bluuebunny/crossref_metadata_2025 huggingface dataset:
Apoptosis and the selective survival of host animals following thermal bleaching in zooxanthellate corals
Authors: Tchernov Dan , Kvitt Hagit , Haramaty Liti , Bibby Thomas S. , Gorbunov Maxim Y. , Rosenfeld Hanna , Falkowski Paul G.
Published: June 2011

During the past several decades, numerous reports from disparate geographical areas have documented an increased frequency of “bleaching” in reef-forming corals. The phenomenon, triggered by increased sea surface temperatures, occurs when the cnidarian hosts digest and/or expel their intracellular, photosynthetic dinoflagellate symbionts (“zooxanthellae” in the genus
Symbiodinium
). Although coral bleaching is often followed by the death of the animal hosts, in some cases, the animal survives and can be repopulated with viable zooxanthellae. The physiological factors determining the ability of the coral to survive bleaching events are poorly understood. In this study, we experimentally established that bleaching and death of the host animal involve a caspase-mediated apoptotic cascade induced by reactive oxygen species produced primarily by the algal symbionts. In addition, we demonstrate that, although some corals naturally suppress caspase activity and significantly reduce caspase concentration under high temperatures as a mechanism to prevent colony death from apoptosis, even sensitive corals can be prevented from dying by application of exogenous inhibitors of caspases. Our results indicate that variability in response to thermal stress in corals is determined by a four-element, combinatorial genetic matrix intrinsic to the specific symbiotic association. Based on our experimental data, we present a working model in which the phenotypic expression of this symbiont/host relationship places a selective pressure on the symbiotic association. The model predicts the survival of the host animals in which the caspase-mediated apoptotic cascade is down-regulated.
Functional interaction between dynein light chain and intermediate chain is required for mitotic spindle positioning
Authors: Stuchell-Brereton Melissa D. , Siglin Amanda , Li Jun , Moore Jeffrey K. , Ahmed Shubbir , Williams John C. , Cooper John A.
Published: June 2011

Cytoplasmic dynein is a large multisubunit complex involved in retrograde transport and the positioning of various organelles. Dynein light chain (LC) subunits are conserved across species; however, the molecular contribution of LCs to dynein function remains controversial. One model suggests that LCs act as cargo-binding scaffolds. Alternatively, LCs are proposed to stabilize the intermediate chains (ICs) of the dynein complex. To examine the role of LCs in dynein function, we used Saccharomyces cerevisiae, in which the sole function of dynein is to position the spindle during mitosis. We report that the LC8 homologue, Dyn2, localizes with the dynein complex at microtubule ends and interacts directly with the yeast IC, Pac11. We identify two Dyn2-binding sites in Pac11 that exert differential effects on Dyn2-binding and dynein function. Mutations disrupting Dyn2 elicit a partial loss-of-dynein phenotype and impair the recruitment of the dynein activator complex, dynactin. Together these results indicate that the dynein-based function of Dyn2 is via its interaction with the dynein IC and that this interaction is important for the interaction of dynein and dynactin. In addition, these data provide the first direct evidence that LC occupancy in the dynein motor complex is important for function.
A mechanism of Rap1-induced stabilization of endothelial cell–cell junctions
Authors: Liu Jian J. , Stockton Rebecca A. , Gingras Alexandre R. , Ablooglu Ararat J. , Han Jaewon , Bobkov Andrey A. , Ginsberg Mark H.
Published: June 2011

Activation of Rap1 small GTPases stabilizes cell–cell junctions, and this activity requires Krev Interaction Trapped gene 1 (KRIT1). Loss of KRIT1 disrupts cardiovascular development and causes autosomal dominant familial cerebral cavernous malformations. Here we report that native KRIT1 protein binds the effector loop of Rap1A but not H-Ras in a GTP-dependent manner, establishing that it is an authentic Rap1-specific effector. By modeling the KRIT1–Rap1 interface we designed a well-folded KRIT1 mutant that exhibited a ∼40-fold-reduced affinity for Rap1A and maintained other KRIT1-binding functions. Direct binding of KRIT1 to Rap1 stabilized endothelial cell–cell junctions in vitro and was required for cardiovascular development in vivo. Mechanistically, Rap1 binding released KRIT1 from microtubules, enabling it to locate to cell–cell junctions, where it suppressed Rho kinase signaling and stabilized the junctions. These studies establish that the direct physical interaction of Rap1 with KRIT1 enables the translocation of microtubule-sequestered KRIT1 to junctions, thereby supporting junctional integrity and cardiovascular development.
A memory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly
Authors: Dinh Hieu , Rajasekaran Sanguthevar
Published: June 2011

Motivation: Exact-match overlap graphs have been broadly used in the context of DNA assembly and the shortest super string problem where the number of strings n ranges from thousands to billions. The length ℓ of the strings is from 25 to 1000, depending on the DNA sequencing technologies. However, many DNA assemblers using overlap graphs suffer from the need for too much time and space in constructing the graphs. It is nearly impossible for these DNA assemblers to handle the huge amount of data produced by the next-generation sequencing technologies where the number n of strings could be several billions. If the overlap graph is explicitly stored, it would require Ω(n  2) memory, which could be prohibitive in practice when n is greater than a hundred million. In this article, we propose a novel data structure using which the overlap graph can be compactly stored. This data structure requires only linear time to construct and and linear memory to store.

Results: For a given set of input strings (also called reads), we can informally define an exact-match overlap graph as follows. Each read is represented as a node in the graph and there is an edge between two nodes if the corresponding reads overlap sufficiently. A formal description follows. The maximal exact-match overlap of two strings x and y, denoted by ov  max(x, y), is the longest string which is a suffix of x and a prefix of y. The exact-match overlap graph of n given strings of length ℓ is an edge-weighted graph in which each vertex is associated with a string and there is an edge (x, y) of weight ω=ℓ−|ov  max(x, y)| if and only if ω≤λ, where |ov  max(x, y)| is the length of ov  max(x, y) and λ is a given threshold. In this article, we show that the exact-match overlap graphs can be represented by a compact data structure that can be stored using at most (2λ−1)(2⌈logn⌉+⌈logλ⌉)n bits with a guarantee that the basic operation of accessing an edge takes O(log λ) time. We also propose two algorithms for constructing the data structure for the exact-match overlap graph. The first algorithm runs in O(λℓnlogn) worse-case time and requires O(λ) extra memory. The second one runs in O(λℓn) time and requires O(n) extra memory. Our experimental results on a huge amount of simulated data from sequence assembly show that the data structure can be constructed efficiently in time and memory.

Availability: Our DNA sequence assembler that incorporates the data structure is freely available on the web at http://www.engr.uconn.edu/~htd06001/assembler/leap.zip

Contact:  hdinh@engr.uconn.edu; rajasek@engr.uconn.edu
Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction
Authors: Zhang Zengming , Li Yu , Lin Biaoyang , Schroeder Michael , Huang Bingding
Published: June 2011

Motivation: Protein–ligand binding sites are the active sites on protein surface that perform protein functions. Thus, the identification of those binding sites is often the first step to study protein functions and structure-based drug design. There are many computational algorithms and tools developed in recent decades, such as LIGSITEcs/c, PASS, Q-SiteFinder, SURFNET, and so on. In our previous work, MetaPocket, we have proved that it is possible to combine the results of many methods together to improve the prediction result.

Results: Here, we continue our previous work by adding four more methods Fpocket, GHECOM, ConCavity and POCASA to further improve the prediction success rate. The new method MetaPocket 2.0 and the individual approaches are all tested on two datasets of 48 unbound/bound and 210 bound structures as used before. The results show that the average success rate has been raised 5% at the top 1 prediction compared with previous work. Moreover, we construct a non-redundant dataset of drug–target complexes with known structure from DrugBank, DrugPort and PDB database and apply MetaPocket 2.0 to this dataset to predict drug binding sites. As a result, >74% drug binding sites on protein target are correctly identified at the top 3 prediction, and it is 12% better than the best individual approach.

Availability: The web service of MetaPocket 2.0 and all the test datasets are freely available at http://projects.biotec.tu-dresden.de/metapocket/ and http://sysbio.zju.edu.cn/metapocket.

Contact:  bhuang@biotec.tu-dresden.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections
Authors: Lagorce David , Maupetit Julien , Baell Jonathan , Sperandio Olivier , Tufféry Pierre , Miteva Maria A. , Galons Hervé , Villoutreix Bruno O.
Published: June 2011

Summary:The FAF-Drugs2 server is a web application that prepares chemical compound libraries prior to virtual screening or that assists hit selection/lead optimization before chemical synthesis or ordering. The FAF-Drugs2 web server is an enhanced version of the FAF-Drugs2 package that now includes Pan Assay Interference Compounds detection. This online toolkit has been designed through a user-centered approach with emphasis on user-friendliness. This is a unique online tool allowing to prepare large compound libraries with in house or user-defined filtering parameters.

Availability: The FAF-Drugs2 server is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/FAF-Drugs/.

Contact:  david.lagorce@inserm.fr; bruno.villoutreix@inserm.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Myocarditis as a precipitating factor for heart failure: evaluation and 1‐year follow‐up using cardiovascular magnetic resonance and endomyocardial biopsy
Authors: Mavrogeni Sophie , Spargias Costas , Bratis Costas , Kolovou Genovefa , Markussis Vyron , Papadopoulou Evangelia , Constadoulakis Pantelis , Papadimitropoulos Miltiadis , Douskou Marouso , Pavlides Gregory , Cokkinos Denis
Published: June 2011

Aims

The aim of this study was to evaluate myocarditis as a precipitating factor for heart failure using cardiovascular magnetic resonance (CMR) and endomyocardial biopsy

Methods and results

Eighty‐five patients with suspected myocarditis and 20 controls were evaluated. Seventy‐one patients with positive CMR were referred for endomyocardial biopsy and re‐evaluation after 1 year. Cardiovascular magnetic resonance was performed using STIR T2‐weighted (T2W), early T1‐weighted (EGE), and late gadolinium‐enhanced (LGE) images. Immunohistological and polymerase chain reaction (PCR) analysis of myocardial specimens was employed.

In patients with myocarditis, T2 and EGE were increased compared with controls (2.6 ± 0.9 vs. 1.57 ± 0.13, P < 0.001 and 7.9 ± 5.5 vs. 3.59 ± 0.08, P < 0.001, respectively). Late gadolinium enhancement was found in all myocarditis patients. Endomyocardial biopsy performed in 50 of 71 patients with positive CMR showed positive immunohistology in 48% and presence of infectious genomes in 80% (mainly Chlamydia, Herpes, and Parvovirus B19). Left ventricular ejection fraction (LVEF) was significantly decreased compared with controls (47.7 ± 19.2 vs. 64 ± 0.2, P < 0.001). After 1 year, CMR showed normalization of T2 and EGE, and decreased LGE. Left ventricular ejection fraction increased in 36.5% of patients, remained stable in 56.5% and decreased in 7% of patients, in whom biopsy showed persistence of the initial infective agents. A negative correlation was identified between EGE, LGE, and LVEF. Patients with positive biopsies had lower LVEFs.

Conclusion

In a Greek population with myocarditis, Chlamydia with viruses was a common finding. Cardiovascular magnetic resonance and PCR proved useful for the detection of myocarditis; EGE and LGE had the best correlation for the development of heart failure. Persistence of the initially detected infective agents was identified in patients who deteriorated further.
Novel and Highly Specific Monoclonal Antibody to Acidovorax citrulli and Development of ELISA-Based Detection in Cucurbit Leaves and Seed
Authors: Himananto Orawan , Thummabenjapone Petcharat , Luxananil Plearnpis , Kumpoosiri Mallika , Hongprayoon Ratchanee , Kositratana Wichai , Gajanandana Oraprapai
Published: June 2011

A novel monoclonal antibody (MAb) specific to the seedborne bacterium Acidovorax citrulli was produced. MAb 11E5 reacted specifically with 19 strains of A. citrulli but not with three closely related bacteria in the family Comamonadaceae (i.e., A. facilis, Comamonas acidovorans, and C. testosteroni) and another seven phytopathogenic bacteria. Moreover, this MAb detected a strain of A. citrulli that was not detected by a commercial enzyme-linked immunosorbent assay (ELISA)-based kit and a commercial immunochromatographic strip test. In Western blot analysis, MAb 11E5 reacted with an A. citrulli protein of a molecular mass >170 kDa. MAb 11E5 was employed to develop two sandwich ELISA systems: MAb captured-sandwich ELISA (MC-sELISA) and polyclonal antibody captured-sandwich ELISA (PC-sELISA). MC-sELISA was 10 times more sensitive than PC-sELISA for detection of A. citrulli in cucurbit leaf and seed extracts. The detection limit of the MC-sELISA was 5 × 104 CFU/ml. Detection of A. citrulli in naturally infected cucurbit leaves, fruit, and seed was also feasible using MC-sELISA. The newly established MCsELISA provides another alternative for specific detection of A. citrulli in cucurbits and can be applied for routine field inspection.
Pathogenicity, Symptom Development, and Mycotoxin Formation in Wheat by Fusarium Species Frequently Isolated from Sugar Beet
Authors: Christ Daniela S. , Gödecke Ruben , von Tiedemann Andreas , Varrelmann Mark
Published: June 2011

Crop rotations with putative non-host crops such as sugar beet are often recommended to reduce Fusarium head blight (FHB) in cereals. However, recent observations have shown pathogenic, endophytic, and saprotrophic colonization of sugar beet with various Fusarium spp. Therefore, strains of seven species frequently isolated from sugar beet were tested for pathogenicity on wheat. Species-specific symptoms on heads and kernels were evaluated and the grains were analyzed for 20 mycotoxins with liquid chromatography–tandem mass spectrometry. Fusarium graminearum, F. culmorum, and F. cerealis from sugar beet caused typical FHB symptoms and mycotoxin contamination with deoxynivalenol and nivalenol, while a high incidence of black point was observed in heads inoculated with F. tricinctum or F. equiseti. Black point kernels revealed 3.4 to 14.5 times higher mycotoxin concentrations than symptomless grains, containing enniatin B1 at 38,000 μg/kg, moniliformin at 4,900 μg/kg, and 2-amino-14,16-dimethyloctadecan-3-ol at 5,500 μg/kg, as well as monoacetoxyscirpenol at 2,600 μg/kg and nivalenol at 3,800 μg/kg. Monitoring of these latter two species in the field is hampered by the lack of typical head symptoms after infection. In further experiments, the impact of sugar beet residues on FHB severity and the correlation between mycotoxin contamination of cereal lots and the amount of black point have to be evaluated.
Vitamin D Deficiency Is Prevalent in Girls and Women With Rett Syndrome
Authors: Motil Kathleen J. , Barrish Judy O. , Lane Jane , Geerts Suzanne P. , Annese Fran , McNair Lauren , Percy Alan K. , Skinner Steven A. , Neul Jeffrey L. , Glaze Daniel G.
Published: June 2011

Objectives:

The aim of the study was to determine the prevalence of vitamin D deficiency and identify the relation between 25‐hydroxyvitamin D (25‐(OH)D) levels and the consumption of dietary sources of vitamin D or exposure to anticonvulsants in girls and women with Rett syndrome (RTT).

Subjects and Methods:

Retrospective review of the medical records of 284 girls and women with RTT to determine serum 25‐(OH)D and parathyroid hormone levels, nutritional status, dietary sources of vitamin D, exposure to anticonvulsants, degree of mobility, and MECP2 status.

Results:

Twenty percent of girls and women who were tested (n = 157) had 25‐(OH)D levels <50 nmol/L. Multivitamin supplements, vitamin D–fortified milk, and commercial formulas were consumed by 40%, 52%, and 54%, respectively. Anticonvulsants were used by 57%, and 39% ambulated independently. Median 25‐(OH)D levels were lower in individuals who did not receive multivitamin supplements (P < 0.05) or commercial formulas (P < 0.001) than in those who did. Median 25‐(OH)D levels differed (P < 0.01) among racial and ethnic groups, but the number in some groups was small. Nutritional status, use of anticonvulsants, degree of mobility, and MECP2 status did not influence 25‐(OH)D levels.

Conclusions:

Vitamin D deficiency is prevalent in girls and women with RTT. The use of multivitamin supplements or commercial formulas is associated with improved vitamin D levels. Attention to vitamin D may enhance bone mineral deposition and reduce the frequency of bone fractures in these individuals.
Navigating a tool end in a specific direction: stick-tool use in kea (
Nestor notabilis
)
Authors: Auersperg Alice M. I. , Huber Ludwig , Gajdon Gyula K.
Published: June 2011

This study depicts how captive kea, New Zealand parrots, which are not known to use tools in the wild, employ a stick-tool to retrieve a food reward after receiving demonstration trials. Four out of six animals succeeded in doing so despite physical (beak curvature) and ecological (no stick-like materials used during nest construction) constraints when handling elongated objects. We further demonstrate that the same animals can thereafter direct the functional end of a stick-tool into a desired direction, aiming at a positive option while avoiding a negative one.
Malagasy dialects and the peopling of Madagascar
Authors: Serva Maurizio , Petroni Filippo , Volchenkov Dima , Wichmann Søren
Published: June 2011

The origin of Malagasy DNA is half African and half Indonesian, nevertheless the Malagasy language, spoken by the entire population, belongs to the Austronesian family. The language most closely related to Malagasy is Maanyan (Greater Barito East group of the Austronesian family), but related languages are also in Sulawesi, Malaysia and Sumatra. For this reason, and because Maanyan is spoken by a population which lives along the Barito river in Kalimantan and which does not possess the necessary skill for long maritime navigation, the ethnic composition of the Indonesian colonizers is still unclear. There is a general consensus that Indonesian sailors reached Madagascar by a maritime trek, but the time, the path and the landing area of the first colonization are all disputed. In this research, we try to answer these problems together with other ones, such as the historical configuration of Malagasy dialects, by types of analysis related to lexicostatistics and glottochronology that draw upon the automated method recently proposed by the authors. The data were collected by the first author at the beginning of 2010 with the invaluable help of Joselinà Soafara Néré and consist of Swadesh lists of 200 items for 23 dialects covering all areas of the island.
Patterning as a signature of human epidermal stem cell regulation
Authors: Klein Allon M. , Nikolaidou-Neokosmidou Varvara , Doupé David P. , Jones Philip H. , Simons Benjamin D.
Published: June 2011

Understanding how stem cells are regulated in adult tissues is a major challenge in cell biology. In the basal layer of human epidermis, clusters of almost quiescent stem cells are interspersed with proliferating and differentiating cells. Previous studies have shown that the proliferating cells follow a pattern of balanced stochastic cell fate. This behaviour enables them to maintain homeostasis, while stem cells remain confined to their quiescent clusters. Intriguingly, these clusters reappear spontaneously in culture, suggesting that they may play a functional role in stem cell auto-regulation. We propose a model of pattern formation that explains how clustering could regulate stem cell activity in homeostatic tissue through contact inhibition and stem cell aggregation.
Acyl depsipeptide (ADEP) resistance in Streptomyces
Authors: Gominet Myriam , Seghezzi Nicolas , Mazodier Philippe
Published: June 2011

ADEP, a molecule of the acyl depsipeptide family, has an antibiotic activity with a unique mode of action. ADEP binding to the ubiquitous protease ClpP alters the structure of the enzyme. Access of protein to the ClpP proteolytic chamber is therefore facilitated and its cohort regulatory ATPases (ClpA, ClpC, ClpX) are not required. The consequent uncontrolled protein degradation in the cell appears to kill the ADEP-treated bacteria. ADEP is produced byStreptomyces hawaiiensis. Most sequenced genomes ofStreptomyceshave fiveclpPgenes, organized as two distinct bicistronic operons,clpP1clpP2andclpP3clpP4, and a singleclpP5gene. We investigated whether the different Clp proteases are all sensitive to ADEP. We report that ClpP1 is a target of ADEP whereas ClpP3 is largely insensitive. In wild-typeStreptomyces lividans,clpP3clpP4expression is constitutively repressed and the reason for the maintenance of this operon inStreptomyceshas been elusive. ClpP activity is indispensable for survival of actinomycetes; we therefore tested whether theclpP3clpP4operon, encoding an ADEP-insensitive Clp protease, contributes to a mechanism of ADEP resistance by target substitution. We report that inS. lividans, inactivation of ClpP1ClpP2 production or protease activity is indeed a mode of resistance to ADEP although it is neither the only nor the most frequent mode of resistance. The ABC transporter SclAB (orthologous to theStreptomyces coelicolormultidrug resistance pump SCO4959–SCO4960) is also able to confer ADEP resistance, and analysis of strains withsclABdeletions indicates that there are also other mechanisms of ADEP resistance.
Cell envelope gene expression in phosphate-limited Bacillus subtilis cells
Authors: Botella Eric , Hübner Sebastian , Hokamp Karsten , Hansen Annette , Bisicchia Paola , Noone David , Powell Leagh , Salzberg Letal I. , Devine Kevin M.
Published: June 2011

The high phosphate content of Bacillus subtilis cell walls dictates that cell wall metabolism is an important feature of the PhoPR-mediated phosphate limitation response. Here we report the expression profiles of cell-envelope-associated and PhoPR regulon genes, determined by live cell array and transcriptome analysis, in exponentially growing and phosphate-limited B. subtilis cells. Control by the WalRK two-component system confers a unique expression profile and high level of promoter activity on the genes of its regulon with yocH and cwlO expression differing both qualitatively and quantitatively from all other autolysin-encoding genes examined. The activity of the PhoPR two-component system is restricted to the phosphate-limited state, being rapidly induced in response to the cognate stimulus, and can be sustained for an extended phosphate limitation period. Constituent promoters of the PhoPR regulon show heterogeneous induction profiles and very high promoter activities. Phosphate-limited cells also show elevated expression of the actin-like protein MreBH and reduced expression of the WapA cell wall protein and WprA cell wall protease indicating that cell wall metabolism in this state is distinct from that of exponentially growing and stationary-phase cells. The PhoPR response is very rapidly deactivated upon removal of the phosphate limitation stimulus with concomitant increased expression of cell wall metabolic genes. Moreover expression of genes encoding enzymes involved in sulphur metabolism is significantly altered in the phosphate-limited state with distinct perturbations being observed in wild-type 168 and AH024 (ΔphoPR) cells.
RNA helicase retinoic acid-inducible gene I as a sensor of Hantaan virus replication
Authors: Lee Min-Hi , Lalwani Pritesh , Raftery Martin J. , Matthaei Markus , Lütteke Nina , Kirsanovs Sina , Binder Marco , Ulrich Rainer G. , Giese Thomas , Wolff Thorsten , Krüger Detlev H. , Schönrich Günther
Published: June 2011

Hantaan virus (HTNV) causes severe human disease. The HTNV genome consists of three ssRNA segments of negative polarity that are complexed with viral nucleocapsid (N) protein. How the human innate immune system detects HTNV is unclear. RNA helicase retinoic acid-inducible gene I (RIG-I) does not sense genomic HTNV RNA. So far it has not been analysed whether pathogen-associated molecular patterns generated during the HTNV replication trigger RIG-I-mediated innate responses. Indeed, we found that knock‐down of RIG-I in A549 cells, an alveolar epithelial cell line, increases HTNV replication and prevents induction of 2′,5′-oligoadenylate synthetase, an interferon-stimulated gene. Moreover, overexpression of wild-type or constitutive active RIG-I in Huh7.5 cells lacking a functional RIG-I diminished HTNV virion production. Intriguingly, reporter assays revealed thatin vitro-transcribed HTNV N RNA and expression of the HTNV N ORF triggers RIG-I signalling. This effect was completely blocked by the RNA-binding domain of vaccinia virus E3 protein, suggesting that dsRNA-like secondary structures of HTNV N RNA stimulate RIG-I. Finally, transfection of HTNV N RNA into A549 cells resulted in a 2 log-reduction of viral titres upon challenge with virus. Our study is the first demonstration that RIG-I mediates antiviral innate responses induced by HTNV N RNA during HTNV replication and interferes with HTNV growth.
A novel mechanism for the inhibition of interferon regulatory factor-3-dependent gene expression by human respiratory syncytial virus NS1 protein
Authors: Ren Junping , Liu Tianshuang , Pang Lan , Li Kui , Garofalo Roberto P. , Casola Antonella , Bao Xiaoyong
Published: June 2011

Human respiratory syncytial virus (RSV), a leading cause of respiratory tract infections in infants, inhibits type I interferon (IFN)-dependent signalling, as well as IFN synthesis. RSV non-structural protein NS1 plays a significant role in this inhibition; however, the mechanism(s) responsible is not fully known. The transcription factor interferon regulatory factor (IRF)-3 is essential for viral-induced IFN-β synthesis. In this study, we found that NS1 protein inhibits IRF-3-dependent gene transcription in constitutively active IRF-3 overexpressing cells, demonstrating that NS1 directly targets IRF-3. Our data also demonstrate that NS1 associates with IRF-3 and its transcriptional coactivator CBP, leading to disrupted association of IRF-3 to CBP and subsequent reduced binding of IRF-3 to the IFN-β promoter without blocking viral-induced IRF-3 phosphorylation, nuclear translocation and dimerization, thereby identifying a novel molecular mechanism by which RSV inhibits IFN-β synthesis.
H2B homology region of major immediate–early protein 1 is essential for murine cytomegalovirus to disrupt nuclear domain 10, but is not important for viral replication in cell culture
Authors: Cosme-Cruz Ruth , Martínez Francisco Puerta , Perez Kareni J. , Tang Qiyi
Published: June 2011

Cytomegalovirus (CMV) major immediate–early protein 1 (IE1) has multiple functions and is important for efficient viral infection. As does its counterpart in human CMV, murine CMV (MCMV) IE1 also functions as a disruptor of mouse-cell nuclear domain 10 (ND10), where many different gene-regulation proteins congregate. It still remains unclear how MCMV IE1 disperses ND10 and whether this dispersion could have any effect on viral replication. MCMV IE1 is 595 aa long and has multiple functional domains that have not yet been fully analysed. In this study, we dissected the IE1 molecule by truncation and/or deletion and found that the H2B homology domain (amino acid sequence NDIFERI) is required for the dispersion of ND10 by IE1. Furthermore, we made additional deletions and point mutations and found that the minimal truncation in the H2B homology domain required for IE1 to lose the ability to disperse ND10 is just 3 aa (IFE). Surprisingly, the mutated IE1 still interacted with PML and co-localized with ND10 but failed to disperse ND10. This suggests that binding to ND10 key protein is essential to, but not sufficient for, the dispersal of ND10, and that some other unknown mechanism must be involved in this biological procedure. Finally, we generated MCMV with IFE-deleted IE1 (MCMVdlIFE) and its revertant (MCMVIFERQ). Although MCMVdlIFE lost the ability to disperse ND10, plaque assays and viral gene production assays showed that the deletion of IFE did not increase viral replication in cell culture. We conclude that the dispersion of ND10 appears not to be important for MCMV replication in a mouse-cell culture.
Ethical and practical challenges of sharing data from genome-wide association studies: The eMERGE Consortium experience
Authors: McGuire Amy L. , Basford Melissa , Dressler Lynn G. , Fullerton Stephanie M. , Koenig Barbara A. , Li Rongling , McCarty Cathy A. , Ramos Erin , Smith Maureen E. , Somkin Carol P. , Waudby Carol , Wolf Wendy A. , Clayton Ellen Wright
Published: June 2011

In 2007, the National Human Genome Research Institute (NHGRI) established the Electronic MEdical Records and GEnomics (eMERGE) Consortium (www.gwas.net) to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. One of the major ethical and administrative challenges for the eMERGE Consortium has been complying with existing data-sharing policies. This paper discusses the challenges of sharing genomic data linked to health information in the electronic medical record (EMR) and explores the issues as they relate to sharing both within a large consortium and in compliance with the National Institutes of Health (NIH) data-sharing policy. We use the eMERGE Consortium experience to explore data-sharing challenges from the perspective of multiple stakeholders (i.e., research participants, investigators, and research institutions), provide recommendations for researchers and institutions, and call for clearer guidance from the NIH regarding ethical implementation of its data-sharing policy.
Gene status of head and neck squamous cell carcinoma cell lines and cetuximab‐mediated biological activities
Authors: Kondo Norio , Tsukuda Mamoru , Taguchi Takahide , Nakazaki Kouichi , Sakakibara Atsuko , Takahashi Hideaki , Toth Gabor , Nishimura Goshi
Published: June 2011

Cetuximab is a chimeric IgG1 monoclonal antibody that targets epidermal growth factor receptor (EGFR). Cetuximab binds to EGFR and prevents phosphorylation of EGFR. Moreover, preclinical results have shown the ability of cetuximab to induce either complement‐mediated tumor cell killing (CDC) or antibody‐dependent cell‐mediated‐cytotoxicity (ADCC). We previously reported mutation in EGFR regarding head and neck squamous cell carcinoma (HNSCC) cell lines. In the present study, we analyzed the same 16 HNSCC cell lines for mutations in KRAS, PIK3CA, BRAF and PTEN. Furthermore, we evaluated cetuximab‐mediated biological activities (antiproliferative effect by the MTT assay and ADCC) regarding these cell lines. Mutations in PIK3CA and PTEN were observed in two cell lines (2/16, 12.5%), but no mutation was observed in KRAS and BRAF. The antiproliferative effect of cetuximab by the MTT assay was not strong, and no correlation was observed between the antiproliferative effect of cetuximab and mutations in EGFR, KRAS, PIK3CA, BRAF and PTEN in these cell lines. Therefore, the mutation status of EGFR and downstream molecules were not useful for predicting the antitumor effects of cetuximab on HNSCC. Cetuximab‐mediated ADCC was observed in these cell lines and might have been influenced by the expression of EGFR. Therefore, cetuximab‐mediated ADCC seems to be an important part of the antitumor mechanisms of cetuximab and the expression levels of EGFR might influence the antitumor activity of cetuximab. Therefore, besides the antiproliferative effect of cetuximab by the MTT assay, it appeared important to evaluate cetuximab‐mediated ADCC as well as EGFR expression in HNSCC cells. (Cancer Sci 2011; 102: 1717–1723)
Analysis of the role of the coat protein N‐terminal segment in Potato virus X virion stability and functional activity
Authors: LUKASHINA ELENA , KSENOFONTOV ALEXANDER , FEDOROVA NATALIA , BADUN GENNADY , MUKHAMEDZHANOVA ANNA , KARPOVA OLGA , RODIONOVA NINA , BARATOVA LYUDMILA , DOBROV EVGENY
Published: June 2011

Previously, we have reported that intact Potato virus X (PVX) virions cannot be translated in cell‐free systems, but acquire this capacity by the binding of PVX‐specific triple gene block protein 1 (TGBp1) or after phosphorylation of the exposed N‐terminal segment of intravirus coat protein (CP) by protein kinases. With the help of in vitro mutagenesis, a nonphosphorylatable PVX mutant (denoted ST PVX) was prepared in which all 12 S and T residues in the 20‐residue‐long N‐terminal CP segment were substituted by A or G. Contrary to expectations, ST PVX was infectious, produced normal progeny and was translated in vitro in the absence of any additional factors. We suggest that the N‐terminal PVX CP segment somehow participates in virion assembly in vivo and that CP subunits in ST virions may differ in structure from those in the wild‐type (UK3 strain). In the present work, to test this suggestion, we performed a comparative tritium planigraphy study of CP structure in UK3 and ST virions. It was found that the profile of tritium incorporation into ST mutant virions in some CP segments differed from that of normal UK3 virions and from UK3 complexed with the PVX movement protein TGBp1. It is proposed that amino acid substitutions in ST CP and the TGBp1‐driven remodelling of UK3 virions induce structural alterations in intravirus CPs. These alterations affect the predicted RNA recognition motif of PVX CP, but in different ways: for ST PVX, labelling is increased in α‐helices 6 and 7, whereas, in remodelled UK3, labelling is increased in the β‐sheet strands β3, β4 and β5.
CorA, the magnesium/nickel/cobalt transporter, affects virulence and extracellular enzyme production in the soft rot pathogen Pectobacterium carotovorum
Authors: KERSEY CALEB M. , AGYEMANG PAUL A. , DUMENYO C. KORSI
Published: June 2011

Pectobacterium carotovorum (formerly Erwinia carotovora ssp. carotovora) is a phytopathogenic bacterium that causes soft rot disease, characterized by water‐soaked soft decay, resulting from the action of cell wall‐degrading exoenzymes secreted by the pathogen. Virulence in soft rot bacteria is regulated by environmental factors, host and bacterial chemical signals, and a network of global and gene‐specific bacterial regulators. We isolated a mini‐Tn5 mutant of P. carotovorum that is reduced in the production of extracellular pectate lyase, protease, polygalacturonase and cellulase. The mutant is also decreased in virulence as it macerates less host tissues than its parent and is severely impaired in multiplication in planta. The inactivated gene responsible for the reduced virulent phenotype was identified as corA. CorA, a magnesium/nickel/cobalt membrane transporter, is the primary magnesium transporter for many bacteria. Compared with the parent, the CorA‐ mutant is cobalt resistant. The mutant phenotype was confirmed in parental strain P. carotovorum by marker exchange inactivation of corA. A functional corA+ DNA from P. carotovorum restored exoenzyme production and pathogenicity to the mutants. The P. carotovorum corA+ clone also restored motility and cobalt sensitivity to a CorA‐ mutant of Salmonella enterica. These data indicate that CorA is required for exoenzyme production and virulence in P. carotovorum.
Atrium electromechanical interval in left ventricular diastolic dysfunction
Authors: Chao Tze‐Fan , Wang Kang‐Ling , Chuang Chi‐Fang , Chen Shih‐Ann , Yu Wen‐Chung
Published: June 2011

Eur J Clin Invest 2011

Background  Left ventricular (LV) diastolic dysfunction has great effects on the left atrium (LA). A recently developed electromechanical interval (PA‐TDI), which was determined as the time interval from the initiation of P wave deflection to the peak of local lateral LA tissue Doppler imaging signal, was reported to be associated with LA electrophysiological properties. The goal of our study was to evaluate the association between the PA‐TDI interval and LV diastolic function.

Materials and methods  A total of 224 consecutive patients were enrolled. LV diastolic dysfunction was defined as either (i) impaired relaxation: E/A ratio < 0·75 and E/E′ ratio < 10, (ii) pseudonormal pattern: 0·75 ≤ E/A ratio < 1·5 and E/E′ ratio > 10 or (iii) restrictive pattern: E/A ratio ≥ 1·5 and E/E′ ratio > 10. The PA‐TDI intervals were measured and compared between patients with and without diastolic dysfunction.

Results  Fifty‐six per cent of the study population had abnormal diastolic function. The PA‐TDI interval was significantly longer in the diastolic dysfunction group than that in the normal group (147·8 ± 18·2 vs. 130·4 ± 17·0 ms, P < 0·01). In patients with diastolic dysfunction, the PA‐TDI intervals became progressively longer as the diastolic dysfunction progressed from impaired relaxation (141·2 ± 11·4 ms), pseudonormal pattern (147·6 ± 18·0 ms) to restrictive pattern (164·1 ± 20·9 ms).

Conclusions  The PA‐TDI interval was significantly longer in patients with LV diastolic dysfunction than those without it. Its prolongation may reflect the severity of atrial remodelling because of the abnormal diastolic function of LV.
Stable extramarital affairs are breaking the heart
Authors: Fisher A. D. , Bandini E. , Corona G. , Monami M. , Cameron Smith M. , Melani C. , Balzi D. , Forti G. , Mannucci E. , Maggi M.
Published: June 2011

The relationship between extramarital affairs and cardiovascular risk is still not completely clarified. The aim of this study was to investigate whether extramarital affairs have a protective effect on cardiovascular risk or, conversely, a deleterious one. Among patients studied, 91.8% of the whole sample reported no or occasional extramarital affairs, while 8.2% declared a stable secondary relationship. During a median follow‐up of 4 [0–8] years, 95 major adverse cardiovascular events (MACE), eight of which were fatal, were observed. Cox analysis, after adjustment for confounding factors, showed that presence of stable extramarital affair was associated with a higher incidence of MACE (HR = 2.13 [1.12; 4.07], p = 0.023). The introduction in the Cox model of patient perceived partner’s hypoactive sexual desire (PPPHSD) attenuates the association (HR 1.86 [0.93; 3.70], p = 0.078). The sample was therefore divided according to PPPHSD. We observed that unadjusted incidence of MACE was significantly associated with presence of extramarital affairs only in men reporting a primal partner without PPPHSD. This association was also confirmed in a Cox regression model, after adjusting for confounders (HR = 2.87 [1.81; 6.98], p = 0.020). We can conclude that to be unfaithful represents an independent risk factor for MACE. Therefore, infidelity induces not only heart trouble in the betrayed partners, but seems to be also able to increase the betrayer’s heart‐related events.
The pharmacokinetics and metabolism of meloxicam in camels after intravenous administration
Authors: WASFI I. A. , AL ALI W. A. , AGHA B. A. , KAMEL A. M. , AL BIRIKI N. A , AL NEAIMI K. M.
Published: June 2011

Wasfi, I. A., Al Ali, W. A., Agha, B. A., Kamel, A. M., Al Biriki, N. A, Al Neaimi, K. M. The pharmacokinetics and metabolism of meloxicam in camels after intravenous administration.J. vet. Pharmacol. Therap. 35, 155–162.

The pharmacokinetics and metabolism of meloxicam was studied in camels (Camelus dromedarus) (n = 6) following intravenous (i.v.) administration of a dose of 0.6 mg·kg/body weight. The results obtained (mean ± SD) were as follows: the terminal elimination half‐life (t1/2β) was 40.2 ± 16.8 h and total body clearance (ClT) was 1.94 ± 0.66 mL·kg/h. The volume of distribution at steady state (VSS) was 92.8 ± 13.7 mL/kg. One metabolite of meloxicam was tentatively identified as methylhydroxy meloxicam. Meloxicam and metabolite were excreted unconjugated in urine. Meloxicam could be detected in plasma 10 days following i.v. administration in camels using a sensitive liquid chromatography tandem mass spectrometry (LC/MS/MS) method.
Heterologous protein transfer within structured myxobacteria biofilms
Authors: Wei Xueming , Pathak Darshankumar T. , Wall Daniel
Published: June 2011

Microbial biofilms represent heterogeneous populations of cells that form intimate contacts. Within these populations cells communicate, cooperate and compete. Myxobacteria are noted for their complex social interactions, including gliding motility and lipoprotein exchange. Here, we investigated cis protein sequence and cellular behaviour requirements for lipoprotein transfer between Myxococcus xanthus cells. Specifically, an outer membrane (OM) type II signal sequence (SS) fused to the heterologous mCherry fluorescent reporter resulted in OM localization. When donor cells harbouring SSOM–mCherry were mixed with GFP‐labelled recipient cells they developed red fluorescence. Our results surprisingly showed that a type II SS for OM localization, but not inner membrane localization, was necessary and sufficient for rapid and efficient heterologous protein transfer. Importantly, transfer did not occur in liquid or on surfaces where cells were poorly aligned. We conclude that cell–cell contact and alignment is a critical step for lipoprotein exchange. We hypothesize that protein transfer facilitates cooperative myxobacteria behaviours.
A mutation within the C‐terminal domain of Sup35p that affects [PSI+] prion propagation
Authors: Kabani Mehdi , Cosnier Bruno , Bousset Luc , Rousset Jean‐Pierre , Melki Ronald , Fabret Céline
Published: June 2011

The epigenetic factor [PSI+] in the yeast Saccharomyces cerevisiae is due to the prion form of Sup35p. The N‐terminal domain of Sup35p (N), alone or together with the middle‐domain (NM), assembles in vitro into fibrils that induce [PSI+] when introduced into yeast cells. The Sup35p C‐terminal domain (C), involved in translation termination, is essential for growth. The involvement of Sup35p C‐terminal domain into [PSI+] propagation is subject to debate. We previously showed that mutation of threonine 341 within Sup35p C‐domain affects translation termination efficiency. Here, we demonstrate that mutating threonine 341 to aspartate or alanine results in synthetic lethality with [PSI+] and weakening of [PSI+] respectively. The corresponding Sup35D and Sup35A proteins assemble into wild‐type like fibrils in vitro, but with a slower elongation rate. Moreover, cross‐seeding between Sup35p and Sup35A is inefficient both in vivo and in vitro, suggesting that the point mutation alters the structural properties of Sup35p within the fibrils. Thus, Sup35p C‐terminal domain modulates [PSI+] prion propagation, possibly through a functional interaction with the N and/or M domains of the protein. Our results clearly demonstrate that Sup35p C‐terminal domain plays a critical role in prion propagation and provide new insights into the mechanism of prion conversion.
Lipoamide dehydrogenase is essential for both bloodstream and procyclic Trypanosoma brucei
Authors: Roldán Angela , Comini Marcelo A. , Crispo Martina , Krauth‐Siegel R. Luise
Published: June 2011

Lipoamide dehydrogenase (LipDH) is a component of four mitochondrial multienzyme complexes. RNA interference or the deletion of both alleles in bloodstream Trypanosoma brucei resulted in an absolute requirement for exogenous thymidine. In the absence of thymidine, lipdh−/− parasites showed a severely altered morphology and cell cycle distribution. Most probably, in bloodstream cells with their only rudimentary mitochondrion, LipDH is required as component of the glycine cleavage complex which generates methylene‐tetrahydrofolate for dTMP and thus DNA synthesis. The essential role of LipDH in bloodstream parasites was confirmed by an in vivo model. Lipdh−/− cells were unable to infect mice. Our data further revealed that degradation of branched‐chain amino acids takes place but is dispensable. In cultured bloodstream – but not procyclic – African trypanosomes, the total cellular concentration of LipDH increases with increasing cell densities. In procyclic parasites, LipDH mRNA depletion caused an even stronger proliferation defect that was not reversed by thymidine suggesting that in the fully elaborated mitochondrion of these cells the primary effect is not on the glycine cleavage complex. Since the medium used for the cultivation of procyclic cells was not supplemented with glucose, impairment of the 2‐ketoglutarate dehydrogenase complex is probably the main effect of LipDH depletion.
Regulation of RhSUC2, a sucrose transporter, is correlated with the light control of bud burst in Rosa sp.
Authors: HENRY CLEMENCE , RABOT AMELIE , LALOI MARYSE , MORTREAU ERIC , SIGOGNE MONIQUE , LEDUC NATHALIE , LEMOINE RÉMI , SAKR SOULAIMAN , VIAN ALAIN , PELLESCHI‐TRAVIER SANDRINE
Published: June 2011

In roses, light is a central environmental factor controlling bud break and involves a stimulation of sugar metabolism. Very little is known about the role of sucrose transporters in the bud break process and its regulation by light. In this study, we show that sugar promotes rose bud break and that bud break is accompanied by an import of sucrose. Radio‐labelled sucrose accumulation is higher in buds exposed to light than to darkness and involves an active component. Several sucrose transporter (RhSUC1, 2, 3 and 4) transcripts are expressed in rose tissues, but RhSUC2 transcript level is the only one induced in buds exposed to light after removing the apical dominance. RhSUC2 is preferentially expressed in bursting buds and stems. Functional analyses in baker's yeast demonstrate that RhSUC2 encodes a sucrose/proton co‐transporter with a Km value of 2.99 mm at pH 4.5 and shows typical features of sucrose symporters. We therefore propose that bud break photocontrol partly depends upon the modulation of sucrose import into buds by RhSUC2.
Tn5 transposase‐assisted transformation of indica rice
Authors: Wu Jun , Du Hongwei , Liao Xuewei , Zhao Yu , Li Liguan , Yang Liuyan
Published: June 2011

Here, we describe experiments on Tn5 transposase‐assisted transformation of indica rice. Transposomes were formed in vitro as a result of hyperactive Tn5 transposase complexing with a transposon that contained a 19‐bp tetracycline operator (tetO) sequence. To form modified projectiles for transformation, the Tn10‐derived prokaryotic tetracycline repressor (TetR) proteins, which can bind transposomes via the high affinity of TetR for tetO, were immobilized onto the surface of bare gold microscopic particles. These projectiles were introduced into cells of the indica rice cultivar Zhuxian B by particle bombardment. Once projectiles were inside the cell, tetracycline induced an allosteric conformational change in TetR that resulted in the dissociation of TetR from tetO, and thus generated free transposomes. Molecular evidence of transposition was obtained by the cloning of insertion sites from many transgenic plants. We also demonstrated that the introduced foreign DNA was inherited stably over several generations. This technique is a promising transformation method for other plant species as it is species independent.