An integrated transcriptomics and proteomics analysis of the secretome of the helminth pathogen Fasciola hepatica: Proteins associated with invasion and infection of the mammalian host

To infect their mammalian hosts, Fasciola hepatica larvae must penetrate and traverse the intestinal wall of the duodenum, move through the peritoneum, and penetrate the liver. After migrating through and feeding on the liver, causing extensive tissue damage, the parasites move to their final niche in the bile ducts where they mature and produce eggs. Here we integrated a transcriptomics and proteomics approach to profile Fasciola secretory proteins that are involved in host-pathogen interactions and to correlate changes in their expression with the migration of the parasite. Prediction of F. hepatica secretory proteins from 14,031 expressed sequence tags (ESTs) available from the Wellcome Trust Sanger Centre using the semiautomated EST2Secretome pipeline showed that the major components of adult parasite secretions are proteolytic enzymes including cathepsin L, cathepsin B, and asparaginyl endopeptidase cysteine proteases as well as novel trypsin-like serine proteases and carboxypeptidases. Proteomics analysis of proteins secreted by infective larvae, immature flukes, and adult F. hepatica showed that these proteases are developmentally regulated and correlate with the passage of the parasite through host tissues and its encounters with different host macromolecules. Proteases such as FhCL3 and cathepsin B have specific functions in larvae activation and intestinal wall penetration, whereas FhCL1, FhCL2, and FhCL5 are required for liver penetration and tissue and blood feeding. Besides proteases, the parasites secrete an array of antioxidants that are also highly regulated according to their migration through host tissues. However, whereas the proteases of F. hepatica are secreted into the parasite gut via a classical endoplasmic reticulum/Golgi pathway, we speculate that the antioxidants, which all lack a signal sequence, are released via a non-classical trans-tegumental pathway.

Helminth pathogen cathepsin proteases:it's a family affair

Helminth pathogens express papain-like cysteine peptidases, termed cathepsins, which have important roles in virulence, including host entry, tissue migration and the suppression of host immune responses. The liver fluke Fasciola hepatica, an emerging human pathogen, expresses the largest cathepsin L cysteine protease family yet described. Recent phylogenetic, biochemical and structural studies indicate that this family contains five separate clades, which exhibit overlapping but distinct substrate specificities created by a process of gene duplication followed by subtle residue divergence within the protease active site. The developmentally regulated expression of these proteases correlates with the passage of the parasite through host tissues and its encounters with different host macromolecules.

Detached-Eddy Simulation of a Louver-Cooling Scheme for Turbine Blades

The performance of a louver-cooling scheme on a flat plate was analyzed using a detached-eddy-simulation turbulence model. It was assumed that the louver-cooling scheme was tested in a wind tunnel with the mainstream flow velocity of 20 m/s, equivalent to a Reynolds number of 16,200, based on the jet diameter. Turbulence closure was achieved by a realizable k-e-based detached-eddy-simulation turbulence model. Solutions of two blowing ratios of 0.5 and 1 were successfully obtained by running parallel on 16 nodes on a computer cluster. The flowfields were found to be highly unsteady and oscillatory in nature, with the maximum fluctuation of the adiabatic effectiveness as high as 15% of the time-averaged value. It is shown that the fluctuations in the adiabatic effectiveness are mainly caused by the spanwise fluctuation of the coolant jet and the unsteady vortical structures created by the interaction of the jet and the mainstream.

Numerically Investigating the Effects of Cross-Links in Scaled Microchannel Heat Sinks

Thermal management as a method of heightening performance in miniaturized electronic devices using microchannel heat sinks has recently become of interest to researchers and the industry. One of the current challenges is to design heat sinks with uniform flow distribution. A number of experimental studies have been conducted to seek appropriate designs for microchannel heat sinks. However, pursuing this goal experimentally can be an expensive endeavor. The present work investigates the effect of cross-links on adiabatic two-phase flow in an array of parallel channels. It is carried out using the three dimensional mixture model from the computational fluid dynamics software, FLUENT 6.3. A straight channel and two cross-linked channel models were simulated. The cross-links were located at 1/3 and 2/3 of the channel length, and their widths were one and two times larger than the channel width. All test models had 45 parallel rectangular channels, with a hydraulic diameter of 1.59 mm. The results showed that the trend of flow distribution agrees with experimental results. A new design, with cross-links incorporated, was proposed and the results showed a significant improvement of up to 55% on flow distribution compared with the standard straight channel configuration without a penalty in the pressure drop. Further discussion about the effect of cross-links on flow distribution, flow structure, and pressure drop was also documented.

yambo: An ab initio tool for excited state calculations

yambo is an ab initio code for calculating quasiparticle energies and optical properties of electronic systems within the framework of many-body perturbation theory and time-dependent density functional theory. Quasiparticle energies are calculated within the GW approximation for the self-energy. Optical properties are evaluated either by solving the Bethe-Salpeter equation or by using the adiabatic local density approximation. yambo is a plane-wave code that, although particularly suited for calculations of periodic bulk systems, has been applied to a large variety of physical systems. yambo relies on efficient numerical techniques devised to treat systems with reduced dimensionality, or with a large number of degrees of freedom. The code has a user-friendly command-line based interface, flexible 110 procedures and is interfaced to several publicly available density functional ground-state codes.

Romanticism and Blackwood's Magazine:'An Unprecedented Phenomenon'

Romanticism and Blackwood's Magazine is inspired by the ongoing critical fascination with Blackwood's Edinburgh Magazine, and the burgeoning recognition of its centrality to the Romantic age. Though the magazine itself was published continuously for well over a century and a half, this volume concentrates specifically on those years when William Blackwood was at the helm, beginning with his founding of the magazine in 1817 and closing with his death in 1834. These were the years when, as Samuel Taylor Coleridge put it in 1832, Blackwood's reigned as 'an unprecedented Phenomenon in the world of letters.' The magazine placed itself at the centre of the emerging mass media, commented decisively on all the major political and cultural issues that shaped the Romantic movement, and published some of the leading writers of the day, including Coleridge, Thomas De Quincey, John Galt, Felicia Hemans, James Hogg, Walter Scott, and Mary Shelley.

'This much-needed volume reminds us not only why Blackwood's was the most influential periodical publication of the time, but also how its writers, writings, and critical agendas continue to shape so many of the scholarly concerns of Romantic studies in the twenty-first century.' - Charles Mahoney, Associate Professor, University of Connecticut, USA

List of Illustrations
Acknowledgements
Abbreviations
Notes on Contributors
'A character so various, and yet so indisputably its own': A Passage to Blackwood's Edinburgh Magazine; R.Morrison & D.S.Roberts
PART I: BLACKWOOD'S AND THE PERIODICAL PRESS
Beginning Blackwood's: The Right Mix of Dulce and Ùtile; P.Flynn
John Gibson Lockhart and Blackwood's: Shaping the Romantic Periodical Press; T.Richardson
From Gluttony to Justified Sinning: Confessional Writing in Blackwood's and the London Magazine; D.Higgins
Camaraderie and Conflict: De Quincey and Wilson on Enemy Lines; R.Morrison
Selling Blackwood's Magazine, 1817-1834; D.Finkelstein
PART II: BLACKWOOD'S CULTURE AND CRITICISM
Blackwood's 'Personalities'; T.Mole
Communal Reception, Mary Shelley, and the 'Blackwood's School' of Criticism; N.Mason
Blackwoodian Allusion and the Culture of Miscellaneity; D.Stewart
Blackwood's Edinburgh Magazine in the Scientific Culture of Early Nineteenth-Century Edinburgh; W.Christie
The Art and Science of Politics in Blackwood's Edinburgh Magazine, c. 1817-1841; D.Kelly
Prosing Poetry: Blackwood's and Generic Transposition, 1820-1840; J.Camlot
PART III: BLACKWOOD'S FICTIONS
Blackwood's and the Boundaries of the Short Story; T.Killick
The Edinburgh of Blackwood's Edinburgh Magazine and James Hogg's Fiction; G.Hughes
'The Taste for Violence in Blackwood's Magazine'; M.Schoenfield
PART IV: BLACKWOOD'S AT HOME
John Wilson and Regency Authorship; R.Cronin
John Wilson and Sport; J.Strachan
William Maginn and the Blackwood's 'Preface' of 1826; D.E.Latané, Jr.
All Work and All Play: Felicia Hemans's Edinburgh Noctes; N.Sweet
PART V: BLACKWOOD'S ABROAD
Imagining India in Early Blackwood's; D.S.Roberts
Tales of the Colonies: Blackwood's, Provincialism, and British Interests Abroad; A.Jarrells
Selected Bibliography
Index

ROBERT MORRISON is Queen's National Scholar at Queen's University, Kingston, Ontario, Canada. His book, The English Opium-Eater: A Biography of Thomas De Quincey was a finalist for the James Tait Black Prize. He has edited writings by Jane Austen, Leigh Hunt, Thomas De Quincey, and John Polidori.
DANIEL SANJIV ROBERTS is Reader in English at Queen's University Belfast, UK. His publications include a monograph, Revisionary Gleam: De Quincey, Coleridge, and the High Romantic Argument (2000), and major critical editions of Thomas De Quincey's Autobiographic Sketches and Robert Southey's The Curse of Kehama; the latter was cited as a Distinguished Scholarly Edition by the MLA. He is currently working on an edition of Charles Johnstone's novel The History of Arsaces, Prince of Betlis for the Early Irish Fiction series.

Topoisomerase IIα promotes activation of RNA polymerase I transcription by facilitating pre-initiation complex formation

Type II DNA topoisomerases catalyse DNA double-strand cleavage, passage and re-ligation to effect topological changes. There is considerable interest in elucidating topoisomerase II roles, particularly as these proteins are targets for anti-cancer drugs. Here we uncover a role for topoisomerase IIa in RNA polymerase I-directed ribosomal RNA gene transcription, which drives cell growth and proliferation and is upregulated in cancer cells. Our data suggest that topoisomerase IIa is a component of the initiation-competent RNA polymerase Iß complex and interacts directly with RNA polymerase I-associated transcription factor RRN3, which targets the polymerase to promoter-bound SL1 in pre-initiation complex formation. In cells, activation of rDNA transcription is reduced by inhibition or depletion of topoisomerase II, and this is accompanied by reduced transient double-strand DNA cleavage in the rDNA-promoter region and reduced pre-initiation complex formation. We propose that topoisomerase IIa functions in RNA polymerase I transcription to produce topological changes at the rDNA promoter that facilitate efficient de novo pre-initiation complex formation.

Linking Parliamentary Records through Metatdata

The LIPARM schema links the parliamentary record together for the first time by creating a unified metadata scheme for all of its key elements. People, bills, acts, items of business, debates, divisions and sessions will all be described by the scheme and will be linked together across resources which are currently spread out and isolated. For the first time, it will be possible to trace a given MP’s entire voting record or to find every speech they made. It will be possible to follow the passage of every bill or act, and every contribution to the debates that accompany it. Both the historical and the contemporary record of parliamentary proceedings will become accessible in this way for the first time.

A novel three-dimensional culture system for isolation and clonal propagation of neural stem cells using a thermo-reversible gelation polymer

In the present study, we examined the possible utility of a three-dimensional culture system using a thermo-reversible gelation polymer to isolate and expand neural stem cells (NSCs). The polymer is a synthetic biologically inert polymer and gelates at temperatures higher than the gel-sol transition point ( approximately 20 degrees C). When fetal mouse brain cells were inoculated into the gel, spherical colonies were formed ( approximately 1% in primary culture and approximately 9% in passage cultures). The spheroid-forming cells were positive for expression of the NSC markers nestin and Musashi. Under conditions facilitating spontaneous neural differentiation, the spheroid-forming cells expressed genes characteristic to astrocytes, oligodendrocytes, and neurons. The cells could be successively propagated at least to 80 poly-D-lysines over a period of 20 weeks in the gel culture with a growth rate higher than that observed in suspension culture. The spheroids formed by fetal mouse brain cells in the gel were shown to be of clonal origin. These results indicate that the spheroid culture system is a convenient and powerful tool for isolation and clonal expansion of NSCs in vitro.

An investigation into the acceleration response of a damaged beam-type structure to a moving force

In recent years there have been a growing number of publications on procedures for damage detection in beams from analysing their dynamic response to the passage of a moving force. Most of this research demonstrates their effectiveness by showing that a singularity that did not appear in the healthy structure is present in the response of the damaged structure. This paper elucidates from first principles how the acceleration response can be assumed to consist of ‘static’ and ‘dynamic’ components, and where the beam has experienced a localised loss in stiffness, an additional ‘damage’ component. The combination of these components establishes how the damage singularity will appear in the total response. For a given damage severity, the amplitude of the ‘damage’ component will depend on how close the damage location is to the sensor, and its frequency content will increase with higher velocities of the moving force. The latter has implications for damage detection because if the frequency content of the ‘damage’ component includes bridge and/or vehicle frequencies, it becomes more difficult to identify damage. The paper illustrates how a thorough understanding of the relationship between the ‘static‘ and ‘damage’ components contributes to establish if damage has occurred and to provide an estimation of its location and severity. The findings are corroborated using accelerations from a planar finite element simulation model where the effects of force velocity and bridge span are examined.

Tip leakage flow and heat transfer on turbine blade tip and casing, Part 1: Effect of tip clearance height and rotation speed

Steady simulations were performed to investigate tip leakage flow and heat transfer characteristics on the rotor blade tip and casing in a single-stage gas turbine engine. A typical high-pressure gas turbine stage was modeled with a pressure ratio of 3.2. The predicted isentropic Mach number and adiabatic wall temperature on the casing showed good agreement with available experimental data under similar operating condition. The present numerical study focuses extensively on the effects of tip clearance heights and rotor rotational speeds on the blade tip and casing heat transfer characteristics. It was observed that the tip leakage flow structure is highly dependent on the height of the tip gap and the speed of the rotor. In all cases, the tip leakage flow was seen to separate and recirculate just around the corner of the pressure side of the blade tip. This region of re-circulating flow enlarges with increasing clearance heights. The separated leakage flow reattaches afterwards on the tip surface. Leakage flow reattachment was shown to enhance surface heat transfer at the tip. The interaction between tip leakage flow and secondary flows that is induced by the relative casing motion is found to significantly influence the blade tip and casing heat transfer distribution. A region of critical heat transfer exists on the casing near the blade tip leading edge and along the pressure-side edge for all the clearance heights that were investigated. At high rotation speed, the region of critical heat transfer tends to move towards the trailing edge due to the change in inflow angle.

Gapped Two-Body Hamiltonian for Continuous-Variable Quantum Computation

We introduce a family of Hamiltonian systems for measurement-based quantum computation with continuous variables. The Hamiltonians (i) are quadratic, and therefore two body, (ii) are of short range, (iii) are frustration-free, and (iv) possess a constant energy gap proportional to the squared inverse of the squeezing. Their ground states are the celebrated Gaussian graph states, which are universal resources for quantum computation in the limit of infinite squeezing. These Hamiltonians constitute the basic ingredient for the adiabatic preparation of graph states and thus open new venues for the physical realization of continuous-variable quantum computing beyond the standard optical approaches. We characterize the correlations in these systems at thermal equilibrium. In particular, we prove that the correlations across any multipartition are contained exactly in its boundary, automatically yielding a correlation area law. © 2011 American Physical Society.

Re-organisation of the cytoskeleton during developmental programmed cell death in Picea abies embryos

Cell and tissue patterning in plant embryo development is well documented. Moreover, it has recently been shown that successful embryogenesis is reliant on programmed cell death (PCD). The cytoskeleton governs cell morphogenesis. However, surprisingly little is known about the role of the cytoskeleton in plant embryogenesis and associated PCD. We have used the gymnosperm, Picea abies , somatic embryogenesis model system to address this question. Formation of the apical-basal embryonic pattern in P. abies proceeds through the establishment of three major cell types: the meristematic cells of the embryonal mass on one pole and the terminally differentiated suspensor cells on the other, separated by the embryonal tube cells. The organisation of microtubules and F-actin changes successively from the embryonal mass towards the distal end of the embryo suspensor. The microtubule arrays appear normal in the embryonal mass cells, but the microtubule network is partially disorganised in the embryonal tube cells and the microtubules disrupted in the suspensor cells. In the same embryos, the microtubule-associated protein, MAP-65, is bound only to organised microtubules. In contrast, in a developmentally arrested cell line, which is incapable of normal embryonic pattern formation, MAP-65 does not bind the cortical microtubules and we suggest that this is a criterion for proembryogenic masses (PEMs) to passage into early embryogeny. In embryos, the organisation of F-actin gradually changes from a fine network in the embryonal mass cells to thick cables in the suspensor cells in which the microtubule network is completely degraded. F-actin de-polymerisation drugs abolish normal embryonic pattern formation and associated PCD in the suspensor, strongly suggesting that the actin network is vital in this PCD pathway.

The Role of Arg228 in the phosphorylation of galactokinase: The mechanism of GHMP kinases by QM/MM studies

GHMP kinases are a group of structurally-related small molecule kinases. They have been found in all kingdoms of life and are mostly responsible for catalysing the ATP-dependent phosphorylation of intermediary metabolites. Although the GHMP kinases are of clinical, pharmaceutical and biotechnological importance, the mechanism of GHMP-kinases is controversial. A catalytic base mechanism was suggested for mevalonate kinase that has a structural feature of the ?-phosphate of ATP close to an aspartate residue; however, for one GHMP member, homoserine kinase, where the residue acting as general base is absent, a direct phosphorylation mechanism was suggested. Furthermore, it has been proposed by some authors that all the GHMP kinases function via the direct phosphorylation mechanism. This controversy in mechanism has limited our ability to exploit these enzymes as drug targets and in biotechnology. Here the phosphorylation reaction mechanism of the human galactokinase, a member of GHMP kinase was investigated using molecular dynamics simulations and density functional theory-based QM/MM calculations (B3LYP-D/AMBER99). The reaction coordinates were localized by potential energy scan using adiabatic mapping method. Our results indicate that a highly conserved Glu174 captures Arg105 to the proximity of the a-phosphate of ATP forming a H-bond network, therefore the mobility of ATP in the large oxyanion hole is restricted. Arg228 functions to stabilize the negative charge developed at the ß,?-bridging oxygen of the ATP during bond cleavage. The reaction occurs via direct phosphorylation mechanism and the Asp186 in proximity of ATP does not directly participate in the reaction pathway. Since Arg228 is not conserved among GHMP kinases, reagents which form interactions with Arg228, and therefore can interrupt its function in phosphorylation may be developed into potential selective inhibitors for galactokinase.

Resistance Development of Cystic Fibrosis Respiratory Pathogens When Exposed to Fosfomycin and Tobramycin Alone and in Combination under Aerobic and Anaerobic Conditions

Although antibiotics from different classes are frequently prescribed in combination to prevent the development of resistance amongst Cystic Fibrosis (CF) respiratory pathogens, there is a lack of data as to the efficacy of this approach. We have previously shown that a 4:1 (w/w) combination of fosfomycin and tobramycin (F:T) has excellent activity against CF pathogens with increased activity under physiologically relevant anaerobic conditions. Therefore, the aim of this study was to determine whether F:T could delay or prevent the onset of resistance compared to either fosfomycin or tobramycin alone under aerobic and anaerobic conditions. The frequency of spontaneous mutants arising following exposure to fosfomycin, tobramycin and F:T was determined for clinical Pseudomonas aeruginosa and MRSA isolates under aerobic and anaerobic conditions. The effect of sub-inhibitory concentrations of fosfomycin, tobramycin and F:T on the induction of resistance was also investigated, with the stability of resistance and fitness cost associated with resistance assessed if it developed. P. aeruginosa and MRSA isolates had a lower frequency of spontaneous mutants to F:T compared to fosfomycin and tobramycin under both aerobic and anaerobic conditions. There was a maximum two-fold increase in F:T MICs when P. aeruginosa and MRSA isolates were passaged in sub-inhibitory F:T for 12 days. In contrast, sequential resistance to fosfomycin and tobramycin developed quickly (n = 3 days for both) after passage in sub-inhibitory concentrations. Once developed, both fosfomycin and tobramycin resistance was stable and not associated with a biological fitness cost to either P. aeruginosa or MRSA isolates. The results of this study suggest that F:T may prevent the development of resistance compared to fosfomycin or tobramycin alone under aerobic and physiologically relevant anaerobic conditions. F:T may be a potential treatment option in CF patients chronically colonised by MRSA and/or P. aeruginosa.