bluuebunny/crossref_metadata_2025 huggingface dataset:
Model selection in Bayesian segmentation of multiple DNA alignments
Authors: Oldmeadow Christopher , Keith Jonathan M.
Published: January 2011

Motivation: The analysis of multiple sequence alignments is allowing researchers to glean valuable insights into evolution, as well as identify genomic regions that may be functional, or discover novel classes of functional elements. Understanding the distribution of conservation levels that constitutes the evolutionary landscape is crucial to distinguishing functional regions from non-functional. Recent evidence suggests that a binary classification of evolutionary rates is inappropriate for this purpose and finds only highly conserved functional elements. Given that the distribution of evolutionary rates is multi-modal, determining the number of modes is of paramount concern. Through simulation, we evaluate the performance of a number of information criterion approaches derived from MCMC simulations in determining the dimension of a model.

Results: We utilize a deviance information criterion (DIC) approximation that is more robust than the approximations from other information criteria, and show our information criteria approximations do not produce superfluous modes when estimating conservation distributions under a variety of circumstances. We analyse the distribution of conservation for a multiple alignment comprising four primate species and mouse, and repeat this on two additional multiple alignments of similar species. We find evidence of six distinct classes of evolutionary rates that appear to be robust to the species used.

Availability: Source code and data are available at http://dl.dropbox.com/u/477240/changept.zip

Contact:  jonathan.keith@monash.edu; christopher.oldmeadow@newcastle.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
MBRole: enrichment analysis of metabolomic data
Authors: Chagoyen Monica , Pazos Florencio
Published: January 2011

Summary: While many tools exist for performing enrichment analysis of transcriptomic and proteomic data in order to interpret them in biological terms, almost no equivalent tools exist for metabolomic data. We present Metabolite Biological Role (MBRole), a web server for carrying out over-representation analysis of biological and chemical annotations in arbitrary sets of metabolites (small chemical compounds) coming from metabolomic data of any organism or sample.

Availability and Implementation: The web server is freely available at http://csbg.cnb.csic.es/mbrole. It was tested in the main web browsers.

Contact:  monica.chagoyen@cnb.csic.es
flowPhyto: enabling automated analysis of microscopic algae from continuous flow cytometric data
Authors: Ribalet Francois , Schruth David M. , Armbrust E. Virginia
Published: January 2011

Motivation: Flow cytometry is a widely used technique among biologists to study the abundances of populations of microscopic algae living in aquatic environments. A new generation of high-frequency flow cytometers collects up to several hundred samples per day and can run continuously for several weeks. Automated computational methods are needed to analyze the different phytoplankton populations present in each sample. Software packages in the programming environment R provide powerful tools for conducting such analyses.

Results: We introduce flowPhyto, an R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.

Availability: Freely accessible at http://www.bioconductor.org

Contact:  armbrust@u.washington.edu
Clinical Practice Guidelines by the Infectious Diseases Society of America for the Treatment of Methicillin-Resistant Staphylococcus aureus Infections in Adults and Children
Authors: Liu Catherine , Bayer Arnold , Cosgrove Sara E. , Daum Robert S. , Fridkin Scott K. , Gorwitz Rachel J. , Kaplan Sheldon L. , Karchmer Adolf W. , Levine Donald P. , Murray Barbara E. , Rybak Michael J. , Talan David A. , Chambers Henry F.
Published: January 2011

Evidence-based guidelines for the management of patients with methicillin-resistant Staphylococcus aureus (MRSA) infections were prepared by an Expert Panel of the Infectious Diseases Society of America (IDSA). The guidelines are intended for use by health care providers who care for adult and pediatric patients with MRSA infections. The guidelines discuss the management of a variety of clinical syndromes associated with MRSA disease, including skin and soft tissue infections (SSTI), bacteremia and endocarditis, pneumonia, bone and joint infections, and central nervous system (CNS) infections. Recommendations are provided regarding vancomycin dosing and monitoring, management of infections due to MRSA strains with reduced susceptibility to vancomycin, and vancomycin treatment failures.
Myocardial fibrosis in isolated left ventricular non‐compaction and its relation to disease severity
Authors: Nucifora Gaetano , Aquaro Giovanni D. , Pingitore Alessandro , Masci Pier Giorgio , Lombardi Massimo
Published: January 2011

Aims

The aim of the present study was to evaluate the prevalence and extent of myocardial fibrosis in patients with isolated left ventricular non‐compaction (LVNC) and to determine its relation to clinical status and LV systolic function.

Methods and results

The cardiac magnetic resonance imaging (MRI) database of our institution was searched for all patients with a first diagnosis of isolated LVNC. The diagnosis of isolated LVNC was based on the presence of standard cardiac MRI and clinical criteria. For each patient, cine and contrast‐enhanced cardiac MR images were analysed to evaluate LV systolic function and the prevalence and extent of late gadolinium enhancement (LGE), a surrogate of myocardial fibrosis. A total of 42 patients (mean age 46 ± 20 years, 62% male) were identified. Late gadolinium enhancement was observed in 23 (55%) patients with isolated LVNC, occupying 4.8 ± 6.7% of the LV mass. Both the presence and extent of LGE were significantly related to the number of abnormal clinical features (i.e. symptomatic status, resting electrocardiogram abnormalities, and 24 h Holter monitoring abnormalities; P< 0.001 and P= 0.001, respectively). Similarly, LGE was more prevalent and extensive in patients with LV ejection fraction (EF) <50% compared with patients with LVEF ≥50% (90 vs. 23%; P< 0.001 and 8.9 ± 7.6 vs. 1.1 ± 2.4%; P< 0.001, respectively). At multivariate analysis, both the presence and extent of LV LGE were independently related to LVEF (β = −0.63; P< 0.001 and β = −0.62; P< 0.001, respectively).

Conclusion

Myocardial fibrosis is related to clinical disease severity and LV systolic dysfunction in isolated LVNC.
Male fish use prior knowledge about rivals to adjust their mate choice
Authors: Bierbach David , Girndt Antje , Hamfler Sybille , Klein Moritz , Mücksch Frauke , Penshorn Marina , Schwinn Michael , Zimmer Claudia , Schlupp Ingo , Streit Bruno , Plath Martin
Published: January 2011

Mate choice as one element of sexual selection can be sensitive to public information from neighbouring individuals. Here, we demonstrate that males of the livebearing fish
Poecilia mexicana
gather complex social information when given a chance to familiarize themselves with rivals prior to mate choice. Focal males ceased to show mating preferences when being observed by a rival (which prevents rivals from copying mating decisions), but this effect was only seen when focal males have perceived rivals as sexually active. In addition, focal males that were observed by a familiar, sexually active rival showed a stronger behavioural response when rivals were larger and thus, more attractive to females. Our study illustrates an unparalleled adjustment in the expression of mating preferences based on social cues, and suggests that male fish are able to remember and strategically exploit information about rivals when performing mate choice.
An offspring signal of quality affects the timing of future parental reproduction
Authors: Mas Flore , Kölliker Mathias
Published: January 2011

Solicitation signals by offspring are well known to influence parental behaviour, and it is commonly assumed that this behavioural effect translates into an effect on residual reproduction of parents. However, this equivalence assumption concerning behavioural and reproductive effects caused by offspring signals remains largely untested. Here, we tested the effect of a chemical offspring signal of quality on the relative timing and amount of future reproduction in the European earwig (Forficula auricularia). We manipulated the nutritional condition of earwig nymphs and exposed females to their extract, or to solvent as a control. There were no significant main effects of exposure treatment on 2nd clutch production, but exposure to extracts of well-fed nymphs induced predictable timing of the 2nd relative to the 1st clutch. This result demonstrates for the first time that an offspring signalper se, in the absence of any maternal behaviour, affects maternal reproductive timing, possibly through an effect on maternal reproductive physiology.
Synthesis and functionalization of superparamagnetic poly-
ɛ
-caprolactone microparticles for the selective isolation of subpopulations of human adipose-derived stem cells
Authors: Balmayor Elizabeth R. , Pashkuleva Iva , Frias Ana M. , Azevedo Helena S. , Reis Rui L.
Published: January 2011

There has been a growing interest in using biofunctionalized magnetic particles for cell isolation. This paper describes the synthesis and characterization of magnetite-polymer (Fe
3
O
4
-poly-
ɛ
-caprolactone, magnetite-PCL) microparticles surface functionalized with amino and epoxy groups allowing easy covalent attachment of specific antibodies and subsequent ability to bind target cells. Particles with different sizes (4–135 µm), spherical shape and superparamagnetic behaviour (magnetite content of about 13 wt%) were obtained. The functionalized microparticles presented high protein-binding capacity (coupling efficiency of 47% for epoxy- and 71% for amino-functionalized particles) with a low level of non-specific binding. We have further investigated the influence of initial protein concentration, pH, ionic strength, temperature and incubation time on the capacity of amino-functionalized particles to bind protein molecules. The results showed that maximum protein coupling is rapidly achieved (≤5 h) at pH 5.5 and low ionic strength (0.05 M NaCl). Furthermore, when cultured in direct contact with osteoblast-like cells (Saos-2) or human-derived adipose stem cells (ASCs), the amino-functionalized particles did not affect the proliferation and morphology of the cells. As a proof of principle for the application of magnetic microparticles for cell isolation, CD105 (endoglin) antibody was coupled to the magnetic particle surface to bind subpopulations of human ASCs expressing the CD105 antigen. The isolation of CD105+ ASCs from a heterogeneous cell population was confirmed by flow cytometry analysis. Given the demonstrated potential of functionalized magnetite-PCL microparticles for selective cell isolation, we expect that these particles may be further applied in immuno-magnetic cell separation owing to their versatility and ease of surface modification.
Barnacles resist removal by crack trapping
Authors: Hui Chung-Yuen , Long Rong , Wahl Kathryn J. , Everett Richard K.
Published: January 2011

We study the mechanics of pull-off of a barnacle adhering to a thin elastic layer which is bonded to a rigid substrate. We address the case of barnacles having acorn shell geometry and hard, calcarious base plates. Pull-off is initiated by the propagation of an interface edge crack between the base plate and the layer. We compute the energy release rate of this crack as it grows along the interface using a finite element method. We also develop an approximate analytical model to interpret our numerical results and to give a closed-form expression for the energy release rate. Our result shows that the resistance of barnacles to interfacial failure arises from a crack-trapping mechanism.
The macroecology of rapid evolutionary radiation
Authors: Parnell Nicholas F. , Streelman J. Todd
Published: January 2011

A long-standing debate in ecology addresses whether community composition is the result of stochastic factors or assembly rules. Non-random, over-dispersed patterns of species co-occurrence have commonly been attributed to competition—a particularly important force in adaptive radiation. We thus examined the macroecology of the recently radiated cichlid rock-fish assemblage in Lake Malawi, Africa at a spectrum of increasingly fine spatial scales (entire lake to depth within rock-reef sites). Along this range of spatial scales, we observed a signal of community structure (decreased co-occurrence of species) at the largest and smallest scales, but not in between. Evidence suggests that the lakewide signature of structure is driven by extreme endemism and micro-allopatric speciation, while patterns of reduced co-occurrence with depth are indicative of species interactions. We identified a ‘core’ set of rock-reef species, found in combination throughout the lake, whose depth profiles exhibited replicated positive and negative correlation. Our results provide insight into how ecological communities may be structured differently at distinct spatial scales, re-emphasize the importance of local species interactions in community assembly, and further elucidate the processes shaping speciation in this model adaptive radiation.
Mammal pollinators lured by the scent of a parasitic plant
Authors: Johnson Steven D. , Burgoyne Priscilla M. , Harder Lawrence D. , Dötterl Stefan
Published: January 2011

To communicate with animals, plants use signals that are distinct from their surroundings. Animals generally learn to use these signals through associative conditioning; however, signals are most effective when they elicit innate behavioural responses. Many plant species have flowers specialized for pollination by ground-dwelling mammals, but the signals used to attract these pollinators have not been elucidated. Here, we demonstrate the chemical basis for attraction of mammal pollinators to flowers of the dioecious parasitic plant
Cytinus visseri
(Cytinaceae). Two aliphatic ketones dominate the scent of this species; 3-hexanone, which elicits strong innate attraction in rodents, and 1-hexen-3-one, which repels them in isolation, but not in combination with 3-hexanone. The aliphatic ketone-dominated scent of
C. visseri
contrasts with those of insect-pollinated plants, which are typically dominated by terpenoids, aromatic or non-ketone aliphatic compounds. 3-hexanone is also known from some bat-pollinated species, suggesting independent evolution of plant signals in derived, highly specialized mammal-pollination systems.
Information theory and the neuropeptidergic regulation of seasonal reproduction in mammals and birds
Authors: Stevenson Tyler J. , Ball Gregory F.
Published: January 2011

Seasonal breeding in the temperate zone is a dramatic example of a naturally occurring change in physiology and behaviour. Cues that predict periods of environmental amelioration favourable for breeding must be processed by the brain so that the appropriate responses in reproductive physiology can be implemented. The neural integration of several environmental cues converges on discrete hypothalamic neurons in order to regulate reproductive physiology. Gonadotrophin-releasing hormone-1 (GnRH1) and Kisspeptin (Kiss1) neurons in avian and mammalian species, respectively, show marked variation in expression that is positively associated with breeding state. We applied the constancy/contingency model of predictability to investigate how GnRH1 and Kiss1 integrate different environmental cues to regulate reproduction. We show that variation in GnRH1 from a highly seasonal avian species exhibits a predictive change that is primarily based on contingency information. Opportunistic species have low measures of predictability and exhibit a greater contribution of constancy information that is sex-dependent. In hamsters, Kiss1 exhibited a predictive change in expression that was predominantly contingency information and is anatomically localized. The model applied here provides a framework for studies geared towards determining the impact of variation in climate patterns to reproductive success in vertebrate species.
Phylogenetic conservatism of environmental niches in mammals
Authors: Cooper Natalie , Freckleton Rob P. , Jetz Walter
Published: January 2011

Phylogenetic niche conservatism is the pattern where close relatives occupy similar niches, whereas distant relatives are more dissimilar. We suggest that niche conservatism will vary across clades in relation to their characteristics. Specifically, we investigate how conservatism of environmental niches varies among mammals according to their latitude, range size, body size and specialization. We use the Brownian rate parameter,σ2, to measure the rate of evolution in key variables related to the ecological niche and define the more conserved group as the one with the slower rate of evolution. We find that tropical, small-ranged and specialized mammals have more conserved thermal niches than temperate, large-ranged or generalized mammals. Partitioning niche conservatism into its spatial and phylogenetic components, we find that spatial effects on niche variables are generally greater than phylogenetic effects. This suggests that recent evolution and dispersal have more influence on species' niches than more distant evolutionary events. These results have implications for our understanding of the role of niche conservatism in species richness patterns and for gauging the potential for species to adapt to global change.
Trapped in the darkness of the night: thermal and energetic constraints of daylight flight in bats
Authors: Voigt Christian C. , Lewanzik Daniel
Published: January 2011

Bats are one of the most successful mammalian groups, even though their foraging activities are restricted to the hours of twilight and night-time. Some studies suggested that bats became nocturnal because of overheating when flying in daylight. This is because—in contrast to feathered wings of birds—dark and naked wing membranes of bats efficiently absorb short-wave solar radiation. We hypothesized that bats face elevated flight costs during daylight flights, since we expected them to alter wing-beat kinematics to reduce heat load by solar radiation. To test this assumption, we measured metabolic rate and body temperature during short flights in the tropical short-tailed fruit batCarollia perspicillataat night and during the day. Core body temperature of flying bats differed by no more than 2°C between night and daytime flights, whereas mass-specific CO2production rates were higher by 15 per cent during daytime. We conclude that increased flight costs only render diurnal bat flights profitable when the relative energy gain during daytime is high and risk of predation is low. Ancestral bats possibly have evolved dark-skinned wing membranes to reduce nocturnal predation, but a low degree of reflectance of wing membranes made them also prone to overheating and elevated energy costs during daylight flights. In consequence, bats may have become trapped in the darkness of the night once dark-skinned wing membranes had evolved.
Geographically pervasive effects of urban noise on frequency and syllable rate of songs and calls in silvereyes (Zosterops lateralis)
Authors: Potvin Dominique A. , Parris Kirsten M. , Mulder Raoul A.
Published: January 2011

Recent studies in the Northern Hemisphere have shown that songbirds living in noisy urban environments sing at higher frequencies than their rural counterparts. However, several aspects of this phenomenon remain poorly understood. These include the geographical scale over which such patterns occur (most studies have compared local populations), and whether they involve phenotypic plasticity or microevolutionary change. We conducted a field study of silvereye (Zosterops lateralis) vocalizations over more than 1 million km2of urban and rural south-eastern Australia, and compared possible effects of urban noise on songs (which are learned) and contact calls (which are innate). Across 14 paired urban and rural populations, silvereyes consistently sang both songs and contact calls at higher frequencies in urban environments. Syllable rate (syllables per second) decreased in urban environments, consistent with the hypothesis that reflective structures degrade song and encourage longer intervals between syllables. This comprehensive study is, to our knowledge, the first to demonstrate varied adaptations of urban bird vocalizations over a vast geographical area, and to provide insight into the mechanism responsible for these changes.
Relative effects of time for speciation and tropical niche conservatism on the latitudinal diversity gradient of phyllostomid bats
Authors: Stevens Richard D.
Published: January 2011

Determinants of contemporary patterns of diversity, particularly those spanning extensive latitudinal gradients, are some of the most intensely debated issues in ecology. Recently, focus has shifted from a contemporary environmental perspective to a historical one in an attempt to better understand the construction of latitudinal gradients. Although the vast majority of research on historical mechanisms has focused on tropical niche conservatism (TNC), other historical scenarios could produce similar latitudinal gradients. Herein, I formalize predictions to distinguish between two such historical processes—namely time for speciation (TFS) and TNC—and test relative support based on diversity gradients of New World bats. TFS and TNC are distinctly spatial and environmental mechanisms, respectively. Nonetheless, because of the way that environmental characteristics vary spatially, these two mechanisms are hard to distinguish. Evidence provided herein suggests that TNC has had a more important effect than TFS in determining diversity gradients of New World bats. Indeed, relative effects of different historical mechanisms, as well as relative effects of historical and contemporary environmental determinants, are probably context-dependent. Future research should move away from attempting to identify the mechanism with primacy and instead attempt to understand the particular contexts in which different mechanisms have greater influence on diversity gradients.
Fitness costs of disrupting circadian rhythms in malaria parasites
Authors: O'Donnell Aidan J. , Schneider Petra , McWatters Harriet G. , Reece Sarah E.
Published: January 2011

Circadian biology assumes that biological rhythms maximize fitness by enabling organisms to coordinate with their environment. Despite circadian clocks being such a widespread phenomenon, demonstrating the fitness benefits of temporal coordination is challenging and such studies are rare. Here, we tested the consequences—for parasites—of being temporally mismatched to host circadian rhythms using the rodent malaria parasite,
Plasmodium chabaudi
. The cyclical nature of malaria infections is well known, as the cell cycles across parasite species last a multiple of approximately 24 h, but the evolutionary explanations for periodicity are poorly understood. We demonstrate that perturbation of parasite rhythms results in a twofold cost to the production of replicating and transmission stages. Thus, synchronization with host rhythms influences in-host survival and between-host transmission potential, revealing a role for circadian rhythms in the evolution of host–parasite interactions. More generally, our results provide a demonstration of the adaptive value of circadian rhythms and the utility of using an evolutionary framework to understand parasite traits.
Adaptation to climate change: contrasting patterns of thermal-reaction-norm evolution in Pacific versus Atlantic silversides
Authors: Baumann Hannes , Conover David O.
Published: January 2011

How organisms may adapt to rising global temperatures is uncertain, but concepts can emerge from studying adaptive physiological trait variations across existing spatial climate gradients. Many ectotherms, particularly fish, have evolved increasing genetic growth capacities with latitude (i.e. countergradient variation (CnGV) in growth), which are thought to be an adaptation primarily to strong gradients in seasonality. In contrast, evolutionary responses to gradients in mean temperature are often assumed to involve an alternative mode, ‘thermal adaptation’. We measured thermal growth reaction norms in Pacific silverside populations (
Atherinops affinis
) occurring across a weak latitudinal temperature gradient with invariant seasonality along the North American Pacific coast. Instead of thermal adaptation, we found novel evidence for CnGV in growth, suggesting that CnGV is a ubiquitous mode of reaction-norm evolution in ectotherms even in response to weak spatial and, by inference, temporal climate gradients. A novel, large-scale comparison between ecologically equivalent Pacific versus Atlantic silversides (
Menidia menidia
) revealed how closely growth CnGV patterns reflect their respective climate gradients. While steep growth reaction norms and increasing growth plasticity with latitude in
M. menidia
mimicked the strong, highly seasonal Atlantic coastal gradient, shallow reaction norms and much smaller, latitude-independent growth plasticity in
A. affinis
resembled the weak Pacific latitudinal temperature gradient.
Risk-sensitivity and the mean-variance trade-off: decision making in sensorimotor control
Authors: Nagengast Arne J. , Braun Daniel A. , Wolpert Daniel M.
Published: January 2011

Numerous psychophysical studies suggest that the sensorimotor system chooses actions that optimize the average cost associated with a movement. Recently, however, violations of this hypothesis have been reported in line with economic theories of decision-making that not only consider the mean payoff, but are also sensitive to risk, that is the variability of the payoff. Here, we examine the hypothesis that risk-sensitivity in sensorimotor control arises as a mean-variance trade-off in movement costs. We designed a motor task in which participants could choose between a sure motor action that resulted in a fixed amount of effort and a risky motor action that resulted in a variable amount of effort that could be either lower or higher than the fixed effort. By changing the mean effort of the risky action while experimentally fixing its variance, we determined indifference points at which participants chose equiprobably between the sure, fixed amount of effort option and the risky, variable effort option. Depending on whether participants accepted a variable effort with a mean that was higher, lower or equal to the fixed effort, they could be classified as risk-seeking, risk-averse or risk-neutral. Most subjects were risk-sensitive in our task consistent with a mean-variance trade-off in effort, thereby, underlining the importance of risk-sensitivity in computational models of sensorimotor control.
Just a heartbeat away from one's body: interoceptive sensitivity predicts malleability of body-representations
Authors: Tsakiris Manos , Jiménez Ana Tajadura- , Costantini Marcello
Published: January 2011

Body-awareness relies on the representation of both interoceptive and exteroceptive percepts coming from one's body. However, the exact relationship and possible interaction of interoceptive and exteroceptive systems for body-awareness remain unknown. We sought to understand for the first time, to our knowledge, the interaction between interoceptive and exteroceptive awareness of the body. First, we measured interoceptive awareness with an established heartbeat monitoring task. We, then, used a multi-sensory-induced manipulation of body-ownership (e.g. Rubber Hand Illusion (RHI)) and we quantified the extent to which participants experienced ownership over a foreign body-part using behavioural, physiological and introspective measures. The results suggest that interoceptive sensitivity predicts the malleability of body representations, that is, people with low interoceptive sensitivity experienced a stronger illusion of ownership in the RHI. Importantly, this effect was not simply owing to a poor proprioceptive representation or differences in autonomic states of one's body prior to the multi-sensory stimulation, suggesting that interoceptive awareness modulates the online integration of multi-sensory body-percepts.
Seasonal interactions in the black-legged kittiwake,
Rissa tridactyla
: links between breeding performance and winter distribution
Authors: Bogdanova Maria I. , Daunt Francis , Newell Mark , Phillips Richard A. , Harris Michael P. , Wanless Sarah
Published: January 2011

Relationships between events in one period of the annual cycle and behaviour in subsequent seasons are key determinants of individual life histories and population dynamics. However, studying such associations is challenging, given the difficulties in following individuals across seasons, particularly in migratory species. Relationships between breeding performance and subsequent winter ecology are particularly poorly understood, yet are likely to be profoundly important because of the costs of reproduction. Using geolocation technology, we show that black-legged kittiwakes that experienced breeding failure left their colony in southeast Scotland earlier than successful breeders. Moreover, a greater proportion of unsuccessful breeders (94% versus 53% successful) travelled over 3000 km to the West Atlantic, whereas fewer visited the East Atlantic (31% versus 80% successful), less than 1000 km from the colony. The two groups did not differ in the timing of return to the colony the following spring. However, 58 per cent of males made a previously undescribed long-distance pre-breeding movement to the central Atlantic. Our results demonstrate important links between reproductive performance and winter distribution, with significant implications for population dynamics. Furthermore, macro-scale segregation associated with breeding outcome is relevant to defining important wintering areas, in particular among declining species experiencing increasingly regular breeding failure.
Adaptive seeds tame genomic sequence comparison
Authors: Kiełbasa Szymon M. , Wan Raymond , Sato Kengo , Horton Paul , Frith Martin C.
Published: January 2011

The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern multi-billionbase DNA data sets. The difficulty is caused by the nonuniform (oligo)nucleotide composition of these sequences, rather than their size per se. To solve this problem, we modified the standard seed-and-extend approach (e.g., BLAST) to use adaptive seeds. Adaptive seeds are matches that are chosen based on their rareness, instead of using fixed-length matches. This method guarantees that the number of matches, and thus the running time, increases linearly, instead of quadratically, with sequence length. LAST, our open source implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition.
A Novel Interaction between CCaMK and a Protein Containing the Scythe_N Ubiquitin-Like Domain in Lotus japonicus
Authors: Kang Heng , Zhu Hui , Chu Xiaojie , Yang Zhenzhen , Yuan Songli , Yu Dunqiang , Wang Chao , Hong Zonglie , Zhang Zhongming
Published: January 2011

In the Rhizobium-legume symbiosis, calcium/calmodulin-dependent protein kinase (CCaMK) is a key regulator for both rhizobial infection and nodule organogenesis. Deregulation of CCaMK by either a point mutation in the autophosphorylation site or the deletion of the carboxyl-terminal regulatory domain results in spontaneous nodule formation without rhizobia. However, the underlying biochemical mechanisms are poorly understood. Here, using the kinase domain of CCaMK as a bait in yeast two-hybrid screening, we identify a novel protein, CIP73 (for CCaMK-interacting protein of approximately 73 kD), that interacts with CCaMK. CIP73 contains a Scythe_N ubiquitin-like domain and belongs to the large ubiquitin superfamily. Deletion and mutagenesis analysis demonstrate that CIP73 could only interact with CCaMK when the calmodulin-binding domain and three EF-hand motifs are removed from the kinase domain. The amino-terminal 80 amino acid residues (80–160) of CCaMK are required for interacting with CIP73 in yeast cells. On the other hand, protein pull-down assay and bimolecular fluorescence complementation assay in Nicotiana benthamiana show that the full-length CCaMK could interact with CIP73 in vitro and in planta. Importantly, CCaMK phosphorylates the amino terminus of CIP73 in a Ca2+/calmodulin-dependent manner in vitro. CIP73 transcripts are preferentially expressed in roots, and very low expression is detected in leaves, stems, and nodules. The expression in roots is significantly decreased after inoculation of Mesorhizobium  loti. RNA interference knockdown of CIP73 expression by hairy root transformation in Lotus japonicus led to decreased nodule formation, suggesting that CIP73 performed an essential role in nodulation.
Long‐term protection against tobacco mosaic virus induced by the marine alga oligo‐sulphated‐galactan Poly‐Ga in tobacco plants
Authors: VERA JEANNETTE , CASTRO JORGE , GONZÁLEZ ALBERTO , BARRIENTOS HERNA , MATSUHIRO BETTY , ARCE PATRICIO , ZUÑIGA GUSTAVO , MOENNE ALEJANDRA
Published: January 2011

In order to study the antiviral effect of the oligo‐sulphated galactan Poly‐Ga, the leaves of tobacco plants XhantiNN were sprayed with water (control), with increasing concentrations of Poly‐Ga, for increasing numbers of treatments or cultivated for increasing times after treatment. Control and treated plants were infected with tobacco mosaic virus (TMV) and the numbers of necrotic lesions were measured in infected leaves. The number of necrotic lesions decreased with increasing concentrations of Poly‐Ga, with increasing numbers of treatments and with increasing time after treatment, indicating a long‐term protection against TMV that mimicks vaccination. In addition, control Xhantinn plants and plants treated with Poly‐Ga and cultivated for increasing times after treatment were infected with TMV in the middle part of the plant, and the levels of TMV‐capsid protein (CP) transcripts were measured in apical leaves. TMV‐CP transcripts decreased in distant leaves, indicating that Poly‐Ga induces systemic protection against TMV. The activities of the defence enzymes phenylalanine ammonia lyase (PAL) and lipoxygenase (LOX) and the amounts of several phenylpropanoid compounds (PPCs) were measured in control and treated plants without infection. A progressive increase in PAL activity was observed with increasing time after treatment, together with the accumulation of free and conjugated PPCs. In contrast, LOX activity remained unchanged. Interestingly, the increase in PAL activity showed a linear correlation with the decrease in necrotic lesions and the decrease in TMV‐CP transcript level. Thus, Poly‐Ga induced systemic and long‐term protection against TMV in tobacco plants that is determined, at least in part, by a sustained activation of PAL and the accumulation of PPCs with potential antiviral activity.
The FRP1 F‐box gene has different functions in sexuality, pathogenicity and metabolism in three fungal pathogens
Authors: JONKERS WILFRIED , VAN KAN JAN A. L. , TIJM PATRICK , LEE YIN‐WON , TUDZYNSKI PAUL , REP MARTIJN , MICHIELSE CAROLINE B.
Published: January 2011

Plant‐pathogenic fungi employ a variety of infection strategies; as a result, fungi probably rely on different sets of proteins for successful infection. The F‐box protein Frp1, only present in filamentous fungi belonging to the Sordariomycetes, Leotiomycetes and Dothideomycetes, is required for nonsugar carbon catabolism and pathogenicity in the root‐infecting fungus Fusarium oxysporum. To assess the role of Frp1 in other plant‐pathogenic fungi, FRP1 deletion mutants were generated in Fusarium graminearum and Botrytis cinerea, and their phenotypes were analysed. Deletion of FgFRP1 in F. graminearum led to impaired infection of barley roots, but not of aerial plant parts. Deletion of BcFRP1 in B. cinerea did not show any effect on pathogenicity. Sexual reproduction, however, was impaired in both F. graminearum and B. cinerea FRP1 deletion mutants. The mutants of all three fungi displayed different phenotypes when grown on an array of carbon sources. The F. oxysporum and B. cinerea deletion mutants showed opposite growth phenotypes on sugar and nonsugar carbon sources. Replacement of FoFRP1 in F. oxysporum with the B. cinerea BcFRP1 resulted in the restoration of pathogenicity, but also in a switch from impaired growth on nonsugar carbon sources to impaired growth on sugar carbon sources. This effect could be ascribed in part to the B. cinerea BcFRP1 promoter sequence. In conclusion, the function of the F‐box protein Frp1, despite its high sequence conservation, is not conserved between different fungi, leading to differential requirements for pathogenicity and carbon source utilization.
Narrowing down the apricot Plum pox virus resistance locus and comparative analysis with the peach genome syntenic region
Authors: VERA RUIZ ELSA MARÍA , SORIANO JOSÉ MIGUEL , ROMERO CARLOS , ZHEBENTYAYEVA TETYANA , TEROL JAVIER , ZURIAGA ELENA , LLÁCER GERARDO , ABBOTT ALBERT GLENN , BADENES MARÍA LUISA
Published: January 2011

Sharka disease, caused by the Plum pox virus (PPV), is one of the main limiting factors for stone fruit crops worldwide. Only a few resistance sources have been found in apricot (Prunus armeniaca L.), and most studies have located a major PPV resistance locus (PPVres) on linkage group 1 (LG1). However, the mapping accuracy was not sufficiently reliable and PPVres was predicted within a low confidence interval. In this study, we have constructed two high‐density simple sequence repeat (SSR) improved maps with 0.70 and 0.68 markers/cm, corresponding to LG1 of ‘Lito’ and ‘Goldrich’ PPV‐resistant cultivars, respectively. Using these maps, and excluding genotype–phenotype incongruent individuals, a new binary trait locus (BTL) analysis for PPV resistance was performed, narrowing down the PPVres support intervals to 7.3 and 5.9 cm in ‘Lito’ and ‘Goldrich’, respectively. Subsequently, 71 overlapping oligonucleotides (overgo) probes were hybridized against an apricot bacterial artificial chromosome (BAC) library, identifying 870 single BACs from which 340 were anchored onto a map region of approximately 30–40 cm encompassing PPVres. Partial BAC contigs assigned to the two allelic haplotypes (resistant/susceptible) of the PPVres locus were built by high‐information content fingerprinting (HICF). In addition, a total of 300 BAC‐derived sequences were obtained, and 257 showed significant homology with the peach genome scaffold_1 corresponding to LG1. According to the peach syntenic genome sequence, PPVres was predicted within a region of 2.16 Mb in which a few candidate resistance genes were identified.
Optimising harvest strategies in a multi‐species bivalve fishery
Authors: GORMAN D. , MAYFIELD S. , WARD T. M. , BURCH P.
Published: January 2011

Abstract  Optimising harvests from fishery resources requires appropriate data. In this study, fishery‐independent survey and size‐at‐first maturity (L50) data were used to assess the suitability of current minimum legal sizes (MLS) and total allowable commercial catches (TACC) in the South Australian, mixed‐species, mud‐cockle (Katelysia spp.) fishery. Estimates of L50 suggested the MLS was conservative in one fishing zone (Coffin Bay), but appropriate elsewhere. Harvestable‐biomass estimates (HB) demonstrated that TACCs were excessive in the Port River (41% of HB), suitable in Coffin Bay (10% of HB) and precautionary in the West Coast (1.5% of HB) fishing zones. Consequently, the MLS was decreased by 5 mm shell length in Coffin Bay and the TACCs for the Port River (reduced by 80%) and West Coast (increased by 40%) amended. This study demonstrated that harvest strategies in mixed‐species fisheries can be optimised by explicitly considering data on species composition, abundance and population biology.
Evidence for branching in cryptococcal capsular polysaccharides and consequences on its biological activity
Authors: Cordero Radames J. B. , Frases Susana , Guimaräes Allan J. , Rivera Johanna , Casadevall Arturo
Published: January 2011

The encapsulated fungus Cryptococcus neoformans is a common cause of life‐threatening disease in immunocompromised individuals. Its major virulence determinant is the polysaccharide (PS) capsule. An unsolved problem in cryptococcal biology is whether the PSs composing the capsule are linear or complex branched polymers, as well as the implications of this structural composition in pathogenesis. In this study we approached the problem by combining static and dynamic light scattering, viscosity analysis, and high‐resolution microscopy and correlated the findings with biological properties. Analysis of the dependence of capsular PS molecular mass and the radius of gyration provided strong evidence against a simple linear PS configuration. Shape factors calculated from light scattering measurements in solution revealed values consistent with polymer branching. Furthermore, viscosity measurements provided complementary evidence for structural branching. Electron microscopy showed PS spherical‐like structures similar to other branched PS. Finally, we show that the capacity of capsular PS to interfere in complement‐mediated phagocytosis, inhibit nitric oxide production by macrophage‐like cells, protect against reactive oxygen species, antibody reactivity and half‐life in serum were influenced by the degree of branching, providing evidence for the notion that PS branching is an important parameter in determining the biological activity of C. neoformans PS.
Vascular endothelial growth factor receptor 2 (VEGFR‐2) signalling activity in paediatric pilocytic astrocytoma is restricted to tumour endothelial cells
Authors: Sikkema A. H. , de Bont E. S. J. M. , Molema G. , Dimberg A. , Zwiers P. J. , Diks S. H. , Hoving E. W. , Kamps W. A. , Peppelenbosch M. P. , den Dunnen W. F. A.
Published: January 2011

A. H. Sikkema, E. S. J. M. de Bont, G. Molema, A. Dimberg, P. J. Zwiers, S. H. Diks, E. W. Hoving, W. A. Kamps, M. P. Peppelenbosch and W. F. A. den Dunnen (2011) Neuropathology and Applied Neurobiology37, 538–548

Vascular endothelial growth factor receptor 2 (VEGFR‐2) signalling activity in paediatric pilocytic astrocytoma is restricted to tumour endothelial cells

Aims: Tumours depend on angiogenesis for enhanced tumour cell survival and progression. Vascular endothelial growth factor receptor (VEGFR) signalling plays a major part in this process. Previously, we evaluated tyrosine kinase activity in paediatric brain tumour tissue lysates using a peptide microarray containing 144 different tyrosine kinase peptide substrates. When applied to paediatric pilocytic astrocytoma tissue, this analysis revealed extensive phosphorylation of VEGFR‐derived peptides. The aim of the current study was to validate this result and determine the presence of VEGFR‐2 activity in paediatric pilocytic astrocytoma as the main VEGFR in terms of mitogenic signalling. In addition, the localization of VEGFR1–3 mRNA expression was assessed. Methods: VEGFR‐2 phosphorylation was determined by adopting a proximity ligation assay approach. Enrichment of endothelial markers and VEGFRs in tumour endothelium was determined by quantitative polymerase chain reaction (qPCR) analysis of laser‐microdissected blood vessels. Results: Proximity ligation assays on tumour cryosections showed the presence of phosphorylation of VEGFR‐2, which primarily localized to vascular endothelium. qPCR analysis of endothelial markers and VEGFRs showed a 13.6‐fold average enrichment of VEGFR‐2 expression in the laser‐microdissected endothelium compared to whole tumour. Also the expression of VEGFR‐1 and ‐3 was highly enriched in the endothelium fraction with an average fold‐enrichment of 16.5 and 50.8 respectively. Conclusions: Phosphorylated VEGFR‐2 is detected on endothelial cells in paediatric pilocytic astrocytoma. Furthermore, endothelial cells are the main source of VEGFR1–3 mRNA expression. This suggests a crucial role for VEGF/VEGFR‐induced angiogenesis in the progression and maintenance of these tumours.
A calcium‐activated apyrase from Teladorsagia circumcincta: an excretory/secretory antigen capable of modulating host immune responses?
Authors: NISBET A. J. , ZARLENGA D. S. , KNOX D. P. , MEIKLE L. I. , WILDBLOOD L. A. , MATTHEWS J. B.
Published: January 2011

A cDNA representing the gene Teladorsagia circumcincta apyrase‐1 (Tci‐apy‐1) was isolated, by PCR, from a T. circumcincta fourth‐stage larval (L4) cDNA library. The closest orthologue of this gene is a Ca2+‐dependent apyrase from Ostertagia ostertagi, with 92% amino acid identity across all 339 residues. Tci‐apy‐1 is transcribed in a stage‐specific manner, the transcript being predominant in L4, detectable in the adult cDNA, but absent from eggs and infective third‐stage larvae (L3). The protein, Tci‐APY‐1, was detected by immunoblotting in extracts of L4 nematodes and was present in excretory/secretory products from the same developmental stage. A recombinant version of Tci‐APY‐1 was expressed in bacteria as an active enzyme that hydrolysed nucleoside triphosphate substrates with a preference of ATP over other nucleoside triphosphates. Recombinant Tci‐APY‐1 hydrolysed ATP and ADP but not AMP. Apyrase activity was divalent cation‐dependent, with no hydrolysis in the presence of Mg2+, but activation in the presence of Ca2+. Recombinant Tci‐APY‐1 was bound by IgG present in serum and both IgG and IgA present in abomasal mucus from trickle‐infected, immune sheep but not in material derived from lambs exposed to a single infection. The potential immunomodulatory roles of this Tci‐APY‐1 are discussed in relation to purinergic signalling.
Novel aspects in the evaluation of an automated blood group analyser
Authors: Strobel E. , Betten S.
Published: January 2011

Background: In contrast to other studies evaluating machines by testing a great number of samples, we focused here on the sensitivity and on the influence of possible disturbing factors on automated blood group testing.

Materials and Methods: As the gelcards of the DiaMed‐ID Micro Typing System are well known, this study examines reading and interpretation of the gelcards by the automated analyser Techno TwinStation. The results of automated reading were compared with visual reading of the gelcards taken out from the machine.

Results: The sensitivity, tested by the titers of some complete and incomplete antibodies, was at least the same for automated as for visual reading. Samples with weak antigens were well recognised by the analyser. Mixed field agglutinations were recognised as questionable results by automated reading up to a relation of 1 : 10 for the most part. Antibody screening and reverse typing were not influenced by hyperbilirubinaemia, whereas in lipemic and haemolytic samples doubtful results were reported.

Conclusion: Interpretation of the results by the automated analyser Techno TwinStation may be disturbed in some difficult samples, but in most of these cases the analyser reports not a false, but a doubtful result, thus triggering visual reading by the operator.