bluuebunny/crossref_metadata_2025 huggingface dataset:
The development of the body wall ofPolymorphus minutus(Acanthocephala) in its intermediate hostGammarus pulex
Authors: Butterworth Penelope E.
Published: June 2009

The ultrastructure and development of the body wall ofPolymorphus minutusis described during the acanthella stages in the intermediate hostGammarus pulex.

The cortex of the early acanthella is simple in structure, consisting of a syncytium containing giant nuclei, mitochondria, Golgi bodies, endoplasmic reticulum and a few lipid bodies. The cuticle is penetrated by pores which open into vesicles in a vesicular region.

The cortex gives rise to the body wall, neck and lemnisci of the adult, and may be considered as divided initially into two and later three functionally different regions: an outer absorptive region, an inner storage region and a layer between which develops to provide firm, resistant skeletal protection.

Absorption is facilitated by the increase in surface area due to the pores which penetrate the surface. This region is functional throughout development and the pores increase in number, possibly by division, as the animal grows. Beneath the pores a pore canal layer develops towards the end of the late acanthella stage.

During development supporting fibres are deposited throughout the cortex. Beneath the vesicular layer a concentration of mitochondria, Golgi bodies and endoplasmic reticulum deposit the fibres of the felt layer. In the anterior meta-soma no felt layer is found, but the body spines originate from this region.

The inner region of the cortex, or radial layer, contains the giant nuclei, which are arranged in the early acanthella in 5 rings of 4, 6, 5 or 6, 6 and 5 nuclei respectively. During development they produce dendritic process and finally fragment. They are considered here to be concerned with the formation of the felt layer and lemnisci rather than the ‘lacunar channels’. The inner cortical region becomes ensely packed with lipid bodies, and it is suggested that these may be responsible, owing to fixation artifact, for the so-called ‘lacunar channels’ previously described in these regions, the extensive cavities seen in some light microscope preparations being filled with a fluid lipid rather than an aqueous solution.

The lemnisci are similar in appearance to the cortex except for regions of concentrated endoplasmic reticulum.

The mitochondria in the cortex of the acanthella appear to be aerobic rather than anaerobic, as they possess many cristae and are larger than the mitochondria of the adults.

My thanks are due to Dr D. W. T. Crompton for advice and encouragement, and to Dr D. H. Northcote and Dr F. B. P. Wooding for time on the Phillips Electron Microscope 100. This work was carried out during the tenure of an S.R.C. studentship.
Trypanosoma (Megatrypanum) hoarei sp.nov. (Protozoa: Trypanosomatidae) from shrews of the genus Sorex in California
Authors: Davis Betty S.
Published: June 2009

A new species of Trypanosoma, T. (Megatrypanum) hoarei, is described from shrews of the genus Sorex (S. trowbridgii, S. vagrans, S. ornatus, and S. palustris) in California. Four body types are found in adult populations of T. hoarei, two common and two rare, as well as intermediate stages, indicating a tendency to-ward polymorphism in this species. Multiplication is discontinuous, with a reproductive and growth period characterized by moderate numbers of diverse and bizarre developmental forms in the blood and high coefficients of variation for total length (20–30 %), succeeded by an adult phase with few trypanosomes in the blood and lower coefficients of variation for total length (7–12 %). The method and site of multiplication in T. hoarei is unknown but evidence indicates that reproduction by multiple fission or binary fission of amastigote forms may occur in tissue capillaries, with the production of large, rounded amastigote individuals. The latter develop, without intervention of epimastigote stages, into large, rounded trypomastigote individuals from which a wide variety of other developmental forms proceed, including certain distinctive, very long ribbon-like trypanosomes. A review of the literature on mole and shrew trypanosomes suggests that T. hoarei of Sorex, T. petrodromi from Petrodrorrms, and T. talpae from Talpa are related, primitive insectivore forms, clearly distinguishable from the lewisi-type trypanosomes also found in insectivores.
Immunity in trypanosomiasis
Authors: Soltys M. A.
Published: June 2009

Success in immunizing rabbits, rats and sheep with dead trypanosomes depends on the method of killing trypanosomes, the frequency of inoculations, and the strain used for immunization. Positive results were obtained when trypanosomes were killed by formalin or by freezing and thawing five times. Negative results were obtained when trypanosomes were killed by 56° C. for half an hour.

Animals which received 10 doses of the mixture produced better results than those which received the same amount but only in 2 doses. An addition of Freund's adjuvant improved results, but 10 doses without an adjuvant were still better than 2 doses with an adjuvant. When trypanosomes were killed by 0·5% formalin, only an M variant of T. brucei, which was maintained by frequent passage in mice and was an antibody-sensitive variant, was able to produce in animals protective antibodies and resistance to a homologous ‘M’ variant, but not to an ‘R’ variant. On the other hand, if an ‘R’ variant of the same strain, which was passaged forty-eight times through rabbits and became resistant to antibodies, was killed by 0·5 % formalin and inoculated into animals, no antibodies and resistance could be demonstrated to a homologous ‘R’ variant and an ‘M’ variant.

Although it is possible to produce immunity in animals with dead trypanosomes further studies, particularly in the field, are necessary to find its practical application.
Non-linear phenomena in host—parasite interactions
Authors: Anderson R. M. , May R. M. , Gupta S.
Published: June 2009

The paper examines non-linear dynamical phenomena in host—parasite interactions by reference to a series of different problems ranging from the impact on transmission of control measures based on vaccination and chemotherapy, to the effects of immunological responses targeted at different stages in a parasite's life-cycle. Throughout, simple mathematical models are employed to aid in interpretation. Analyses reveal that the influence of a defined control measure on the prevalence or intensity of infection, whether vaccination or drug treatment, is non-linearly related to the magnitude of control effort (as defined by the proportion of individuals vaccinated or treated with a drug). Consideration of the relative merits of gametocyte and sporozoite vaccines against malarial parasites suggests that very high levels of cohort immunization will be required to block transmission in endemic areas, with the former type of vaccine being more effective in reducing transmission for a defined level of coverage and the latter being better with respect to a reduction in morbidity. The inclusion of genetic elements in analyses of the transmission of helminth parasites reveals complex non-linear patterns of change in the abundance of different parasite genotypes under selection pressures imposed by either the host immunological defences or the application of chemotherapeutic agents. When resistance genes are present in parasite populations, the degree to which abundance can be suppressed by chemotherapy depends critically on the frequency and intensity of application, with intermediate values of the former being optimal. A more detailed consideration of the impact of immunological defences on parasite population growth within an individual host, by reference to the erythrocytic cycle of malaria, suggests that the effectiveness of a given immunological response is inversely related to the life-expectancy of the target stage in the parasite's developmental cycle.
Novel biochemical pathways in parasitic protozoa
Authors: Fairlamb A. H.
Published: June 2009

Throughout evolution, enzymes and their metabolites have been highly conserved. Parasites are no exception to this and differ most markedly by the absence of metabolic pathways that are present in the mammalian host. In general, parasites are metabolically lazy and rely on the metabolism of the host both for a supply of prefabricated components such as purines, fatty acids, sterols and amino acids and for the removal of end-products. Nonetheless, parasites are metabolically highly sophisticated in that (1) they retain the genetic capacity to induce many pathways, when needed, and (2) they have developed complex mechanisms for their survival in the host. Certain unique features of the metabolism of trypanosomes, leishmania, malaria and anaerobic protozoa will be discussed. This will include (1) glycolysis and electron transport with reference to the unique organelles: the glycosome and the hydrogenosome, (2) purine salvage, pyrimidine biosynthesis and folic acid metabolism and (3) polyamine and thiol metabolism with special reference to the role of the unique metabolite of trypanosomes and leishmanias, trypanothione.
The ecology of immature phases of Trichostrongyle nematodes: II. The effect of climatic factors on the availability of the infective larvae of Trichostrongylus retortaeformis to the host
Authors: Crofton H. D.
Published: June 2009

1. Eggs and larvae of Trichostrongylus retortaeformis were used.

2. The rate of hatching of eggs was shown to be mainly related to temperature. From November to March, when maximum temperatures were below 50° F., there was no hatching. When maximum temperatures of 50–55° F. occurred eggs hatched on or before the fifteenth day, but never during the first 8 days. Eggs hatched in 8 days or less when maximum temperatures of 60–80° F. occurred.

3. When the rate of evaporation in the air was high, eggs still hatched and reached the infective stage, the grass blades reducing the rate of loss of moisture from the faecal pellet. Laboratory experiments show that eggs may not develop to the infective stage if the faecal pellets are on a grassless portion of the pasture. This is most likely to occur when the rate of evaporation is high and the temperature low.

4. Hatching may be delayed by cold conditions, but some eggs remain viable for long periods and they hatch when the temperature rises. Eggs passed by the host in the autumn can survive a cold winter and hatch in the spring, but eggs passed during the coldest period die.

5. During periods when the maximum temperature never exceeded 55° F., little or no migration of larvae occurred. When temperatures rose above 55° F. the number of larvae migrating increased; but rise of temperature was associated with increase in the rate of evaporation. High rates of evaporation reduced the number of larvae migrating on the grass blades.

6. Some infective larvae died soon after exposure on grass plots, but a small number survived long periods. In cold weather some larvae were still alive after 20 weeks. A high death-rate occurred in warm weather. A large proportion of the larvae died during periods in which the rate of evaporation was high; in one of these periods 95% of the larvae were dead at the end of 4 weeks' exposure.

7. The number of larvae on grass blades of a pasture was shown to be dependent, at any time, upon the climate at that time, and upon past conditions which had influenced hatching and survival:
On the genusDinobothriumvan Beneden (Cestoda), with a description of two new species from sharks, and a note onMonorygmasp. from the electric ray
Authors: Sproston Nora G.
Published: June 2009

A new species of the giant phyllobothriid genusDinobothrium(D. keilinin.sp.) is described from the blue shark (Carcharinus glaucus); it is compared withD. planumLinton, found for the first time from British waters, in the basking shark (Cetorhinus maximus), and the structure of both is discussed in relation to that of the genotype,D. septariavan Beneden. A fourth species,D. paciferumn.sp., also from the basking shark, is described, and though only a tenth the size of the other species, it shares most of their diagnostic scolex characters. It has eight true suckers above the four pendent bothria: inD. planumthere are four true suckers and four pseudo-suckers, while inD. keilinithere are only four true suckers, andD. septariais said to have four pseudo-suckers alone. The nomenclature of the older species is revised, and the genus redefined.

Attention is directed to the adaptations in these large cestodes which facilitate interchange with the substratum: the development of lateral furrows through which the main excretory canals open to the exterior. There is also a ventral furrow, which in the nascent segments is an open cleft: this accommodates the growing uterus and permits a protracted gravid phase of the proglottidesin situ. The effect is of five longitudinal hinges, which allow of considerable lateral expansion of the thick-walled strobilus. The smallerD. paciferumlacks these modifications, and the cylindrical segments are apparently detached in the gravid state. An explanation is offered for the conflicting accounts of the lateral extent of the vitellaria in this genus: there is a lateral contraction of the ventral vitelline reticulum as the ovarian phase waxes. InD. paciferumthe vitellaria completely encircle the proglottis at the inception of the ovarian phase.

Notes are given on the selachiàn hosts examined, their food and the other parasites present. The relationships ofDinobothriumto other phyllobothriid genera and toTetrabothriusare discussed.

In one electric ray,Torpedo nobiliana, a single immature strobilus of another kind of phyllobothriid was found; it is probably a new species ofMonorygma, though it has slight resemblances toCalyptrobothrium—a genus characteristic of electric rays. The boat-shaped bothria are held at an angle from the scolex by contractile buttress-like wings, and at their proximal end there is a relatively large and complex sucker. Affinities with related genera are discussed and the nomenclature ofMonorygma angusta(Linton) is emended.
Pseudoporrorchis teliger, a new species of acanthocephala from Java
Authors: van Cleave Harley J.
Published: June 2009

Joyeux & Baer, in 1935, recognized a new genus when they described Pseudoporrorchis houdemeri, a new species of Acanthocephala taken from the intestine of Centropus sinensis intermedius at Tonkin, Indo-China. They reviewed the literature and assigned four additional species to this genus as follows: Echinorhynchus rotundatus von Linstow, 1897; E. centropi Porta, 1910; E. bulbocaudatus Southwell & Macfie, 1925; and E. centropusi Tubangui, 1933. These same authors presented a tabular comparison of the five species, based upon all of the usual morphological details utilized in formulating specific descriptions. Morphologically the five species show close conformity in all essential features. In their host relations they are equally uniform in that each species utilizes some species of the avian genus Centropus as its definitive host. In the present paper a sixth species of this genus is described in which the same adherence to general morphological pattern is observed, although the definitive hosts are mammals instead of the customary bird hosts.
The seasonal and diurnal activities of individual sheep ticks (Ixodes ricinus L.)
Authors: Lees A. D. , Milne A.
Published: June 2009

1. Activity in Ixodes ricinus was studied by laying down newly emerged ticks in natural clumps of vegetation from which all hosts (with the possible exception of ‘mice’) were excluded. After a period of quiescence the ticks climbed to the ‘active’ position at the vegetation tips. Activity was assessed either by simple observation (in adults which were marked individually) or by ‘brushing’ the vegetation with the hands (nymphs and larvae). 52 % of the adults and 44 % of the nymphs were recovered.

2. The seasonal activity behaviour was followed in three series of ticks set out during May, July and October 1945. The results were used in interpreting the time relations of seasonal activity in ‘wild’ populations. The timing of the activity cycle appears to be largely determined by the availability of unfed ticks rather than by the prevailing meteorological conditions.

3. The diurnal pattern of behaviour in active ticks was closely examined during a 24 hr. period. Many remained at the tips without moving. The others began or ended a phase of activity by night or by day; but among these, the proportion ending a phase at night was significantly greater. This is the main reason for the previously reported diurnal fluctuation of activity in a tick population.

4. Two hundred and seven adult ticks spent, on an average, a total of 9 days at the vegetation tips (individual limits 1 and 54 days). This activity was spread over an ‘active period’ (interval between first and last appearances) averaging 30 days. Very active ticks rarely remained continuously at the tips. The mean number of visits to the tips was 4 (limits 1 and 19), each lasting for an average of 2·5 days. Where long spells of activity alternate with short periods of quiescence, the behaviour is probably regulated by the humidity reaction, the quiescent phase providing an opportunity for restoring the depleted water balance.

5. Newly moulted adult ticks possess reserves of fat adequate for many months of quiescence. During activity these reserves are exhausted in a few weeks or even days. Duration of survival mainly depended on whether the onset of activity was immediate or delayed. Some adults remained quiescent for 1 year before becoming active for the first time.

6. Several types of orientations were observed in the field. In attaining the position at the tips favourable for encountering a host, the gravity response (upward-turning near the tip) is of major importance. The tick avoids wind and direct sunlight by sheltering behind its supporting stem. In sensing the approach of a ‘host’ (the observer's finger) the perception of eddies of warm air is particularly significant. The response (questing, then orientation) is elicited much less readily if the stimulus is applied from the leeward.
Egyptian fever of cattle
Authors: Daubney R. , Said M. Sami
Published: June 2009

The disease, Egyptian fever of cattle, has been observed at the Serum Institute, Abbassiah, in Cyrenaican and Cyprus cattle, and less frequently in native Egyptian cattle. The responsible Theileria has been determined as T. annulata (Dzchunkowsky & Luhz, 1904), and both natural and experimental transmission has been demonstrated with Hyalomma excavatum Koch 1844, of Delpy (1949b).

H. excavatum in Egypt is a three-host tick, which hibernates during the winter months in the walls of buildings in the engorged nymphal and fasting adult stages. Transmission has been effected with nymphae and adults, infected in each case by feeding the preceding stage on reacting or recovered cattle. On no occasion has infection been observed to pass through the egg to the larval stage. Infection can also be transmitted by inoculation of the blood of a reacting animal in which schizonts are demonstrable.
Failure to produce resistance to chloroquine in Plasmodium gallinaceum in chicks
Authors: Bishop Ann , McConnachie Elspeth W.
Published: June 2009

A strain of Plasmodium gallinaceum has been treated for 16 months with chloroquine, under conditions which previously have produced strains resistant to proguanil, sulphonamides and pamaquin, but no change in reaction to the drug has occurred.
Description of two new species of Ascodipteron from africa and one species of Nycteribosca from madagascar (Diptera, streblidae)
Authors: Jobling B.
Published: June 2009

The description of one new species of Ascodipteron and another one of Nycteribosca is based on the material collected in Africa and Madagascar respectively by Mr H. Hoogstraal, of the United States Naval Medical Research Unit No. 3. These specimens represent a part of the collection which was sent to me for identification by Mr R. L. Wenzel of the Chicago Natural History Museum. In this paper I have also included the description of another new species of Ascodipteron of which two specimens were collected by Mr T. S. Jones in West Africa.
Number, Form, Content: Hume's Dialogues, Number Nine
Authors: Fendt Gene
Published: June 2009

This paper's aim is threefold. First, I wish to show that there is an analogy in section nine that arises out of the interaction of the interlocutors; this analogy is, or has, a certain comic adequatic to the traditional (e.g. Aquinas's) arguments about proofs for the existence of God. Second, Philo's seemingly inconsequential example of the strange necessity of products of 9 in section nine is a perfected analogy of the broken arguments actually given in that section, destroying Philo's earlier arguments. Finally, I raise the question of the designer's intent in creating such a humourous piece.
Selective class II HDAC inhibitors impair myogenesis by modulating the stability and activity of HDAC–MEF2 complexes
Authors: Nebbioso Angela , Manzo Fabio , Miceli Marco , Conte Mariarosaria , Manente Lucrezia , Baldi Alfonso , De Luca Antonio , Rotili Dante , Valente Sergio , Mai Antonello , Usiello Alessandro , Gronemeyer Hinrich , Altucci Lucia
Published: June 2009

Histone deacetylase (HDAC) inhibitors are promising new epi‐drugs, but the presence of both class I and class II enzymes in HDAC complexes precludes a detailed elucidation of the individual HDAC functions. By using the class II‐specific HDAC inhibitor MC1568, we separated class I‐ and class II‐dependent effects and defined the roles of class II enzymes in muscle differentiation in cultured cells and in vivo. MC1568 arrests myogenesis by (i) decreasing myocyte enhancer factor 2D (MEF2D) expression, (ii) by stabilizing the HDAC4–HDAC3–MEF2D complex, and (iii) paradoxically, by inhibiting differentiation‐induced MEF2D acetylation. In vivo MC1568 shows an apparent tissue‐selective HDAC inhibition. In skeletal muscle and heart, MC1568 inhibits the activity of HDAC4 and HDAC5 without affecting HDAC3 activity, thereby leaving MEF2–HDAC complexes in a repressed state. Our results suggest that HDAC class II‐selective inhibitors might have a therapeutic potential for the treatment of muscle and heart diseases.
Structure and functional relevance of the Slit2 homodimerization domain
Authors: Seiradake Elena , von Philipsborn Anne C , Henry Maud , Fritz Martin , Lortat‐Jacob Hugues , Jamin Marc , Hemrika Wieger , Bastmeyer Martin , Cusack Stephen , McCarthy Andrew A
Published: June 2009

Slit proteins are secreted ligands that interact with the Roundabout (Robo) receptors to provide important guidance cues in neuronal and vascular development. Slit–Robo signalling is mediated by an interaction between the second Slit domain and the first Robo domain, as well as being dependent on heparan sulphate. In an effort to understand the role of the other Slit domains in signalling, we determined the crystal structure of the fourth Slit2 domain (D4) and examined the effects of various Slit2 constructs on chick retinal ganglion cell axons. Slit2 D4 forms a homodimer using the conserved residues on its concave face, and can also bind to heparan sulphate. We observed that Slit2 D4 frequently results in growth cones with collapsed lamellipodia and that this effect can be inhibited by exogenously added heparan sulphate. Our results show that Slit2 D4–heparan sulphate binding contributes to a Slit–Robo signalling mechanism more intricate than previously thought.
Engineering and characterization of a bispecific HER2 × EGFR‐binding affibody molecule
Authors: Friedman Mikaela , Lindström Sara , Ekerljung Lina , Andersson‐Svahn Helene , Carlsson Jörgen , Brismar Hjalmar , Gedda Lars , Frejd Fredrik Y. , Ståhl Stefan
Published: June 2009

HER2 (human epidermal‐growth‐factor receptor‐2; ErbB2) and EGFR (epidermal‐growth‐factor receptor) are overexpressed in various forms of cancer, and the co‐expression of both HER2 and EGFR has been reported in a number of studies. The simultaneous targeting of HER2 and EGFR has been discussed as a strategy with which to potentially increase efficiency and selectivity in molecular imaging and therapy of certain cancers. In an effort to generate a molecule capable of bispecifically targeting HER2 and EGFR, a gene fragment encoding a bivalent HER2‐binding affibody molecule was genetically fused in‐frame with a bivalent EGFR‐binding affibody molecule via a (G4S)3 [(Gly4‐Ser)3]‐encoding gene fragment. The encoded 30 kDa affibody construct (ZHER2)2–(G4S)3–(ZEGFR)2, with potential for bs (bispecific) binding to HER2 and EGFR, was expressed in Escherichia coli and characterized in terms of its binding capabilities. The retained ability to bind HER2 and EGFR separately was demonstrated using both biosensor technology and flow‐cytometric analysis, the latter using HER2‐ and EGFR‐overexpressing cells. Furthermore, simultaneous binding to HER2 and EGFR was demonstrated in: (i) a sandwich format employing real‐time biospecific interaction analysis where the bs affibody molecule bound immobilized EGFR and soluble HER2; (ii) immunofluorescence microscopy, where the bs affibody molecule bound EGFR‐overexpressing cells and soluble HER2; and (iii) a cell–cell interaction analysis where the bs affibody molecule bound HER2‐overexpressing SKBR‐3 cells and EGFR‐overexpressing A‐431 cells. This is, to our knowledge, the first reported bs affinity protein with potential ability for the simultaneous targeting of HER2 and EGFR. The potential future use of this and similar constructs, capable of bs targeting of receptors to increase the efficacy and selectivity in imaging and therapy, is discussed.
Primary care implications of parents' nutrition beliefs
Authors: Pettigrew Simone
Published: June 2009

The present study investigated nutrition-related beliefs and behaviours among parents of varying socioeconomic profiles to facilitate more effective primary care interventions to improve parents’ child-feeding practices. A questionnaire comprising attitudinal and behavioural items was administered to parents at three Perth primary schools. A response rate of 21% (n = 181) was obtained. Respondents exhibited a good understanding of most of the issues under investigation, indicating that efforts could focus on changing specific behaviours rather than attempting to increase general awareness of the importance of children’s diets to their health and wellbeing. The results suggest that education relating to appetite regulation could be beneficial to all parents, although medium socioeconomic status families appear to be most in need of this information as well as knowledge relating to repeatedly offering new foods to children to foster preference. Information about the need for healthy school canteens and the desirability of reducing television viewing during meals may be more productively targeted to low and medium socioeconomic status families.
Prospective Incidence Study of Bloodstream Infection in Infants and Children With Central Venous Catheters After Cardiac Surgery in Italy
Authors: Bezzio Stefania , Scolfaro C. , Broglia R. , Calabrese R. , Mignone F. , Abruzzese P. A. , Aidala E. , Valori A. , Grassitelli S. , Rizzo A. , Iannandrea S. , Tovo P. A.
Published: June 2009

This prospective observational study was designed to assess the incidence of, risk factors for, and outcome of catheter-related bloodstream infection in children undergoing cardiac surgery. A staff specifically trained to handle the central venous catheters with proper aseptic techniques and an appropriate patient to medical staff ratio remain the most effective measures to prevent this infection.
Deuterium inventory in Tore Supra: reconciling particle balance and post-mortem analysis
Authors: Tsitrone E. , Brosset C. , Pégourié B. , Gauthier E. , Bouvet J. , Bucalossi J. , Carpentier S. , Corre Y. , Delchambre E. , Desgranges L. , Dittmar T. , Douai D. , Ekedahl A. , Escarguel A. , Ghendrih Ph. , Grisolia C. , Grosman A. , Gunn J. , Hong S.H. , Jacob W. , Kazarian F. , Kocan M. , Khodja H. , Linez F. , Loarer T. , Marandet Y. , Martinez A. , Mayer M. , Meyer O. , Monier Garbet P. , Moreau P. , Pascal J.Y. , Pasquet B. , Rimini F. , Roche H. , Roure I. , Rosanvallon S. , Roubin P. , Roth J. , Saint-Laurent F. , Samaille F. , Vartanian S.
Published: June 2009

Fuel retention, a crucial issue for next step devices, is assessed in present-day tokamaks using two methods: particle balance performed during shots and post-mortem analysis carried out during shutdowns between experimental campaigns. Post-mortem analysis generally gives lower estimates of fuel retention than integrated particle balance. In order to understand the discrepancy between these two methods, a dedicated experimental campaign has been performed in Tore Supra to load the vessel walls with deuterium (D) and monitor the trapped D inventory through particle balance. The campaign was followed by an extensive post-mortem analysis phase of the Tore Supra limiter. This paper presents the status of the analysis phase, including the assessment of the D content in the castellated tile structure of the limiter. Indeed, using combined surface analysis techniques, it was possible to derive the relative contributions of different zones of interest on the limiter (erosion, thick deposits, thin deposits), showing that the post-mortem inventory is mainly due to codeposition (90% of the total), in particular due to gap deposits. However, deuterium was also evidenced deep into the material in erosion zones (10% of the total). At the present stage of the analysis, 50% of the inventory deduced from particle balance has been found through post-mortem analysis, a significant progress with respect to previous studies (factor 8–10 discrepancy). This shows that post-mortem analysis can be consistent with particle balance provided specific procedures are implemented (dedicated campaign followed by extensive post-mortem analysis). Both techniques are needed for a reliable assessment of fuel retention in tokamaks, giving complementary information on how much and where fuel is retained in the vessel walls.
Progress in research and development of mirrors for ITER diagnostics
Authors: Litnovsky A. , Voitsenya V. , Sugie T. , De Temmerman G. , Costley A.E. , Donné A.J.H. , Vukolov K.Yu. , Orlovskiy I. , Brooks J.N. , Allain J.P. , Kotov V. , Semerok A. , Thro P.-Y. , Akiyama T. , Yoshida N. , Tokunaga T. , Kawahata K.
Published: June 2009

Metallic mirrors will be used as plasma-viewing elements in all optical and laser diagnostic systems in ITER. In the harsh environment of ITER, the performance of mirrors will decrease mainly because of the erosion of their surfaces and deposition of impurities. The deterioration of the optical properties of diagnostic mirrors will directly affect the entire performance of the respective ITER diagnostics, possibly leading to their shutdown. Therefore, R&D on mirrors is of crucial importance for ITER diagnostics. There is a coordinated worldwide R&D programme supervised by the Specialists Working Group on first mirrors of the International Tokamak Physics Activity, Topical Group on Diagnostics. This paper provides an overview of new results in the field of first mirrors, covering the manufacturing of ITER mirror prototypes, investigations of mitigation of deposition and mirror cleaning and the predictive modelling of the mirror performance in ITER. The current status of research on beryllium deposition—a new critical area of mirror research—is given along with an outlook for future activities.
Spectral effects on fast wave core heating and current drive
Authors: Phillips C.K. , Bell R.E. , Berry L.A. , Bonoli P.T. , Harvey R.W. , Hosea J.C. , Jaeger E.F. , LeBlanc B.P. , Ryan P.M. , Taylor G. , Valeo E.J. , Wilgen J.B. , Wilson J.R. , Wright J.C. , Yuh H.
Published: June 2009

Recent results obtained with high harmonic fast wave (HHFW) heating and current drive (CD) on NSTX strongly support the hypothesis that the onset of perpendicular fast wave propagation right at or very near the launcher is a primary cause for a reduction in core heating efficiency at long wavelengths that is also observed in ICRF heating experiments in numerous tokamaks. A dramatic increase in core heating efficiency was first achieved in NSTX L-mode helium majority plasmas when the onset for perpendicular wave propagation was moved away from the antenna and nearby vessel structures. Efficient core heating in deuterium majority L-mode and H-mode discharges, in which the edge density is typically higher than in comparable helium majority plasmas, was then accomplished by reducing the edge density in front of the launcher with lithium conditioning and avoiding operational points prone to instabilities. These results indicate that careful tailoring of the edge density profiles in ITER should be considered to limit radio frequency (rf) power losses to the antenna and plasma facing materials. Finally, in plasmas with reduced rf power losses in the edge regions, the first direct measurements of HHFW CD were obtained with the motional Stark effect (MSE) diagnostic. The location and radial dependence of HHFW CD measured by MSE are in reasonable agreement with predictions from both full wave and ray tracing simulations.
Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity
Authors: Zhu Shanfeng , Zeng Jia , Mamitsuka Hiroshi
Published: June 2009

Motivation: Clustering MEDLINE documents is usually conducted by the vector space model, which computes the content similarity between two documents by basically using the inner-product of their word vectors. Recently, the semantic information of MeSH (Medical Subject Headings) thesaurus is being applied to clustering MEDLINE documents by mapping documents into MeSH concept vectors to be clustered. However, current approaches of using MeSH thesaurus have two serious limitations: first, important semantic information may be lost when generating MeSH concept vectors, and second, the content information of the original text has been discarded.

Methods: Our new strategy includes three key points. First, we develop a sound method for measuring the semantic similarity between two documents over the MeSH thesaurus. Second, we combine both the semantic and content similarities to generate the integrated similarity matrix between documents. Third, we apply a spectral approach to clustering documents over the integrated similarity matrix.

Results: Using various 100 datasets of MEDLINE records, we conduct extensive experiments with changing alternative measures and parameters. Experimental results show that integrating the semantic and content similarities outperforms the case of using only one of the two similarities, being statistically significant. We further find the best parameter setting that is consistent over all experimental conditions conducted. We finally show a typical example of resultant clusters, confirming the effectiveness of our strategy in improving MEDLINE document clustering.

Contact:  zhushanfeng@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Our changing oceans: conclusions of the first International Symposium on the Effects of climate change on the world's oceans
Authors: Valdés Luis , Peterson William , Church John , Brander Keith , Marcos Marta
Published: June 2009

Valdés, L., Peterson, W., Church, K., and Marcos, M. 2009. Our changing oceans: conclusions of the first International Symposium on the Effects of climate change on the world's oceans. – ICES Journal of Marine Science, 66: 1435–1438.
Construction of a derivative of Tn917 containing an outward-directed promoter and its use in Bacillus subtilis
Authors: Zagorec Monique , Steinmetz Michel
Published: June 2009

Summary: Engineered variants of the transposon Tn917 have been widely used to obtain insertion mutations and transcriptional fusions in Bacillus subtilis and other Gram-positive bacteria. We have developed a novel Tn917-based methodology useful for isolation and characterization of mutants resulting from gene over-expression. A Tn917 variant was constructed which contains a strong out-facing promoter near one end, able to promote transcription of genes in the vicinity of its insertion target. This transposon, designated Tn917PF1, was tested in model conditions. Three Tn917PF1 mutants of B. subtilis, with phenotypes presumed to result from gene over-expression, were analysed. Their phenotypes were shown to be due to transcription from the transposon promoter. In one mutant the promoter activated a deg gene, probably degQ. The other two contained different insertions decryptifying a B. subtilis gene encoding β-galactosidase.
Variation of colony morphology and chromosomal rearrangement in Candida tropicalis pK233
Authors: Suzuki Takahito , Miyamae Yuki , Ishida Ikuko
Published: June 2009

Summary: UV irradiation treatment of the asexual yeastCandida tropicalisgave rise to morphological mutants exhibiting at least four different types of abnormal colonies on glucose-containing solid medium. These mutants were named according to their colony morphologies: ‘doughnut’, ‘frilly’, ‘echinoid’ and ‘walnut’ mutants. The doughnut mutant produced a wrinkled colony with a hollow in its central region that was rich in filamentous pseudohyphal cells. With increased incubation time, the colony gradually changed to a reticulate shape. The parent strain, which normally produced smooth colonies, gave similar colonies to those of the doughnut mutant when grown in medium containing oleic acid as carbon source. Both the frilly and the walnut mutants produced pseudohyphal cells in a similar fashion to the doughnut mutant. The echinoid mutant produced an echinulate colony morphology with aerial hyphae and contained true hyphal cells as well as pseudohyphal ones. Pulsed-field gel electrophoresis showed that the echinoid and frilly mutants had different karyotypes from that of their parent strain, suggesting the occurrence of chromosomal rearrangements associated with these morphological mutations.
Morphology of three polycentric rumen fungi and description of a procedure for the induction of zoosporogenesis and release of zoospores in cultures
Authors: Ho Y. W. , Bauchop T.
Published: June 2009

Summary: Three polycentric rumen fungi, LL, LC2 and Ruminomyces elegans (C2), isolated from the rumen of cattle were grown in six culture media. LL and LC2 were morphologically similar. Their characteristics resembled those of Orpinomyces and Neocallimastix joyonii, and they grew well and produced sporangia after 3–4 d growth in all the media. R. elegans differed morphologically from LL and LC2, but although it also grew well in all media, abundant sporangia occurred only after 2–3 d growth in media containing cellulose. Undifferentiated sporangia were produced by all three isolates; differentiation of the sporangia did not occur in the spent growth media. However, if thalli possessing recently-formed sporangia were transferred to, or flooded with, fresh liquid medium or rumen fluid, zoosporogenesis and liberation of zoospores occurred within 17–20 min for isolates LL and LC2 and 30 min for R. elegans. Procedures for inducing zoosporogenesis by polycentric anaerobic fungi are described.
Purification and properties of an acid endo-1,4-β-glucanase from Bacillus sp. KSM-330
Authors: Ozaki Katsuya , Ito Susumu
Published: June 2009

Summary: A novel acid cellulase (endo-1,4-β-glucanase, EC 3.2.1.4) was found in a culture of Bacillus sp. KSM-330 isolated from soil. One-step chromatography on a column of CM-Bio-Gel A yielded a homogeneous enzyme, as determined by silver staining of both sodium dodecyl sulphate (SDS) and nondenaturing gels. The enzyme had a molecular mass of 42 kDa, as determined by SDS-polyacrylamide gel electrophoresis. The isoelectric point was higher than pH 10. The N-terminal amino acid sequence of the enzyme was Val-Ala-Lys-Glu-Met-Lys-Pro-Phe-Pro-GIn-GIn-Val-Asn-Tyr-Ser-Gly-Ile-Leu-Lys-Pro. This enzyme had an optimum pH for activity of 5·2, being active over an extremely narrow range of pH values, from 4·2 to 6·9; below and above these pH values no activity was detectable. The optimum temperature at pH 5·2 was around 45 °. The enzyme efficiently hydrolysed carboxymethylcellulose (CMC) and lichenan, but more crystalline forms of cellulose, curdlan, laminarin, 4-nitrophenyl-β-D-glucopyranoside and 4-nitrophenyl-β-d-cellobioside were barely hydrolysed. The enzymic activity was inhibited by Hg2+ but was not affected by other inhibitors of thiol enzymes, such as 4-chloromercuribenzoate, N-ethylmaleimide and monoiodoacetate. N-Bromosuccinimide abolished the enzymic activity, and CMC protected the enzyme from inactivation by this tryptophan-specific oxidant. It is suggested that a tryptophan residue(s) is involved in the mechanism of action of the Bacillus cellulase and that the inhibition of enzymic activity by Hg2+ is ascribable to interactions with the tryptophan residue(s) rather than with thiol group(s).
Differentiation of Coxiella burnetii isolates by analysis of restriction-endonuclease-digested DNA separated by SDS-PAGE
Authors: Hendrix Laura R. , Samuel James E. , Mallavia Louis P.
Published: June 2009

Thirty-two isolates of Coxiella burnetii collected from various hosts ranging from arthropods to man were compared by restriction endonuclease (RE) digestion patterns of chromosomal DNA using SDS-PAGE. SDS-PAGE provided better DNA fragment separation than agarose gel electrophoresis and enabled the differentiation of these isolates into six distinct groups on the basis of DNA restriction fingerprints. Two groups of chronic disease isolates could be distinguished, each having unique RE digestion patterns of chromosomal DNA. Three similar but distinct RE digestion patterns were seen among the group of acute disease isolates. Three additional isolates included in this study exhibited a unique RE digestion pattern and also had a unique plasmid type, designated QpDG. DNA-DNA hybridization on selected isolates quantified the relatedness between several groups and supported the classification of these groups as distinct strains.
Structural and stereospecific requirements for the nucleoside-triggered germination of Bacillus cereus spores
Authors: Senesi Sonia , Cercignani Giovanni , Freer Giulia , Batoni Giovanna , Barnini Simona , Ota Fusao
Published: June 2009

A selection of adenosine analogues was tested for their ability to trigger germination of Bacillus cereus NCIB 8122 spores. The germination-inducing activity was governed by the structural properties of the sugar rather than the base moieties of the nucleosides. Among the sugar-modified analogues, only those containing a 2′-deoxy-D-ribose moiety promoted spore germination. Requirements for a specific molecular structure of the base were not clearly identified, although the highest activity was observed when substituents were inserted at position 6 of the purine ring. All the base-modified analogues, even those such as coformycin and 2′-deoxycoformycin with an expanded base ring, retained the germination-inducing activity of adenosine. However, of the two 2′-deoxycoformycin diastereoisomers characterized by an asymmetric carbon atom at position 8 of the homopurine ring, only the 8 S-isomer induced germination, thus indicating that stereospecific configuration of the inducer, at least in the case of 2′-deoxycoformycin, appears to be essential for the initiation of spore germination. The differences in the germination-inducing activity of the various analogues tested were not affected significantly by spore activation at different temperatures, although the higher the activation temperature, the lower was the concentration of each analogue required for maximum germination.
Caesium accumulation and interactions with other monovalent cations in the cyanobacterium Synechocystis PCC 6803
Authors: Avery Simon V. , Codd Geoffrey A. , Gadd Geoffrey M.
Published: June 2009

Growth ofSynechocystisPCC 6803 in BG-11 medium supplemented with 1 mM-CsCl resulted in intracellular accumulation of Cs+to a final level of approximately 510 nmol (109cells)-1after incubation for 10 d. The doubling time was increased by 64% and the final cell yield was decreased by 70% during growth in the presence of Cs+as compared to growth in control BG-11 medium. When the total monovalent cation concentration of the medium was doubled by adding either K+or Na+, levels of accumulated Cs+were decreased by approximately 50% to 220 and 270 nmol (109cells)-1, respectively, after 28 d with little inhibition of growth being apparent. Short-term experiments revealed that extracellular K+and Na+inhibited Cs+accumulation to a similar extent, with 90% inhibition of Cs+accumulation occurring at the highest concentrations used (50 mM-K+or Na+; 1 mM-Cs+). In all experiments, Cs+accumulation resulted in a reduction in intracellular K+, except when cells were grown in K+-depleted medium, although a stoichiometric relationship was not apparent, the amount of Cs+accumulated generally being greater than the amount of K+released. Cs+accumulation had no discernible effect on intracellular Na+. When K+, Na+, Rb+, Li+or Tl+were supplied at equimolar (1 mM) concentrations to Cs+, only Tl+significantly reduced Cs+accumulation. However, an approximately 50% inhibition of Cs+accumulation resulted when concentrations of K+, Na+, Rb+or Li+were increased to 10 mM, which suggests that Cs+may have a higher affinity for the monovalent cation transport system than K+, Rb+and TI+also caused a decrease in intracellular K+, whereas Na+and Li+stimulated K+uptake. Cs+accumulation was dependent on the external Cs+concentration and showed a linear relationship to external Cs+concentrations≤2 mM over 12 h incubation. However, prolonged incubation in external Cs+concentrations≥ 0·8 mM resulted in Cs+release from the cells and after 48 h, similar amounts of Cs+and K+were present in cells incubated at these higher concentrations. Cs+accumulation was energy- and pH-dependent. Incubation in the light at 4 °C, or in the presence of 3(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), or at 22 °C in the dark resulted in decreased Cs+accumulation and decreased K+release from the cells. Increased amounts of Cs+were accumulated as the pH of the external medium was increased, with maximal accumulation [approximately 1330 nmol Cs+(109cells)-1after 24 h incubation] occurring at pH 10, the highest pH value used. It is suggested that an important mechanism of Cs+toxicity inSynechocystisPCC 6803 arises through replacement of cellular K+by Cs+. The possible role of primary producers such as cyanobacteria in the mobilization of this radionuclide in aquatic habitats is discussed.
Two multifunctional peptide synthetases and an O-methyltransferase are involved in the biosynthesis of the DNA-binding antibiotic and antitumour agent saframycin Mx1 from Myxococcus xanthus
Authors: Pospiech Andreas , Bietenhader Jürg , Schupp Thomas
Published: June 2009

Saframycin Mx1 is a DNA-binding antibiotic and antitumour agent produced by Myxococcus xanthus. It is a heterocyclic quinone, thought to be synthesized via the linear pepide intermediate AlaGlyTyrTyr. Analysis of 14.1 kb DNA sequence involved in saframycin production revealed genes for two large multifunctional peptide synthetases of 1770 and 2605 amino acids, respectively, and a putative O-methyltransferase of 220 amino acids. The three ORFs read in the same direction and are separated by short non-translated gaps of 44 and 49 bp. The peptide synthetases contain two amino-acid-activating domains each. The first domain lacks two of the most conserved ‘core’ sequences, and the last domain is followed by a putative reductase functionality, not previously seen in peptide synthetases. Complementation tests showed that antibiotic-nonproducing mutant strains lacking one of the peptide synthetases secrete a substrate, presumably a modified amino acid precursor, that can be used by O-methyltransferase-deficient mutant strains to synthesize saframycin Mx1.