bluuebunny/crossref_metadata_2025 huggingface dataset:
Domain compliance and elastic power transmission in rotary F
O
F
1
-ATPase
Authors: Sielaff Hendrik , Rennekamp Henning , Wächter André , Xie Hao , Hilbers Florian , Feldbauer Katrin , Dunn Stanley D. , Engelbrecht Siegfried , Junge Wolfgang
Published: November 2008

The 2 nanomotors of rotary ATP synthase, ionmotive F
O
and chemically active F
1
, are mechanically coupled by a central rotor and an eccentric bearing. Both motors rotate, with 3 steps in F
1
and 10–15 in F
O
. Simulation by statistical mechanics has revealed that an elastic power transmission is required for a high rate of coupled turnover. Here, we investigate the distribution in the F
O
F
1
structure of compliant and stiff domains. The compliance of certain domains was restricted by engineered disulfide bridges between rotor and stator, and the torsional stiffness (κ) of unrestricted domains was determined by analyzing their thermal rotary fluctuations. A fluorescent magnetic bead was attached to single molecules of F
1
and a fluorescent actin filament to F
O
F
1
, respectively. They served to probe first the functional rotation and, after formation of the given disulfide bridge, the stochastic rotational motion. Most parts of the enzyme, in particular the central shaft in F
1
, and the long eccentric bearing were rather stiff (torsional stiffness κ > 750 pNnm). One domain of the rotor, namely where the globular portions of subunits γ and ε of F
1
contact the c-ring of F
O
, was more compliant (κ ≅ 68 pNnm). This elastic buffer smoothes the cooperation of the 2 stepping motors. It is located were needed, between the 2 sites where the power strokes in F
O
and F
1
are generated and consumed.
An interferon-related gene signature for DNA damage resistance is a predictive marker for chemotherapy and radiation for breast cancer
Authors: Weichselbaum Ralph R. , Ishwaran Hemant , Yoon Taewon , Nuyten Dimitry S. A. , Baker Samuel W. , Khodarev Nikolai , Su Andy W. , Shaikh Arif Y. , Roach Paul , Kreike Bas , Roizman Bernard , Bergh Jonas , Pawitan Yudi , van de Vijver Marc J. , Minn Andy J.
Published: November 2008

Individualization of cancer management requires prognostic markers and therapy-predictive markers. Prognostic markers assess risk of disease progression independent of therapy, whereas therapy-predictive markers identify patients whose disease is sensitive or resistant to treatment. We show that an experimentally derived IFN-related DNA damage resistance signature (IRDS) is associated with resistance to chemotherapy and/or radiation across different cancer cell lines. The IRDS genes STAT1, ISG15, and IFIT1 all mediate experimental resistance. Clinical analyses reveal that IRDS(+) and IRDS(−) states exist among common human cancers. In breast cancer, a seven–gene-pair classifier predicts for efficacy of adjuvant chemotherapy and for local-regional control after radiation. By providing information on treatment sensitivity or resistance, the IRDS improves outcome prediction when combined with standard markers, risk groups, or other genomic classifiers.
Environmental signatures associated with cholera epidemics
Authors: Constantin de Magny Guillaume , Murtugudde Raghu , Sapiano Mathew R. P. , Nizam Azhar , Brown Christopher W. , Busalacchi Antonio J. , Yunus Mohammad , Nair G. Balakrish , Gil Ana I. , Lanata Claudio F. , Calkins John , Manna Byomkesh , Rajendran Krishnan , Bhattacharya Mihir Kumar , Huq Anwar , Sack R. Bradley , Colwell Rita R.
Published: November 2008

The causative agent of cholera,
Vibrio cholerae
, has been shown to be autochthonous to riverine, estuarine, and coastal waters along with its host, the copepod, a significant member of the zooplankton community. Temperature, salinity, rainfall and plankton have proven to be important factors in the ecology of
V. cholerae
, influencing the transmission of the disease in those regions of the world where the human population relies on untreated water as a source of drinking water. In this study, the pattern of cholera outbreaks during 1998–2006 in Kolkata, India, and Matlab, Bangladesh, and the earth observation data were analyzed with the objective of developing a prediction model for cholera. Satellite sensors were used to measure chlorophyll a concentration (CHL) and sea surface temperature (SST). In addition, rainfall data were obtained from both satellite and
in situ
gauge measurements. From the analyses, a statistically significant relationship between the time series for cholera in Kolkata, India, and CHL and rainfall anomalies was determined. A statistically significant one month lag was observed between CHL anomaly and number of cholera cases in Matlab, Bangladesh. From the results of the study, it is concluded that ocean and climate patterns are useful predictors of cholera epidemics, with the dynamics of endemic cholera being related to climate and/or changes in the aquatic ecosystem. When the ecology of
V. cholerae
is considered in predictive models, a robust early warning system for cholera in endemic regions of the world can be developed for public health planning and decision making.
Tpl2 kinase regulates T cell interferon-γ production and host resistance to Toxoplasma gondii
Authors: Watford Wendy T. , Hissong Bruce D. , Durant Lydia R. , Yamane Hidehiro , Muul Linda M. , Kanno Yuka , Tato Cristina M. , Ramos Haydeé L. , Berger Alan E. , Mielke Lisa , Pesu Marko , Solomon Benjamin , Frucht David M. , Paul William E. , Sher Alan , Jankovic Dragana , Tsichlis Philip N. , O'Shea John J.
Published: November 2008

Tpl2 (Tumor progression locus 2), also known as Cot/MAP3K8, is a hematopoietically expressed serine-threonine kinase. Tpl2 is known to have critical functions in innate immunity in regulating tumor necrosis factor–α, Toll-like receptor, and G protein–coupled receptor signaling; however, our understanding of its physiological role in T cells is limited. We investigated the potential roles of Tpl2 in T cells and found that it was induced by interleukin-12 in human and mouse T cells in a Stat4-dependent manner. Deficiency of Tpl2 was associated with impaired interferon (IFN)-γ production. Accordingly, Tpl2−/− mice had impaired host defense against Toxoplasma gondii with reduced parasite clearance and decreased IFN-γ production. Furthermore, reconstitution of Rag2−/− mice with Tpl2-deficient T cells followed by T. gondii infection recapitulated the IFN-γ defect seen in the Tpl2-deficient mice, confirming a T cell–intrinsic defect. CD4+ T cells isolated from Tpl2−/− mice showed poor induction of T-bet and failure to up-regulate Stat4 protein, which is associated with impaired TCR-dependent extracellular signal-regulated kinase activation. These data underscore the role of Tpl2 as a regulator of T helper cell lineage decisions and demonstrate that Tpl2 has an important functional role in the regulation of Th1 responses.
Altered kinetics of nonhomologous end joining and class switch recombination in ligase IV–deficient B cells
Authors: Han Li , Yu Kefei
Published: November 2008

Immunoglobulin heavy chain class switch recombination (CSR) is believed to occur through the generation and repair of DNA double-strand breaks (DSBs) in the long and repetitive switch regions. Although implied, the role of the major vertebrate DSB repair pathway, nonhomologous end joining (NHEJ), in CSR has been controversial. By somatic gene targeting of DNA ligase IV (Lig4; a key component of NHEJ) in a B cell line (CH12F3) capable of highly efficient CSR in vitro, we found that NHEJ is required for efficient CSR. Disruption of the Lig4 gene in CH12F3 cells severely inhibits the initial rate of CSR and causes a late cell proliferation defect under cytokine stimulation. However, unlike V(D)J recombination, which absolutely requires NHEJ, CSR accumulates to a substantial level in Lig4-null cells. The data revealed a fast-acting NHEJ and a slow-acting alterative end joining of switch region breaks during CSR.
Development and Validation of Prediction Models for Rice Surface Lipid Content and Color Parameters Using Near‐Infrared Spectroscopy: A Basis for Predicting Rice Degree of Milling
Authors: Saleh M. I. , Meullenet J. F. , Siebenmorgen T. J.
Published: November 2008

Degree of milling (DOM) of rice plays a key role in determining rice quality and value. Therefore, accurate, nondestructive, quick, and automated surface lipid content (SLC) measurement would be useful in a commercial milling environment. This study was undertaken to provide calibration models for commercial use to provide quick and accurate evaluation of milled rice SLC and Hunterlab color parameters (L,a,b) as indications of rice DOM. In all, 960 samples, including seven cultivars from seven southern United States locations, stored for 0, 1, 2, 3, and 6 months, were milled for four durations to obtain samples of varying DOM. The samples were used to develop calibration models of milled rice SLC and L,a,b values. Another sample set (n = 58) was commercially milled and used to validate the developed models. A DA 7200 diode array analyzer was used to scan milled rice samples in wavelength spectra of 950–1,650 nm. SLC and color parameters were measured using a Soxtec system and a HunterLab colorimeter, respectively. The partial least squares regression (PLS) method using the full near‐infrared spectra was used to develop prediction models for rice SLC and color parameters. Milled rice SLC was well fitted with a correlation of determination of predicted and measured values of (R2 = 0.934). Color parameters were also successfully fitted for L (R2 = 0.943), a (R2 = 0.870), and b (R2 = 0.855). Performance of the developed models to predict rice DOM was superior in predicting SLC and L,a,b values with R2 predicted and measured values of 0.958, 0.836, 0.924, and 0.661, respectively.
Role of rpfF in Virulence and Exoenzyme Production of Xanthomonas axonopodis pv. glycines, the Causal Agent of Bacterial Pustule of Soybean
Authors: Thowthampitak J. , Shaffer B. T. , Prathuangwong S. , Loper J. E.
Published: November 2008

Ten strains of Xanthomonas axonopodis pv. glycines, the causal agent of bacterial pustule of soybean, which were isolated from various soybean growing regions of Thailand, produced an extracellular diffusible factor (DSF) related to a well-characterized quorum sensing molecule produced by other Xanthomonas spp. Genomic DNA of the 10 strains of X. axonopodis pv. glycines contained rpfF, a gene encoding for the biosynthesis of the DSF in X. campestris pv. campestris. The rpfF gene from one strain of X. axonopodis pv. glycines was fully sequenced, and the 289 aa product is closely related to RpfF of other Xanthomonas spp. (95 to 98% identical). Three independently generated rpfF mutants of X. axonopodis pv. glycines strain No12-2 were defective in the production of a DSF, as expected if rpfF encodes for DSF biosynthesis in X. axonopodis pv. glycines. The rpfF mutants of X. axonopodis pv. glycines exhibited reduced virulence on soybean and produced less than wild-type levels of extracellular polysaccharide and the extracellular enzymes carboxylmethylcellulase, protease, endo-β-1,4-mannanase, and pectate lyase. Transcripts for three genes that encode for the extracellular enzymes protease, endoglucanase, and pectate lyase were at lower abundance in an rpfF mutant than in the parental strain of X. axonopodis pv. glycines. These results indicate that X. axonopodis pv. glycines produces a diffusible signal related to the DSF of X. campestris pv. campestris, which contributes to virulence and exoenzyme production by this phytopathogenic bacterium.
Rapid Development of Fungicide Resistance by Sclerotinia homoeocarpa on Turfgrass
Authors: Jo Young-Ki , Won Chang Seog , Boehm Michael , Jung Geunhwa
Published: November 2008

Dollar spot, caused by Sclerotinia homoeocarpa, is the most prevalent and economically important turfgrass disease in North America. Increasing levels of fungicide resistance, coupled with tightening environmental scrutiny of existing fungicides, has left fewer options for managing dollar spot. More knowledge about S. homoeocarpa populations is needed to improve dollar spot management strategies, especially with respect to minimizing the development of fungicide resistance. Population diversity of S. homoeocarpa was examined using inter-simple sequence repeat markers and vegetative compatibility assays. Two subgroups were found in S. homoeocarpa field populations on both fairway and putting green turfgrass at a research field in Wisconsin. These subgroups were genetically different, vegetatively incompatible, and had different fungicide sensitivities. The frequency of the two genetic subgroups differed significantly between the fairway and putting green, but was uniform within the fairway or within the green. Population dynamics of S. homoeocarpa in response to two systemic fungicides (thiophanate-methyl and propiconazole) were assessed based on in vitro fungicide sensitivity. Dynamics of S. homoeocarpa populations depended on the presence of fungicide-resistant isolates in the initial populations before fungicide applications and changed rapidly after fungicide applications. Shifting of the population toward propiconazole resistance was gradual, whereas thiophanate-methyl resistance developed rapidly in the population. In conclusion, field populations of S. homoeocarpa containing genetically distinct, vegetatively incompatible groups were different on turfgrass that was managed differently, and they were changed rapidly after exposure to fungicides.
Haplotype Diversity at the Pi-ta Locus in Cultivated Rice and Its Wild Relatives
Authors: Wang X. , Jia Y. , Shu Q. Y. , Wu D.
Published: November 2008

The Pi-ta gene in rice confers resistance to races of Magnaporthe oryzae that contain AVR-Pita. Pi-ta encodes a predicted cytoplasmic receptor protein with a nucleotide-binding site and a leucine-rich domain. A panel of 51 Oryza accessions of AA genome species Oryza sativa, O. glaberrima, O. rufipogon, O. nivara, and O. barthii, and CC genome species O. officinalis were sequenced to investigate the diversity present in the exon and intron regions of the Pi-ta gene. Two major clades were identified, consisting of 16 different sequences with numerous insertion and deletions. Only one Pi-ta resistance allele was identified despite DNA sequences revealing 16 Pi-ta variants. Most differences were identified in the intron region, and obvious selection of any motif was not observed in the coding region of Pi-ta variants. Reverse-transcription polymerase chain reaction analysis of seedlings revealed that all Pi-ta variants were expressed with or without pathogen inoculation. The 15 Pi-ta variants can be translated into nine proteins highly similar to the Pi-ta protein. Resistance to M. oryzae expressing AVR-Pita correlates with alanine and susceptibility correlates with serine at position 918 of Pi-ta in most accessions examined. These data confirm that a single amino acid controlling resistance specificity underlies the evolution of resistance of Pi-ta genes in rice.
Sexual Recombination in the Botrytis cinerea Populations in Hungarian Vineyards
Authors: Váczy Kálmán Z. , Sándor Erzsébet , Karaffa Levente , Fekete Erzsébet , Fekete Éva , Árnyasi Mariann , Czeglédi Levente , Kövics György J. , Druzhinina Irina S. , Kubicek Christian P.
Published: November 2008

Botrytis cinerea (anamorph of Botryotinia fuckeliana) causes gray mold on a high number of crop plants including grapes. In this study, we investigated the genetic properties of a grape pathogenic population of B. cinerea in the area of Eger, Hungary. A total of 109 isolates from 12 areas were sampled. Based on the sequence of the β-tubulin (tub1) locus, they all belong to group II, a phylogenetic species within B. cinerea. Seventy-four isolates were classified as transposa, with both the Flipper and Boty transposons, and 10 were classified as vacuma, lacking both transposons. The remaining isolates contained either only Flipper (13) or Boty (12). Multilocus analysis of sequences from tub1 and two other loci (elongation factor 1-alpha, tef1, and a minisatellite from the intron of an ATPase, MSB1) led to poor phylogenetic resolution of strains in individual clades. Analysis of five microsatellites (Bc2, Bc3, Bc5, Bc6, and Bc10) resulted in 55 microsatellite haplotypes within the 109 strains. No correlation was detected among individual haplotypes and the presence/absence of Flipper and/or Boty, the geographic origin, or the year of isolation. Application of the index of association, the chi-square test, and the phi test consistently indicated that the population of Hungarian isolates of B. cinerea undergoes sexual reproduction. However, the index of association test suggested the presence of some clonality, and the fixation index showed a low or occasionally moderate level of fixation in the Flipper populations. We conclude that the B. cinerea populations in Hungary consist of a strongly recombining group II phylogenetic species.
RNA-Mediated Gene Silencing of Superoxide Dismutase (bcsod1) in Botrytis cinerea
Authors: Patel R. M. , van Kan J. A. L. , Bailey A. M. , Foster G. D.
Published: November 2008

Gene silencing is a powerful tool utilized for identification of gene function and analysis in plants, animals, and fungi. Here, we report the silencing of superoxide dismutase (bcsod1) in Botrytis cinerea through sense and antisense-mediated silencing mechanisms. Because superoxide dismutase (SOD) is a virulence factor, transformants were tested for phenotypic silencing in vitro and reduction in pathogenicity in planta. Plate-based assays with and without paraquat were performed to screen initial silencing efficiency, and a subset of transformants was used for in planta studies of virulence. Transformants exhibiting strongly decreased transcripts levels were recovered with both constructs but none of those exhibited a reduction in virulence in planta. Our investigations may help optimize a high-throughput gene silencing system useful for identifying potential gene targets for future fungal control.
An experimental study of the decay of turbulent puffs in pipe flow
Authors: de Lozar Alberto , Hof Björn
Published: November 2008

As reported in a number of recent studies, turbulence in pipe flow is transient for
Re
<2000 and the flow eventually always returns to the laminar state. Generally, the lifetime of turbulence has been observed to increase rapidly with Reynolds number but there is currently no accord on the exact scaling behaviour. In particular, it is not clear whether a critical point exists where turbulence becomes sustained or if it remains transient. We here aim to clarify if these conflicting results may have been caused by the different experimental and numerical protocols used to trigger turbulence in these studies.
Introduction. Turbulence transition in pipe flow: 125th anniversary of the publication of Reynolds' paper
Authors: Eckhardt Bruno
Published: November 2008

The 125th anniversary of Osborne Reynolds' seminal publication on the transition to turbulence in pipe flow offers an opportunity to survey our understanding of the nature of the transition. Dynamical systems concepts, computational methods and dedicated experiments have helped to elucidate some of Reynolds' observations and to extract new quantitative characteristics of the transition. This introduction summarizes some of the developments and indicates how the various papers in this volume contribute to an improved understanding of Reynolds' observations.
The critical layer in pipe flow at high Reynolds number
Authors: Viswanath D
Published: November 2008

We report the computation of a family of travelling wave solutions of pipe flow up to
Re
=75 000. As in all lower branch solutions, streaks and rolls feature prominently in these solutions. For large
Re
, these solutions develop a critical layer away from the wall. Although the solutions are linearly unstable, the two unstable eigenvalues approach 0 as
Re
→∞ at rates given by
Re
−0.41
and
Re
−0.87
; surprisingly, the solutions become more stable as the flow becomes less viscous. The formation of the critical layer and other aspects of the
Re
→∞ limit could be universal to lower branch solutions of shear flows. We give implementation details of the GMRES-hookstep and Arnoldi iterations used for computing these solutions and their spectra, while pointing out the new aspects of our method.
Camouflage, communication and thermoregulation: lessons from colour changing organisms
Authors: Stuart-Fox Devi , Moussalli Adnan
Published: November 2008

Organisms capable of rapid physiological colour change have become model taxa in the study of camouflage because they are able to respond dynamically to the changes in their visual environment. Here, we briefly review the ways in which studies of colour changing organisms have contributed to our understanding of camouflage and highlight some unique opportunities they present. First, from a proximate perspective, comparison of visual cues triggering camouflage responses and the visual perception mechanisms involved can provide insight into general visual processing rules. Second, colour changing animals can potentially tailor their camouflage response not only to different backgrounds but also to multiple predators with different visual capabilities. We present new data showing that such facultative crypsis may be widespread in at least one group, the dwarf chameleons. From an ultimate perspective, we argue that colour changing organisms are ideally suited to experimental and comparative studies of evolutionary interactions between the three primary functions of animal colour patterns: camouflage; communication; and thermoregulation.
The critical swimming speed of Iberian barbel Barbus bocagei in relation to size and sex
Authors: Mateus C. S. , Quintella B. R. , Almeida P. R.
Published: November 2008

The swimming capacity of Barbus bocagei was measured with the critical swimming speed (Ucrit) standard test in a modified Blažka‐type swim tunnel. Sixty B. bocagei were tested and they exhibited a mean ±s.d. Ucrit of 0·81 ± 0·11 m s−1 or 3·1 ± 0·86 total lengths per second (LT s−1). Sex had no effect on Ucrit but significant differences were found between the swimming performance of fish with distinct sizes.
Reproduction in an invasive exotic catfish Pterygoplichthys disjunctivus in Volusia Blue Spring, Florida, U.S.A.
Authors: Gibbs M. A. , Shields J. H. , Lock D. W. , Talmadge K. M. , Farrell T. M.
Published: November 2008

Morphology and reproductive strategies of a population of invasive loricariid catfish, Pterygoplichthys disjunctivus, in Volusia Blue Spring, Florida, were examined using morphological characters, gonado‐somatic indices and batch fecundity. This species has cystovarian ovaries, a left ovary that is significantly larger than the right ovary, and is highly fecund. Ovaries contained multiple oocyte size classes and completely spent females were not found, both of which indicate that this species is a multiple spawner. Reproductive patterns changed significantly between the first (2005) and the last (2007) years of this study; female fish became capable of spawning at a smaller size, a greater proportion of the captured population were capable of spawning each year and female batch fecundity increased, as did male and female gonado‐somatic indices. Plasticity of P. disjunctivus reproductive patterns is discussed in relation to resource availability and environmental stability.
Latitudinal variations in age and size at maturity among allis shad Alosa alosa populations
Authors: Lassalle G. , Trancart T. , Lambert P. , Rochard E.
Published: November 2008

Age and total length (LT) at maturity of allis shad Alosa alosa exhibited a significant negative latitudinal gradient over the species’ distribution range. Particular thermal conditions experienced over the distribution area could be the key factor involved to explain this negative trend.
Do northern riverine anadromous Arctic charrSalvelinus alpinusand sea troutSalmo truttaoverwinter in estuarine and marine waters?
Authors: Jensen J. L. A. , Rikardsen A. H.
Published: November 2008

By use of acoustic telemetry, the present study showed that both riverine anadromous brown trout (sea trout)Salmo truttaand Arctic charrSalvelinus alpinusin a north Norwegian river descended the river within the first 4 months after spawning in late September and spent long parts of the remaining winter period in the estuary and also possibly partly in salt water. This contradicts the general assumption, based on studies of lake‐dwelling populations, that both species, and in particularS.alpinus, overwinter and spend 9–11 months in fresh water at northern latitudes and the rest of the year in salt water.
Behavioural interactions between the introduced plague minnow Gambusia holbrooki and the vulnerable native Australian ornate rainbowfish Rhadinocentrus ornatus, under experimental conditions
Authors: Keller K. , Brown C.
Published: November 2008

The impact of the plague minnow Gambusia holbrooki on the ornate rainbowfish Rhadinocentrus ornatus was investigated by comparing the behavioural response and microhabitat preferences of populations of R. ornatus collected from locations that are sympatric and allopatric with G. holbrooki. Rhadinocentrus ornatus populations from sympatric areas exhibited a significantly higher frequency of intraspecific chases, spent significantly more time at an intermediate depth and were nipped significantly less often by G. holbrooki compared to the allopatric R. ornatus populations. The frequency of intraspecific chases by all R. ornatus populations were greatest immediately following G. holbrooki exposure and increased further with repeated exposure. Activity levels were also significantly higher in the presence of G. holbrooki. Gambusia holbrooki and the allopatric R. ornatus populations showed very similar microhabitat preferences, whereas the preferences for the sympatric R. ornatus populations have shifted to facilitate cohabitation with G. holbrooki. The results suggest that sympatric populations of R. ornatus have evolved or developed behavioural responses to G. holbrooki through niche and character shifts. The implications are discussed in relation to the conservation management of R. ornatus and other threatened species.
Cold shock and fish
Authors: Donaldson M. R. , Cooke S. J. , Patterson D. A. , Macdonald J. S.
Published: November 2008

Rapid decreases in water temperature may result in a number of physiological, behavioural and fitness consequences for fishes termed ‘cold shock’. Cold‐shock stress occurs when a fish has been acclimated to a specific water temperature or range of temperatures and is subsequently exposed to a rapid decrease in temperature, resulting in a cascade of physiological and behavioural responses and, in some cases, death. Rapid temperature decreases may occur from either natural (e.g. thermocline temperature variation, seiches and storm events) or anthropogenic sources (e.g. varied thermal effluents from power generation and production industries). The magnitude, duration and frequency of the temperature change as well as the initial acclimation temperatures of individuals can influence the extent of the consequences of cold shock on fishes. Early research on cold shock focused on documenting mortality events associated with cold shock. However, in recent years, a shift in research has occurred where the focus of cold‐shock studies now involves characterizing the sublethal effects of cold shock in terms of the stress response in fishes. This shift has revealed that cold shock can actually be used as a tool for fisheries science (e.g. to induce polyploidy). The cold‐shock stress response offers opportunities to develop many exciting research questions, yet to date, cold‐shock research has been largely unfocused. Few studies attempt to link laboratory physiology experiments with ecologically relevant field data on behaviour, growth, bioenergetics and fitness. Additional research will allow for the development of more focused and robust management policies and conservation initiatives. This review synthesizes the sublethal physiological and behavioural consequences of cold‐shock stress on fishes, identifies natural and anthropogenic sources of cold shock, discusses the benefits of cold shock to fisheries science and describes mitigation and management efforts. Existing knowledge gaps and opportunities for future cold‐shock research are presented.
Interspecific variation in distributions and diets of coral reef butterflyfishes (Teleostei: Chaetodontidae)
Authors: Pratchett M. S. , Berumen M. L.
Published: November 2008

This study examined within‐reef distributions for 19 species of butterflyfishes (Chaetodontidae) at Lizard Island, northern Great Barrier Reef, Australia, and compared spatial patterns of abundance among species with contrasting diets. Spatial variation in abundance of butterflyfishes was most prominent among physiognomic reef zones mainly due to significant zonation of eight species, including four obligate hard‐coral feeders (Chaetodon trifascialis, Chaetodon baronessa, Chaetodon plebeius and Chaetodon lunulatus) and four generalist species (Chaetodon auriga, Chaetodon citrinellus, Chaetodon kleinii and Chaetodon rafflesi). Distributions of obligate hard‐coral feeders were closely associated with spatial variation in percentage cover of scleractinian corals, but no more restricted compared with facultative hard‐coral feeders or non‐coral feeders. Species with highest dietary specialization (C. trifascialis and C. baronessa), however, exhibited the most pronounced zonation patterns and were restricted to habitats with greatest abundance of their preferred prey. While there are conspicuous links between dietary specialization v. spatial patterns in abundance of butterflyfishes, it remains unclear whether dietary specialization is the cause or consequence of more restricted distributions.
Detection heterogeneity in underwater visual‐census data
Authors: MacNeil M. A. , Graham N. A. J. , Conroy M. J. , Fonnesbeck C. J. , Polunin N. V. C. , Rushton S. P. , Chabanet P. , McClanahan T. R.
Published: November 2008

This study shows how capture–mark–recapture (CMR) models can provide robust estimates of detection heterogeneity (sources of bias) in underwater visual‐census data. Detection biases among observers and fish family groups were consistent between fished and unfished reef sites in Kenya, even when the overall level of detection declined between locations. Species characteristics were the greatest source of detection heterogeneity and large, highly mobile species were found to have lower probabilities of detection than smaller, site‐attached species. Fish family and functional‐group detectability were also found to be lower at fished locations, probably due to differences in local abundance. Because robust CMR models deal explicitly with sampling where not all species are detected, their use is encouraged for studies addressing reef‐fish community dynamics.
Comparison of blood pressure measured at the arm, ankle and calf
Authors: Moore C. , Dobson A. , Kinagi M. , Dillon B.
Published: November 2008

The suitability of alternative sites for non‐invasive blood pressure (NIBP) measurement was investigated in 100 awake healthy volunteers. The calf and the ankle were chosen for comparison with the arm, and the results analysed subjected to Bland–Altman analysis. Discomfort was graded using a Visual Analogue Scale. There was a poor agreement between the different sites with respect to systolic blood pressure: the agreement was closer for diastolic and mean measurements. The mean blood pressure calf measurement was on average 4 mmHg (95% limits of agreement −12 to 20), higher than the arm. The ankle was 8 mmHg higher (−8 to 24) than the arm. ANOVA demonstrated a statistically significant difference in the discomfort scores between the sites (p < 0.001). The calf demonstrated the highest discomfort score and the ankle the lowest. We suggest that the ankle should be considered in preference to the calf as an alternative site for NIBP measurement if use of an arm is undesirable or impossible.
Partial deletion of the LAMA3 gene is responsible for hereditary junctional epidermolysis bullosa in the American Saddlebred Horse
Authors: Graves K. T. , Henney P. J. , Ennis R. B.
Published: November 2008

Laminin 5 is a heterotrimeric basement membrane protein integral to the structure and function of the dermal–epidermal junction. It consists of three glycoprotein subunits: the α3, β3 and γ2 chains, which are encoded by the LAMA3, LAMB3 and LAMC2 genes respectively. A mutation in any of these genes results in the condition known as hereditary junctional epidermolysis bullosa (JEB). A 6589‐bp deletion spanning exons 24–27 was found in the LAMA3 gene in American Saddlebred foals born with the skin‐blistering condition epitheliogenesis imperfecta. The deletion confirms that this autosomal recessive condition in the American Saddlebred Horse can indeed be classified as JEB and corresponds to Herlitz JEB in humans. A diagnostic test was developed and nine of 175 randomly selected American Saddlebred foals from the 2007 foal crop were found to be carriers of the mutation (frequency of 0.026).
Re‐sequencing regions of the ovine Y chromosome in domestic and wild sheep reveals novel paternal haplotypes
Authors: Meadows J. R. S. , Kijas J. W.
Published: November 2008

The male‐specific region of the ovine Y chromosome (MSY) remains poorly characterized, yet sequence variants from this region have the potential to reveal the wild progenitor of domestic sheep or examples of domestic and wild paternal introgression. The 5′ promoter region of the sex‐determining gene SRY was re‐sequenced using a subset of wild sheep including bighorn (Ovis canadensis), thinhorn (Ovis dalli spp.), urial (Ovis vignei), argali (Ovis ammon), mouflon (Ovis musimon) and domestic sheep (Ovis aries). Seven novel SNPs (oY2–oY8) were revealed; these were polymorphic between but not within species. Re‐sequencing and fragment analysis was applied to the MSY microsatellite SRYM18. It contains a complex compound repeat structure and sequencing of three novel size fragments revealed that a pentanucleotide element remained fixed, whilst a dinucleotide element displayed variability within species. Comparison of the sequence between species revealed that urial and argali sheep grouped more closely to the mouflon and domestic breeds than the pachyceriforms (bighorn and thinhorn). SNP and microsatellite data were combined to define six previously undetected haplotypes. Analysis revealed the mouflon as the only species to share a haplotype with domestic sheep, consistent with its status as a feral domesticate that has undergone male‐mediated exchange with domestic animals. A comparison of the remaining wild species and domestic sheep revealed that O. aries is free from signatures of wild sheep introgression.
Assessing SNP markers for assigning individuals to cattle populations
Authors: Negrini R. , Nicoloso L. , Crepaldi P. , Milanesi E. , Colli L. , Chegdani F. , Pariset L. , Dunner S. , Leveziel H. , Williams J. L. , Ajmone Marsan P.
Published: November 2008

The effectiveness of single nucleotide polymorphisms (SNPs) for the assignment of cattle to their source breeds was investigated by analysing a panel of 90 SNPs assayed on 24 European breeds. Breed assignment was performed by comparing the Bayesian and frequentist methods implemented in the structure 2.2 and geneclass 2 software programs. The use of SNPs for the reallocation of known individuals to their breeds of origin and the assignment of unknown individuals was tested. In the reallocation tests, the methods implemented in structure 2.2 performed better than those in geneclass 2, with 96% vs. 85% correct assignments respectively. In contrast, the methods implemented in geneclass 2 showed a greater correct assignment rate in allocating animals treated as unknowns to a reference dataset (62% vs. 51% and 80% vs. 65% in field tests 1 and 2 respectively). These results demonstrate that SNPs are suitable for the assignment of individuals to reference breeds. The results also indicate that structure 2.2 and geneclass 2 can be complementary tools to assess breed integrity and assignment. Our findings also stress the importance of a high‐quality reference dataset in allocation studies.
The concordance test emerges as a powerful tool for identifying quantitative trait nucleotides: lessons from BTA6 milk yield QTL
Authors: Seroussi E.
Published: November 2008

The lack of conventions for confirming the discovery of quantitative trait nucleotides in livestock was evidenced by the proposals of mutations in two different genes (SPP1 and ABCG2) as the underlying functional mutation for a major quantitative trait locus (QTL) for milk concentration on bovine chromosome 6 (BTA6). Of these conflicting candidates, SPP1 was excluded by follow‐up studies and by the data described here. A simple test for concordance of the zygosity state between QTL segregation status and the candidate polymorphism was shown, in this case, to be a critical step towards establishing the proof. If a given sample effectively represents the genetic variation across the QTL region, haplotype‐based concordance may further enhance the functionality and resolution power of this test, allowing identification of the causative gene.
Outcomes of older patients (≥60 years) with acquired aplastic anaemia treated with immunosuppressive therapy
Authors: Kao Susan Y. , Xu Wei , Brandwein Joseph M. , Lipton Jeffrey H. , Messner Hans A. , Minden Mark D. , Schimmer Aaron D. , Schuh Andre C. , Yee Karen , Gupta Vikas
Published: November 2008

We report a single center experience in treating 24 consecutive patients ≥60 years old for aplastic anaemia (AA) with immunosuppressive therapy (IST). The main outcomes of interest were the tolerability and toxicity of IST, response rate and survival. Median age was 70 years (range 61–78). Seven patients received standard IST consisting of standard dose antithymocyte‐globulin (ATG) with or without ciclosporin (CsA), and 17 patients received attenuated IST consisting of at least a 50% dose reduction of ATG with CsA or CsA alone. Six patients (25%) had early deaths, mostly due to infection. Early mortality appeared higher in the standard IST group although this was not statistically significant (43% vs. 18%, P = 0·4). The 2‐year cumulative incidence of response was 42% [95% confidence interval (CI) 26–69%]. Responders had significantly better survival than non‐responders (P = 0·0002). The 3‐year probability of overall survival was 49% (95% CI 27–68%). Moderate or severe co‐morbidities (P = 0·03) as determined by Charlson Co‐morbidity Index and very severe AA (P = 0·007) were associated with significantly inferior overall survival while age was not. Nine out of 14 evaluable patients in the attenuated IST group had durable responses to treatment, suggesting that patients not suitable for standard IST can still benefit from attenuated IST.
Peripheral blood monocytes are responsible for γδ T cell activation induced by zoledronic acid through accumulation of IPP/DMAPP
Authors: Roelofs Anke J. , Jauhiainen Marjo , Mönkkönen Hannu , Rogers Michael J. , Mönkkönen Jukka , Thompson Keith
Published: November 2008

Nitrogen‐containing bisphosphonates indirectly activate Vγ9Vδ2 T cells through inhibition of farnesyl pyrophosphate synthase and intracellular accumulation of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), but the cells responsible for Vγ9Vδ2 T cell activation through IPP/DMAPP accumulation are unknown. Treatment of human peripheral blood mononuclear cells (PBMCs) with a pharmacologically relevant concentration of zoledronic acid induced accumulation of IPP/DMAPP selectively in monocytes, which correlated with efficient drug uptake by these cells. Furthermore, zoledronic acid‐pulsed monocytes triggered activation of γδ T cells in a cell contact‐dependent manner. These observations identify monocytes as the cell type directly affected by bisphosphonates responsible for Vγ9Vδ2 T cell activation.
Familial aggregation of food allergy and sensitization to food allergens: a family‐based study
Authors: Tsai H.‐J. , Kumar R. , Pongracic J. , Liu X. , Story R. , Yu Y. , Caruso D. , Costello J. , Schroeder A. , Fang Y. , Demirtas H. , Meyer K. E. , O'Gorman M. R. G. , Wang X.
Published: November 2008

BackgroundThe increasing prevalence of food allergy (FA) is a growing clinical and public health problem. The contribution of genetic factors to FA remains largely unknown.

ObjectiveThis study examined the pattern of familial aggregation and the degree to which genetic factors contribute to FA and sensitization to food allergens.

MethodsThis study included 581 nuclear families (2,004 subjects) as part of an ongoing FA study in Chicago, IL, USA. FA was defined by a set of criteria including timing, clinical symptoms obtained via standardized questionnaire interview and corroborative specific IgE cut‐offs for 95% positive predictive value (PPV) for food allergens measured by Phadia ImmunoCAP. Familial aggregation of FA as well as sensitization to food allergens was examined using generalized estimating equation (GEE) models, with adjustment for important covariates including age, gender, ethnicity and birth order. Heritability was estimated for food‐specific IgE measurements.

ResultsFA in the index child was a significant and independent predictor of FA in other siblings (OR=2.6, 95% CI: 1.2–5.6,P=0.01). There were significant and positive associations among family members (father–offspring, mother–offspring, index–other siblings) for total IgE and specific IgE to all the nine major food allergens tested in this sample (sesame, peanut, wheat, milk, egg white, soy, walnut, shrimp and cod fish). The estimated heritability of food‐specific IgE ranged from 0.15 to 0.35 and was statistically significant for all the nine tested food allergens.

ConclusionThis family‐based study demonstrates strong familial aggregation of FA and sensitization to food allergens, especially, among siblings. The heritability estimates indicate that food‐specific IgE is likely influenced by both genetic and environmental factors. Together, this study provides strong evidence that both host genetic susceptibility and environmental factors determine the complex trait of IgE‐mediated FA.
Development and validation of a self‐administered Food Allergy Quality of Life Questionnaire for children
Authors: Flokstra‐de Blok B. M. J. , DunnGalvin A. , Vlieg‐Boerstra B. J. , Oude Elberink J. N. G. , Duiverman E. J. , Hourihane J. O'B. , Dubois A. E. J.
Published: November 2008

Background
Having a food allergy may affect health‐related quality of life (HRQL). Currently, no validated, self‐administered, disease‐specific HRQL questionnaire exists for children with food allergy.

Objective
The aim of this study was to develop and validate the Food Allergy Quality of Life Questionnaire – Child Form (FAQLQ‐CF) in the Dutch language.

Methods
Interviews with food‐allergic children (n=13, 8–12 years) generated 139 HRQL items. The most important items were identified by 51 food‐allergic children using the clinical impact method. This resulted in the FAQLQ‐CF containing 24 items (total score range 1 ‘not troubled’ to 7 ‘extremely troubled’). The FAQLQ‐CF, the Food Allergy Independent Measure (FAIM) and a generic HRQL questionnaire (CHQ‐CF87) were sent to 115 food‐allergic children for cross‐sectional validation of the FAQLQ‐CF.

Results
Construct validity was demonstrated by the correlation between the FAQLQ‐CF and the FAIM (rho=0.60, P<0.001). The FAQLQ‐CF had an excellent internal consistency (Cronbach's α=0.94) and discriminated between children who differed in number of food allergies (>2 food allergies vs. 2 food allergies; total FAQLQ‐CF score, 4.3 vs. 3.6; P=0.036), but did not discriminate between reported anaphylaxis or not. The total FAQLQ‐CF score correlated with 8 of the 11 CHQ‐CF87 sub‐scales which demonstrated convergent/discriminant validity.

Conclusion
The FAQLQ‐CF is the first self‐administered disease‐specific HRQL questionnaire for food‐allergic children. This questionnaire has a strong internal consistency and cross‐sectional validity. It discriminates between children who differ in number of food allergies, and it was short and easy to use in the population studied. Therefore, the FAQLQ‐CF may be a useful tool in clinical research.
Combination of omalizumab and specific immunotherapy is superior to immunotherapy in patients with seasonal allergic rhinoconjunctivitis and co‐morbid seasonal allergic asthma
Authors: Kopp M. V. , Hamelmann E. , Zielen S. , Kamin W. , Bergmann K.‐C. , Sieder C. , Stenglein S. , Seyfried S. , Wahn U. ,   for the DUAL study group
Published: November 2008

Background
The treatment of allergic asthma by specific immunotherapy (SIT) is hampered by potential side‐effects.

Objective
The aim of this study was to study the effect of omalizumab, a monoclonal anti‐IgE antibody, in combination with SIT in patients with seasonal allergic rhinoconjunctivitis (SAR) and co‐morbid seasonal allergic asthma (SAA) incompletely controlled by conventional pharmacotherapy.

Methods
A randomized, double‐blind, placebo‐controlled, multi‐centre trial was performed to assess the efficacy and safety of omalizumab (Xolair®) vs. placebo in combination with depigmented SIT (Depigoid®) during the grass pollen season. Omalizumab or placebo was started 2 weeks before SIT; the whole treatment lasted 18 weeks. Primary endpoint was daily ‘symptom load’, the sum of daily scores for symptom severity and rescue medication use.

Results
A total of 140 patients (age 11–46 years) were randomized; and a total of 130 finished the study. Combination therapy reduced the symptom load by 39% (P=0.0464, Wilcoxon test) over SIT monotherapy. This difference was mainly due to reduced symptom severity (P=0.0044), while rescue medication use did not change significantly. Combination therapy also improved asthma control (Asthma Control Questionnaire, P=0.0295) and quality of life in the case of asthma (Asthma Quality of Life Questionnaire, P=0.0293) and rhinoconjunctivitis (Rhinoconjunctivitis Quality of Life Questionnaire, P=0.0537). Numbers of patients with ‘excellent or good’ treatment efficacy according to ratings of investigators (75.0% vs. 36.9%) or patients (78.5% vs. 46.1%) were markedly higher in the combination group than under SIT alone.

Conclusion
Combination of omalizumab with SIT for treatment of patients with SAR and co‐morbid SAA was safe and reduced the symptom load in a statistically significant and clinically meaningful manner.
The environmental and socio‐economic impacts of Eichhornia crassipes in the Victoria Falls/Mosi‐oa‐Tunya World Heritage Site, Livingstone, Zambia1
Authors: Nang’alelwa M.
Published: November 2008

The exotic water hyacinth (Eichhornia crassipes) has invaded the Maramba River, a tributary of the Zambezi River in the Victoria Falls World Heritage Site in Zambia presenting several negative environmental and economic impacts. The major impacts identified by recent studies are on the generation of hydro electric power, tourism development, native biodiversity, fish catches and human health. Other recorded impacts are reduced quality and quantity of water for domestic use, restricted navigation of waterways and the threat posed to vital infrastructure. This has led to the initiation of efforts to manage this infestation and address the resultant impacts. Methods proposed for control of water hyacinth in the Victoria Falls/Musi‐oa‐Tunya Pilot Site are an integration of mechanical and biological control measures. This paper discusses the impacts of water hyacinth invasion on the Maramba River and isolated clusters on the backwaters of the Zambezi. Two field surveys undertaken over the last three years and recent interviews with resource persons representing interested and affected institutions and local communities impacted by water hyacinth provide the basis for the data in this paper and the current intervention activities. The field surveys and questionnaires targeted government institutions involved in the management of the area and persons from the private sector engaged in tourism activities. Local peoples found in and around the project area were also interviewed. A pioneering effort is made to quantify the impacts and detail the costs arising from these impacts. Recommendations for the future control and management of E. crassipes are also made.