bluuebunny/crossref_metadata_2025 huggingface dataset:
Graph minor theory
Authors: Lovász László
Published: January 2006

A monumental project in graph theory was recently completed. The project, started by Robertson and Seymour, and later joined by Thomas, led to entirely new concepts and a new way of looking at graph theory. The motivating problem was Kuratowski’s characterization of planar graphs, and a far-reaching generalization of this, conjectured by Wagner: If a class of graphs is minor-closed (i.e., it is closed under deleting and contracting edges), then it can be characterized by a finite number of excluded minors. The proof of this conjecture is based on a very general theorem about the structure of large graphs: If a minor-closed class of graphs does not contain all graphs, then every graph in it is glued together in a tree-like fashion from graphs that can almost be embedded in a fixed surface. We describe the precise formulation of the main results and survey some of its applications to algorithmic and structural problems in graph theory.
The scientific library of the earls of Macclesfield
Authors: Quarrie Paul
Published: January 2006

The dispersal at auction of the renowned scientific library of the earls of Macclesfield from Shirburn Castle has been held at Sotheby's, London, in the period March 2004 to November 2005 in six sales following upon the sale to the Cambridge University Library of the Macclesfield scientific papers. This paper discusses aspects of the history of the library, its genesis and composition, the personal history of those who created it, and certain individual volumes.
A steady vortex ring in Poiseuille flow and rearrangements of a function
Authors: Rebah Dirar
Published: January 2006

This study proves the existence of a steady vortex ring of an ideal fluid in Poiseuille flow. The method that was used is a variational method proposed by Benjamin (Benjamin 1976
The alliance of practical and analytical insight into the nonlinear problems of fluid mechanics
, vol. 503, pp. 8–29), in which a steady vortex ring can be obtained as a maximizer of a functional that is related to kinetic energy and the impulse over the set of rearrangements of a prescribed function.
Paedocypris
, a new genus of Southeast Asian cyprinid fish with a remarkable sexual dimorphism, comprises the world's smallest vertebrate
Authors: Kottelat Maurice , Britz Ralf , Hui Tan Heok , Witte Kai-Erik
Published: January 2006

Paedocypris
is a new genus of paedomorphic cyprinid fish from highly acidic blackwater peat swamps in Southeast Asia. It includes two new species, one of which (
Paedocypris progenetica
) appears to be the smallest fish and vertebrate known, with the smallest mature female measuring a mere 7.9 mm.
Paedocypris
has many ’larval’ features typically associated with paedomorphic fish (e.g. narrow frontals that leave the brain unprotected dorsally by bone and a precaudal larval-fin-fold), but, uniquely among fishes, males also possess highly modified pelvic fins with hypertrophied muscles and a keratinized pad in front of the pelvic girdle, which, we hypothesize, function together as a clasping or holding device, thereby suggesting an unusual reproductive mode. Unfortunately, habitat destruction jeopardizes the survival of these fishes and thus opportunities for further research.
Bumble-bee foragers infected by a gut parasite have an impaired ability to utilize floral information
Authors: Gegear Robert J , Otterstatter Michael C , Thomson James D
Published: January 2006

Parasitic infection can influence a variety of behavioural mechanisms in animals, but little is known about the effects of infection on the cognitive processes underlying ecologically relevant behaviours. Here, we examined whether parasitic infection alters cognitive aspects of foraging in a social insect, the bumble-bee (
Bombus impatiens
). In controlled experiments, we assessed the ability of foraging bees to discriminate rewarding from non-rewarding flowers on the basis of colour and odour. We found that natural and experimental infection by a protozoan parasite (
Crithidia bombi
, which lives exclusively within the gut tract), impaired the ability of foragers to learn the colour of rewarding flowers. Parasitic infection can thus disrupt central nervous system pathways that mediate cognitive processes in bumble-bees and as a consequence, can reduce their ability to monitor floral resources and make economic foraging decisions. It is postulated that this infection-induced change to cognitive function in bumble-bees is the result of communication between immune and nervous systems. Parasitized animals, including invertebrates, can therefore show subtle behavioural changes that are nonetheless ecologically significant and reflect complex mechanisms.
Extreme convergence in the body plans of an early suchian (Archosauria) and ornithomimid dinosaurs (Theropoda)
Authors: Nesbitt Sterling J , Norell Mark A
Published: January 2006

Living archosaurs comprise birds (dinosaurs) and crocodylians (suchians). The morphological diversity of birds and stem group dinosaurs is tremendous and well-documented. Suchia, the archosaurian group including crocodylians, is generally considered more conservative. Here, we report a new Late Triassic suchian archosaur with unusual, highly specialized features that are convergent with ornithomimid dinosaurs. Several derived features of the skull and postcranial skeleton are identical to conditions in ornithomimids. Such cases of extreme convergence in multiple regions of the skeleton in two distantly related vertebrate taxa are rare. This suggests that these archosaurs show iterative patterns of morphological evolution. It also suggests that this group of suchians occupied the adaptive zone that was occupied by ornithomimosaurs later in the Mesozoic.
Soil moisture mediates association between the winter North Atlantic Oscillation and summer growth in the Park Grass Experiment
Authors: Kettlewell P.S , Easey J , Stephenson D.B , Poulton P.R
Published: January 2006

Several aspects of terrestrial ecosystems are known to be associated with the North Atlantic Oscillation (NAO) through effects of the NAO on winter climate, but recently the winter NAO has also been shown to be correlated with the following summer climate, including drought. Since drought is a major factor determining grassland primary productivity, the hypothesis was tested that the winter NAO is associated with summer herbage growth through soil moisture availability, using data from the Park Grass Experiment at Rothamsted, UK between 1960 and 1999. The herbage growth rate, mean daily rainfall, mean daily potential evapotranspiration (PE) and the mean and maximum potential soil moisture deficit (PSMD) were calculated between the two annual cuts in early summer and autumn for the unlimed, unfertilized plots. Mean and maximum PSMD were more highly correlated than rainfall or PE with herbage growth rate. Regression analysis showed that the natural logarithm of the herbage growth rate approximately halved for a 250 mm increase in maximum PSMD over the range 50–485 mm. The maximum PSMD was moderately correlated with the preceding winter NAO, with a positive winter NAO index associated with greater maximum PSMD. A positive winter NAO index was also associated with low herbage growth rate, accounting for 22% of the interannual variation in the growth rate. It was concluded that the association between the winter NAO and summer herbage growth rate is mediated by the PSMD in summer.
Termite-egg mimicry by a sclerotium-forming fungus
Authors: Matsuura Kenji
Published: January 2006

Mimicry has evolved in a wide range of organisms and encompasses diverse tactics for defence, foraging, pollination and social parasitism. Here, I report an extraordinary case of egg mimicry by a fungus, whereby the fungus gains competitor-free habitat in termite nests. Brown fungal balls, called ‘termite balls’, are frequently found in egg piles of
Reticulitermes
termites. Phylogenetic analysis illustrated that termite-ball fungi isolated from different hosts (
Reticulitermes speratus
,
Reticulitermes flavipes
and
Reticulitermes virginicus
) were all very similar, with no significant molecular differences among host species or geographical locations. I found no significant effect of termite balls on egg survivorship. The termite-ball fungus rarely kills termite eggs in natural colonies. Even a termite species (
Reticulitermes okinawanus
) with no natural association with the fungus tended termite balls along with its eggs when it was experimentally provided with termite balls. Dummy-egg bioassays using glass beads showed that both morphological and chemical camouflage were necessary to induce tending by termites. Termites almost exclusively tended termite balls with diameters that exactly matched their egg size. Moreover, scanning electron microscopic observations revealed sophisticated mimicry of the smooth surface texture of eggs. These results provide clear evidence that this interaction is beneficial only for the fungus, i.e. termite balls parasitically mimic termite eggs.
Chryseobacterium soldanellicola sp. nov. and Chryseobacterium taeanense sp. nov., isolated from roots of sand-dune plants
Authors: Park Myung Soo , Jung Se Ra , Lee Kang Hyun , Lee Myung-Sook , Do Jin Ok , Kim Seung Bum , Bae Kyung Sook
Published: January 2006

Two Gram-negative, yellow-pigmented bacteria designated PSD1-4T and PHA3-4T, isolated from two sand-dune plant species inhabiting coastal areas in Tae-an, Korea, were subjected to taxonomic investigation. 16S rRNA gene sequence analysis indicated that both isolates should be placed in the genus Chryseobacterium of the family Flavobacteriaceae. The phenotypic properties of the strains were also consistent with their classification into this genus. The levels of 16S rRNA gene sequence similarity between strain PSD1-4T and other Chryseobacterium species were 95·2–97·2 %; those between PHA3-4T and others were 93·7–97·8 %. The DNA–DNA relatedness data indicated that strains PSD1-4T and PHA3-4T were clearly different from the nearest species, Chryseobacterium indoltheticum and Chryseobacterium taichungense. The major fatty acids were 13-methyltetradecanoic acid (iso-C15 : 0), 3-hydroxy-15-methylhexadecanoic acid (iso-C17 : 0 3-OH) and omega-9-cis-15-methylhexadecenoic acid (iso-C17 : 1ω9c) for both strains. On the basis of polyphasic taxonomic analysis results, it is evident that each of these strains represents a novel species of Chryseobacterium, for which the names Chryseobacterium soldanellicola sp. nov. (type strain PSD1-4T=KCTC 12382T=NBRC 100864T) and Chryseobacterium taeanense sp. nov. (type strain PHA3-4T=KCTC 12381T=NBRC 100863T) are proposed.
Microbacterium koreense sp. nov., from sea water in the South Sea of Korea
Authors: Lee Jung-Sook , Lee Keun Chul , Park Yong-Ha
Published: January 2006

Microbacterium strains JS53-2T and JS53-5 were isolated from sea water in the South Sea of Korea and subjected to phenotypic, chemotaxonomic and genetic characterization. The cells were found to be Gram-positive. These strains contained MK-11 and MK-12 as the main respiratory quinones and anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as the major cellular fatty acids. The DNA G+C content was 68 mol%. The cell-wall sugars of the isolates were galactose and xylose, and the diamino acid in the cell-wall hydrolysates was lysine. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represented an evolutionary lineage distinct from those of other Microbacterium species. DNA–DNA reassociation values between the isolates and reference strains Microbacterium terregens KCTC 19034T, Microbacterium lacticum KCTC 9230T, Microbacterium aurum KCTC 19091T and Microbacterium schleiferi KCTC 19095T were below 23 %. On the basis of evaluation of the morphological, physiological and chemotaxonomic characteristics, 16S rRNA gene sequence comparisons and DNA–DNA hybridizations, a novel species, Microbacterium koreense sp. nov., is proposed for these isolates. The type strain is JS53-2T (=KCTC 19074T=CIP 108696T=CCUG 50754T).
Three novel species of the genus Catellatospora, Catellatospora chokoriensis sp. nov., Catellatospora coxensis sp. nov. and Catellatospora bangladeshensis sp. nov., and transfer of Catellatospora citrea subsp. methionotrophica Asano and Kawamoto 1988 to Catellatospora methionotrophica sp. nov., comb. nov.
Authors: Ara Ismet , Kudo Takuji
Published: January 2006

Three Gram-positive, aerobic, non-motile, mesophilic strains, designated 2-25(1)T, 2-29(17)T and 2-70(23)T, were isolated from sandy soil from Chokoria, Cox's Bazar, Bangladesh. The organisms produce short chains of non-motile spores that emerge singly or in tufts from vegetative hyphae on the surface of agar media. A comparative phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates formed a distinct clade within the evolutionary radiation of the family Micromonosporaceae and clustered with members of the genus Catellatospora. The nearest neighbours were Catellatospora citrea subsp. citrea and C. citrea subsp. methionotrophica. Chemotaxonomic data, such as the presence of meso- and 3-hydroxy-diaminopimelic acids, N-glycolyl type muramic acid, arabinose and xylose and glucose in whole-cell hydrolysates, phosphatidylethanolamine as a diagnostic phospholipid, a tetrahydrogenated menaquinone with 9 isoprene units as a major menaquinone and fatty acid profiles predominated by iso-branched hexadecanoic acid and iso-branched pentadecanoic acid, supported the affiliation of the novel isolates to the genus Catellatospora. The results of DNA–DNA hybridization and physiological and biochemical tests allowed the novel isolates to be differentiated genotypically and phenotypically from the three recognized Catellatospora species. The three isolates therefore represent novel species for which the names Catellatospora chokoriensis sp. nov. [type strain 2-25(1)T=JCM 12950T=DSM 44900T], Catellatospora coxensis sp. nov. [type strain 2-29(17)T=JCM 12951T=DSM 44901T] and Catellatospora bangladeshensis sp. nov. [type strain 2-70(23)T=JCM 12949T=DSM 44899T], are proposed. DNA–DNA hybridization tests with C. citrea subsp. citrea and C. citrea subsp. methionotrophica, in combination with chemotaxonomic and physiological data, demonstrated that C. citrea subsp. methionotrophica should be elevated to a separate species for which the name Catellatospora methionotrophica sp. nov., comb. nov. is proposed (type strain JCM 7543T=DSM 44098T).
Bacillus macauensis sp. nov., a long-chain bacterium isolated from a drinking water supply
Authors: Zhang Tong , Fan Xiaojun , Hanada Satoshi , Kamagata Yoichi , Fang Herbert H. P.
Published: January 2006

A novel long-chain, Gram-positive, rod-shaped, endospore-forming strain was isolated from the influent of a drinking water treatment plant in Macau, China. This facultatively anaerobic isolate (2·0–5·0 μm in length and 0·8–1·2 μm in diameter) formed long chains over 100 μm in length in both liquid and solid media. It had a growth temperature range of 20–40 °C, with an optimum at about 30 °C, and a growth pH range of 6·0–10·0, with an optimum at pH 8·5. The G+C content of the DNA extracted was 40·8 mol%. The main fatty acid components were anteiso-C15 : 0(67·2 %) and iso-C15 : 0(21·7 %), with small quantities of iso-C14 : 0, C14 : 0, iso-C16 : 0and iso-C17 : 0. The main quinone component was MK-7. Phylogenetic analyses based on its 16S rRNA gene sequence revealed that this isolate is a member of the genusBacillus, with no close relatives at the species level (sequence similarity <96·1 %). These phenotypic and genetic properties suggested that this strain represents a novel species, for which the nameBacillus macauensissp. nov. is proposed. The type strain is ZFHKF-1T(=JCM 13285T=DSM 17262T).
Janibacter anophelis sp. nov., isolated from the midgut of Anopheles arabiensis
Authors: Kämpfer Peter , Terenius Olle , Lindh Jenny M. , Faye Ingrid
Published: January 2006

A Gram-positive, aerobic, non-motile strain, H2.16BT, isolated from the midgut of the mosquito Anopheles arabiensis was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity studies, strain H2.16BT was shown to belong to the genus Janibacter, being most closely related to Janibacter melonis (98·3 %), Janibacter terrae (98·5 %) and Janibacter limosus (98·5 %). Chemotaxonomic data (meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall and major fatty acids of iso-C16 : 0, C17 : 1
ω8c and C17 : 0) supported the allocation of the strain to the genus Janibacter. The results of DNA–DNA hybridization and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain H2.16BT from closely related species. Thus, H2.16BT represents a novel species of the genus Janibacter, for which the name Janibacter anophelis sp. nov. is proposed. The type strain is H2.16BT (=CCUG 49715T=CIP 108728T).
Extremely halophilic denitrifying bacteria from hypersaline inland lakes, Halovibrio denitrificans sp. nov. and Halospina denitrificans gen. nov., sp. nov., and evidence that the genus name Halovibrio Fendrich 1989 with the type species Halovibrio variabilis should be associated with DSM 3050
Authors: Sorokin D. Yu. , Tourova T. P. , Galinski E. A. , Belloch C. , Tindall B. J.
Published: January 2006

Anaerobic enrichments with acetate as electron donor and nitrate as electron acceptor at 4 M NaCl from inland, hypersaline lake sediments from Central Asia resulted in the isolation of several extremely halophilic bacteria that comprised two subgroups, most with vibrio-shaped cells and a single strain with rod-shaped cells. Members of both subgroups were extremely halophilic, with growth occurring in 2–5 M NaCl with an optimum at 2–3 M. 16S rRNA gene sequence analysis showed a close affiliation of the new isolates with Pseudomonas halophila DSM 3050 in the Gammaproteobacteria. However, phenotypic comparison of the denitrifying halophiles with the original description of P. halophila demonstrated that they were more similar to another bacterium isolated from the same source at the same time, the extremely halophilic Halovibrio variabilis, which has since been reclassified as Halomonas variabilis (DSM 3051). Direct cross-comparison showed that the characteristics of these two halophilic bacteria do not correspond with the original descriptions associated with these names and DSM numbers. While it is desirable that this problem be solved, in connection with the present investigations, this is a matter that can only be solved by a Request for an Opinion. On the basis of the phenotypic and genetic comparison of these isolates, it is proposed that the new denitrifying vibrio-shaped isolates represent a novel species, Halovibrio denitrificans sp. nov. (type strain HGD 3T=DSM 15503T=UNIQEM U232T) and that the rod-shaped isolate represents a novel genus and species, Halospina denitrificans gen. nov., sp. nov. (type strain HGD 1-3T=DSM 15505T=UNIQEM U233T).
The influence of temperature on the stage at hatch of laboratory reared Gadus morhua and implications for comparisons of length and morphology
Authors: Jordaan A. , Hayhurst S. E. , Kling L. J.
Published: January 2006

A staging table for yolk‐sac larvae of Atlantic cod Gadus morhua was developed and applied to determine the development stage at hatch. Larvae (n = 20) were sampled during the period from 50% hatch to first‐feeding from four temperature treatments (c. 2, 4, 8 and 12° C). Data recorded included standard length, development stage, yolk‐sac area and evidence of feeding by larvae. The results indicated that the stage of development at hatch was positively correlated to larval size. Furthermore, developmentally based changes in morphology shortly after hatch reduced much of the initial difference in size, although some difference still existed. No relationship between size at hatch and the incidence of first‐feeding larvae was found. Based on these observations, it is recommended that the development stage of hatching larvae be reported in studies investigating size and morphological differences when observing individual larval fish that originate from different populations, batches or species.
Age structure and growth of Semotilus atromaculatus(Mitchill) in PCB‐contaminated streams
Authors: Henshel D. S. , Sparks D. W. , Simon T. P. , Tosick M. J.
Published: January 2006

Creek chub Semotilus atromaculatus from two PCB contaminated streams (Clear Creek and Richland Creek) at three locations and a reference stream (Little Indian Creek), Indiana, U.S.A., were examined to determine if age class structure and growth variables were correlated with in‐situ PCB exposure. Approximately five to 15 fish were captured weekly during the spring spawning season and monthly thereafter for a 12 month period. Fish collected ranged from 25 to 267 mm total length (LT). Throughout the course of this study, no spawning activity was observed at either location in Clear Creek, although some very small young‐of‐the‐year (YOY) creek chub fry were observed at the downstream location by late summer. Creek chub nests were observed in both Richland Creek and Little Indian Creek but YOY were common only in Little Indian Creek. Exposure to PCBs was shown to both enhance and decrease growth in varied laboratory tests; subtle but significant gender‐specific differences in the growth of creek chub populations between the sites were observed. Creek chub up to 24 months in age from Clear Creek and Richland Creek were significantly larger (both LT and mass for males and LT for females) than reference site creek chub. This trend was reversed for creek chub aged ≥24 months as the reference site fish were consistently larger with reference males weighing significantly more. Older age classes of creek chub were missing in areas of higher PCB contamination. Female population growth rates and individual instantaneous growth rates were consistently higher at the reference site in comparison to the PCB‐contaminated sites. Calculation of ‘functional b’(as a condition factor) did indicate that growth enhancement in young males did occur at the most contaminated site and reductions in growth (mass relative to LT) occurred in females from all contaminated sites. Furthermore, long‐term survivorship for females was reduced in the PCB‐contaminated streams. All of these subtle alterations in growth would not have been observed if males and females had not been analysed separately.
Morphological differentiation and resource polymorphism in three sympatric whitefishCoregonus lavaretus(L.) forms in a subarctic lake
Authors: Kahilainen K. , Østbye K.
Published: January 2006

Three field‐identified whitefishCoregonus lavaretusforms in Lake Muddusjärvi, Finland, were compared in morphology, diet and prey size. First, these forms were studied with univariate and multivariate analysis to assess morphological divergence at a higher resolution level than in the field. Second, stomach contents were analysed to estimate diet‐overlap among forms. Finally, the relationship between prey size and morphology was examined. The whitefish were assigned to the initial field‐classification with 99·2% and 98·8% accuracy for morphologic and meristic traits, respectively. The small sparsely‐rakered form (SSR) had the shortest rakers and largest gillraker space, followed by the large sparsely‐rakered form (LSR) with intermediate gillraker length and gillraker space, while densely‐rakered whitefish (DR) had the longest rakers and smallest gillraker space. The two sparsely‐rakered whitefish forms (LSR and SSR), consumed mainly benthic macroinvertebrates, while densely‐rakered whitefish (DR), utilized pelagic food items. Average diet‐overlaps between whitefish forms were low in June‐September (Schoener's α = 0·02 − 0·23). Gillraker number and length were negatively correlated to prey length in the diet (r = −0·73, andr = −0·60), while gillraker space was positively correlated with prey length (r = 0·81). The fact that these whitefish forms were morphologically and ecologically segregated, and that gillraker traits probably have a functional value in food selection, further suggests that natural selection has been important in structuring life‐history trajectories into divergent niche use.
The influence of environmental temperature and oxygen concentration on the recovery of largemouth bass from exercise: implications for live–release angling tournaments
Authors: Suski C. D. , Killen S. S. , Kieffer J. D. , Tufts B. L.
Published: January 2006

The impact of variation in water temperature and dissolved oxygen on recovery of largemouth bass Micropterus salmoides from exercise was examined. For this, largemouth bass were first exercised and recovered for either 1, 2 or 4 h at ambient water temperatures (25° C) in fully oxygenated water. Results showed that exercise forced fish to utilize anaerobic metabolism to meet energy demands, and resulted in reductions in anaerobic energy stores adenosine triphosphate (ATP), Phosphocreatine (PCr) and glycogen. Exercise also resulted in a seven‐fold increase in lactate within white muscle. After 2 h of recovery in oxygenated water at acclimation temperature, physiological recovery from exercise was under way, and by 4 h most variables examined had returned to control levels. Next, largemouth bass were exercised at ambient temperatures and recovered for 2 h in environments with either elevated temperature (32° C), reduced temperature (14 and 20° C), hypoxia or hyperoxia. Both elevated and reduced temperature impaired recovery of tissue lactate and tissue ATP relative to fish recovered in water at acclimation temperature, while hyperoxic water impaired recovery of tissue ATP. Moderately hypoxic waters impaired the recovery of plasma glucose, plasma lactate and tissue PCr relative to fish recovered in fully oxygenated water. Results from this study are discussed in the context of critical oxygen and temperature guidelines for largemouth bass. In addition, several recommendations are made concerning remedial treatments used in livewells (tanks) during angling tournaments when fish are recovering from exercise associated with angling.
Factors structuring reproductive habitat suitability of Engraulis encrasicolus in the south coast of Sicily
Authors: Cuttitta A. , Guisande C. , Riveiro I. , Maneiro I. , Patti B. , Vergara A. R. , Basilone G. , Bonanno A. , Mazzola S.
Published: January 2006

Egg and larval abundance, obtained from annual summer cruises carried out in the Strait of Sicily during 6 years (1997 to 2002), was used to identify the spawning and retention areas of the anchovy Engraulis encrasicolus. Larval amino acid composition was used to analyse the nutritional condition of the larvae collected during the 2002 survey. As the anchovy spawns along the south Sicilian coast, but mainly in the north‐west and middle parts of the coast, the higher number and larger size larvae in the south‐east end of the Sicilian coast indicated that larvae were transported by the main branch of the Atlantic‐Ionian Stream and retained in the south‐east end of the Sicilian coast (Cape Passero). This retention process, however, did not always favour the nutritional condition of the larvae, because the larvae were not transported to an area with a higher primary production or with a higher stability. In 2002 larval amino acid concentration was higher in the spawning areas than in those areas where the larvae were transported to, indicating a lower nutritional condition of the larvae in the nursery areas. The lack of enrichment and concentration processes, and low primary production in this area which limited body growth rate may explain the low locally reproducing anchovy population in the south coast of Sicily.
The influence of broad scale climatic phenomena on long term trends in Atlantic salmon population size: an example from the River Foyle, Ireland
Authors: Boylan P. , Adams C. E.
Published: January 2006

The effect of marine climatic conditions in the North Atlantic on the abundance of returning migrant Atlantic salmon Salmo salar in the River Foyle, Ireland was examined. Catches of Atlantic salmon from commercial netting stations significantly predicted a measure of population size independent of catches over a 48 year period, thus commercial net catches were used as a measure of relative population size over a longer period in this study. The North Atlantic Oscillation index in winter (wNAOI) provides a generalized measure of climate variation for the northern hemisphere and between 1875 and 2001, the wNAOI was a highly significant predictor of the 5 year running mean of catches of migrant Atlantic salmon returning to the River Foyle. When the index was <0·151, the wNAOI correlated significantly and negatively with Atlantic salmon catches, with 70% of the variance in population size explained by variation in conditions in the marine environment between 1875 and 2001. When the wNAOI was >0·151, however, this relationship uncoupled. The probability of catches exceeding the long‐term median was 2·34 times lower in years where the wNAOI was above the 0·151 breakpoint than for years when it was <0·151. The wNAOI exceeded the 0·151 threshold on 8 out of the 10 years prior to 2001. Models of climate change indicated that the NAOI is likely to increase significantly with time. If these models are correct, this study would lead to the conclusion that a decoupling of these broad scale climate effects on Atlantic salmon population size will become the norm. Data presented here suggests two consequences of this. Firstly that the value of the NAOI as a predictive tool for forecasting adult Atlantic salmon population size will be limited and secondly that the median population size will become lower in the future.
Effects of temperature on persistence times of native and invasive gammarid species in the stomachs of Cottus gobio
Authors: Lagrue C. , Bollache L.
Published: January 2006

Gastric lavage was used to investigate the effects of temperature on persistence time of two amphipod species, one native Gammarus pulex and one invasive Gammarus roeseli, in the stomachs of bullhead Cottus gobio. Persistence time was strongly influenced by temperature and prey type, such that G. pulex species degraded faster than G. roeseli.
Turning T‐cell receptor β recombination on and off: more questions than answers
Authors: Jackson Annette M. , Krangel Michael S.
Published: January 2006

Summary:  Successful V(D)J recombination at the T‐cell receptor β (Tcrb) locus is critical for early thymocyte development. The locus is subject to a host of regulatory mechanisms that impart a strict developmental order to Tcrb recombination events and that insure that Tcrb recombination occurs in an allelically excluded fashion. Progress has been made in the understanding of the cis‐acting control of Tcrb locus chromatin structure and the extent to which such accessibility control can account for the developmental regulation of Tcrb recombination. However, recent studies in our laboratory and elsewhere have made it abundantly clear that accessibility control is only part of the story, and multiple additional mechanisms impact both the developmental activation and inactivation of locus recombination events. Here we evaluate our current understanding of developmental regulation at the Tcrb locus. We highlight the many unresolved issues and we discuss how recent concepts emerging from studies of other antigen receptor loci may (or may not) help to resolve these issues.
Negative selection of the T‐cell repertoire: where and when does it occur?
Authors: Von Boehmer Harald , Kisielow Pawel
Published: January 2006

Summary:  Because of the use of somewhat artificial models for the elucidation of negative selection [superantigen, T‐cell receptor (TCR) transgenic mice], there is still considerable uncertainty at what stages of T‐cell development negative selection can occur and whether it becomes manifest as developmental arrest, lineage diversion, or induction of apoptotic cell death. Here, experimental evidence is reviewed that excludes developmental arrest and lineage diversion as the sole mechanisms of negative selection. The data emphasize that both CD4+CD8+ double‐positive cortical as well as semi‐mature, single‐positive, medullary thymocytes are targets of deletion in experimental models employing superantigen and TCR transgenic mice with premature as well as ‘timely’ onset of TCR expression.
Recent insights into the signals that control αβ/γδ‐lineage fate
Authors: Lauritsen Jens Peter H. , Haks Mariëlle C. , Lefebvre Juliette M. , Kappes Dietmar J. , Wiest David L.
Published: January 2006

Summary:  During thymopoiesis, two major types of mature T cells are generated that can be distinguished by the clonotypic subunits contained within their T‐cell receptor (TCR) complexes: αβ T cells and γδ T cells. Although there is no consensus as to the exact developmental stage where αβ and γδ T‐cell lineages diverge, γδ T cells and precursors to the αβ T‐cell lineage (bearing the pre‐TCR) are thought to be derived from a common CD4−CD8− double‐negative precursor. The role of the TCR in αβ/γδ lineage commitment has been controversial, in particular whether different TCR isotypes intrinsically favor adoption of the corresponding lineage. Recent evidence supports a signal strength model of lineage commitment, whereby stronger signals promote γδ development and weaker signals promote adoption of the αβ fate, irrespective of the TCR isotype from which the signals originate. Moreover, differences in the amplitude of activation of the extracellular signal‐regulated kinase‐ mitogen‐activated protein kinase‐early growth response pathway appear to play a critical role. These findings will be placed in context of previous analyses in an effort to more precisely define the signals that control T‐lineage fate during thymocyte development.
T‐cell development, doing it in a dish
Authors: Schmitt Thomas M , Zúñiga‐Pflücker Juan Carlos
Published: January 2006

Summary:  The thymus provides a unique environment for the development of T lymphocytes from bone marrow‐derived progenitor cells. Several environmental factors have been identified that influence the development of T cells in the thymus. In particular, the Notch pathway has emerged as critical for the induction of T‐lineage commitment and differentiation. Until recently, however, the precise nature of the thymus‐derived signals that drive T‐cell development were unclear, and the only reliable in vitro culture system that supported T‐cell differentiation required the use of thymus organ cultures. Here, we discuss recent advances in the identification of critical Notch receptor ligands that have facilitated the development of a simple in vitro model for the differentiation of T cells ‘in a dish’, providing an alternate approach for studying T lymphopoiesis.
Strength of signal: a fundamental mechanism for cell fate specification
Authors: Hayes Sandra M. , Love Paul E.
Published: January 2006

Summary:  How equipotent cells develop into complex tissues containing many diverse cell types is still a mystery. However, evidence is accumulating from different tissue systems in multiple organisms that many of the specific receptor families known to regulate cell fate decisions target conserved signaling pathways. A mechanism for preserving specificity in the cellular response that has emerged from these studies is one in which quantitative differences in receptor signaling regulate the cell fate decision. A signal strength model has recently gained support as a means to explain αβ/γδ lineage commitment. In this review, we compare the αβ/γδ fate decision with other cell fate decisions that occur outside of the lymphoid system to attain a better picture of the quantitative signaling mechanism for cell fate specification.
Regulation of intrathymic T‐cell development by Lunatic Fringe– Notch1 interactions
Authors: Visan Ioana , Yuan Julie S. , Tan Joanne B. , Cretegny Kira , Guidos Cynthia J.
Published: January 2006

Summary:  Intrathymic Notch1 signaling critically regulates T‐lineage specification and commitment as well as T‐cell progenitor survival and differentiation. Notch1 activation is continuously required during progression of early CD4/CD8‐double‐negative thymocytes to the CD4/CD8‐double‐positive stage. This developmental transition occurs as thymocytes migrate from the corticomedullary junction (CMJ) to the outer subcapsular zone (SCZ) of the thymus. Members of two families of structurally distinct Notch ligands, Delta‐like 1 and Jagged‐1, are expressed by cortical thymic epithelial cells, but it is not known which ligands are functionally required within the CMJ and SCZ microenvironmental niches. Our laboratory has investigated this question by genetically manipulating thymocyte expression of Lunatic Fringe (L‐Fng), a glycosyltransferase that enhances sensitivity of Notch receptors to Delta‐like ligands. This approach has revealed that low‐threshold intrathymic Notch1 signals instruct multipotent thymus‐seeding progenitors to suppress their B‐cell potential and choose the T‐cell fate. This strategy has also revealed that Delta‐like Notch ligands are functionally limiting in both the CMJ and SCZ microenvironmental niches. Finally, we discuss our recent demonstration that L‐Fng‐mediated competition for Delta‐like ligands is an important mechanism for regulating thymus size.
Gnathostomulid phylogeny inferred from a combined approach of four molecular loci and morphology
Authors: Sørensen Martin V. , Sterrer Wolfgang , Giribet Gonzalo
Published: January 2006

The phylogeny of the obscure metazoan phylum Gnathostomulida has previously only been addressed with cladistic analyses of morphological data. In the present study DNA sequence data from four molecular loci, including 18S rRNA, 28S rRNA, histone H3 and cytochrome c oxidase subunit I, are added to a revised morphological data matrix. The data set represents 23 gnathostomulid species that are analyzed under direct optimization using parsimony as the optimality criterion. The results obtained from analyzing the four molecular loci and combined morphological and molecular data under different parameter sets are generally very congruent, and differ only on minor points. The results clearly support gnathostomulid monophyly, as well as the basal division of Gnathostomulida into Filospermoidea and Bursovaginoidea. Filospermoidea were represented by species of Haplognathia and Cosmognathia, and generic monophyly is supported for both groups. Within Bursovaginoidea, Conophoralia (= Austrognathiidae) and Scleroperalia appear as sister groups. Monophyly of Mesognathariidae was confirmed as well, whereas the relationships between species of Gnathostomulidae and Onychognathiidae were contradicted by the molecular data when compared to morphological observations.

©The Willi Hennig Society 2006.
Relapse in common lymphoma subtypes: salvage treatment options for follicular lymphoma, diffuse large cell lymphoma and Hodgkin disease
Authors: Seyfarth Bärbel , Josting Andreas , Dreyling Martin , Schmitz Norbert
Published: January 2006

Over the last decade diagnostic techniques such as immunophenotyping as well as cytogenetic and molecular profiling gave new insights into the pathogenesis of malignant lymphoma and helped to establish the WHO classification. The recognition of well‐defined biological entities with distinct response and relapse patterns led to the development of more specific treatment strategies for individual lymphoma subtypes. New treatment modalities such as the monoclonal antibody rituximab have improved the results of first‐line treatment of patients with certain B‐cell lymphoma subtypes substantially. Furthermore, new prognostic factors were described for different lymphoma entities leading to further differentiation of treatment. As a consequence, the quality of relapse after first‐line therapy has changed and treatment strategies for relapsed disease need to be redefined. This review summarises current salvage treatment options for common lymphoma subtypes taking into account variables which should be considered before an individual patient is treated. We focus on follicular lymphoma, diffuse large B‐cell lymphoma and Hodgkin disease since these are most frequent and evidence‐based salvage strategies are beginning to emerge.
Genetic polymorphisms at FCER1B and PAI‐1 and asthma susceptibility
Authors: Hizawa N. , Maeda Y. , Konno S. , Fukui Y. , Takahashi D. , Nishimura M.
Published: January 2006

Background
We previously detected a promoter polymorphism (−109C/T) in the gene for the β‐chain of the high‐affinity receptor for IgE (FCER1B), which was associated with total serum IgE levels but not with asthma in a Japanese population. A genetic interaction is biologically plausible between FcεRI‐β and the plasminogen activator inhibitor 1 (PAI‐1), which is highly expressed in mast cells in asthmatics and plays an essential role in airway remodelling. We hypothesized that FCER1B promoter polymorphisms, by modifying the intensity of mast cell activation signals, modulate the genetic effects of a functional 4G/5G polymorphism in the PAI‐1 gene on asthma.

Objective
To examine whether FCER1B promoter polymorphisms (−109C/T and −654C/T) influence the genetic effects of the functional polymorphism (4G/5G) at the PAI‐1 promoter region on asthma susceptibility using a case–control analysis.

Methods
Subjects (374 asthmatic patients and 374 non‐asthmatic controls) were divided into combined genotype groups based on the presence of FCER1B−109TT and −654CC genotypes and the PAI‐1 4G allele. Logistic regression analysis was used to estimate adjusted odds ratios for asthma associated with the different genotype groups.

Results
Individuals homozygous for the FCER1B−109T/−654C haplotype and the PAI‐1 5G allele had a reduced susceptibility to asthma; the odds ratio for the development of asthma was 0.20 (95% confidence interval, 0.084–0.46; P=0.00015) for them, compared with individuals also homozygous for the −109T/−654C haplotype at FCER1B but carrying the 4G allele at PAI‐1. The regression model also showed an interaction of the PAI‐1 4G/5G genotype with the FCER1B−109C/T (P for interaction=0.0017) or FCER1B−654C/T (P for interaction=0.031) on asthma.

Conclusion
The present findings suggest a synergistic interaction between FCER1B and PAI‐1 genes in asthma susceptibility.
Taming the killer lakes of Cameroon
Authors: Eby G. Nelson , Evans William C.
Published: January 2006

A chain of volcanoes, some of them still active, extends from the Atlantic Ocean into the highlands of Cameroon. Mount Cameroon, located at the edge of the continent, erupted in 1999 and 2000 and spewed lava part‐way down its flanks, cutting off a coastal road. A number of the now extinct (or dormant) volcanic craters on the continental part of the line are filled with water, forming crater lakes. These lakes have achieved mythical status in local tribal lore. Lacking a written history, prior to the arrival of the colonial powers, much of our understanding of past natural phenomena relating to the lakes is based on these myths.
Nursing attitudes and beliefs in pain assessment and management
Authors: Layman Young Jennifer , Horton Faith M. , Davidhizar Ruth
Published: January 2006

Aims.  This paper reports a study to determine nurses’ attitudes towards pain assessment tools and the relationship of these attitudes to education and experience.

Background.  The issue of pain management is of interest to caregivers nationally and internationally. For example, in the United States of America, the National Health and Medical Research Council set guidelines to assist clinicians in pain management. Research on whether healthcare teams use pain assessment tools has yielded contradictory findings.

Methods.  Using an open‐ended questionnaire developed for this study, which was based on Fishbein and Ajzen expectancy‐value model, a convenience sample of 52 nurses on an acute care unit were asked: (1) What do you believe about the assessment of pain? (2) What do you believe about the use of pain assessment tools? and (3) What do you believe about the use of pain assessment tools in improving the patient's outcome? The nurses then rated their attitudes about each belief and how each belief made them feel. The data were collected in 2003.

Results.  When Fishbein and Ajzen's formula for calculating attitude was used, attitude scores ranged from −6 to 28 with an overall mean score of +8·3. The amount of education and experience of each nurse and the attitude measure in regard to the use of pain assessment tools were compared.

Conclusions.  The Fishbein and Ajzen model provides a useful way to obtain information on the attitude of nurses towards the use of pain assessment instruments. To provide further information, this study with an open‐ended instrument should be followed with a fixed‐response survey with a larger sample size and in various settings.
The impact of a gluten‐free diet on adults with coeliac disease: results of a national survey
Authors: Zarkadas M. , Cranney A. , Case S. , Molloy M. , Switzer C. , Graham I. D. , Butzner J. D. , Rashid M. , Warren R. E. , Burrows V.
Published: January 2006

Objective We sought to evaluate the impact of the gluten‐free diet on the 5,240 members of the Canadian Celiac Association (CCA). Data are presented on 2,681 adults (≥16 years) with biopsy‐proven celiac disease (CD).

Methods A mail‐out survey was used. Quality of life was evaluated using the ‘SF12’, and celiac‐specific questions.

Results Mean age was 56 years, mean age at diagnosis was 45 years, and 75% were female. The ‘SF12’ summary scores were similar to normative Canadian data, but were significantly lower for females and newly diagnosed patients.

Respondents reported: following a gluten‐free (GF) diet (90%), improvement on the diet (83%), and difficulties following the diet (44%), which included: determining if foods were GF (85%), finding GF foods in stores (83%), avoiding restaurants (79%), and avoiding travel (38%). Most common reactions to consumed gluten (among 73%) included pain, diarrhea, bloating, fatigue, nausea, and headache.

Excellent information on CD and its treatment was provided by the CCA (64%), gastroenterologists (28%), dietitians (26%) and family doctor (12%).

Conclusions Quality of life in those with CD could be increased with early diagnosis, increased availability of gluten‐free foods, improved food labelling, and better dietary instruction. Education of physicians and dietitians about CD and its treatment is essential.
Trends in energy and macronutrient intakes in non‐under‐reporters vary with the method used to identify under‐reporters
Authors: Warwick P.
Published: January 2006

Objective  To investigate effects of using different methods to identify under‐reporters on trends in dietary intake and physical activity level (PAL) in non‐under‐reporters.

Design  Dietary intake and activity pattern were recorded by 887 female university students from 1988 to 2003. Energy expenditure (EE) and PAL were measured using a factorial method. Nine methods were used to identify under‐reporters. Trends between 1988 and 2003 were determined from linear regression of median data for each year.

Results  Prevalence of under‐reporting varied with the method used, ranging from 22.2% to 66.7%. Trends that were consistent using all methods were a decrease in per cent of energy from fat and no change in alcohol intake or PAL (P < 0.05). Trends in energy and macronutrient intakes varied with the method used. Using the four methods that excluded the most under‐reporters there were increases in energy and gram carbohydrate (CHO) intakes (P < 0.05), but no change in gram fat intake. Using the four methods that excluded the fewest under‐reporters there was no change in energy or gram CHO intake, but a decrease in gram fat intake (P < 0.05).

Conclusion  Trends in energy, fat and CHO intakes in non‐under‐reporters varied with the method used to identify under‐reporters.