bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulation of valanimycin biosynthesis in Streptomyces viridifaciens: characterization of VlmI as a Streptomyces antibiotic regulatory protein (SARP)
Authors: Garg Ram P. , Parry Ronald J.
Published: November 2009

Streptomyces antibiotic regulatory proteins (SARPs) have been shown to activate transcription by binding to a tandemly arrayed set of heptameric direct repeats located around the −35 region of their cognate promoters. Experimental evidence is presented here showing that vlmI is a regulatory gene in the valanimycin biosynthetic gene cluster of Streptomyces viridifaciens and encodes a protein belonging to the SARP family. The organization of the valanimycin biosynthetic gene cluster suggests that the valanimycin biosynthetic genes are located on three potential transcripts, vlmHORBCD, vlmJKL and vlmA. Disruption of vlmI abolished valanimycin biosynthesis. Western blot analyses showed that VlmR and VlmA are absent from the vlmI mutant and that the production of VlmK is severely diminished. These results demonstrate that the expression of these genes from the three potential transcripts is under the positive control of VlmI. The vlmA–vlmH and vlmI–vlmJ intergenic regions both exhibit a pattern of heptameric direct repeats. Gel shift assays with VlmI overproduced in Escherichia coli as a C-terminal FLAG-tagged protein clearly demonstrated that VlmI binds to DNA fragments from both regions that contain these heptameric repeats. When a high-copy-number vlmI expression plasmid was introduced into Streptomyces coelicolor M512, which contains mutations in the undecylprodigiosin and actinorhodin activators redD and actII-orf4, undecylprodigiosin production was restored, showing that vlmI can complement a redD mutation. Introduction of the same vlmI expression plasmid into an S. viridifaciens vlmI mutant restored valanimycin production to wild-type levels.
The SOS response of Listeria monocytogenes is involved in stress resistance and mutagenesis
Authors: van der Veen Stijn , van Schalkwijk Saskia , Molenaar Douwe , de Vos Willem M. , Abee Tjakko , Wells-Bennik Marjon H. J.
Published: November 2009

The SOS response is a conserved pathway that is activated under certain stress conditions and is regulated by the repressor LexA and the activator RecA. The food-borne pathogenListeria monocytogenescontains RecA and LexA homologues, but their roles inListeriahave not been established. In this study, we identified the SOS regulon inL. monocytogenesby comparing the transcription profiles of a wild-type strain and a ΔrecAmutant strain after exposure to the DNA-damaging agent mitomycin C. In agreement with studies in other bacteria, we identified an imperfect palindrome AATAAGAACATATGTTCGTTT as the SOS operator sequence. The SOS regulon ofL. monocytogenesconsists of 29 genes in 16 LexA-regulated operons, encoding proteins with functions in translesion DNA synthesis and DNA repair. We furthermore identified a role for the product of the LexA-regulated geneyneAin cell elongation and inhibition of cell division. As anticipated, RecA ofL. monocytogenesplays a role in mutagenesis; ΔrecAcultures showed considerably lower rifampicin- and streptomycin-resistant fractions than the wild-type cultures. The SOS response is activated after stress exposure as shown byrecA- andyneA-promoter reporter studies. Stress-survival studies showed ΔrecAmutant cells to be less resistant to heat, H2O2and acid exposure than wild-type cells. Our results indicate that the SOS response ofL. monocytogenescontributes to survival upon exposure to a range of stresses, thereby likely contributing to its persistence in the environment and in the host.
From spores to antibiotics via the cell cycle
Authors: Errington Jeff
Published: November 2009

Spore formation inBacillus subtilisis a superb experimental system with which to study some of the most fundamental problems of cellular development and differentiation. Work begun in the 1980s and ongoing today has led to an impressive understanding of the temporal and spatial regulation of sporulation, and the functions of many of the several hundred genes involved. Early in sporulation the cells divide in an unusual asymmetrical manner, to produce a small prespore cell and a much larger mother cell. Aside from developmental biology, this modified division has turned out to be a powerful system for investigation of cell cycle mechanisms, including the components of the division machine, how the machine is correctly positioned in the cell, and how division is coordinated with replication and segregation of the chromosome. Insights into these fundamental mechanisms have provided opportunities for the discovery and development of novel antibiotics. This review summarizes how the bacterial cell cycle field has developed over the last 20 or so years, focusing on opportunities emerging from theB. subtilissystem.
The MORPHEUS protein crystallization screen
Authors: Gorrec Fabrice
Published: November 2009

A 96-condition initial screen for protein crystallization, called MORPHEUS, has been developed at the MRC Laboratory of Molecular Biology, Cambridge, England (MRC-LMB). The concept integrates several innovative approaches, such as chemically compatible mixes of potential ligands, new buffer systems and precipitant mixes that also act as cryoprotectants. Instead of gathering a set of crystallization conditions that have already been successful, a selection of molecules frequently observed in the Protein Data Bank (PDB) to co-crystallize with proteins has been made. These have been put together in mixes of similar chemical behaviour and structure, and combined with buffers and precipitant mixes that were also derived from PDB searches, to build the screende novo. Observations made at the MRC-LMB and many practical aspects were also taken into account when formulating the screen. The resulting screen is easy to use, comprehensive yet small, and has already yielded a list of crystallization hits using both known and novel samples. As an indicator of success, the screen has now become one of the standard screens used routinely at the MRC-LMB when searching initial crystallization conditions for biological macromolecules.
The role of predation in variation in body shape in guppies Poecilia reticulata: a comparison of field and common garden phenotypes
Authors: Burns J. G. , Di Nardo P. , Rodd F. H.
Published: November 2009

The body shapes of both wild‐caught and laboratory‐reared male and female Trinidadian guppies Poecilia reticulata from two low‐predation and two high‐predation populations were studied, but predation regime did not seem to be the most important factor affecting body shape. Instead, complicated patterns of plasticity in body shape among populations and the sexes were found. In particular, populations differed in the depth of the caudal peduncle, which is the muscular region just anterior to the tail fin rays and from which most swimming power is generated. Strikingly, the direction of population differences in caudal peduncle depth observed in wild‐caught individuals was reversed when P. reticulata were raised in a common laboratory environment.
Effects of the timing of initial feeding on growth and survival of spotted mandarin fish Siniperca scherzeri larvae
Authors: Zhang L. , Wang Y. J. , Hu M. H. , Fan Q. X. , Chenung S. G. , Shin P. K. S. , Li H. , Cao L.
Published: November 2009

The effects of delayed first feeding on growth and survival of spotted mandarin fish Siniperca scherzeri larvae were examined under controlled conditions. Morphometric characters [yolk‐sac volume, oil globule volume, head depth (HD), body depth (BD), eye diameter (ED), musculature height (MH), mouth diameter (MD) and total length (LT)], body mass (M), specific growth rate (SGR) and survival were evaluated under different first‐feeding time (2, 3, 4 and 5 days after hatching). Larvae began to feed exogenously at 2 days after hatching (DAH) and the point of no return (PNR) occurred between 5 and 6 DAH at 23° C, range ±1·0° C. The yolk volume of larvae first‐fed at 2 days had a significant difference compared with that of larvae first‐fed at 3, 4 and 5 days on 3 and 4 DAH. The larvae first‐fed at 2 days achieved comparatively better growth performance than that of 3, 4 and 5 days. On 5 DAH, all morphometric characters had significant differences between 2 and 5 days and 2 and 4 days initial feeding, respectively. Total mortality was recorded on 9 DAH for the larvae first‐fed at 5 days. On 12 DAH, significant differences were observed between 2 and 4 days and 3 and 4 days initial feeding for all morphometric characters. From 16 DAH to the end of experiment, all growth variables of the larvae first‐fed at 2 days were significantly higher than those in other treatments. The SGR (2–9 DAH) first‐fed at 2 and 3 days were significantly higher than 4 and 5 day treatments, and the SGR (9–16 DAH) first‐fed at 2 days was significantly higher than 3 and 4 day treatments. There was no significant difference, however, of SGR (16–28 DAH) among treatments. Survival rate was significantly higher at 2 days initial feeding (27·42%) when compared with 3 (15·96%) and 4 days (7·92%) initial feeding at the end of experiment. The present study suggests that the first feeding of S. scherzeri larvae should be initiated at 2 days after hatching for achieving good growth and survival.
Spatio‐temporal variation in the elemental compositions of otoliths of southern bluefin tuna Thunnus maccoyii in the Indian Ocean and its ecological implication
Authors: Wang C. H. , Lin Y. T. , Shiao J. C. , You C. F. , Tzeng W. N.
Published: November 2009

The elements Na, Mg, Mn, Ca, Sr and Ba in otoliths of southern bluefin tuna Thunnus maccoyii, collected from their feeding ground in the central Indian Ocean and spawning ground between southern Java and north‐western Australia were measured by laser‐ablation inductively coupled plasma mass spectrometry (LA‐ICPMS) and compared among sampling locations and developmental stages. The Na, Mg and Mn to Ca concentration ratios were significantly higher at the larval stage than at the adult stage, and the ratio reached a peak at the first inflection point of the otolith, mean ±s.d. 43·3 ± 4·9 days after hatching and decreased sharply to a low level thereafter. The temporal change of the elements:Ca ratios in the first inflection point corresponded to the life stage transition from larva to juvenile, indicating that the uptake rate of elements from ambient waters was significantly influenced by the ontogenetic change in the fish. The elemental composition at the otolith edge differed significantly in sub‐adults on the feeding grounds and adults on the spawning grounds. Thus, the otolith elemental composition can be used as a biological tracer to study the time of the ontogenetic shift and to reconstruct the past migratory environmental history of T. maccoyii. In addition, the elemental composition of the otolith core of the adult was similar between feeding and spawning grounds, indicating that the fish in the Indian Ocean had the same larval origin, which is consistent with the single spawning population hypothesis.
Localization of tyrosine hydroxylase immunoreactive neurons in the forebrain of the guppy Poecilia reticulata
Authors: Parafati M. , Senatori O. , Nicotra A.
Published: November 2009

The current study reports for the first time the distribution of tyrosine hydroxylase immunoreactive (TH‐ir) neurons in the forebrain of the guppy Poecilia reticulata. Numerous small TH‐ir neurons were observed in the olfactory bulbs, located mainly in the periphery of the bulbs. The TH‐ir telencephalic neurons are localized in the ventral telencephalic area where they are grouped in three distinct nuclei (Vv,Vd and Vp) composed of a small number of cells forming a continuous strip. The largest number of forebrain TH‐ir neurons was observed in the diencephalon where both small and larger neurons are present. Diencephalic TH‐ir neurons are subdivided in large nuclei located in the preoptic region (nSC, nPOp and nPOm), the thalamus (nDM), the pretectal region (nPPv and nAP), the hypothalamus (nPP and nRP) and the posterior tuberculum (nPT). Many diencephalic nuclei are distributed in periventricular regions and no TH‐ir cells were observed in the paraventricular organ. A comparative analysis indicates that the present observations are consistent with the general pattern of TH‐ir neurons distribution reported for the forebrain of other teleosts, but with some interspecies variability present, mainly in the diencephalon. This paper also provides valuable neuroanatomical information for P. reticulata, a teleost frequently used in toxicological tests, for future studies investigating the effects of environmental pollutants on the catecholaminergic system.
Behavioural and morphological differences between feral and domesticated strains of common carp Cyprinus carpio
Authors: Matsuzaki S. S. , Mabuchi K. , Takamura N. , Nishida M. , Washitani I.
Published: November 2009

Morphological and behavioural traits of a feral strain of the common carp Cyprinus carpio from Lake Biwa in Japan were compared with those of two domesticated strains reared in Japan (one commercial strain and one ornamental koi). To compare genetically inherited traits, all fish were reared from eggs under similar environmental conditions. Using these fish, the following five traits were compared among the three strains: body shape, consumption rate of two types of free‐swimming shrimp, medaka Oryzias latipes and bottom‐dwelling chironomid larvae prey items, preference for a bottom habitat, feeding skills in detecting prey and escape response to predator attack. The feral strain of fish had more streamlined bodies, higher consumption rates for free‐swimming prey, a greater preference for a bottom habitat, possessed greater skill in detecting prey and were more cautious of predator attacks, compared with the fish of the two domesticated strains. These characteristics shown by the feral fish are probably adaptive to the natural environment. A genetic analysis based on five nuclear single nucleotide polymorphism markers, however, suggested that the feral strain was relatively recently derived from domesticated stocks. Considering this, the present results appear to indicate the possibility that domesticated C. carpio could re‐adapt to the wild environment during a short evolutionary period, although further research using more feral strains is required.
A histological investigation of the occurrence of non‐reproductive female bluefin tuna Thunnus thynnus in the Mediterranean Sea
Authors: Zupa R. , Corriero A. , Deflorio M. , Santamaria N. , Spedicato D. , Marano C. , Losurdo M. , Bridges C. R. , De Metrio G.
Published: November 2009

The presence of non‐reproductive Atlantic bluefin tuna Thunnus thynnus females in the Mediterranean Sea was investigated through histological analysis of the gonads. Three hundred and twenty‐six ovary samples were collected from adults captured at different locations in the Mediterranean Sea during the reproductive seasons between 1998 and 2008. Only three specimens were considered to be in a non‐reproductive state: two of them were in a reabsorbing state showing ovaries with early vitellogenic oocytes and extensive α and β atresia of vitellogenic follicles; the third showed gonads with perinucleolar oocytes and was considered to be in a resting state. The low occurrence of non‐reproductive individuals found in this study makes it unlikely that non‐reproductive individuals aggregate with reproductive ones during their migration towards spawning grounds. Further research is suggested in order to investigate the potential presence of non‐reproductive individuals on non‐spawning grounds during the reproductive season.
The influence of maternal condition on offspring performance in sockeye salmon Oncorhynchus nerka
Authors: Tierney K. B. , Patterson D. A. , Kennedy C. J.
Published: November 2009

Eggs were taken from adult sockeye salmon Oncorhynchus nerka that had reached their journey's end in spawn‐ready and moribund condition, and fertilized by healthy males. Egg number, size, hatching success and offspring growth did not differ with maternal condition, which suggests the absence of any persisting physiological maternal effects. Differences were noted in the swimming behaviour and physiology of the offspring at parr stage. In a 30 min schooling test conducted using groups of five in a flume, parr from moribund females were more likely to fatigue, were not as tightly schooled, and had a diminished startle response, both in the per cent responding and the burst distance. In individual, confined swimming tests conducted within a tube, post‐exercise plasma lactate concentration, which is an indicator of white muscle use, was greater for parr from moribund adult females. The moribund females also had elevated lactate following exercise (their migration), which suggests heritable differences may exist in muscle use. This study shows that juvenile O. nerka artificially propagated from females exhausted by their return migration can exhibit swimming performance differences, indicating that maternal condition may need to be considered in breeding programmes.
Assessment of the dorsal fin spine for chimaeroid (Holocephali: Chimaeriformes) age estimation
Authors: Barnett L. A. K. , Ebert D. A. , Cailliet G. M.
Published: November 2009

Previous attempts to age chimaeroids have not rigorously tested assumptions of dorsal fin spine growth dynamics. Here, novel imaging and data‐analysis techniques revealed that the dorsal fin spine of the spotted ratfish Hydrolagus colliei is an unreliable structure for age estimation. Variation among individuals in the relationship between spine width and distance from the spine tip indicated that the technique of transverse sectioning may impart imprecision and bias to age estimates. The number of growth‐band pairs observed by light microscopy in the inner dentine layer was not a good predictor of body size. Mineral density gradients, indicative of growth zones, were absent in the dorsal fin spine of H. colliei, decreasing the likelihood that the bands observed by light microscopy represent a record of growth with consistent periodicity. These results indicate that the hypothesis of aseasonal growth remains plausible and it should not be assumed that chimaeroid age is quantifiable by standard techniques.
Multi‐scale recruitment patterns and effects on local population size of a temperate reef fish
Authors: Fontes J. , Caselle J. E. , Afonso P. , Santos R. S.
Published: November 2009

Recruitment of the temperate reef fish Coris julis was studied across the Azores Archipelago (central North Atlantic), over four consecutive recruitment seasons and at three spatial scales: between islands (separated by 100s of km), sites within islands (separated by 10s of km) and transects within sites (separated by 10s of m). At the largest scale (i.e. between islands) spatial recruitment patterns were highly variable, suggesting the influence of stochastic processes. Recruitment was spatially consistent within islands, even though magnitude was unpredictable between years, indicating that processes at meso‐scales are probably more deterministic. Recruits settled randomly at the transect scale, probably reflecting habitat homogeneity. It was proposed that large and island‐scale patterns reflect larval availability, driven by physical and biological processes occurring in the plankton. No evidence was found for a density‐dependent relationship between newly settled and 2 week settled C. julis nor between cumulative recruitment and young‐of‐the‐year. It appears that adult density is limited by larval supply (pre‐settlement regulation) at low recruitment sites, and determined by post‐settlement, density‐dependent processes at high recruitment sites. This work is one of few to investigate multiple spatial and temporal scales of recruitment for a coastal fish species inhabiting isolated, temperate oceanic islands and hence, provides a novel comparison to the many studies of recruitment on coral reefs and other, more connected systems.
Early development of the digestive tract (pharynx and gut) in the embryos and pre‐larvae of the European sea bass Dicentrarchus labrax
Authors: Sucré E. , Charmantier‐Daures M. , Grousset E. , Charmantier G. , Cucchi‐Mouillot P.
Published: November 2009

The European sea bass Dicentrarchus labrax is a marine teleost important in Mediterranean aquaculture. The development of the entire digestive tract of D. labrax, including the pharynx, was investigated from early embryonic development to day 5 post hatching (dph), when the mouth opens. The digestive tract is initialized at stage 12 somites independently from two distinct infoldings of the endodermal sheet. In the pharyngeal region, the anterior infolding forms the pharynx and the first gill slits at stage 25 somites. The other three gill arches and slits are formed between 1 and 5 dph. Posteriorly, in the gut tube region, a posterior infolding forms the foregut, midgut and hindgut. The anus opens before hatching, at stage 28 somites. Associated organs (liver, pancreas and gall bladder) are all discernable from 3 dph. Some aspects of the development of the two independent initial infoldings seem original compared with data in the literature. These results are discussed and compared with embryonic and post‐embryonic development patterns in other teleosts.
Female guppiesPoecilia reticulataprefer males that can learn fast
Authors: Shohet A. J. , Watt P. J.
Published: November 2009

The role of learning ability as a potentially desirable male trait in sexual selection was investigated in the guppyPoecilia reticulata. Mate preference tests and the rate at which a male learnt two mazes were used to determine whether female preference was related to male learning ability. In addition, male body size and saturation of the orange patches were measured. Female preference was found to be related to rate of learning, such that males that learnt the mazes faster were found to be more attractive to females, but was not found to be related to body size or saturation.
Population subdivision in Siamese mud carp Henicorhynchus siamensis in the Mekong River basin: implications for management
Authors: Adamson E. A. S. , Hurwood D. A. , Baker A. M. , Mather P. B.
Published: November 2009

A molecular approach was employed to investigate stock structure in Siamese mud carp Henicorhynchus siamensis populations collected from 14 sites across mainland south‐east Asia, with the major focus being the lower Mekong River basin. Spatial analysis of a mitochondrial DNA fragment (ATPase 6 and 8) identified four stocks in the Mekong River basin that were all significantly differentiated from a population in the nearby Khlong River, Thailand. In the Mekong River basin, populations in northern Lao People's Democratic Republic and northern Thailand represent two independent stocks, and samples from Thai tributaries group with those from adjacent Mekong sites above the Khone Falls to form a third stock. All sites below the Khone Falls constituted a single vast stock that includes Cambodia and the Mekong Delta in Vietnam. While H. siamensis is considered currently to undertake extensive annual migrations across the Mekong River basin, the data presented here suggest that natural gene flow may occur over much more restricted geographical scales within the basin, and hence populations may need to be managed at finer spatial scales than at the whole‐of‐drainage‐basin level.
Behavioural type in newly emerged steelhead Oncorhynchus mykiss does not predict growth rate in a conventional hatchery rearing environment
Authors: Conrad J. L. , Sih A.
Published: November 2009

Behavioural assays were conducted on newly emerged steelhead Oncorhynchus mykiss to investigate the presence of behavioural syndromes and to determine whether behavioural type in young fish predicts growth rate in a conventional hatchery rearing environment. Individual fry were consistent in their position choice and activity behaviours across safe and unsafe contexts, as well as among assays conducted on different days. Position choice and activity behaviours, however, were not necessarily correlated to each other. Both behaviours predicted feeding rates during behavioural assays, but there was no relationship between fry behaviour and subsequent growth rate or survival during the first 3 months of hatchery rearing. These results support the hypothesis that selection in captivity may be relaxed with respect to behavioural type rather than directional, allowing for increased behavioural variance in domesticated populations. Modest magnitudes of correlations among fry behaviours, however, suggest that behavioural type may be unstable at the onset of the juvenile feeding stage.
Effects of temperature on biological and biochemical indicators of the life‐history strategy of bullheadCottus gobio
Authors: Reyjol Y. , Léna J.‐P. , Hervant F. , Pont D.
Published: November 2009

The biological and biochemical effects of temperature on life‐history strategy of female bullheadCottus gobiowere investigated. Fish from two populations (Bez Basin, south‐east France) experiencing contrasted thermal environments (i.e. more or less stable) were reared during 4 months at three distinct temperatures (7, 9 or 12° C). Both somatic (soma fresh mass and muscle triglyceride content) and reproductive (gonad fresh mass, fecundity, mean diameter of eggs and gonad triglyceride content) indicators were examined. Mixed models indicated that an increasing temperature had significant negative effects on all life‐history indicators except for soma fresh mass. Differences in life‐history strategy with regard to muscle and gonad triglyceride contents, however, suggest that populations experiencing more variable thermal environments may be better adapted than others to cope with an increasing temperature. These findings may have important implications forC. gobiopopulations, within the context of climate warming.
First record of Randall's snapper Randallichthys filamentosus (Perciformes: Lujanidae) from the eastern Indian Ocean (north‐western Australia)
Authors: Newman S. J.
Published: November 2009

The rare Randall's snapper Randallichthys filamentosus is recorded here for the first time in the eastern Indian Ocean from Scott Reef, north‐western Australia. A single specimen of R. filamentosus, measuring 495 mm fork length, was captured on 9 July 2006 at a depth of 211 m on the outer reef slopes of Scott Reef. The capture of this specimen indicates that this deepwater fish is more widely distributed than was previously acknowledged and further implies that this species has a dispersal capacity that extends across ocean boundaries.
Ecological niche specialization inferred from morphological variation and otolith strontium of Arctic charr Salvelinus alpinus L. found within open lake systems of southern Baffin Island, Nunavut, Canada
Authors: Loewen T. N. , Gillis D. , Tallman R. F.
Published: November 2009

The presence of two morphotypes of Arctic charr Salvelinus alpinus was confirmed via morphological variation and otolith strontium (Sr) within three open‐lake systems of southern Baffin Island, Nunavut, Canada: Qinngu (LH001), Iqalugaarjuit Lake (PG082) and Qasigiat (PG015). Analysis of otolith Sr indicates that a component of each S. alpinus population within lakes LH001 and PG082 is migratory (large–maturing S. alpinus), whereas another component is lake‐resident (small–maturing S. alpinus). Alternatively, small and large maturing S. alpinus may both inhabit tidal habitats during their lifetime in lake PG015. Three morphological characters were identified by principal factor analysis (PFA) as characters that were different between maturity groups for all lakes studied: eye diameter, pectoral fin length and pelvic fin length. As well, upper jaw length (LH001 and PG082) and fork depth (PG015) were identified in PFA as traits that differed between morphs. Univariate tests of morphological characters identified by PFA demonstrated maturity group differences with the exception of eye diameter in Lake PG015 and upper jaw length and pelvic fin length in lake LH001. No difference was found in the MANOVA test of upper and lower gill raker number between small–maturing and undeveloped fish within all lakes studied. Clear morphological variation observed between small–maturing and undeveloped fish in all three lakes of the study suggests ecological niche separation between morphotypes. This is the first documented case of lake‐resident S. alpinus use of the tidal habitat in the presence of a migratory large–maturing morphotype.
An increased frequency of 13q deletions detected by fluorescence in situ hybridization and its impact on survival in children and adolescents with Burkitt lymphoma: results from the Children’s Oncology Group study CCG‐5961
Authors: Nelson Marilu , Perkins Sherrie L. , Dave Bhavana J. , Coccia Peter F. , Bridge Julia A. , Lyden Elizabeth R. , Heerema Nyla A. , Lones Mark A. , Harrison Lauren , Cairo Mitchell S. , Sanger Warren G.
Published: November 2009

Burkitt lymphoma (BL), an aggressive B‐cell malignancy, is often curable with short intensive treatment regiments. Nearly all BLs contain rearrangements of the MYC/8q24 region; however, recent cytogenetic studies suggest that certain secondary chromosomal aberrations in BL correlate with an adverse prognosis. In this multi‐centre study, the frequency and impact on clinical outcome of del(13q) and +7 in addition to MYC rearrangements as detected by fluorescence in situ hybridization (FISH) in children and adolescents with intermediate and high‐risk BL registered on Children’s Cancer Group study CCG‐5961 were investigated. Analysis with 13q14.3 and 13q34 loci specific probes demonstrated deletions of 13q in 38/90 (42%) cases. The loss of either 13q14.3 or 13q34 alone occurred in 14% and 8% respectively, while 20% exhibited loss of both regions. Gain of chromosome 7 was observed in 7/68 (10%) cases and MYC rearrangements were detected in 84/90 (93%). Prognostic analysis controlling for known risk factors demonstrated that patients exhibiting loss of 13q, particularly 13q14.3, had a significant decrease in 5‐year overall survival (77% vs. 95%, P = 0·012). These observations indicate that del(13q) occurs in childhood BL at frequencies higher than previously detected by classical cytogenetics and underscores the importance of molecular cytogenetics in risk stratification.
A comprehensive evaluation of the prognostic significance of 13q deletions in patients with B‐chronic lymphocytic leukaemia
Authors: Van Dyke Daniel L. , Shanafelt Tait D. , Call Timothy G. , Zent Clive S. , Smoley Stephanie A. , Rabe Kari G. , Schwager Susan M. , Sonbert Jessica C. , Slager Susan L. , Kay Neil E.
Published: November 2009

Deletion 13q14 on fluorescence in situ hybridization (FISH) analysis is the most common cytogenetic abnormality in chronic lymphocytic leukaemia (CLL), and is a favourable prognostic biomarker when detected as a sole abnormality. We intensively interrogated clinical outcome in 323 consecutive, untreated CLL patients with isolated 13q‐ identified within 2 years of diagnosis. We also analyzed outcome in 217 additional patients with deletion 11q22.3 or 17p13.1, or trisomy 12, based on whether these occurred in isolation or in conjunction with 13q‐. Patients with a heterozygous 13q‐ and those with a homozygous deletion had similar time to first treatment (TFT) and overall survival (OS). In contrast, a higher percentage of 13q‐ nuclei was associated with significantly shorter TFT (P < 0·001). The 5‐year untreated rate was 79% for patients with isolated 13q‐ in ≤65·5% of nuclei compared to 38% among those with 13q‐ in >65·5% of nuclei (P < 0·001). The percentage of nuclei exhibiting 13q‐ remained an independent predictor of TFT after controlling for ZAP‐70, IGHV, or CD38 (all P < 0·001). Among patients with 13q‐ plus one other FISH abnormality, concomitant 13q‐ appeared to attenuate the shorter survival associated with 17p‐ (P = 0·019). The clinical implications of 13q‐ in CLL appear more complex than originally appreciated.
Molecular variability of group 1 and 5 grass pollen allergens between Pooideae species: implications for immunotherapy
Authors: Chabre H. , Gouyon B. , Huet A. , Boran‐Bodo V. , Nony E. , Hrabina M. , Fenaille F. , Lautrette A. , Bonvalet M. , Maillère B. , Bordas‐Le Floch V. , Van Overtvelt L. , Jain K. , Ezan E. , Batard T. , Moingeon P.
Published: November 2009

Background
Differences between major allergens from distinct grass species remain to be investigated, both in terms of structure and antigenicity.

Methods
Group 1 and 5 allergens purified from five common Pooideae species were analysed by mass spectrometry (MS). Major histocompatibility complex (MHC) class II‐restricted T cell epitopes were identified using predictive algorithms and human leucocyte antigen (HLA)‐binding assays. CD4+ T cell reactivity and IgE binding were assessed based on the induction of CD154 expression in peripheral blood mononuclear cells and using competitive ELISA assays, respectively.

Results
MS analysis of group 5 pollen allergens reveals considerable intra‐ and inter‐species variability in amino acid sequence, with 30–50 predominant isoforms found for each species. Differences in the amino acid sequence as well as N‐ and O‐glycosylation contribute to the variability of group 1 allergens, yielding 5–10 main isoforms, depending on the species. Out of 14 MHC class II‐restricted T cell epitopes identified within group 1, only one is conserved among the five grass species. Significant differences in binding affinities for HLA‐DR molecules result in variable CD4+ T cell recognition of group 1 and 5 allergens purified from the various species. Up to 38% and 85% of patients exhibit seric IgE responses to species‐restricted (or semi‐restricted) epitopes associated with group 1 or 5 allergens, respectively.

Conclusion
Major pollen allergens from distinct grass species bear both shared and species‐restricted T and B cell immune epitopes. When compared with single extracts, a five grass pollen extract is thus more suitable for specific immunotherapy, as it contains a broader repertoire of the IgE epitopes to which patients are sensitized.

Cite this as: H. Chabre, B. Gouyon, A. Huet, V. Baron‐Bodo, E. Nony, M. Hrabina, F. Fenaille, A. Lautrette, M. Bonvalet, B. Maillère, V. Bordas‐Le Floch, L. Van Overtvelt, K. Jain, E. Ezan, T. Batard and P. Moingeon, Clinical & Experimental Allergy, 2010 (40) 505–519.
Outcomes of cervical liquid‐based cytology suggesting a glandular abnormality
Authors: Finall A. I. , Olafsdottir R.
Published: November 2009

Objective:  To ascertain the positive predictive value of both ?glandular neoplasia (national standard code 6) and borderline change (national standard code 8) in glandular cells in liquid‐based cervical cytology specimens in Cardiff and Vale NHS Trust and to outline the histological outcomes of these cases.

Method:  Eighty‐nine liquid‐based (Surepath™) cervical cytology cases were retrospectively identified from a 2‐year period (January 2005 to December 2006) and correlated with histopathological diagnoses.

Results:  Initial punch biopsy histology revealed 18 cases (21%) of cervical glandular intraepithelial neoplasia (CGIN). A further nine cases (10%) of CGIN were identified following local excision or hysterectomy. Ten cases of invasive malignancy were identified: four endocervical adenocarcinomas (all node negative, TNM stage T1b1), five endometrial adenocarcinomas and one squamous cell carcinoma. There were 10 with high‐grade cervical intraepithelial neoplasia (CIN) alone. Women diagnosed with endometrial malignancy presented later with an average age of 64.6 years compared with 34.9 years for endocervical lesions. Taking high‐grade CIN or worse as a positive outcome, the overall positive predictive value (PPV) of glandular abnormalities on cytology (both code 6 and 8) was 58.1% [95% confidence interval (CI) 47.8, 68.4]. PPV for borderline change in glandular cells alone was 24.1% (95% CI 8.5, 39.6) and for ?glandular neoplasia alone 75.4% (95% CI 64.3, 86.5).

Conclusion:  With our interpretation of the classification, women with cytological diagnoses of glandular neoplasia of the cervix should initially be investigated by local resection rather than punch biopsy, and those with borderline change in glandular cells with repeat cytology.
The birth of sedimentology: Henry Clifton Sorby and Johannes Walther
Authors: Okada Hakuyu , Kenyon‐Smith Alec
Published: November 2009

Sedimentology is the study of naturally occurring particulate matter with special emphasis on understanding the factors controlling the creation, distribution and accumulation of that matter. Consequently, sedimentology can, and does, embrace geomorphology and climatology, transport mechanisms, depositional environments and lithifaction processes. Its significance lies in the ability of practitioners of the subject—sedimentologists—to determine each and all of the foregoing through the study of samples of sediments and sedimentary rocks. It is, therefore, a basic discipline for the study of past and present environments on Earth, its satellite and its planetary neighbours. The long‐standing contributions of two of the nineteenth century founders of the subject, Henry Clifton Sorby (1826–1908) and Johannes Walther (1860–1937), are discussed here.
Acquisition and processing of simultaneous vibroseis data
Authors: Bagaini Claudio
Published: November 2009

Numerous methods have been developed in the past three decades to speed up vibroseis acquisition. This paper gives an overview of the most promising ones and proposes a classification of them into three categories: simultaneous shooting, cascaded sweeps and slip‐sweep. The principles upon which these methods are based, the processing techniques developed to separate the simultaneously acquired data and their main features are also discussed. Finally, some criteria for the selection of the most suitable methods for the acquisition and the separation stages are proposed.
Validity, reliability and acceptability of the Imperial Nutritional Screening System (INSYST): a tool that does not require the body mass index
Authors: Tammam J. D. , Gardner L. , Hickson M.
Published: November 2009

Background: Nutritional screening tools are central to identifying malnourished patients, but their efficacy is often reduced as a result of difficulties in obtaining height for body mass index (BMI) calculations. The present study aimed to evaluate the validity, reliability and acceptability of the Imperial Nutritional Screening System (INSYST); a tool that does not require the BMI.

Methods: Patients were screened by the researcher within 72 h of admission using INSYST I & II, Malnutrition Universal Screening Tool (MUST) and Mini Nutritional Assessment (MNA), including taking height and weight. Routine INSYST data, completed by nursing staff, were subsequently collected. At risk and malnourished patients were combined for statistical analysis. Inter‐tool and inter‐rater agreement (kappa, κ) was evaluated. Sensitivity and specificity were calculated. Nurses were timed using INSYST. Acceptability, including ease and speed of use, was evaluated.

Results: Kappa (agreement) scores (allP < 0.001) were substantial for INSYST I versus MUST and MNA (κ = 0.73 and κ = 0.76, respectively) and moderate for INSYST II (both κ = 0.53). The sensitivity of INSYST I and II was high (95–100%), whereas specificity was lower (65–83%). The agreement between dietitian and nurse for INSYST I was substantial κ = 0.77 and that for INSYST II was fair κ = 0.39 (bothP ≤ 0.001). There was little disagreement for INSYST I, although nurses tended to underestimate malnutrition risk when using INSYST II. INSYST I took a median of 60 s to complete, INSYST II took 102 s and weighing took 100 s, giving a total time of approximately 5 min. Likert scales showed that the majority of nurses scored INSYST as being fast and easy to use.

Conclusions: INSYST has shown promising levels of concurrent validity (versus MUST and MNA), inter‐rater reliability and acceptability, suggesting that BMI (and therefore height) is unnecessary for identifying malnourished patients.
The Malnutrition Screening Tool is a useful tool for identifying malnutrition risk in residential aged care
Authors: Isenring E. A. , Bauer J. D. , Banks M. , Gaskill D.
Published: November 2009

Background:  The Malnutrition Screening Tool (MST) is a valid nutrition screening tool in the acute hospital setting but has not been assessed in residential aged care facilities. The aim of this secondary analysis was to determine whether the MST could be a useful nutrition screening tool when compared with a full nutrition assessment by Subjective Global Assessment (SGA) in the residential aged care setting.

Methods:  Two hundred and eighty‐five residents (29% male; mean age 84 ± 9 years) from eight residential aged care facilities in Australia participated in the study. A secondary analysis of data collected during a nutrition intervention study was conducted. The MST consists of two questions related to recent weight loss and appetite. Although the MST was not specifically applied, weight loss and appetite information was available and an estimated MST score (0–5) was calculated. Nutritional status was assessed by a research assistant trained in using the SGA.

Results:  Malnutrition prevalence was 42.8% (122 malnourished out of 285 residents). Compared to the SGA, the MST was an effective predictor of nutritional risk (sensitivity = 83.6%, specificity = 65.6%, positive predictive value = 0.65, negative predictive value = 0.84).

Conclusions:  The components of the MST have acceptable sensitivity and specificity, suggesting that it can play a valuable role in quickly identifying the risk of malnutrition in the residential aged care setting. Further prospective research using the MST tool against a broader array of objective and subjective nutritional parameters is required to confirm its validity as a screening tool in aged care settings.
Conventional protein kinase C plays a critical role in negative regulation of CD98‐induced homotypic aggregation
Authors: Cho J. Y. , Katz D. R. , Skubitz K. M. , Chain B. M.
Published: November 2009

Abstract

CD98, a heterodimeric type II transmembrane protein, is involved in many different cellular events, ranging from amino acid transport to cell–cell adhesion. Little is known about the positive and negative signalling pathways involved in these responses. Therefore, we examined the role of conventional protein kinase C (PKC) isoforms during CD98‐induced intracellular signalling and homotypic aggregation of U937 cells. The CD98‐induced aggregation was enhanced by the general protein kinase inhibitors GF109203X and staurosporin, and by specific PKC‐α/‐β peptide inhibitor 19–27, but inhibited by PKC activators such as phorbol 12‐myristate 13‐acetate (PMA). PMA‐inhibition was reversed by PKC inhibitors recognising the ATP‐binding site in PKC (e.g. staurosporin, GF109203X and Go6983). Inhibitors which bind to diacylglycerol (DAG) or Ca2+‐binding sites of PKC (calphostin C and Go6967) had no effect. PMA‐induced translocation of conventional PKC (cPKC) isozymes (α, β and γ), but decreased the expression of PKC‐δ, which plays an important role in CD98‐induced homotypic aggregation. PMA treatment also suppressed the surface level of CD98 but not CD29, CD18 and CD147, dose‐ and time‐dependently. These data provide evidence that PMA‐responsive cPKC isoforms (α, β and γ) play a key role in negative regulation of CD98 signalling and homotypic aggregation.
Morphological evolution in Tropidurinae squamates: an integrated view along a continuum of ecological settings
Authors: GRIZANTE M. B. , NAVAS C. A. , GARLAND Jr T. , KOHLSDORF T.
Published: November 2009

Variation in squamate foot morphology is likely relevant during evolutionary processes of habitat colonization because distinct surfaces differ in energetic and functional demands for locomotion. We combined new foot morphological data with published information of limb and tail lengths to investigate evolutionary changes possibly associated with the differential usage of ecological settings by Tropidurinae species. Several traits exhibited significant phylogenetic signal, and we performed conventional and phylogenetic regressions of PC scores (retained from Principal Components Analyses of morphometric traits) on continuous ecological indices. Tropidurines from sandy habitats exhibit larger foot soles, opposite to the evolution of narrow feet in species that use branches and rocks. Also, species that usually move along trunks present longer femora. This study provides evidence for morphological adaptations associated with substrate usage in Tropidurinae, and suggests that opposite morphological profiles might evolve associated with the use of surfaces energetically and functionally contrasting, possibly leading to trade‐offs.
Bcl‐2 overexpression in hepatic stellate cell line CFSC‐2G, induces a pro‐fibrotic state
Authors: González‐Puertos Viridiana Y , Hernández‐Pérez Elizabeth , Nuño‐Lámbarri Natalia , Ventura‐Gallegos José L , López‐Diázguerrero Norma E , Robles‐Díaz Guillermo , Gutiérrez‐Ruiz María C , Konigsberg Mina
Published: November 2009

Background and Aim:  Development of hepatic fibrosis is a complex process that involves oxidative stress (OS) and an altered balance between pro‐ and anti‐apoptotic molecules. Since Bcl‐2 overexpression preserves viability against OS, our objective was to address the effect of Bcl‐2 overexpression in the hepatic stellate cells (HSC) cell‐line CFSC‐2G under acetaldehyde and H2O2 challenge, and explore if it protects these cells against OS, induces replicative senescence and/or modify extracellular matrix (ECM) remodeling potential.

Methods:  To induce Bcl‐2 overexpression, HSC cell line CFSC‐2G was transfected by lipofection technique. Green fluorescent protein‐only CFSC‐2G cells were used as a control. Cell survival after H2O2 treatment and total protein oxidation were assessed. To determine cell cycle arrest, proliferation‐rate, DNA synthesis and senescence were assessed. Matrix metalloproteinases (MMP), tissue‐inhibitor of MMP (TIMP), transglutaminases (TG) and smooth muscle a‐actin (α‐SMA) were evaluated by western blot in response to acetaldehyde treatment as markers of ECM remodeling capacity in addition to transforming growth factor‐β (TGF‐β) mRNA.

Results:  Cells overexpressing Bcl‐2 survived ≈ 20% more than control cells when exposed to H2O2 and ≈ 35% proteins were protected from oxidation, but Bcl‐2 did not slow proliferation or induced senescence. Bcl‐2 overexpression did not change α‐SMA levels, but it increased TIMP‐1 (55%), tissue transglutaminases (tTG) (25%) and TGF‐β mRNA (49%), when exposed to acetaldehyde, while MMP‐13 content decreased (47%).

Conclusions:  Bcl‐2 overexpression protected HSC against oxidative stress but it did not induce replicative senescence. It increased TIMP‐1, tTG and TGF‐β mRNA levels and decreased MMP‐13 content, suggesting that Bcl‐2 overexpression may play a key role in the progression of fibrosis in chronic liver diseases.