bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing the potassium requirements of five pasture species
Authors: Brennan R. F. , Bolland M. D. A.
Published: May 2006

Potassium (K) deficiency is now common in sandy soils of south-western Australia and the K requirements of most pasture species grown in rotation with crops in the region are not known. In a glasshouse experiment using a K deficient yellow sand, we compared the K requirements of 5 pasture species now commonly grown in the region: French serradella (Ornithopus sativus Brot.) cv. Cadiz, yellow serradella (Ornithopus compressus Brot.) cv. Santorini, balansa clover [Trifolium balansae, classified as T. michelianum Savi var. balansae (Boiss)] cv. Paradana, 2 subterranean clover (Trifolium subterraneum L.) cultivars, cv. Seaton Park (subspecies subterraneum) and cv. Trikkala (subspecies yanninicum), and annual ryegrass (Lolium rigidum Gaud) cv. Wimmera. After 56 days of growth, above-ground growth was harvested and analysed for total K. Mitscherlich curves were fitted to yield of dried shoots, K concentration and K content (K concentration multiplied by yield) of the shoots. These fitted curves were used to determine the amount of K required to produce 75% of the maximum yield of dried shoots, K required to attain a K concentration in dried shoots of 25 g/kg, and K required to achieve a K content in dried shoots of 250 mg K/pot.
Annual ryegrass and yellow serradella more effectively used indigenous soil K and applied K to produce dried shoots than the other species and cultivars, with the other species and cultivars requiring about 55% more applied K to produce 75% of the maximum shoot yield. The K content in dried shoots estimated the total K taken up from the soil, and annual ryegrass took up least K from soil, but it required least applied K to produce 75% of the maximum shoot yield, indicating it used the K it took up very effectively to produce shoots. Yellow serradella took up most K and, after annual ryegrass, it needed least applied K to produce the target yield of dried shoots. After yellow serradella, subterranean clover cv. Trikkala took up most K from soil, but it required nearly the most applied K to produce the target shoot yield so it was inefficient at using K taken up to produce the shoots. For all the other species and cultivars, K requirement was similar as assessed by yield or K content data. The critical concentration of K required for 90% maximum yield of dried shoots was about (g K/kg) 24 for balansa clover, 23 for both subterranean clover cultivars, 21 for yellow and French serradella, and 15 for annual ryegrass.
Persistence and leaching of imazethapyr and flumetsulam herbicides over a 4-year period in the highly alkaline soils of south-eastern Australia
Authors: Hollaway K. L. , Kookana R. S. , Noy D. M. , Smith J. G. , Wilhelm N.
Published: May 2006

Imazethapyr and flumetsulam are acetolactate synthase herbicides commonly used in the cereal belt of south-eastern Australia. As their labels recommend recropping periods of up to 34 months for imazethapyr and 24 months for flumetsulam, there are concerns that in some cases their persistence may damage subsequent rotation crops. This is the first major study in south-eastern Australia to investigate their leaching and persistence for up to 4 years after treatment. Imazethapyr persisted for more than 3 years at 2 sites and flumetsulam for more than 2 years at 3 sites. For imazethapyr, soil type (clay content) rather than soil pH seemed to be most important in determining persistence, with residues of 10% of applied imazethapyr predicted to persist for 24 months after treatment in clay soil and 5 months after treatment in sandy soil. The potential for leaching below our studied soil depth of 40 cm is of concern for imazethapyr but not for flumetsulam. The current labels appear to provide adequate information for safe recropping periods, but may be conservative for imazethapyr in sandy soils.
Effects of postharvest methyl jasmonate treatments against Botrytis cinerea on Geraldton waxflower (Chamelaucium uncinatum)
Authors: Eyre J. X. , Faragher J. , Joyce D. C. , Franz P. R.
Published: May 2006

Cut Geraldton waxflower (Chamelaucium uncinatum Schauer) flowers are often infected with Botrytis cinerea. Release of infection from quiescence can cause ethylene production by invaded host tissues and result in flower abscission. Postharvest floral organ abscission is a major problem for the commercial waxflower industry. Methyl jasmonate (MeJA) occurs naturally in plant tissue and has a signalling role in eliciting induced systemic resistance against disease. MeJA treatments have been shown to suppress B. cinerea infecting cut rose flowers. The present experiments investigated the potential of exogenous MeJA treatments for B. cinerea management on harvested waxflower. MeJA treatments of 10 and 100 µL liquid MeJA/L of air applied to cv. Purple Pride and 1 µL MeJA/L to cv. Mullering Brook gave reductions in disease severity for uninoculated stems. However, concentrations of 100 µL MeJA/L applied to Purple Pride in addition to 1 and 10 µL MeJA/L applied to Mullering Brook increased the incidence of floral organ fall. Flower abscission upon treatment with MeJA may be due to induced systemic resistance-associated upregulation of ethylene biosynthesis. MeJA treatments had no direct effect on B. cinerea hyphal elongation in vitro. Collectively, these results show that while MeJA treatment may elicit defence in waxflower against Botrytis, the chemical also causes floral organ fall. Thus, exogenous MeJA treatments do not have potential for B. cinerea management on harvested waxflower.
In vitro detection of hepatocytotoxic metabolites from Drechslera biseptata: a contributing factor to acute bovine liver disease?
Authors: Aslani M. R. , Pascoe I. , Kowalski M. , Michalewicz A. , Retallick M. A. S. , Colegate S. M.
Published: May 2006

Acute bovine liver disease, which causes photosensitisation and sudden death in dairy cattle in the southern parts of Australia, has been tentatively associated with the presence of Cynosurus echinatus L. (rough dog’s tail) in the pasture. Also tentatively implicated is the known phytopathogenic fungus Drechslera biseptata that has been isolated from C. echinatus collected at the time of, and from the sites of, outbreaks of acute bovine liver disease. Aqueous and hexane extracts of in vitro cultures of D. biseptata caused binucleation of cultured rat hepatocytes whereas the methanolic extracts caused severe degeneration and necrosis. A methanolic extract of entire C. echinatus collected from a toxic paddock showed the same degenerative toxic effect on the cultured rat hepatocytes. High pressure liquid chromatographic separation and mass spectrometric analysis of the isolated hepatocytotoxic metabolites indicated the possibility of cytochalasin-like compounds.
Fluorescence resonance energy transfer in living cells reveals dynamic membrane changes in the initiation of B cell signaling
Authors: Sohn Hae Won , Tolar Pavel , Jin Tian , Pierce Susan K.
Published: May 2006

B cell responses are initiated by the clustering of the B cell receptor (BCR) by the binding of multivalent antigens. Clustering leads to phosphorylation of tyrosines in the cytoplasmic domains of the BCR by the inner plasma membrane leaflet-associated Src-family kinase Lyn. At present, little is known about the earliest events after BCR clustering that precede the BCR's phosphorylation by Lyn. Here we use fluorescence resonance energy transfer (FRET) in living cells to detect the interaction of the BCR with a Lyn-based membrane-targeted reporter in the first several seconds after BCR clustering. The results showed that, within seconds of antigen binding, the BCR selectively and transiently associated with the Lyn construct and that this association preceded by several seconds the triggering of Ca
2+
fluxes and could be prolonged by the engagement of the B cell coreceptor complex, CD19/CD21. Thus, FRET measurements in living B cells revealed highly dynamic and regulated antigen-induced changes in the plasma membrane, allowing association of the BCR with the earliest components of its signaling cascade.
Toward the structural genomics of complexes: Crystal structure of a PE/PPE protein complex from
Mycobacterium tuberculosis
Authors: Strong Michael , Sawaya Michael R. , Wang Shuishu , Phillips Martin , Cascio Duilio , Eisenberg David
Published: May 2006

The developing science called structural genomics has focused to date mainly on high-throughput expression of individual proteins, followed by their purification and structure determination. In contrast, the term structural biology is used to denote the determination of structures, often complexes of several macromolecules, that illuminate aspects of biological function. Here we bridge structural genomics to structural biology with a procedure for determining protein complexes of previously unknown function from any organism with a sequenced genome. From computational genomic analysis, we identify functionally linked proteins and verify their interaction
in vitro
by coexpression/copurification. We illustrate this procedure by the structural determination of a previously unknown complex between a PE and PPE protein from the
Mycobacterium tuberculosis
genome, members of protein families that constitute ≈10% of the coding capacity of this genome. The predicted complex was readily expressed, purified, and crystallized, although we had previously failed in expressing individual PE and PPE proteins on their own. The reason for the failure is clear from the structure, which shows that the PE and PPE proteins mate along an extended apolar interface to form a four-α-helical bundle, where two of the α-helices are contributed by the PE protein and two by the PPE protein. Our entire procedure for the identification, characterization, and structural determination of protein complexes can be scaled to a genome-wide level.
'The Value of Civility?'
Authors: Boyd Richard
Published: May 2006

This essay argues for civility's vital place in contemporary urban life. Contrary to many critics who see civility as a conservative or nostalgic virtue deployed to repress difference and frustrate social change, it is argued that civility should be understood as democratic, pluralistic and premised on a sense of moral equality. Civility's most obvious contribution is functional-in easing social conflicts and facilitating social interactions in a complex and diverse market society. However, there is also and maybe more importantly an intrinsic moral value to civility. Observing the formal conditions of civility is one of the ways in which we communicate respect for others and generate habits of moral equality in the everyday life of a democracy.
Absence of β-Catenin Alteration in Hepatic Tumors Induced by p-Nitroanisole in Crj:BDF1 Mice
Authors: Kushida Masahiko , Aiso Sigetoshi , Morimura Keiichirou , Wei Min , Wanibuchi Hideki , Nagano Kasuke , Fukushima Shoji
Published: May 2006

In the present study, β-catenin localization in hepatocellular neoplasms and hepatoblastomas, induced by oral administration of p-Nitroanisole (pNA) in Crj:BDF1 for 2 years, was evaluated by immunohistochemistry along with genetic alterations in exon 2 of β-catenin by the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) approach. Genomic DNA was isolated from paraffin sections of a total of 53 liver tumors. Immunohistochemical analysis revealed no abnormal accumulation of the β-catenin protein in any of the cases. No mutations (0/13), 20% silent mutations (3/15) and 8% silent plus 12% functional mutations (2 + 3/25), not in the multiple phosphorylation sites of β-catenin, were observed in hepatocellular adenomas, carcinomas and hepatoblastomas, respectively. The results indicate that β-catenin does not play an important role in development of hepatic tumors induced by pNA in Crj:BDF1 mice.
Retinal and Peripheral Nerve Toxicity Induced by the Administration of a Pan-Cyclin Dependent Kinase (cdk) Inhibitor in Mice
Authors: Illanes Oscar , Anderson Scott , Niesman Michael , Zwick Laura , Jessen Bart A.
Published: May 2006

Cyclin-dependent kinases (cdks) play a crucial role in cell cycle regulation and are considered promising targets for cancer therapy. Intravenous administration of AG-012986, a pan-cyclin-dependent kinase inhibitor (cdki), resulted in unexpected retinal and peripheral nerve toxicity in mice. AG-012986 was administered daily to CD-1 or B6C3F1 mice for 5 consecutive days. Mice were euthanized 24 h after the last dose (study day 6) or after a 21-day post-dose period (study day 26). Compound related microscopic findings were seen in the sciatic nerves (axonal degeneration) of both strains and in the retina (retinal degeneration/atrophy) of CD-1 mice only after the post-dose period. Although retinal degeneration/atrophy was not detected by routine histology in mice euthanized on day 6, apoptotic retinal cells were evident at this time using TUNEL assay. To our knowledge retinal or peripheral nerve toxicity secondary to the administration of cdkis has not been previously reported. Although the pathogenesis of these lesions is unclear, the toxicities may reflect the unique profile of cdk inhibition, off-target kinase inhibition or receptor binding, or metabolism/distribution properties of AG-012986. Multi-targeted-inhibitors may interfere with cdks and other kinases involved in a wide range of functions other than cell cycle regulation, which could result in unexpected toxicities that may hinder their clinical applications.
A ‘Best Practices’ Approach to Neuropathologic Assessment in Developmental Neurotoxicity Testing—for Today
Authors: Bolon Brad , Garman Robert , Jensen Karl , Krinke Georg , Stuart Barry ,   An Ad Hoc Working Group of the STP Scientific and Regulatory Policy Committee
Published: May 2006

A key trait of developmental neurotoxicants is their ability to cause structural lesions in the immature nervous system. Thus, neuropathologic assessment is an essential element of developmental neurotoxicity (DNT) studies that are designed to evaluate chemically-induced risk to neural substrates in young humans. The guidelines for conventional DNT assays have been established by regulatory agencies to provide a flexible scaffold for conducting such studies; recent experience has launched new efforts to update these recommendations. The present document was produced by an ad hoc subcommittee of the Society of Toxicologic Pathology (STP) tasked with examining conventional methods used in DNT neuropathology in order to define the ‘best practices’ for dealing with the diverse requirements of both national (EPA) and international (OECD) regulatory bodies. Recommendations (including citations for relevant neurobiological and technical references) address all aspects of the DNT neuropathology examination: study design; tissue fixation, collection, processing, and staining; qualitative and quantitative evaluation; statistical analysis; proper control materials; study documentation; and personnel training. If followed, these proposals will allow pathologists to meet the need for a sound risk assessment (balanced to address both regulatory issues and scientific considerations) in this field today while providing direction for the research needed to further refine DNT neuropathology ‘best practices’ in the future.
Molecular Biology of the Nasal Airways: How Do We Assess Cellular and Molecular Responses in the Nose?
Authors: Genter Mary Beth
Published: May 2006

We summarize studies herein that relate to use of molecular techniques to assess mechanism of toxicant and carcinogen action on the nasal mucosa. Specifically, we present the results of an in vivo mutagenesis assay with the herbicide alachlor, which causes olfactory mucosal tumors in rats following dietary administration. A positive response was found in olfactory mucosa after 3 mo of treatment. There was no increase in mutant frequency in the adjacent nasal respiratory mucosa or in liver, which are both non-target tissues for alachlor carcinogenesis. We also summarize previous findings of gene expression studies. One on these was a GeneChip experiment aimed at elucidating the mechanism of alachlor olfactory carcinogenesis, wherein we found that oxidative stress and gelatinase genes were upregulated early in the carcinogenic process, while genes consistent with activation of Wnt signaling were activated later in the carcinogenic process. The final example presented summarizes the results of a microarray experiment designed to identify novel olfactory genes involved in the plasticity of the olfactory mucosa. Those studies identified novel olfactory mucosal genes including Sgpl1 and Pon1. In each instance, precise sampling is emphasized and proper controls are discussed, and examples of independent means of validation of genomics experiments are presented.
Assessment of obesity status in outpatients from three disease states
Authors: Haroun Dalia , Wells Jonathan C. K. , Lau Candice , Hadji‐Lucas Elli , Lawson Margaret S.
Published: May 2006

Aim: To assess obesity status in patients with cystic fibrosis (CF), human immunodeficiency virus (HIV) and various metabolic disorders (MD), through comparison against a) UK reference data and b) contemporary healthy children. Methods: Weight, height, waist circumference (WC), and triceps (TRI) and sub‐scapular (SUBS) skinfold thickness were measured in a total of 57 healthy, 49 HIV, 68 MD and 49 CF children. Using published reference data, standard deviation scores (SDS) were calculated. Results: CF patients had weight, height and BMI SDS significantly below zero. MD patients had height SDS significantly below, and BMI SDS significantly above, zero. Healthy children had BMI SDS significantly above zero. In all three patient groups and healthy children, TRI and WC SDS were significantly above zero. SUBS SDS was also significantly above zero in patients with MD and HIV. WC SDS was greater in patients than in healthy children, but only significantly so for the MD children.

Conclusion: In all three patient groups, even those associated with reduced stature or reduced weight, indices of fatness were significantly increased relative to reference data. The tendency to central fatness was evident in healthy children, but was more extreme in patients, especially those with MD.
Rapid infancy weight gain and subsequent obesity: Systematic reviews and hopeful suggestions
Authors: Ong Ken K. , Loos Ruth J. F.
Published: May 2006

In a systematic review, we identified 21 separate studies with data on the association between rapid infancy weight gain, up to age 2 y, and subsequent obesity risk. Uniformly all studies reported significant positive associations. We transformed the reported effect sizes to a standard infancy weight gain exposure, and found that further differences in study design accounted for much of the variation in risk. An accompanying paper by Melinda Yeung reminds us that there are benefits of postnatal catch‐up growth in certain populations, and suggests that genetic and nutritional factors could moderate the unhealthy translation of rapid infancy weight gain to visceral fat and insulin resistance. Further evidence is needed, and we will need to rigorously test the benefits and risks of any interventions. However, the concept of “healthy” rapid catch‐up infancy growth is an attractive prospect.

Conclusion: Rapid infancy weight gain is consistently associated with increased subsequent obesity risk, but the predictive ability of different weight gain cut‐offs needs to be tested.
Low‐dose warfarin for the prevention of central line‐associated thromboses in children with malignancies—a randomized, controlled study
Authors: Ruud Ellen , Holmstrøm Henrik , De Lange Charlotte , Hogstad Ellen M. , Wesenberg Finn
Published: May 2006

Background: Central venous lines (CVLs) are essential in the care of children with malignancies, but are associated with venous thromboembolism (VTE) and infections. Effective and safe prophylactic approaches are deficient. Aim: To perform a study of adjusted low‐dose warfarin for the prevention of CVL‐related VTE in children with malignancies. Methods: Children with newly diagnosed cancer, a CVL in a jugular vein and an expected treatment period of over 6 mo were eligible for the study. Participants were randomized to low‐dose warfarin, with intended international normalized ratio (INR) 1.3–1.9, or to a control group. Primary outcome was VTE in a jugular vein diagnosed by ultrasonography at 1, 3 and 6 mo after inclusion. Secondary outcome was CVL‐related infections, mainly measured as days on antibiotics or positive blood cultures. Results: The study enrolled 73 children, and 62 completed it fully. Asymptomatic CVL‐related VTE was frequent (42%), but often transient. Regardless of severity, timing and duration, CVL‐related VTE was equally frequent among children on warfarin as compared to controls (p=0.44). Low‐dose warfarin (p=0.59) or jugular CVL‐related VTE (p=0.91) did not have any impact on days on antibiotics, but we observed a tendency towards an association between CVL‐related VTE and positive blood cultures (p=0.15).

Conclusion: Our randomized study of low‐dose oral anticoagulation for the prevention of CVL‐related asymptomatic VTE in children with cancer did not show any benefit of warfarin adjusted to maintain INR between 1.3 and 1.9.
Assembly of the eastern North American herpetofauna: new evidence from lizards and frogs
Authors: Robert Macey J , Schulte James A , Strasburg Jared L , Brisson Jennifer A , Larson Allan , Ananjeva Natalia B , Wang Yuezhao , Parham James F , Papenfuss Theodore J
Published: May 2006

Darwin first recognized the importance of episodic intercontinental dispersal in the establishment of worldwide biotic diversity. Faunal exchange across the Bering Land Bridge is a major example of such dispersal. Here, we demonstrate with mitochondrial DNA evidence that three independent dispersal events from Asia to North America are the source for almost all lizard taxa found in continental eastern North America. Two other dispersal events across Beringia account for observed diversity among North American ranid frogs, one of the most species-rich groups of frogs in eastern North America. The contribution of faunal elements from Asia via dispersal across Beringia is a dominant theme in the historical assembly of the eastern North American herpetofauna.
Seed size variability: from carob to carats
Authors: Turnbull Lindsay A , Santamaria Luis , Martorell Toni , Rallo Joan , Hector Andy
Published: May 2006

The seeds of various plants were used as weights because their mass reputedly varies so little. Carob (
Ceratonia siliqua
), which has given its name to the carat, is particularly famous in this regard. But are carob seeds unusually constant in weight and, if not, how did the myth arise? The variability of seeds sampled from a collection of carob trees (CV=23%) was close to the average of 63 species reviewed from the literature (CV=25%). However, in a perception experiment observers could discriminate differences in carob seed weight of around 5% by eye demonstrating the potential for humans to greatly reduce natural variation. Interestingly, the variability of pre-metrication carat weight standards is also around 5% suggesting that human rather than natural selection gave rise to the carob myth.
Ballooning dispersal in arthropod taxa with convergent behaviours: dynamic properties of ballooning silk in turbulent flows
Authors: Reynolds A.M , Bohan D.A , Bell J.R
Published: May 2006

We present a new model of ballooning behaviour in arthropods in which draglines are regarded as being extendible and completely flexible. Our numerical simulations reveal that silk draglines within turbulent flows can become twisted and stretched into highly contorted shapes. Ballooners are therefore predicted to have little control over their aerodynamic drag and their dispersal within the atmospheric boundary layer. Dragline length is crucial only at lift-off. This prediction runs counter to that of Humphrey who suggested that the length of
rigid
draglines can be used to control dispersal. In contrast with Humphrey's model, the new model accounts naturally for the large distances travelled by some ballooners.
Cooperative growth regulation in coral-dwelling fishes
Authors: Munday Philip L , Cardoni Adrian M , Syms Craig
Published: May 2006

Dominant individuals often grow faster than subordinates because they gain a greater share of important resources. However, dominants should also strategically adjust their growth rates, relative to the size of subordinates, if this improves their reproductive success. Here, we show that individuals in breeding pairs of the coral-dwelling fishGobiodon histrioregulate their growth to reduce the size difference between partners. In pairs where one individual was larger than the other, the smaller individual increased its growth rate and the larger individual decreased its growth rate, compared to individuals in size-matched pairs. The reproductive success of breeding pairs is limited by the size of the smallest individual in the pair. Therefore, it appears that the larger individual trades-off its own growth against that of the smaller individual, thereby improving the reproductive success of both individuals in the pair. This demonstrates a remarkable ability of individuals to strategically adjust their body size to suit the local social environment, and reveals a novel mechanism for size-assortative mating.
The magnetic compass mechanisms of birds and rodents are based on different physical principles
Authors: Thalau Peter , Ritz Thorsten , Burda Hynek , Wegner Regina E , Wiltschko Roswitha
Published: May 2006

Recently, oscillating magnetic fields in the MHz-range were introduced as a useful diagnostic tool to identify the mechanism underlying magnetoreception. The effect of very weak high-frequency fields on the orientation of migratory birds indicates that the avian magnetic compass is based on a radical pair mechanism. To analyse the nature of the magnetic compass of mammals, we tested rodents, Ansell's mole-rats, using their tendency to build their nests in the southern part of the arena as a criterion whether or not they could orient. In contrast to birds, their orientation was not disrupted when a broad-band field of 0.1–10 MHz of 85 nT or a 1.315 MHz field of 480 nT was added to the static geomagnetic field of 46 000 nT. Even increasing the intensity of the 1.315 MHz field (Zeeman frequency in the local geomagnetic field) to 4800 nT, more than a tenth of the static field, the mole-rats remained unaffected and continued to build their nests in the south. These results indicate that in contrast to that of birds, their magnetic compass does not involve radical pair processes; it seems to be based on a fundamentally different principle, which probably involves magnetite.
An application of interval-valued neural networks to a regression problem
Authors: Chetwynd D , Worden K , Manson G
Published: May 2006

This paper is concerned with exploiting uncertainty in order to develop a robust regression algorithm for a pre-sliding friction process based on a Nonlinear Auto-Regressive with eXogenous inputs neural network. Essentially, it is shown that using an interval-valued neural network allows a trade-off between the model error and the interval width of the network weights or a ‘degree of uncertainty’ parameter. The neural network weights are replaced by interval variables and cannot therefore be derived from a conventional optimization algorithm; in this case, the problem is solved by using differential evolution. The paper also shows how to implement the idea of ‘opportunity’ as used in Ben-Haim's information-gap theory.
African cichlid fish: a model system in adaptive radiation research
Authors: Seehausen Ole
Published: May 2006

The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory. The past few years have seen major advances in the phylogenetics, evolutionary biogeography and ecology of cichlid fish. Most of this work has concentrated on the most diverse radiations. Unfortunately, a large number of small radiations and ‘non-radiations’ have been overlooked, potentially limiting the contribution of the cichlid system to our understanding of speciation and adaptive radiation. I have reviewed the literature to identify 33 intralacustrine radiations and 76 failed radiations. For as many as possible I collected information on lake size, age and phylogenetic relationships. I use these data to address two questions: (i) whether the rate of speciation and the resulting species richness are related to temporal and spatial variation in ecological opportunity and (ii) whether the likelihood of undergoing adaptive radiation is similar for different African cichlid lineages. The former is a key prediction of the ecological theory of adaptive radiation that has been presumed true but remains untested for cichlid radiations. The second is based on the hypothesis that the propensity of cichlids to radiate is due to a key evolutionary innovation shared by all African cichlids. The evidence suggests that speciation rate declines through time as niches get filled up during adaptive radiation: young radiations and early stages of old radiations are characterized by high rates of speciation, whereas at least 0.5 Myr into a radiation speciation becomes a lot less frequent. The number of species in cichlid radiations increases with lake size, supporting the prediction that species diversity increases with habitat heterogeneity, but also with opportunity for isolation by distance. Finally, the data suggest that the propensity to radiate within lakes is a derived property that evolved during the evolutionary history of some African cichlids, and the appearance of which does not coincide with the appearance of proposed key innovations in morphology and life history.
Modelling dispersal of a temperate insect in a changing climate
Authors: Walters Richard J , Hassall Mark , Telfer Mark G , Hewitt Godfrey M , Palutikof Jean P
Published: May 2006

We construct a novel individual-based random-walk model to assess how predicted global climate change might affect the dispersal rates of a temperate insect. Using a novel approach we obtained accurate field measurements of daily movements for individuals over time to parameterize our model. Males were found to move significantly further on average than females. Significant variation in movement was evident among individuals; the most dispersive individuals moved up to five (females) and seven (males) times as far on average as the least dispersive individuals. Mean relative daily movement of both males and females were exponentially related to maximum daily temperature recorded within the grass sward. Variability, both within and among individuals, in relative daily movement was incorporated into the model using gamma probability distributions. Resultant dispersal functions for seasonal movement are predicted to be highly leptokurtic, which agrees well with observations from the field. Predictions of the model suggest that for populations at the polewards edge of the current range an increase of 3–5 °C in daily maximum temperature may increase the proportion of long-distance dispersers (those characterized as comprising the top 0.1% of furthest dispersing individuals under local conditions experienced during the 1963–1990 period) by up to 70%.
A UV signal of offspring condition mediates context-dependent parental favouritism
Authors: Bize Pierre , Piault Romain , Moureau Benoît , Heeb Philipp
Published: May 2006

As fitness returns during a breeding attempt are context-dependent, parents are predicted to bias their food allocation within a brood from poor towards good condition nestlings when environmental conditions deteriorate. We tested this prediction in the Alpine swift and the European starling, two migratory bird species, by modifying an ultraviolet (UV) visual signal of condition in nestlings and exploring how parents allocate food to their young as the season progresses. We show in both species that: (i) UV light reflected by the body skin of offspring positively correlates with their stature (i.e. body mass and skeletal size) and (ii) parental favouritism towards young with more UV reflective skin gradually increases as the season progresses. Early-breeding parents supplied food preferentially to UV pale (i.e. small stature) nestlings, whereas late-breeding parents favoured UV bright offspring (i.e. large stature). These results emphasize that parents use UV signals of offspring condition to adjust their feeding strategies depending on the ecological context.
The origin and evolution of Archaea: a state of the art
Authors: Gribaldo Simonetta , Brochier-Armanet Celine
Published: May 2006

Environmental surveys indicate that the Archaea are diverse and abundant not only in extreme environments, but also in soil, oceans and freshwater, where they may fulfil a key role in the biogeochemical cycles of the planet. Archaea display unique capacities, such as methanogenesis and survival at temperatures higher than 90 °C, that make them crucial for understanding the nature of the biota of early Earth. Molecular, genomics and phylogenetics data strengthen Woese's definition of Archaea as a third domain of life in addition to Bacteria and Eukarya. Phylogenomics analyses of the components of different molecular systems are highlighting a core of mainly vertically inherited genes in Archaea. This allows recovering a globally well-resolved picture of archaeal evolution, as opposed to what is observed for Bacteria and Eukarya. This may be due to the fact that no rapid divergence occurred at the emergence of present-day archaeal lineages. This phylogeny supports a hyperthermophilic and non-methanogenic ancestor to present-day archaeal lineages, and a profound divergence between two major phyla, the Crenarchaeota and the Euryarchaeota, that may not have an equivalent in the other two domains of life. Nanoarchaea may not represent a third and ancestral archaeal phylum, but a fast-evolving euryarchaeal lineage. Methanogenesis seems to have appeared only once and early in the evolution of Euryarchaeota. Filling up this picture of archaeal evolution by adding presently uncultivated species, and placing it back in geological time remain two essential goals for the future.
Eukaryotic organisms in Proterozoic oceans
Authors: Knoll A.H , Javaux E.J , Hewitt D , Cohen P
Published: May 2006

The geological record of protists begins well before the Ediacaran and Cambrian diversification of animals, but the antiquity of that history, its reliability as a chronicle of evolution and the causal inferences that can be drawn from it remain subjects of debate. Well-preserved protists are known from a relatively small number of Proterozoic formations, but taphonomic considerations suggest that they capture at least broad aspects of early eukaryotic evolution. A modest diversity of problematic, possibly stem group protists occurs inca1800–1300 Myr old rocks. 1300–720 Myr fossils document the divergence of major eukaryotic clades, but only with the Ediacaran–Cambrian radiation of animals did diversity increase within most clades with fossilizable members. While taxonomic placement of many Proterozoic eukaryotes may be arguable, the presence of characters used for that placement is not. Focus on character evolution permits inferences about the innovations in cell biology and development that underpin the taxonomic and morphological diversification of eukaryotic organisms.
Identification of novel murine parvovirus strains by epidemiological analysis of naturally infected mice
Authors: Besselsen David G. , Romero Melissa J. , Wagner April M. , Henderson Kenneth S. , Livingston Robert S.
Published: May 2006

Random-source DNA samples obtained from naturally infected laboratory mice (n=381) were evaluated by PCR and RFLP analysis to determine the prevalence of murine parvovirus strains circulating in contemporary laboratory mouse colonies. Mouse parvovirus (MPV) was detected in 77 % of samples,Minute virus of mice(MVM) was detected in 16 % of samples and both MVM and MPV were detected in 7 % of samples. MVMm, a strain recently isolated from clinically ill NOD-μchain knockout mice, was detected in 91 % of MVM-positive samples, with the Cutter strain of MVM (MVMc) detected in the remaining samples. The prototypic and immunosuppressive strains of MVM were not detected in any of the samples. MPV-1 was detected in 78 % of the MPV-positive samples and two newly identified murine parvoviruses, tentatively named MPV-2 and MPV-3, were detected in 21 and 1 % of the samples, respectively. The DNA sequence encompassing coding regions of the viral genome and the predicted protein sequences for MVMm, MPV-2 and MPV-3 were determined and compared with those of other rodent parvovirus strains and LuIII parvovirus. The genomic organization for the newly identified viral strains was similar to that of other rodent parvoviruses, and nucleotide sequence identities indicated that MVMm was most similar to MVMc (96.1 %), MPV-3 was most similar to hamster parvovirus (HaPV) (98.1 %) and MPV-2 was most similar to MPV-1 (95.3 %). The genetic similarity of MPV-3 and HaPV suggests that HaPV epizootics in hamsters may result from cross-species transmission, with mice as the natural rodent host for this virus.
Quantifying antagonistic epistasis in a multifunctional RNA secondary structure of the Rous sarcoma virus
Authors: Sanjuán Rafael
Published: May 2006

Recent studies have suggested that antagonistic epistasis (i.e. mutations having smaller effects in combination than alone) may be common among RNA viruses, in contrast to other biological systems. Here, by re-analysing previously published data from a random viral library, selection and epistasis coefficients were estimated in the U5-IR stem and loop of theRous sarcoma virus, a region that adopts a conserved secondary structure and is involved in various essential steps of viral infection. The estimated mutational fitness effects are extremely high and genetic interactions are antagonistic on average. This pattern might be representative of RNA virus genomes, which show high compaction and frequent secondary structures. The implications for RNA virus adaptability are explored.
Nidovirus transcription: how to make sense…?
Authors: Pasternak Alexander O. , Spaan Willy J. M. , Snijder Eric J.
Published: May 2006

Many positive-stranded RNA viruses use subgenomic mRNAs to express part of their genetic information. To produce structural and accessory proteins, members of the order Nidovirales (corona-, toro-, arteri- and roniviruses) generate a 3′ co-terminal nested set of at least three and often seven to nine mRNAs. Coronavirus and arterivirus subgenomic transcripts are not only 3′ co-terminal but also contain a common 5′ leader sequence, which is derived from the genomic 5′ end. Their synthesis involves a process of discontinuous RNA synthesis that resembles similarity-assisted RNA recombination. Most models proposed over the past 25 years assume co-transcriptional fusion of subgenomic RNA leader and body sequences, but there has been controversy over the question of whether this occurs during plus- or minus-strand synthesis. In the latter model, which has now gained considerable support, subgenomic mRNA synthesis takes place from a complementary set of subgenome-size minus-strand RNAs, produced by discontinuous minus-strand synthesis. Sense–antisense base-pairing interactions between short conserved sequences play a key regulatory role in this process. In view of the presumed common ancestry of nidoviruses, the recent finding that ronivirus and torovirus mRNAs do not contain a common 5′ leader sequence is surprising. Apparently, major mechanistic differences must exist between nidoviruses, which raises questions about the functions of the common leader sequence and nidovirus transcriptase proteins and the evolution of nidovirus transcription. In this review, nidovirus transcription mechanisms are compared, the experimental systems used are critically assessed and, in particular, the impact of recently developed reverse genetic systems is discussed.
Characterization of proteinase K-resistant N- and C-terminally truncated PrP in Nor98 atypical scrapie
Authors: Klingeborn Mikael , Wik Lotta , Simonsson Magnus , Renström Lena H. M. , Ottinger Therese , Linné Tommy
Published: May 2006

An increasing number of scrapie cases with atypical characteristics, designated Nor98, have recently been recognized. Here, the proteinase K (PK)-resistant prion protein (PrP) fragments from two Swedish cases of Nor98 atypical scrapie have been characterized. The prominent, fast-migrating band in the distinct Nor98 Western immunoblot electrophoretic profile was determined to be of 7 kDa in size and was accordingly designated Nor98-PrP7. The antigenic composition of Nor98-PrP7, as assayed by a panel of anti-PrP antibodies, revealed that this fragment comprised a mid-region of PrP from around aa 85 to 148. N- and C-terminally truncated fragments spanning the mid-region of PrP have only been observed in the genetic prion disorder Gerstmann–Sträussler–Scheinker disease. It is shown here that the long-term PK resistance of Nor98-PrP7 is reduced compared with that of PrPresin classical scrapie. Enzymic deglycosylation did not change the distinct electrophoretic profile of Nor98-PrP7. A previously unidentified, PK-resistant, C-terminal PrP fragment of around 24 kDa was detected and its PK resistance was investigated. After deglycosylation, this fragment migrated as a 14 kDa polypeptide and was designated PrP-CTF14. Antigenic determination and the size of 14 kDa suggested a fragment spanning approximately aa 120–233. The existence of two PK-resistant PrP fragments, Nor98-PrP7 and PrP-CTF14, that share an overlapping region suggests that at least two distinct PrP conformers with different PK-resistant cores are present in brain extracts from Nor98-affected sheep. The structural gene of PrP in three Nor98-affected sheep was analysed, but no mutations were found that could be correlated to the aberrant PK-resistant profile observed.
Characterization of a new densovirus infecting the German cockroach, Blattella germanica
Authors: Mukha D. V. , Chumachenko A. G. , Dykstra M. J. , Kurtti T. J. , Schal C.
Published: May 2006

A new DNA virus (Parvoviridae:Densovirinae,Densovirus) was isolated and purified from descendants of field-collected German cockroaches,Blattella germanica. Viral DNA and cockroach tissues infected withB. germanicadensovirus (BgDNV) were examined by electron microscopy. Virus particles, about 20 nm in diameter, were observed both in the nucleus and in the cytoplasm of infected cells. Virus DNA proved to be a linear molecule of about 1.2 μm in length.BgDNV isolated from infected cockroaches infected successfully and could be maintained in BGE-2, aB. germanicacell line. The completeBgDNV genome was sequenced and analysed. Five open reading frames (ORFs) were detected in the 5335 nt sequence: two ORFS that were on one DNA strand encoded structural capsid proteins (69.7 and 24.8 kDa) and three ORFs that were on the other strand encoded non-structural proteins (60.2, 30.3 and 25.9 kDa). Three putative promoters and polyadenylation signals were identified. Structural analysis of the inverted terminal repeats revealed the presence of extended palindromes. The genome structure ofBgDNV was compared with that of other members of the familyParvoviridae; the predicted amino acid sequences were aligned and subjected to phylogenetic analyses.
Simian varicella virus gene 28 and 29 promoters share a common upstream stimulatory factor-binding site and are induced by IE62 transactivation
Authors: Ou Yang , Gray Wayne L.
Published: May 2006

Simian varicella virus (SVV) is a neurotropic alphaherpesvirus that causes a natural, varicella-like disease in non-human primates. After resolution of the primary disease, SVV, like its human counterpart, varicella-zoster virus (VZV), establishes latent infection in the neural ganglia of the host. In this study, gene expression of SVV open reading frames (ORFs) 28 and 29, which encode the viral DNA polymerase and DNA-binding protein, respectively, was characterized during lytic infection of Vero cells. The results indicate that the intergenic region controlling gene 28 and 29 expression includes overlapping, divergent promoters. The ORF 28 and 29 promoters are active in SVV-infected Vero cells, but not in uninfected cells. The SVV immediate-early gene 62 (IE62) product transactivates ORF 28 and 29 expression, and a cellular upstream stimulatory factor-binding site is important for efficient IE62 induction of genes 28 and 29. DNA sequence analysis of the 185 bp intergenic region identified putative cellular transcription factor-binding sites. Transcriptional analysis mapped ORF 28 and 29 RNA start sites. A recombinant SVV was employed to demonstrate that the ORF 29 promoter can express a heterologous gene (green fluorescent protein) when inserted into a novel site (the ORF 12/13 intergenic region) within the SVV genome. The findings demonstrate similarities between SVV and VZV ORF 28/29 expression and indicate that the simian varicella model may be useful to investigate the differential regulation of viral genes during lytic and latent infection.
A new subtype of hepatitis C virus genotype 1: complete genome and phylogenetic relationships of an Equatorial Guinea isolate
Authors: Bracho Maria Alma , Carrillo-Cruz Francy Yolima , Ortega Enrique , Moya Andrés , González-Candelas Fernando
Published: May 2006

Hepatitis C virus (HCV) is the leading cause of chronic liver disease and is associated with hepatocellular carcinoma. However, there have been few studies on the distribution and genetic diversity of HCV isolates in non-developed countries. Here, the complete genome sequence of an HCV genotype 1 isolate from Equatorial Guinea is reported, the first complete HCV-1 genome of African origin. Phylogenetic analysis revealed that this sequence always grouped with sequences of genotype 1, but did not group clearly with any subtype described so far. An analysis of partial NS5B gene sequences with additional sequences of African origin also failed to find close similarities between the new sequence and any previously known isolate. Genetic divergence of the coding region of this new sequence with respect to the recognized subtypes of HCV-1 ranged from 20 to 22 %. It is proposed that this isolate is a representative of a new, distinct variant of HCV subtype 1.
Recombinant wild-type measles virus containing a single N481Y substitution in its haemagglutinin cannot use receptor CD46 as efficiently as that having the haemagglutinin of the Edmonston laboratory strain
Authors: Seki Fumio , Takeda Makoto , Minagawa Hiroko , Yanagi Yusuke
Published: May 2006

Signalling lymphocyte activation molecule (SLAM) acts as a cellular receptor forMeasles virus(MV). The recombinant MV, based on a SLAM-using clinical isolate in which asparagine at position 481 of the haemagglutinin was replaced with tyrosine, was generated. Characterization of this recombinant virus revealed that the N481Y substitution in the haemagglutinin allowed it to utilize CD46 as an alternative receptor, but that its ability to use CD46 was rather low in CD46+SLAM−cell lines compared with that of the recombinant virus possessing the haemagglutinin of the Edmonston laboratory strain. Thus, an N481Y substitution alone may not be sufficient to make SLAM-using MVs use CD46 efficiently, suggesting that further substitutions in the haemagglutinin are required for them to grow efficiently in CD46+cells like the Edmonston strain. This may be a reason why few CD46-using MVs are detectedin vivo.