cys174 and Cys224. The electron density extends the structure to include a newly identified conserved cysteine residue, Cys44, which is disulfide-bonded to the fourth conserved cysteine residue, Cys72. A second disulfide bond between Cys72 and Cys174 had been observed previously in a structure with bound SAM. The loop containing Cys44 and Cys72 shifts by nearly 6.5 Å in the arsenic(III)-bound structures compared with the SAM-bound structure, which suggests that this movement leads to formation of the Cys72–Cys174 disulfide bond. A model is proposed for the catalytic mechanism of arsenic(III) SAM methyltransferases in which a disulfide-bond cascade maintains the products in the trivalent state.
Automating the application of smart materials for protein crystallization
Authors: Khurshid Sahir , Govada Lata , EL-Sharif Hazim F. , Reddy Subrayal M. , Chayen Naomi E.
Published: February 2015

The fabrication and validation of the first semi-liquid nonprotein nucleating agent to be administered automatically to crystallization trials is reported. This research builds upon prior demonstration of the suitability of molecularly imprinted polymers (MIPs; known as `smart materials') for inducing protein crystal growth. Modified MIPs of altered texture suitable for high-throughput trials are demonstrated to improve crystal quality and to increase the probability of success when screening for suitable crystallization conditions. The application of these materials is simple, time-efficient and will provide a potent tool for structural biologists embarking on crystallization trials.
Structures of three polycystic kidney disease-like domains fromClostridium histolyticumcollagenases ColG and ColH
Authors: Bauer Ryan , Janowska Katarzyna , Taylor Kelly , Jordan Brad , Gann Steve , Janowski Tomasz , Latimer Ethan C. , Matsushita Osamu , Sakon Joshua
Published: February 2015

Clostridium histolyticumcollagenases ColG and ColH are segmental enzymes that are thought to be activated by Ca2+-triggered domain reorientation to cause extensive tissue destruction. The collagenases consist of a collagenase module (s1), a variable number of polycystic kidney disease-like (PKD-like) domains (s2a and s2b in ColH and s2 in ColG) and a variable number of collagen-binding domains (s3 in ColH and s3a and s3b in ColG). The X-ray crystal structures of Ca2+-bound holo s2b (1.4 Å resolution,R= 15.0%,Rfree= 19.1%) and holo s2a (1.9 Å resolution,R= 16.3%,Rfree= 20.7%), as well as of Ca2+-free apo s2a (1.8 Å resolution,R= 20.7%,Rfree= 27.2%) and two new forms of N-terminally truncated apo s2 (1.4 Å resolution,R= 16.9%,Rfree= 21.2%; 1.6 Å resolution,R= 16.2%,Rfree= 19.2%), are reported. The structurally similar PKD-like domains resemble the V-set Ig fold. In addition to a conserved β-bulge, the PKD-like domains feature a second bulge that also changes the allegiance of the subsequent β-strand. This β-bulge and the genesis of a Ca2+pocket in the archaeal PKD-like domain suggest a close kinship between bacterial and archaeal PKD-like domains. Different surface properties and indications of different dynamics suggest unique roles for the PKD-like domains in ColG and in ColH. Surface aromatic residues found on ColH s2a-s2b, but not on ColG s2, may provide the weak interaction in the biphasic collagen-binding mode previously found in s2b-s3.B-factor analyses suggest that in the presence of Ca2+the midsection of s2 becomes more flexible but the midsections of s2a and s2b stay rigid. The different surface properties and dynamics of the domains suggest that the PKD-like domains of M9B bacterial collagenase can be grouped into either a ColG subset or a ColH subset. The conserved properties of PKD-like domains in ColG and in ColH include Ca2+binding. Conserved residues not only interact with Ca2+, but also position the Ca2+-interacting water molecule. Ca2+aligns the N-terminal linker approximately parallel to the major axis of the domain. Ca2+binding also increases stability against heat and guanidine hydrochloride, and may improve the longevity in the extracellular matrix. The results of this study will further assist in developing collagen-targeting vehicles for various signal molecules.
Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove
Authors: Ivanova Marina E. , Fletcher Georgina C. , O'Reilly Nicola , Purkiss Andrew G. , Thompson Barry J. , McDonald Neil Q.
Published: February 2015

Many components of epithelial polarity protein complexes possess PDZ domains that are required for protein interaction and recruitment to the apical plasma membrane. Apical localization of the Crumbs (Crb) transmembrane protein requires a PDZ-mediated interaction with Pals1 (protein-associated with Lin7, Stardust, MPP5), a member of the p55 family of membrane-associated guanylate kinases (MAGUKs). This study describes the molecular interaction between the Crb carboxy-terminal motif (ERLI), which is required forDrosophilacell polarity, and the Pals1 PDZ domain using crystallography and fluorescence polarization. Only the last four Crb residues contribute to Pals1 PDZ-domain binding affinity, with specificity contributed by conserved charged interactions. Comparison of the Crb-bound Pals1 PDZ structure with an apo Pals1 structure reveals a key Phe side chain that gates access to the PDZ peptide-binding groove. Removal of this side chain enhances the binding affinity by more than fivefold, suggesting that access of Crb to Pals1 may be regulated by intradomain contacts or by protein–protein interaction.
Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states
Authors: Skálová Tereza , Bláha Jan , Harlos Karl , Dušková Jarmila , Koval' Tomáš , Stránský Jan , Hašek Jindřich , Vaněk Ondřej , Dohnálek Jan
Published: February 2015

Human LLT1 is a C-type lectin-like ligand of NKR-P1 (CD161, geneKLRB1), a C-type lectin-like receptor of natural killer cells. Using X-ray diffraction, the first experimental structures of human LLT1 were determined. Four structures of LLT1 under various conditions were determined: monomeric, dimeric deglycosylated after the firstN-acetylglucosamine unit in two forms and hexameric with homogeneous GlcNAc2Man5glycosylation. The dimeric form follows the classical dimerization mode of human CD69. The monomeric form keeps the same fold with the exception of the position of an outer part of the long loop region. The hexamer of glycosylated LLT1 consists of three classical dimers. The hexameric packing may indicate a possible mode of interaction of C-type lectin-like proteins in the glycosylated form.
Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacteriumPsychrobactersp. B6
Authors: Bujacz Anna , Rutkiewicz-Krotewicz Maria , Nowakowska-Sapota Karolina , Turkiewicz Marianna
Published: February 2015

Aminotransferases (ATs) are enzymes that are commonly used in the chemical and pharmaceutical industries for the synthesis of natural and non-natural amino acids by transamination reactions. Currently, the easily accessible enzymes from mesophilic organisms are most commonly used; however, for economical and ecological reasons the utilization of aminotransferases from psychrophiles would be more advantageous, as their optimum reaction temperature is usually significantly lower than for the mesophilic ATs. Here, gene isolation, protein expression, purification, enzymatic properties and structural studies are reported for the cold-active aromatic amino-acid aminotransferase (PsyArAT) fromPsychrobactersp. B6, a psychrotrophic, Gram-negative strain from Antarctic soil. Preliminary computational analysis indicated dual functionality of the enzyme through the ability to utilize both aromatic amino acids and aspartate as substrates. This postulation was confirmed by enzymatic activity tests, which showed that it belonged to the class EC 2.6.1.57. The first crystal structures of a psychrophilic aromatic amino-acid aminotransferase have been determined at resolutions of 2.19 Å for the native enzyme (PsyArAT) and 2.76 Å for its complex with aspartic acid (PsyArAT/D). Both types of crystals grew in the monoclinic space groupP21under slightly different crystallization conditions. ThePsyArAT crystals contained a dimer (90 kDa) in the asymmetric unit, which corresponds to the active form of this enzyme, whereas the crystals of thePsyArAT/D complex included four dimers showing different stages of the transamination reaction.
FEM: feature-enhanced map
Authors: Afonine Pavel V. , Moriarty Nigel W. , Mustyakimov Marat , Sobolev Oleg V. , Terwilliger Thomas C. , Turk Dusan , Urzhumtsev Alexandre , Adams Paul D.
Published: February 2015

A method is presented that modifies a 2mFobs−DFmodelσA-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretability and decreased model bias compared with the starting 2mFobs−DFmodelσA-weighted map.
Automatedde novophasing and model building of coiled-coil proteins
Authors: Rämisch Sebastian , Lizatović Robert , André Ingemar
Published: February 2015

Models generated byde novostructure prediction can be very useful starting points for molecular replacement for systems where suitable structural homologues cannot be readily identified. Protein–protein complexes andde novo-designed proteins are examples of systems that can be challenging to phase. In this study, the potential ofde novomodels of protein complexes for use as starting points for molecular replacement is investigated. The approach is demonstrated using homomeric coiled-coil proteins, which are excellent model systems for oligomeric systems. Despite the stereotypical fold of coiled coils, initial phase estimation can be difficult and many structures have to be solved with experimental phasing. A method was developed for automatic structure determination of homomeric coiled coils from X-ray diffraction data. In a benchmark set of 24 coiled coils, ranging from dimers to pentamers with resolutions down to 2.5 Å, 22 systems were automatically solved, 11 of which had previously been solved by experimental phasing. The generated models contained 71–103% of the residues present in the deposited structures, had the correct sequence and had freeRvalues that deviated on average by 0.01 from those of the respective reference structures. The electron-density maps were of sufficient quality that only minor manual editing was necessary to produce final structures. The method, namedCCsolve, combines methods forde novostructure prediction, initial phase estimation and automated model building into one pipeline.CCsolveis robust against errors in the initial models and can readily be modified to make use of alternative crystallographic software. The results demonstrate the feasibility ofde novophasing of protein–protein complexes, an approach that could also be employed for other small systems beyond coiled coils.
NuProPlot: nucleic acid and protein interaction analysis and plotting program
Authors: Pradhan Lagnajeet , Nam Hyun-Joo
Published: February 2015

Growing numbers of protein and nucleic acid complex structures are being determined and deposited in the Protein Data Bank and the Nucleic Acid Database. With the increasing complexity of these structures, it is challenging to analyse and visualize the three-dimensional interactions. The currently available programs for such analysis and visualization are limited in their applications. They can only analyse a subset of protein–nucleic acid complexes and require multiple iterations before obtaining plots that are suitable for presentation. An interactive web-based program,NuProPlot(http://www.nuproplot.com), has been developed which can automatically identify hydrogen, electrostatic and van der Waals interactions between proteins and nucleic acids and generate a plot showing all of the interactions. Protein–DNA and protein–RNA interactions can be visualized in simple two-dimensional schematics. Interactive schematic drawing options allow selection of the plotted area and repositioning of the individual interactions for better legibility.NuProPlotis a fully automated and user-friendly program providing various custom options.NuProPlotrepresents a greatly improved option for analysis and presentation of protein–nucleic acid interactions.
Structural characterization of substrate and inhibitor binding to farnesyl pyrophosphate synthase fromPseudomonas aeruginosa
Authors: Schmidberger Jason W. , Schnell Robert , Schneider Gunter
Published: February 2015

Locus PA4043 in the genome ofPseudomonas aeruginosaPAO1 has been annotated as coding for a farnesyl pyrophosphate synthase (FPPS). This open reading frame was cloned and expressed recombinantly inEscherichia coli. The dimeric enzyme shows farnesyl pyrophosphate synthase activity and is strongly inhibited by ibandronate and zoledronate, drugs that are presently in clinical use. The structures of the unliganded enzyme and complexes with the substrate geranyl diphosphate (GPP), the inhibitor ibandronate and two compounds obtained from a differential scanning fluorimetry-based screen of a fragment library were determined by X-ray crystallography to resolutions of better than 2.0 Å. The enzyme shows the typical α-helical fold of farnesyl pyrophosphate synthases. The substrate GPP binds in the S1 substrate site in an open conformation of the enzyme. In the enzyme–ibandronate complex three inhibitor molecules are bound in the active site of the enzyme. One inhibitor molecule occupies the allylic substrate site (S1) of each subunit, as observed in complexes of nitrogen-containing bisphosphonate inhibitors of farnesyl synthases from other species. Two (in subunitA) and one (in subunitB) additional ibandronate molecules are bound in the active site. The structures of the fragment complexes show two molecules bound in a hydrophobic pocket adjacent to the active site. This allosteric pocket, which has previously only been described for FPPS from eukaryotic organisms, is thus also present in enzymes from pathogenic prokaryotes and might be utilized for the design of inhibitors of bacterial FPPS with a different chemical scaffold to the highly charged bisphosphonates, which are less likely to pass bacterial membranes.
Coherent imaging at the diffraction limit. Erratum
Authors: Thibault Pierre , Guizar-Sicairos Manuel , Menzel Andreas
Published: February 2015

A correction to the article by Thibaultet al.[J. Synchrotron Rad.(2014),21, 1011–1018] is given.
Contextualizing entrepreneurial learning in basic and vocational education
Authors: Hietanen Lenita , Järvi Taina
Published: February 2015

Purpose

– The purpose of this study is to examine and model entrepreneurial learning processes as a continuum from non-business basic education to vocational education. Previous studies and policy programs in Europe suggest that entrepreneurship education should be a core part of the education system.

Design/methodology/approach

– This is an action research piece of work in which two researchers (the authors) have first studied each other’s own data independently, and then combined these two sets of data. One data set has been collected in a non-business, basic education setting, whereas the other focuses on business studies in vocational education. Here, the entrepreneurial learning process is seen as a synthesis of experimentation with discovered and created opportunities and managing knowledge and competences through reflective practices and decision-making processes.

Findings

– The main finding is that entrepreneurial learning can be enabled and may manifest itself as a useful process both in non-business and business school contexts. Another related essential finding is the importance of developing learners’ reflective practices.

Practical implications

– This research aims to provide scientific evidence that different school levels should cooperate to establish entrepreneurial learning as a continuous process. This case has been researched in the Finnish educational system, but it may also prompt teachers at different school levels in other countries to enable their students’ entrepreneurial learning.

Originality/value

– Although entrepreneurial learning has been researched frequently, there is still a lack of investigation concerning lower educational levels, especially non-business basic education. In addition, the point when growth to become entrepreneurial could begin has not been studied in depth. This research focuses on demonstrating how entrepreneurial learning can be planned and executed as a continuum at lower educational levels.
Cultural heritage and entrepreneurship – inspiration for novel ventures creation
Authors: Summatavet Kärt , Raudsaar Mervi
Published: February 2015

Purpose

– The purpose of this paper is to study the role of networking, creating community, product development and mentoring in the experiential and entrepreneurial learning process. A close look is taken at the experiential knowledge of entrepreneurs to understand and bridge the gap between local cultures and entrepreneurial communities: how to map and implement the tacit knowledge possessed by an entrepreneur, and what sources help trainees find attractive ideas for a new venture?

Design/methodology/approach

– After reviewing the key literature, a phenomenological approach has been applied. Data were collected using not only semi-structured interviews but also secondary data.

Findings

– Creative entrepreneurs consider it important that learning materials are provided according to the learner’s specialist business idea. They need and expect multi-layered support from peers/coaches/mentors and social/local/specialist networks to test the ideas and products and services directly in the community.

Originality/value

– As the conventional teaching methodology is inapplicable for creative and community entrepreneurs, the key factors of their venture-creation process focus on their personal experience, skills, capabilities and motivation.
The association between the regular use of preventive labour induction and improved term birth outcomes: findings of a systematic review and meta‐analysis
Authors: Nicholson JM , Kellar LC , Henning GF , Waheed A , Colon‐Gonzalez M , Ural S
Published: February 2015

Background

Despite a lack of high‐quality evidence, the use of ‘non‐indicated’ term labour induction is increasingly restricted throughout the world.

Objectives

To assess published associations between the regular use of modelled risk‐based ‘non‐indicated’ term labour induction (hereinafter ‘preventive induction’) and rates of common adverse birth outcomes.

Search strategy

MEDLINE and PUBMED databases were searched electronically.

Selection criteria

Studies were identified that compared term birth outcomes following either the current standard approach with its emphasis on the expectant management of intermediate‐level risk or the regular use of preventive induction.

Data collection and analysis

Four studies from four unique databases were identified. A meta‐analysis was performed using STATA IC12.

Main results

Pregnancies exposed to the regular use of preventive induction (n = 1153), as compared with pregnancies receiving the current standard approach (n = 1865), experienced a lower caesarean delivery rate (5.7% versus 14.4%; relative risk 0.39, 95% CI 0.31–0.50; I2 P = 0.21), a lower neonatal intensive care unit admission rate (2.9% versus 6.5%; relative risk 0.45, 95% CI 0.31–0.65; I2 P = 0.57), and a lower weighted adverse outcome index score (2.8 versus 6.1).

Conclusions

The regular use of preventive induction, as compared with the current standard approach, was associated with a more favourable pattern of birth outcomes. Other recently published meta‐analyses have also determined that certain types of ‘non‐indicated’ labour induction are beneficial. Accordingly, the current broad restrictions on ‘non‐indicated’ labour induction should be reconsidered. Adequately powered multi‐site randomised clinical trials are needed to definitively study the risks and benefits of modelled risk‐based ‘non‐indicated’ (i.e. ‘preventive’) term labour induction.
Ethnic differences in postpartum weight retention: a Norwegian cohort study
Authors: Waage CW , Falk RS , Sommer C , Mørkrid K , Richardsen KR , Bærug A , Shakeel N , Birkeland KI , Jenum AK
Published: February 2015

Objective

To explore ethnic differences in weight retention 14 weeks postpartum.

Design

Population‐based cohort study.

Setting

The STORK Groruddalen Study.

Population

A multi‐ethnic cohort of healthy pregnant women attending primary antenatal care at three public Child Health Clinics, in Oslo, Norway (n = 642).

Methods

An explanatory linear regression was performed to model the relationship between ethnicity and postpartum weight retention. Forward selection of 12 explanatory factors was used to adjust for potential confounding factors, based on univariate analysis and adjusted R2.

Main outcome measure

Postpartum weight retention.

Results

Unadjusted mean postpartum weight retention was 2.3 (4.9) kg for women from Western Europe and varied from 3.7 (3.5) to 6.3 (4.7) kg among the five ethnic minority groups. The proportion of women in the highest quintile (postpartum weight retention >8.5–24.4 kg) significantly differed by ethnicity (P < 0.01 for the proportion of women from South Asia, the Middle East and Africa compared with Western Europeans). Women from all ethnic minority groups had a higher relative increase in weight from pre‐pregnancy to postpartum (P < 0.01) compared with Western Europeans. After adjustments for significant exposures, women from the Middle East retained 2.0 kg (95% CI: 1.0–3.0), South Asia 2.8 kg (91.9–3.6), and Africa 4.4 kg (3.1–5.8) more than Western Europeans (P < 0.01).

Conclusions

Significantly more women with an ethnic origin from South Asia, the Middle East and Africa had high postpartum weight retention compared with Western European women.
The Impact of Daubert on the Admissibility of Forensic Anthropology Expert Testimony
Authors: Lesciotto Kate M.
Published: February 2015

Forensic anthropologists anticipated a significant impact from the 1993 Supreme Court Daubert decision, which addressed the standard of admissibility for expert testimony. In response, many forensic articles cited Daubert in the search for objective techniques or a critique of established subjective methods. This study examines challenges to forensic anthropological expert testimony to evaluate whether Daubert has actually affected the admissibility of such testimony. Thirty cases were identified that addressed the admissibility of the testimony, including 14 cases prior to Daubert and 16 after Daubert. Examination of these cases indicates that post‐Daubert cases do not result in more exclusions. Yet, this lack of exclusions may instead be viewed as a manifestation of the field's overall surge toward more objective and quantifiable techniques in a self‐regulating response to Daubert.
Localization of Banana bunchy top virus and cellular compartments in gut and salivary gland tissues of the aphid vector Pentalonia nigronervosa
Authors: Watanabe Shizu , Borthakur Dulal , Bressan Alberto
Published: February 2015

Banana bunchy top virus (BBTV) (Nanoviridae: Babuvirus) is transmitted by aphids of the genus Pentalonia in a circulative manner. The cellular mechanisms by which BBTV translocates from the anterior midgut to the salivary gland epithelial tissues are not understood. Here, we used multiple fluorescent markers to study the distribution and the cellular localization of early and late endosomes, macropinosomes, lysosomes, microtubules, actin filaments, and lipid raft subdomains in the gut and principal salivary glands of Pentalonia nigronervosa. We applied colabeling assays, to colocalize BBTV viral particles with these cellular compartments and structures. Our results suggest that multiple potential cellular processes, including clathrin‐ and caveolae‐mediated endocytosis and lipid rafts, may not be involved in BBTV internalization.
Incidence and management of chylothorax after esophagectomy
Authors: Miao Longsheng , Zhang Yawei , Hu Hong , Ma Longfei , Shun Yihua , Xiang Jiaqing , Chen Haiquan
Published: February 2015

Background

Chylothorax is a rare but serious postoperative complication in esophageal cancer patients. The aim of this study was to identify risk factors associated with chylothorax and the indication for surgical intervention.

Methods

A consecutive series of 1290 patients who underwent esophagectomy for esophageal cancer was included. Peri‐operative data, including postoperative morbidity and mortality, were analyzed.

Results

Thirty‐four patients (2.6%) developed chylothorax and had significantly higher instances of pneumonia (26.5% vs. 11.1%, P = 0.012) and arrhythmia (17.6% vs. 2.9%, P = 0.001), and a longer hospital stay (22 vs. 18 days, P < 0.001). Reoperation was performed in 11 patients at a rate of 77.8%, 42.9%, 20%, and 0% for chylothorax diagnosed in two, three, four, and >= 5 days, respectively, after esophagectomy (P < 0.001). After three days of conservative therapy, the chest tube output was significantly greater in patients whose medical management had failed than in those successfully treated (P < 0.001). All patients who required reoperation had >= 13.5 ml/kg of drainage (sensitivity 100%); four of 23 patients with successful medical management had a chest tube output >= 13.5 ml/kg (specificity 83%). Logistic regression analysis showed that body mass index (BMI) < 25 was an independent risk factor for chylothorax (hazard ratio = 9.256, P = 0.029).

Conclusions

Patients with a BMI < 25 are more likely to develop chylothorax after esophagectomy. Operative therapy should be seriously considered in patients who develop chylothorax early postoperatively. In addition, a high daily chylous output of >= 13.5 ml/kg after three days of conservative therapy might be a reliable indicator for reoperation.
Testing hypotheses on distribution shifts and changes in phenology of imperfectly detectable species
Authors: Chambert Thierry , Kendall William L. , Hines James E. , Nichols James D. , Pedrini Paolo , Waddle J. Hardin , Tavecchia Giacomo , Walls Susan C. , Tenan Simone
Published: February 2015

With ongoing climate change, many species are expected to shift their spatial and temporal distributions. To document changes in species distribution and phenology, detection/non‐detection data have proven very useful. Occupancy models provide a robust way to analyse such data, but inference is usually focused on species spatial distribution, not phenology.

We present a multi‐season extension of the staggered‐entry occupancy model of Kendall et al. (2013, Ecology, 94, 610), which permits inference about the within‐season patterns of species arrival and departure at sampling sites. The new model presented here allows investigation of species phenology and spatial distribution across years, as well as site extinction/colonization dynamics.

We illustrate the model with two data sets on European migratory passerines and one data set on North American treefrogs. We show how to derive several additional phenological parameters, such as annual mean arrival and departure dates, from estimated arrival and departure probabilities.

Given the extent of detection/non‐detection data that are available, we believe that this modelling approach will prove very useful to further understand and predict species responses to climate change.
The skin microbiome: Associations between altered microbial communities and disease
Authors: Weyrich Laura S , Dixit Shreya , Farrer Andrew G , Cooper Alan J , Cooper Alan J
Published: February 2015

A single square centimetre of the human skin can contain up to one billion microorganisms. These diverse communities of bacteria, fungi, mites and viruses can provide protection against disease, but can also exacerbate skin lesions, promote disease and delay wound healing. This review addresses the current knowledge surrounding the healthy skin microbiome and examines how different alterations to the skin microbial communities can contribute to disease. Current methodologies are considered, changes in microbial diversity and colonisation by specific microorganisms are discussed in the context of atopic dermatitis, psoriasis, acne vulgaris and chronic wounds. The recent impact of modern Westernised lifestyles on the human skin microbiome is also examined, as well as the potential benefits and pitfalls of novel therapeutic strategies. Further analysis of the human skin microbiome, and its interactions with the host immune system and other commensal microorganisms, will undoubtedly elucidate molecular mechanisms for disease and reveal gateways for novel therapeutic treatment strategies.