bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanoscale rotational deformation near crack tips in nanocrystalline solids
Authors: Ovid'ko I A , Sheinerman A G
Published: August 2012

A special physical micromechanism of plastic flow in pre-cracked nanocrystalline solids is suggested and theoretically described. The micromechanism represents the fast nanoscale rotational deformation (NRD) occurring through collective events of ideal nanoscale shear near crack tips. We calculated the stress and energy characteristics of the NRD. It has been found that such rotational deformation can effectively occur near crack tips and enhance fracture toughness of nanocrystalline materials. Our theoretical model accounts for the in situ experimental observations (Ke et al 1995 Nanostruct. Mater.

5 689, Shan et al 2008 Phys. Rev. Lett.

100 105502, Cheng et al 2010 Phys. Rev. Lett.

104 255501, Liu et al 2011 Scripta Mater.

64 343) of crystal lattice rotations within nanoscale grains and formation of modulated/agglomerated grain structures near crack tips in deformed nanocrystalline solids with finest grains.
Growth of nanocomposite films from accelerated C60 ions
Authors: Pukha V E , Zubarev E N , Drozdov A N , Pugachov A T , Jeong S H , Nam S C
Published: August 2012

A beam of accelerated C60 ions is used to deposit superhard (∼50 GPa) carbon films that exhibit high index plasticity (∼0.13–0.14) and high conductivity (up to 3000 S m−1). Transmission electron microscopy, Raman spectroscopy and x-ray photoelectron spectroscopy are subsequently used to study the microstructure and bond character of the deposited films. The films consist of textured graphite nanocrystals and diamond-like amorphous carbon (DLC). The graphene plane of the nanocrystals is aligned perpendicular to the film surface. It is shown that sp2 bonds dominate in the films. The percentage of sp3 bonds depends on the ion energy and the substrate temperature, and does not exceed 40%. The obtained results suggest that a new nanocomposite material consisting of oriented graphite nanocrystals reinforced by a DLC matrix is synthesized. A simple model is proposed to correlate the excellent mechanical properties with the observed structure.
Dielectric properties and spectroscopy of large-aspect-ratio ferroelectric thin-film heterostructures
Authors: Narayanan Manoj , Balachandran Uthamalingam , Stoupin Stanislav , Ma Beihai , Tong Sheng , Chao Sheng , Liu Shanshan
Published: August 2012

High energy density and breakdown/operating voltages with lower dielectric film thickness and manufacturing cost are the necessary traits in futuristic capacitors for a variety of applications. Prior studies have reported the successful fabrication of high-k, thin-film ferroelectrics with aspect ratios (diameter/thickness) <1000; however, devices with aspect ratios >104–105 are necessary to meet the large-capacitive requirements in pulsed-power applications such as the inverters in hybrid electric vehicles (HEVs). It is also widely accepted that the breakdown field of thin films decreases logarithmically with an increase in the aspect ratio (area) due to the increased probability of producing a defect spot. These observations raise an important question: can we fabricate ferroelectric high-k film capacitors that have large aspect ratio and can sustain high fields? Here we report the fabrication and characterization of Pb0.92La0.08Zr0.52Ti0.48O3 thin-film capacitors with aspect ratios >104 that can be operated at ∼1 MV cm−1 and are suitable for embedded passives in HEVs. Dielectric spectroscopy showed a low-frequency anomalous relaxation behaviour in large-aspect-ratio heterostructure, which was analysed and interpreted using an equivalent circuit model. The measured anomalous relaxation behaviour was de-convoluted using the model to obtain the actual material response. High capacitances (1–5 µF) and energy densities of (∼9 J cm−3) were routinely measured in these high-aspect-ratio films.
Drosophilatubulin-binding cofactor B is required for microtubule network formation and for cell polarity
Authors: Baffet Alexandre D. , Benoit Béatrice , Januschke Jens , Audo Jennifer , Gourhand Vanessa , Roth Siegfried , Guichet Antoine
Published: August 2012

Microtubules (MTs) are essential for cell division, shape, intracellular transport, and polarity. MT stability is regulated by many factors, including MT-associated proteins and proteins controlling the amount of free tubulin heterodimers available for polymerization. Tubulin-binding cofactors are potential key regulators of free tubulin concentration, since they are required for α-β–tubulin dimerization in vitro. In this paper, we show that mutation of the Drosophila tubulin-binding cofactor B (dTBCB) affects the levels of both α- and β-tubulins and dramatically destabilizes the MT network in different fly tissues. However, we find that dTBCB is dispensable for the early MT-dependent steps of oogenesis, including cell division, and that dTBCB is not required for mitosis in several tissues. In striking contrast, the absence of dTBCB during later stages of oogenesis causes major defects in cell polarity. We show that dTBCB is required for the polarized localization of the axis-determining mRNAs within the oocyte and for the apico-basal polarity of the surrounding follicle cells. These results establish a developmental function for the dTBCB gene that is essential for viability and MT-dependent cell polarity, but not cell division.
Novel PKCα-mediated phosphorylation site(s) on cofilin and their potential role in terminating histamine release
Authors: Sakuma Megumi , Shirai Yasuhito , Yoshino Ken-ichi , Kuramasu Maho , Nakamura Tomofumi , Yanagita Toshihiko , Mizuno Kensaku , Hide Izumi , Nakata Yoshihiro , Saito Naoaki
Published: August 2012

Using specific inhibitors, kinase-negative mutants, and small interfering RNA against protein kinase Cα (PKCα) or PKCβI, we find that PKCβI positively regulates degranulation in rat basophilic leukemia–2H3 cells, whereas PKCα negatively regulates degranulation. Mass spectrometric and mutagenic analyses reveal that PKCα phosphorylates cofilin at Ser-23 and/or Ser-24 during degranulation. Overexpression of a nonphosphorylatable form (S23,24A), but not that of a mutant-mimicking phosphorylated form (S23,24E), increases degranulation. Furthermore, the S23,24A mutant binds to F-actin and retains its depolymerizing and/or cleavage activity; conversely, the S23,24E mutant is unable to sever actin filaments, resulting in F-actin polymerization. In addition, the S23,24E mutant preferentially binds to the 14-3-3ζ protein. Fluorescence-activated cell sorting analysis with fluorescein isothiocyanate–phalloidin and simultaneous observation of degranulation, PKC translocation, and actin polymerization reveals that during degranulation, actin polymerization is dependent on PKCα activity. These results indicate that a novel PKCα-mediated phosphorylation event regulates cofilin by inhibiting its ability to depolymerize F-actin and bind to 14-3-3ζ, thereby promoting F-actin polymerization, which is necessary for cessation of degranulation.
Nonredundant roles of cytoplasmic β- and γ-actin isoforms in regulation of epithelial apical junctions
Authors: Baranwal Somesh , Naydenov Nayden G. , Harris Gianni , Dugina Vera , Morgan Kathleen G. , Chaponnier Christine , Ivanov Andrei I.
Published: August 2012

Association with the actin cytoskeleton is critical for normal architecture and dynamics of epithelial tight junctions (TJs) and adherens junctions (AJs). Epithelial cells express β-cytoplasmic (β-CYA) and γ-cytoplasmic (γ-CYA) actins, which have different cellular localization and functions. This study elucidates the roles of cytoplasmic actins in regulating structure and remodeling of AJs and TJs in model intestinal epithelia. Immunofluorescence labeling and latrunculin B treatment reveal affiliation of dynamic β-CYA filaments with newly assembled and mature AJs, whereas an apical γ-CYA pool is composed of stable perijunctional bundles and rapidly turning-over nonjunctional filaments. The functional effects of cytoplasmic actins on epithelial junctions are examined by using isoform-specific small interfering RNAs and cell-permeable inhibitory peptides. These experiments demonstrate unique roles of β-CYA and γ-CYA in regulating the steady-state integrity of AJs and TJs, respectively. Furthermore, β-CYA is selectively involved in establishment of apicobasal cell polarity. Both actin isoforms are essential for normal barrier function of epithelial monolayers, rapid AJ/TJ reassembly, and formation of three-dimensional cysts. Cytoplasmic actin isoforms play unique roles in regulating structure and permeability of epithelial junctions.
A nuclear-derived proteinaceous matrix embeds the microtubule spindle apparatus during mitosis
Authors: Yao Changfu , Rath Uttama , Maiato Helder , Sharp David , Girton Jack , Johansen Kristen M. , Johansen Jørgen
Published: August 2012

The concept of a spindle matrix has long been proposed. Whether such a structure exists, however, and what its molecular and structural composition are have remained controversial. In this study, using a live-imaging approach in Drosophila syncytial embryos, we demonstrate that nuclear proteins reorganize during mitosis to form a highly dynamic, viscous spindle matrix that embeds the microtubule spindle apparatus, stretching from pole to pole. We show that this “internal” matrix is a distinct structure from the microtubule spindle and from a lamin B–containing spindle envelope. By injection of 2000-kDa dextran, we show that the disassembling nuclear envelope does not present a diffusion barrier. Furthermore, when microtubules are depolymerized with colchicine just before metaphase the spindle matrix contracts and coalesces around the chromosomes, suggesting that microtubules act as “struts” stretching the spindle matrix. In addition, we demonstrate that the spindle matrix protein Megator requires its coiled-coil amino-terminal domain for spindle matrix localization, suggesting that specific interactions between spindle matrix molecules are necessary for them to form a complex confined to the spindle region. The demonstration of an embedding spindle matrix lays the groundwork for a more complete understanding of microtubule dynamics and of the viscoelastic properties of the spindle during cell division.
Actin polymerization controls the activation of multidrug efflux at fertilization by translocation and fine-scale positioning of ABCB1 on microvilli
Authors: Whalen Kristen , Reitzel Adam M. , Hamdoun Amro
Published: August 2012

Fertilization changes the structure and function of the cell surface. In sea urchins, these changes include polymerization of cortical actin and a coincident, switch-like increase in the activity of the multidrug efflux transporter ABCB1a. However, it is not clear how cortical reorganization leads to changes in membrane transport physiology. In this study, we used three-dimensional superresolution fluorescence microscopy to resolve the fine-scale movements of the transporter along polymerizing actin filaments, and we show that efflux activity is established after ABCB1a translocates to the tips of the microvilli. Inhibition of actin poly­merization or bundle formation prevents tip localization, resulting in the patching of ABCB1a at the cell surface and decreased efflux activity. In contrast, enhanced actin polymerization promotes tip localization. Finally, interference with Rab11, a regulator of apical recycling, inhibits activation of efflux activity in embryos. Together our results show that actin-mediated, short-range traffic and positioning of transporters at the cell surface regulates multidrug efflux activity and highlight the multifaceted roles of microvilli in the spatial distribution of membrane proteins.
SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models
Authors: Moal Iain H. , Fernández-Recio Juan
Published: August 2012

Motivation: Empirical models for the prediction of how changes in sequence alter protein–protein binding kinetics and thermodynamics can garner insights into many aspects of molecular biology. However, such models require empirical training data and proper validation before they can be widely applied. Previous databases contained few stabilizing mutations and no discussion of their inherent biases or how this impacts model construction or validation.

Results: We present SKEMPI, a database of 3047 binding free energy changes upon mutation assembled from the scientific literature, for protein–protein heterodimeric complexes with experimentally determined structures. This represents over four times more data than previously collected. Changes in 713 association and dissociation rates and 127 enthalpies and entropies were also recorded. The existence of biases towards specific mutations, residues, interfaces, proteins and protein families is discussed in the context of how the data can be used to construct predictive models. Finally, a cross-validation scheme is presented which is capable of estimating the efficacy of derived models on future data in which these biases are not present.

Availability: The database is available online at http://life.bsc.es/pid/mutation_database/

Contact:  juanf@bsc.es
Adam and Eve’s Shame (And Ours)
Authors: Ward Graham
Published: August 2012

Literature and theology creates a specific interdisciplinary ‘scene’. Over recent years both disciplines have also hosted a wide range of other intellectual sources that have demonstrated the permeability of disciplinary boundaries. This essay explores this permeability by bringing together a theological analysis of shame in the biblical account of Adam and Eve, with the work of affect theory and a reading of shame in Flaubert’s Madame Bovary. The essay concludes, on the basis of the interdisciplinary exercise, with a reflection on the relationship between writing and shame, and the fears that lurk in interdisciplinary engagement. It suggests that the Journal itself has done much to mitigate the shadow and shame of dilettantism associated with interdisciplinary work.
Phenotypic and Molecular Diversity of Cochliobolus sativus Populations from Wheat
Authors: Gurung Suraj , Mahto Baidya N. , Gyawali Sanjaya , Adhikari Tika B.
Published: August 2012

Spot blotch, caused by Cochliobolus sativus, is a devastating foliar disease of wheat in Nepal and in the Northern Great Plains of the United States. However, limited information on variation in virulence and genetic structure of C. sativus from wheat is available. In this study, pathogenic variation of 96 isolates of C. sativus from the Hill and Plain areas in Nepal (n = 48) and in the Central and Northern areas in North Dakota (n = 48) were evaluated on 12 differential wheat lines. DNA polymorphisms in all isolates were analyzed using eight selected amplified fragment length polymorphism primer combinations. Phenotypic data analysis showed the isolates varied greatly and were classified into 47 pathotypes. Cluster analysis indicated the isolates fell into three distinct groups with low, intermediate, and high virulence. Population genetic analysis revealed significant linkage disequilibrium ([Formula: see text] = 0.066 to 0.292), indicating that sexual reproduction plays little or no role in evolution and disease epidemiology in wheat fields. Furthermore, the corrected standardized fixation index (G″ST = 0.05 and 0.02) showed no evidence of genetic differentiation in C. sativus populations. Collectively, these results confirmed high pathogenic and molecular diversity in the C. sativus populations collected from wheat foliar infections and will be useful to assist in developing resistant cultivars to manage this disease.
First Report of Neofusicoccum parvum Associated with Bark Canker and Dieback of Acer pseudoplatanus and Quercus robur in Italy
Authors: Moricca S. , Uccello A. , Ginetti B. , Ragazzi A.
Published: August 2012

Between 2007 and 2011, Acer pseudoplatanus and Quercus robur trees declined in the North Park and the Boscoincittà Park in Milan, Italy (lat. 45° 27′ 47″ N, long. 09° 11′ 16″ E, elev. 121 m). Symptoms included extensive lengthwise bark cracks, with necrosis of the wood tissue underneath. Isolations were conducted from bark and infected wood after surface sterilization with 10% H2O2 for 10 min, followed by five washings in sterilized water. Tissue was placed on potato dextrose agar (PDA) in petri dishes amended with 0.06 g/l streptomycin at pH 6.5. The dishes were incubated in the dark at 24°C. Colonies reached a diameter of 7 to 8 cm in 7 days. They were whitish grey on the upper surface and blackish at the bottom, and consisted of dense aerial mycelia. The conidia were hyaline, ellipsoid, smooth, non-septate, thin-walled, with their upper end wider than their lower end, and measured 14 to 20 × 4.5 to 7 μm. The causal organism was identified as Neofusicoccum parvum (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips (basionym Fusicoccum parvum Pennycook & Samuels; teleomorph Botryosphaeria parva Pennycook & Samuels) based on biometric characteristics, common taxonomic keys, and the sequence information from the rDNA ITS region and the elongation factor 1-alpha (EF1-α) gene (GenBank Accession Nos. HQ893535 and HQ893537, respectively). All morphological traits corresponded to those of the holotype (1), while BLAST searches of the GenBank database revealed for both loci 100% homology with reference sequences. To confirm the involvement of N. parvum in the tree death, and fulfil Koch's postulates, 20 2-year-old seedlings of A. pseudoplatanus and Q. robur (10 each) were artificially infected in May with N. parvum in 2008 and in 2009. A bark portion was removed aseptically and a PDA disc (0.5 cm diameter) of N. parvum mycelium was placed on the wound. Control seedlings (3 per species) received sterile PDA discs. The inoculation site was wrapped in Parafilm for 10 days. After 3 weeks, infected seedlings showed sunken bark lesions associated with necrosis and bark cracks. When the bark was stripped, the wood below these lesions was also necrotic. Control seedlings developed no symptoms. Mycelium of N. parvum was successfully reisolated from the infected tissue. N. parvum is an important member of the Botryosphaeriaceae, a family of cosmopolitan endophytes that have been known for many years (2). The pathogen has been in recent years linked to complex syndromes, in which a prominent symptom is the formation of bark cankers. Although common on fruit crops, it has increasingly been reported on forest trees (3,4).

References: (1) P. Crous et al. Stud. Mycol. 55:248, 2006. (2) P. A. Saccardo. Michelia 1:1, 1877. (3) M. E. Sánchez et al. Plant Dis. 87:1515, 2003. (4) B. Slippers and M. J. Wingfield. Fung. Biol. Rev. 21:90, 2007.
Elderly Age as a Prognostic Marker of 1-year Poor Outcome for Subarachnoid Hemorrhage Patients through Its Interaction with Admission Hydrocephalus
Authors: Degos Vincent , Gourraud Pierre-Antoine , Tursis Virginie Trehel , Whelan Rachel , Colonne Chantal , Korinek Anne Marie , Clarençon Frédéric , Boch Anne-Laure , Nouet Aurélien , Young William L. , Apfel Christian C. , Puybasset Louis
Published: August 2012

Background

An increasing number of elderly patients are treated for aneurysmal subarachnoid hemorrhage. Given that elderly age is associated with both poor outcome and an increased risk of hydrocephalus, we sought to investigate the interaction between age and hydrocephalus in outcome prediction.

Methods

We enrolled 933 consecutive patients treated for subarachnoid hemorrhage between 2002 and 2010 and followed them for 1 yr after intensive care unit discharge. We first performed stepwise analyses to determine the relationship among neurologic events, elderly age (60 or more yr old), and 1-yr poor outcome (defined as Rankin 4-6). Within the most parsimonious model, we then tested for interaction between admission hydrocephalus and elderly age. Finally, we tested the association between age as a stratified variable and 1-yr poor outcome for each subgroup of patients with neurologic events.

Results

24.1% (n=225) of subarachnoid hemorrhage patients were 60 yr old or more and 19.3% (n=180) had 1-yr poor outcomes. In the most parsimonious model (area under the receiver operating characteristic curve, 0.84; 95% CI: 0.82 to 0.88; P<0.001), elderly age and admission hydrocephalus were two independent predictors for 1-yr outcome (P<0.001 and P=0.004, respectively). Including the significant interaction between age and hydrocephalus (P=0.04) improved the model's outcome prediction (P=0.03), but elderly age was no longer a significant predictor. Finally, stratified age was associated with 1-yr poor outcome for hydrocephalus patients (P=0.007), but not for patients without hydrocephalus (P=0.87).

Conclusion

In this observational study, elderly age and admission hydrocephalus predicted poor outcome, but elderly age without hydrocephalus did not. An external validation, however, will be needed to generalize this finding.
Investigating the impact of hepatitis B virus surface gene polymorphism on antigenicity using ex vivo phenotyping
Authors: Ijaz Samreen , Szypulska Renata , Andrews Nick , Tedder Richard S.
Published: August 2012

The hepatitis B virus (HBV) surface antigen (HBsAg) is a complex protein, and understanding accurately the impact of amino acid changes on the antigenicity of the immunodominantadeterminant must take this complexity into consideration. Epitope mapping with four mAbs was used to phenotype HBsAg directly from patients’ sera to investigate the effect of mutations in their native genetic backbone. The expected mAb reactivity was established initially for samples harbouring ‘wild-type’ HBsAg sequences across genotypes A–E. The alteration of HBsAg antigenicity, defined by mAb epitope loss, was demonstrated in a number of samples with sequence-inferred amino acid changes. Individual mutations within the mapped epitopes to which the mAbs were directed usually affected their binding. However, the loss of more than one epitope was observed as the number of mutations within a sequence increased. Conversely, not all mutations occurring in theadeterminant altered the HBsAg conformation. The genotype backbone, the specific amino acid substitution and amino acid changes occurring outside the major antigenic region appeared to be important in determining expression of the predicted epitope loss. These data clearly demonstrate that sequence-based methods alone may not accurately define HBsAg phenotype. This phenotyping methodology allows for the rapid and accurate identification of antigenically altered viruses and will greatly enhance current HBV surveillance, research and diagnostic activities. The data generated can be used to inform on public health issues relating to prevalence, transmission and impact of HBsAg mutants in HBV-infected populations.
Evidence of multiple introductions of beak and feather disease virus into the Pacific islands of Nouvelle-Calédonie (New Caledonia)
Authors: Julian Laurel , Lorenzo Almudena , Chenuet Jean-Paul , Bonzon Marianne , Marchal Celine , Vignon Laurent , Collings David A. , Walters Matthew , Jackson Bethany , Varsani Arvind
Published: August 2012

Beak and feather disease virus (BFDV) is a circular ssDNA virus that causes psittacine beak and feather disease and has almost global presence. Here, we report for the first time the presence of in Nouvelle-Calédonie (New Caledonia). One hundred and sixty-eight exotic and 79 endemic birds were sampled in Nouvelle-Calédonie, 26 were found to be positive for BFDV. We characterized the full genomes of 26 isolates and phylogenetic analysis placed nine of the isolates into the BFDV-J strain, with the remaining 17 isolates from Deplanche’s Rainbow Lorikeet (Trichoglossus haematodus deplanchii) forming a novel strain, BFDV-P. Of more concern was the discovery of an infected bird from the vulnerable and endemic New Caledonian Parakeet (Cyanoramphus saisseti). Our results reveal that there have been at least two introductions of BFDV into Nouvelle-Calédonie.
Germination and Plantlet Regeneration of Encapsulated Microshoots of Aromatic Rice (Oryza sativaL. Cv. MRQ 74)
Authors: Taha Rosna Mat , Saleh Azani , Mahmad Noraini , Hasbullah Nor Azlina , Mohajer Sadegh
Published: August 2012

Plant tissues such as somatic embryos, apical shoot tips, axillary shoot buds, embryogenic calli, and protocom-like bodies are potential micropropagules that have been considered for creating synthetic seeds. In the present study, 3–5 mm microshoots ofOryza sativaL. Cv. MRQ 74 were used as explant sources for obtaining synthetic seeds. Microshoots were induced from stem explants on Murashige and Skoog (MS) medium supplemented with 1.5 mg/L benzylaminopurine (BAP). They were encapsulated in 3% (w/v) sodium alginate, 3% sucrose, 0.1 mg/L BAP, and 0.1 mg/Lα-Naphthalene acetic acid (NAA). Germination and plantlet regeneration of the encapsulated seeds were tested by culturing them on various germination media. The effect of storage period (15–30 days) was also investigated. The maximum germination and plantlet regeneration (100.0%) were recorded on MS media containing 3% sucrose and 0.8% agar with and without 0.1 mg/L BAP. However, a low germination rate (6.67%) was obtained using top soil as a sowing substrate. The germination rate of the encapsulated microshoots decreased from 93.33% to 3.33% after 30 days of storage at 4°C in the dark. Therefore, further research is being done to improve the germination rate of the synthetic seeds.
Voltage-gated potassium channel EAG2 controls mitotic entry and tumor growth in medulloblastoma via regulating cell volume dynamics
Authors: Huang Xi , Dubuc Adrian M. , Hashizume Rintaro , Berg Jim , He Ye , Wang Ji , Chiang Chin , Cooper Michael K. , Northcott Paul A. , Taylor Michael D. , Barnes Michael J. , Tihan Tarik , Chen Justin , Hackett Christopher S. , Weiss William A. , James C. David , Rowitch David H. , Shuman Marc A. , Jan Yuh Nung , Jan Lily Yeh
Published: August 2012

Medulloblastoma (MB) is the most common pediatric CNS malignancy. We identify EAG2 as an overexpressed potassium channel in MBs across different molecular and histological subgroups. EAG2 knockdown not only impairs MB cell growth in vitro, but also reduces tumor burden in vivo and enhances survival in xenograft studies. Mechanistically, we demonstrate that EAG2 protein is confined intracellularly during interphase but is enriched in the plasma membrane during late G2 phase and mitosis. Disruption of EAG2 expression results in G2 arrest and mitotic catastrophe associated with failure of premitotic cytoplasmic condensation. While the tumor suppression function of EAG2 knockdown is independent of p53 activation, DNA damage checkpoint activation, or changes in the AKT pathway, this defective cell volume control is specifically associated with hyperactivation of the p38 MAPK pathway. Inhibition of the p38 pathway significantly rescues the growth defect and G2 arrest. Strikingly, ectopic membrane expression of EAG2 in cells at interphase results in cell volume reduction and mitotic-like morphology. Our study establishes the functional significance of EAG2 in promoting MB tumor progression via regulating cell volume dynamics, the perturbation of which activates the tumor suppressor p38 MAPK pathway, and provides clinical relevance for targeting this ion channel in human MBs.
Meier-Gorlin syndrome mutations disrupt an Orc1 CDK inhibitory domain and cause centrosome reduplication
Authors: Hossain Manzar , Stillman Bruce
Published: August 2012

Like DNA replication, centrosomes are licensed to duplicate once per cell division cycle to ensure genetic stability. In addition to regulating DNA replication, the Orc1 subunit of the human origin recognition complex controls centriole and centrosome copy number. Here we report that Orc1 harbors a PACT centrosome-targeting domain and a separate domain that differentially inhibits the protein kinase activities of Cyclin E–CDK2 and Cyclin A–CDK2. A cyclin-binding motif (Cy motif) is required for Orc1 to bind Cyclin A and inhibit Cyclin A–CDK2 kinase activity but has no effect on Cyclin E–CDK2 kinase activity. In contrast, Orc1 inhibition of Cyclin E–CDK2 kinase activity occurs by a different mechanism that is affected by Orc1 mutations identified in Meier-Gorlin syndrome patients. The cyclin/CDK2 kinase inhibitory domain of Orc1, when tethered to the PACT domain, localizes to centrosomes and blocks centrosome reduplication. Meier-Gorlin syndrome mutations that disrupt Cyclin E–CDK2 kinase inhibition also allow centrosome reduplication. Thus, Orc1 contains distinct domains that control centrosome copy number and DNA replication. We suggest that the Orc1 mutations present in some Meier-Gorlin syndrome patients contribute to the pronounced microcephaly and dwarfism observed in these individuals by altering centrosome duplication in addition to DNA replication defects.
The SNARE Protein SYP71 Expressed in Vascular Tissues Is Involved in Symbiotic Nitrogen Fixation in Lotus japonicus Nodules
Authors: Hakoyama Tsuneo , Oi Ryo , Hazuma Kazuya , Suga Eri , Adachi Yuka , Kobayashi Mayumi , Akai Rie , Sato Shusei , Fukai Eigo , Tabata Satoshi , Shibata Satoshi , Wu Guo-Jiang , Hase Yoshihiro , Tanaka Atsushi , Kawaguchi Masayoshi , Kouchi Hiroshi , Umehara Yosuke , Suganuma Norio
Published: August 2012

Soluble N-Ethylmaleimide Sensitive Factor Attachment Protein Receptor (SNARE) proteins are crucial for signal transduction and development in plants. Here, we investigate a Lotus japonicus symbiotic mutant defective in one of the SNARE proteins. When in symbiosis with rhizobia, the growth of the mutant was retarded compared with that of the wild-type plant. Although the mutant formed nodules, these exhibited lower nitrogen fixation activity than the wild type. The rhizobia were able to invade nodule cells, but enlarged symbiosomes were observed in the infected cells. The causal gene, designated LjSYP71 (for L. japonicus syntaxin of plants71), was identified by map-based cloning and shown to encode a Qc-SNARE protein homologous to Arabidopsis (Arabidopsis thaliana) SYP71. LjSYP71 was expressed ubiquitously in shoot, roots, and nodules, and transcripts were detected in the vascular tissues. In the mutant, no other visible defects in plant morphology were observed. Furthermore, in the presence of combined nitrogen, the mutant plant grew almost as well as the wild type. These results suggest that the vascular tissues expressing LjSYP71 play a pivotal role in symbiotic nitrogen fixation in L. japonicus nodules.
Determinants of Effective Information Technology Governance
Authors: Ferguson Colin , Green Peter , Vaswani Ravi , Wu Gang (Henry)
Published: August 2012

This study examines relations between the overall level of effective information technology (IT) governance and five commonly advocated individual mechanisms of IT governance. It extends the examination of individual IT governance mechanisms to include a wider number of mechanisms, justifies the mechanisms investigated via agency theory, seeks to relate these mechanisms specifically to a perceived overall level of effective IT governance in organizations, and attempts to mitigate the problems of limited generalizability and selection bias by employing a survey and generalized sampling research methodology. The results from a survey of professional auditors reveal significant positive relations between the overall level of effective IT governance and three IT governance mechanisms: IT steering committees, senior management involvement in IT, and corporate performance measurement systems. Ex‐post sensitivity analyses reveal that the primary findings are qualitatively similar across internal auditors and external auditors, as well as information systems auditors (IS) and non‐IS auditors.
Toll‐like receptor‐9 agonists increase cyclin D1 expression partly through activation of activator protein‐1 in human oral squamous cell carcinoma cells
Authors: Min Ruan , Siyi Li , Wenjun Yang , Shengwen Liu , Ow Andrew , Lizheng Wang , Chenping Zhang
Published: August 2012

Increasing evidence suggests that malignant transformation can result from chronic infection, and Toll‐like receptors (TLRs) may play an important role in this process. We have previously reported that the increased expression of TLR‐9 is associated with tumor cell proliferation in oral cancer. However, the mechanisms involved have not been elucidated. The aim of this study was to investigate whether CpG‐oligodeoxynucleotides (CpG‐ODN), a special TLR‐9 agonist, is able to exert the proliferation‐promoting effect in human oral squamous cell carcinoma (OSCC), and to explore the possible underlying molecular mechanism. Flow cytometry, MTT, and colony formation assay were used to evaluate cell proliferation and cell cycle distribution. The mRNA and protein levels were analyzed by quantitative RT‐PCR and Western blot assay. Luciferase reporter gene, EMSA, and ChIP assays were used to detect the activity of activator protein‐1 (AP‐1) and nuclear factor‐κB (NF‐κB) in HB cells. Results showed that CpG‐ODN could stimulate proliferation of HB cells in a dose‐ and time‐dependent manner with a promoted G1/S cell cycle progression. Increased cyclin D1 expression was detected in the nuclear region after CpG‐ODN treatment. Moreover, CpG‐ODN promoted nuclear translocation and activation of AP‐1, which appeared to be required for TLR‐9‐mediated cyclin D1 expression and subsequently cell proliferation, but seemed to have little impact on NF‐κB activity. Our results indicate that CpG‐ODN stimulates tumor cell proliferation through TLR‐9‐mediated AP‐1‐activated cyclin D1 expression in OSCC HB cells. Pharmacologic inhibition of the TLR‐9/AP‐1/cyclin D1 pathway may be a new therapeutic approach for prevention as well as treatment of OSCC.
External evaluation of population pharmacokinetic models of vancomycin in neonates: the transferability of published models to different clinical settings
Authors: Zhao Wei , Kaguelidou Florentia , Biran Valérie , Zhang Daolun , Allegaert Karel , Capparelli Edmund V. , Holford Nick , Kimura Toshimi , Lo Yoke‐Lin , Peris José‐Esteban , Thomson Alison , van den Anker John N. , Fakhoury May , Jacqz‐Aigrain Evelyne
Published: August 2012

Aims

Vancomycin is one of the most evaluated antibiotics in neonates using modeling and simulation approaches. However no clear consensus on optimal dosing has been achieved. The objective of the present study was to perform an external evaluation of published models, in order to test their predictive performances in an independent dataset and to identify the possible study‐related factors influencing the transferability of pharmacokinetic models to different clinical settings.

Method

Published neonatal vancomycin pharmacokinetic models were screened from the literature. The predictive performance of six models was evaluated using an independent dataset (112 concentrations from 78 neonates). The evaluation procedures used simulation‐based diagnostics [visual predictive check (VPC) and normalized prediction distribution errors (NPDE)].

Results

Differences in predictive performances of models for vancomycin pharmacokinetics in neonates were found. The mean of NPDE for six evaluated models were 1.35, −0.22, −0.36, 0.24, 0.66 and 0.48, respectively. These differences were explained, at least partly, by taking into account the method used to measure serum creatinine concentrations. The adult conversion factor of 1.3 (enzymatic to Jaffé) was tested with an improvement in the VPC and NPDE, but it still needs to be evaluated and validated in neonates. Differences were also identified between analytical methods for vancomycin.

Conclusion

The importance of analytical techniques for serum creatinine concentrations and vancomycin as predictors of vancomycin concentrations in neonates have been confirmed. Dosage individualization of vancomycin in neonates should consider not only patients' characteristics and clinical conditions, but also the methods used to measure serum creatinine and vancomycin.
Cell Loss and Autophagy in the Extra‐Adrenal Chromaffin Organ of Zuckerkandl are Regulated by Glucocorticoid Signalling
Authors: Schober Andreas , Parlato Rosanna , Huber Katrin , Kinscherf Ralf , Hartleben Björn , Huber Tobias B. , Schütz Günther , Unsicker Klaus
Published: August 2012

Neuroendocrine chromaffin cells exist in both intra‐ and extra‐adrenal locations; the organ of Zuckerkandl (OZ) constitutes the largest accumulation of extra‐adrenal chromaffin tissue in mammals. The OZ disappears postnatally by modes that are still enigmatic but can be maintained by treatment with glucocorticoids (GC). Whether the response to GC reflects a pharmacological or a physiological role of GC has not been clarified. Using mice with a conditional deletion of the GC‐receptor (GR) gene restricted to cells expressing the dopamine β‐hydroxylase (DBH) gene [GRfl/fl; DBHCre abbreviated (GRDBHCre)], we now present the first evidence for a physiological role of GC signalling in the postnatal maintenance of the OZ: postnatal losses of OZ chromaffin cells in GRDBHCre mice are doubled compared to wild‐type littermates. We find that postnatal cell loss in the OZ starts at birth and is accompanied by autophagy. Electron microscopy reveals autophagic vacuoles and autophagolysosomes in chromaffin cells. Autophagy in OZ extra‐adrenal chromaffin cells is confirmed by showing accumulation of p62 protein, which occurs, when autophagy is blocked by deleting the Atg5 gene (Atg5DBHCre mice). Cathepsin‐D, a lysosomal marker, is expressed in cells that surround chromaffin cells and are positive for the macrophage marker BM8. Macrophages are relatively more abundant in mice lacking the GR, indicating more robust elimination of degenerating chromaffin cells in GRDBHCre mice than in wild‐type littermates. In summary, our results indicate that extra‐adrenal chromaffin cells in the OZ show signs of autophagy, which accompany their postnatal numerical decline, a process that is controlled by GR signalling.
Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate
Authors: LASKY JESSE R. , DES MARAIS DAVID L. , McKAY JOHN K. , RICHARDS JAMES H. , JUENGER THOMAS E. , KEITT TIMOTHY H.
Published: August 2012

Arabidopsis thaliana inhabits diverse climates and exhibits varied phenology across its range. Although A. thaliana is an extremely well‐studied model species, the relationship between geography, growing season climate and its genetic variation is poorly characterized. We used redundancy analysis (RDA) to quantify the association of genomic variation [214 051 single nucleotide polymorphisms (SNPs)] with geography and climate among 1003 accessions collected from 447 locations in Eurasia. We identified climate variables most correlated with genomic variation, which may be important selective gradients related to local adaptation across the species range. Climate variation among sites of origin explained slightly more genomic variation than geographical distance. Large‐scale spatial gradients and early spring temperatures explained the most genomic variation, while growing season and summer conditions explained the most after controlling for spatial structure. SNP variation in Scandinavia showed the greatest climate structure among regions, possibly because of relatively consistent phenology and life history of populations in this region. Climate variation explained more variation among nonsynonymous SNPs than expected by chance, suggesting that much of the climatic structure of SNP correlations is due to changes in coding sequence that may underlie local adaptation.
Genetics of gene expression responses to temperature stress in a sea urchin gene network
Authors: RUNCIE DANIEL E. , GARFIELD DAVID A. , BABBITT COURTNEY C. , WYGODA JENNIFER A. , MUKHERJEE SAYAN , WRAY GREGORY A.
Published: August 2012

Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter the contribution of additive genetic variation to gene expression during development of the purple sea urchin,Strongylocentrotus purpuratus, under increased temperatures that model realistic climate change scenarios. We first measured gene expression responses in the embryos by RNA‐seq to characterize molecular signatures of mild, chronic temperature stress in an unbiased manner. We found that an increase from 12 to 18 °C caused widespread alterations in gene expression including in genes involved in protein folding, RNA processing and development. To understand the quantitative genetic architecture of this response, we then focused on a well‐characterized gene network involved in endomesoderm and ectoderm specification. Using a breeding design with wild‐caught individuals, we measured genetic and gene–environment interaction effects on 72 genes within this network. We found genetic or maternal effects in 33 of these genes and that the genetic effects were correlated in the network. Fourteen network genes also responded to higher temperatures, but we found no significant genotype–environment interactions in any of the genes. This absence may be owing to an effective buffering of the temperature perturbations within the network. In support of this hypothesis, perturbations to regulatory genes did not affect the expression of the genes that they regulate. Together, these results provide novel insights into the relationship between environmental change and developmental evolution and suggest that climate change may not expose large amounts of cryptic genetic variation to selection in this species.
Chemical, genetic and structural assessment of pyridoxal kinase as a drug target in the African trypanosome
Authors: Jones Deuan C. , Alphey Magnus S. , Wyllie Susan , Fairlamb Alan H.
Published: August 2012

Pyridoxal‐5′‐phosphate (vitamin B6) is an essential cofactor for many important enzymatic reactions such as transamination and decarboxylation. African trypanosomes are unable to synthesise vitamin B6de novo and rely on uptake of B6 vitamers such as pyridoxal and pyridoxamine from their hosts, which are subsequently phosphorylated by pyridoxal kinase (PdxK). A conditional null mutant of PdxK was generated in Trypanosoma brucei bloodstream forms showing that this enzyme is essential for growth of the parasite in vitro and for infectivity in mice. Activity of recombinant T. brucei PdxK was comparable to previously published work having a specific activity of 327 ± 13 mU mg−1 and a Kmapp with respect to pyridoxal of 29.6 ± 3.9 µM. A coupled assay was developed demonstrating that the enzyme has equivalent catalytic efficiency with pyridoxal, pyridoxamine and pyridoxine, and that ginkgotoxin is an effective pseudo substrate. A high resolution structure of PdxK in complex with ATP revealed important structural differences with the human enzyme. These findings suggest that pyridoxal kinase is an essential and druggable target that could lead to much needed alternative treatments for this devastating disease.
Does reduction in mycophenolic acid dose compromise efficacy regardless of tacrolimus exposure level? An analysis of prospective data from the Mycophenolic Renal Transplant (MORE) Registry
Authors: Langone Anthony , Doria Cataldo , Greenstein Stuart , Narayanan Mohanram , Ueda Kimi , Sankari Bashir , Pankewycz Oleh , Shihab Fuad , Chan Laurence
Published: August 2012

Prospective data are lacking concerning the effect of reduced mycophenolic acid (MPA) dosing on efficacy and the influence of concomitant tacrolimus exposure. The Mycophenolic Renal Transplant (MORE) Registry is a prospective, observational study of de novo kidney transplant patients receiving MPA therapy under routine management. The effect of MPA dose reduction, interruption, or discontinuation (dose changes) was assessed in 870 tacrolimus‐treated patients: 375 (43.1%) reduced tacrolimus (≤7 ng/mL at baseline) and 495 (56.9%) standard tacrolimus (>7 ng/mL); enteric‐coated mycophenolate sodium 589 (67.7%) and mycophenolate mofetil 281 (32.3%). During baseline to month 1, months 1–3, months 3–6, and months 6–12, 9.3% (78/838), 16.6% (132/794), 20.7% (145/701), and 13.1% (70/535) patients, respectively, required MPA dose changes. These patients experienced an increased risk of biopsy‐proven acute rejection at one yr with tacrolimus exposure either included in the model (hazard ratio [HR] 2.60, 95% CI 1.28–5.29, p = 0.008) or excluded (HR 2.58, 95% CI 1.28–5.23, p = 0.008). MPA dose changes were significantly associated with one yr graft failure when tacrolimus exposure was included (HR 2.23; 95% CI 1.01–4.89, p = 0.047) but not when tacrolimus exposure was excluded (HR 2.16; 95% CI 0.99–4.79; p = 0.054). These results suggest that reducing or discontinuing MPA can adversely affect graft outcomes regardless of tacrolimus trough levels.
Mapping of within‐species segregation distortion in Drosophila persimilis and hybrid sterility between D. persimilis and D. pseudoobscura
Authors: Mcdermott S. R. , Noor M. A. F.
Published: August 2012

In contrast to the prevailing dogma in the 1990s, recent studies have suggested that an evolutionary history of segregation distortion within species may contribute to sterility in species hybrids. However, this recent work identified segregation distortion exclusively in species hybrids that may never have had an evolutionary history of segregation distortion in either parent species. We expand on previous work using a strain of Drosophila persimilis exhibiting segregation distortion within species to generate QTL maps for segregation distortion and hybrid sterility in crosses between D. persimilis and D. pseudoobscura. The maps localize regions along the XR contributing to both phenotypes, and they indicate one region of overlap between the two maps. This overlap could provide preliminary evidence for an association between segregation distortion within species and hybrid sterility, but the localizations are currently too broad to have confidence in this conclusion. This work is a first step towards possibly supporting a genetic conflict model of speciation in this system.
Hoarding patterns of sigmodontine rodent species in the Central Monte Desert (Argentina)
Authors: GIANNONI STELLA M. , CAMPOS VALERIA E. , ANDINO NATALIA , RAMOS‐CASTILLA MARÍA , OROFINO ALEJANDRO , BORGHI CARLOS E. , DE LOS RÍOS CLAUDIA , CAMPOS CLAUDIA M.
Published: August 2012

Hoarding food is an important strategy of rodents in desert environments characterized by unpredictable and poor food resource availability. In the Monte Desert, Prosopis produces abundant food, unevenly in time and space, in the form of pods and seeds. Sigmodontine rodents (Graomys griseoflavus, Akodon molinae, Eligmodontia typus and Calomys musculinus) use Prosopis propagules extensively, and they could be predators or dispersers depending on how they handle and where they leave the propagules. The objectives of this study were: (1) to know what rodent species transported propagules; (2) to evaluate what hoarding pattern was used by species that transport propagules (larder and scatterhoarding); and (3) to analyse in which condition were propagules left by the rodent species, both at the food source and in caches. Our results showed that all four species transported propagules, with G. griseoflavus and E. typus being the species that carried more seeds. Our study supported the evidence that food caching is common among species and that many species both larderhoard and scatterhoard food. Graomys griseoflavus and A. molinae, the largest species, larderhoarded more than did the smaller E. typus. These results uphold the hypothesis that larger species will show greater propensity to larderhoard than smaller species. Considering the interaction between seed‐hoarding patterns and plants, E. typus was the species that could most improve germination because it scatterhoarded propagules and left seeds out of pods. In contrast, G. griseoflavus could have a negative impact on plant populations because this was the species that predated more seeds and larderhoarded a high percentage of them. The smallest C. musculinus was the species that transported propagules least, and left them as seeds inside pods or pod segments mainly at the food source, which makes seeds more vulnerable to predation.