bluuebunny/crossref_metadata_2025 huggingface dataset:
NrdI, a flavodoxin involved in maintenance of the diferric-tyrosyl radical cofactor in
Escherichia coli
class Ib ribonucleotide reductase
Authors: Cotruvo Joseph A. , Stubbe JoAnne
Published: September 2008

Ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to deoxynucleotides and is essential in all organisms. Class I RNRs consist of two homodimeric subunits: α2 and β2. The α subunit contains the site of nucleotide reduction, and the β subunit contains the essential diferric-tyrosyl radical (Y•) cofactor.
Escherichia coli
contains genes encoding two class I RNRs (Ia and Ib) and a class III RNR, which is active only under anaerobic conditions. Its class Ia RNR, composed of NrdA (α) and NrdB (β), is expressed under normal aerobic growth conditions. The class Ib RNR, composed of NrdE (α) and NrdF (β), is expressed under oxidative stress and iron-limited growth conditions. Our laboratory is interested in pathways of cofactor biosynthesis and maintenance in class I RNRs and modulation of Y• levels as a means of regulating RNR activity. Our recent studies have implicated a [2Fe2S]-ferredoxin, YfaE, in the NrdB diferric-Y• maintenance pathway and possibly in the biosynthetic and regulatory pathways. Here, we report that NrdI is a flavodoxin counterpart to YfaE for the class Ib RNR. It possesses redox properties unprecedented for a flavodoxin (
E
ox/sq
= −264 ± 17 mV and
E
sq/hq
= −255 ± 17 mV) that allow it to mediate a two-electron reduction of the diferric cluster of NrdF via two successive one-electron transfers. Data presented support the presence of a distinct maintenance pathway for NrdEF, orthogonal to that for NrdAB involving YfaE.
Teleantagonism: A pharmacodynamic property of the primary nociceptive neuron
Authors: Funez Mani I. , Ferrari Luiz F. , Duarte Djane B. , Sachs Daniela , Cunha Fernando Q. , Lorenzetti Berenice B. , Parada Carlos A. , Ferreira Sérgio H.
Published: September 2008

Previous work from our group showed that intrathecal (i.t.) administration of substances such as glutamate, NMDA, or PGE2induced sensitization of the primary nociceptive neuron (PNN hypernociception) that was inhibited by a distal intraplantar (i.pl.) injection of either morphine or dipyrone. This pharmacodynamic phenomenon is referred to in the present work as “teleantagonism”. We previously observed that the antinociceptive effect of i.t. morphine could be blocked by injecting inhibitors of the NO signaling pathway in the paw (i.pl.), and this effect was used to explain the mechanism of opioid-induced peripheral analgesia by i.t. administration. The objective of the present investigation was to determine whether this teleantagonism phenomenon was specific to this biochemical pathway (NO) or was a general property of the PNNs. Teleantagonism was investigated by administering test substances to the two ends of the PNN (i.e., to distal and proximal terminals; i.pl. plus i.t. or i.t. plus i.pl. injections). We found teleantagonism when: (i) inhibitors of the NO signaling pathway were injected distally during the antinociception induced by opioid agonists; (ii) a nonselective COX inhibitor was tested against PNN sensitization by IL-1β; (iii) selective opioid-receptor antagonists tested against antinociception induced by corresponding selective agonists. Although the dorsal root ganglion seems to be an important site for drug interactions, the teleantagonism phenomenon suggests that, in PNNs, a local sensitization spreads to the entire cell and constitutes an intriguing and not yet completely understood pharmacodynamic property of this group of neurons.
Warlords and militarism in Chad
Authors: Charlton Roger , May Roy
Published: September 2008

After considering the inadequacies of the prevailing concern in African studies with violence and the collapse of the postcolonial state, the authors argue that the uses made of concepts of ‘militarism’ and ‘militarisation’ are equally confused and inadequate, particularly in explaining recent Chad history. They suggest an alternative approach, the elaboration of the warlord model used to discuss Chinese history between 1916 and 1928. They argue that there are striking parallels between the China of that time and Chad from the late seventies in the form of the collapse of central control, the rise of regional centres of power based on personalised rule and military force, and the consequent prevalence of a politics of conflict and war.
Warlordism in China
Authors: Roberts J.A.G.
Published: September 2008

The Reviewis pleased to include this succinct summary of the elements defining, and the debates surrounding, the warlord phenomenon in China's history. Dr Roberts assesses the various ways in which the ‘classical’ warlordism of the period from 1916 to 1928 has been understood and interpreted. The focus is on the collapse of central state authority and the rise of provincial or regional military rulers exercising considerable power and autonomy over the locality. The paper presents a lucid account of how the origins of warlordism have been explained, what are considered to be the main characteristics of warlords and warlordism and what their effects were on the society and polity of China. A number of points raise interesting questions about the extent to which the concept might usefully be applied to some current problems in Africa. These include the decay of nationalism into regionalism and sectarianism; the extent to which such provincial power centres link up with foreign interests; the disintegration of the military hierarchy and the rise of lower‐ranked officer strata; and the burdens imposed on civil society by the extortion and violence occasioned by warlordism and by the obstacles it places in the way of political solutions to problems. The paper concludes with a brief consideration of alternative possibilities that were thrown up in China by the ‘space’ created by the decline of political control which warlordism reflected and perpetuated.
Reviews
Authors: Simons David , Webster Eddie , Williams Roy
Published: September 2008

Unfree Labour and its Persistence into the Capitalist Era: A Critical Review of Recent Books by Robert Miles and Robin Cohen reviewed by Bob Currie The New Helots: Migrants in the International Division of Labourby Robin Cohen;Capitalism and Unfree Labour: Anomaly or Neccessity?by Robert Miles.

War and Society: The Militarisation of South Africaby Jacklyn Cock & Laurie Nathan (Eds); David Phillip, Cape Town, 1989

Coping with Rapid Urban Growth in Africa: An Annotated Bibliography in English and French on Policy and Management of Urban Affairs in the 1980sby Richard Stren with Claire Letemendia, translated by Claude Stren. Bibliography Series no.12, Centre for Developing Area Studies, McGill University, Montreal, 1986
Synaptotagmin-1 Utilizes Membrane Bending and SNARE Binding to Drive Fusion Pore Expansion
Authors: Lynch Kara L. , Gerona Roy R.L. , Kielar Dana M. , Martens Sascha , McMahon Harvey T. , Martin Thomas F.J.
Published: September 2008

In regulated vesicle exocytosis, SNARE protein complexes drive membrane fusion to connect the vesicle lumen with the extracellular space. The triggering of fusion pore formation by Ca2+ is mediated by specific isoforms of synaptotagmin (Syt), which employ both SNARE complex and membrane binding. Ca2+ also promotes fusion pore expansion and Syts have been implicated in this process but the mechanisms involved are unclear. We determined the role of Ca2+-dependent Syt-effector interactions in fusion pore expansion by expressing Syt-1 mutants selectively altered in Ca2+-dependent SNARE binding or in Ca2+-dependent membrane insertion in PC12 cells that lack vesicle Syts. The release of different-sized fluorescent peptide-EGFP vesicle cargo or the vesicle capture of different-sized external fluorescent probes was used to assess the extent of fusion pore dilation. We found that PC12 cells expressing partial loss-of-function Syt-1 mutants impaired in Ca2+-dependent SNARE binding exhibited reduced fusion pore opening probabilities and reduced fusion pore expansion. Cells with gain-of-function Syt-1 mutants for Ca2+-dependent membrane insertion exhibited normal fusion pore opening probabilities but the fusion pores dilated extensively. The results indicate that Syt-1 uses both Ca2+-dependent membrane insertion and SNARE binding to drive fusion pore expansion.
Actin Filament Assembly by Myristoylated, Alanine-rich C Kinase Substrate–Phosphatidylinositol-4,5-diphosphate Signaling Is Critical for Dendrite Branching
Authors: Li Haimin , Chen Gang , Zhou Bing , Duan Shumin
Published: September 2008

Dendrites undergo extensive growth and branching at early stages, but relatively little is known about the molecular mechanisms underlying these processes. Here, we show that increasing the level of myristoylated, alanine-rich C kinase substrate (MARCKS), a prominent substrate of protein kinase C and a phosphatidylinositol-4,5-diphosphate [PI(4,5)P2] sequestration protein highly expressed in the brain, enhanced branching and growth of dendrites both in vitro and in vivo. Conversely, knockdown of endogenous MARCKS by RNA interference reduced dendritic arborization. Results from expression of different mutants indicated that membrane binding is essential for MARCKS-induced dendritic morphogenesis. Furthermore, MARCKS increased the number and length of filamentous actin-based filopodia along neurites, as well as the motility of filopodia, in a PI(4,5)P2-dependent manner. Time-lapse imaging showed that MARCKS increased frequency of filopodia initiation but did not affect filopodia longevity, suggesting that MARCKS may increase dendritic branching through its action on filopodia initiation. These findings demonstrate a critical role for MARCKS–PI(4,5)P2 signaling in regulating dendrite development.
Voa1p Functions in V-ATPase Assembly in the Yeast Endoplasmic Reticulum
Authors: Ryan Margret , Graham Laurie A. , Stevens Tom H.
Published: September 2008

The yeast Saccharomyces cerevisiae vacuolar ATPase (V-ATPase) is a multisubunit complex divided into two sectors: the V1sector catalyzes ATP hydrolysis and the V0sector translocates protons, resulting in acidification of its resident organelle. Four protein factors participate in V0assembly. We have discovered a fifth V0assembly factor, Voa1p (YGR106C); an endoplasmic reticulum (ER)-localized integral membrane glycoprotein. The role of Voa1p in V0assembly was revealed in cells expressing an ER retrieval-deficient form of the V-ATPase assembly factor Vma21p (Vma21pQQ). Loss of Voa1p in vma21QQ yeast cells resulted in loss of V-ATPase function; cells were unable to acidify their vacuoles and exhibited growth defects typical of cells lacking V-ATPase. V0assembly was severely compromised in voa1 vma21QQ double mutants. Isolation of V0–Vma21p complexes indicated that Voa1p associates most strongly with Vma21p and the core proteolipid ring of V0subunits c, c′, and c″. On assembly of the remaining three V0subunits (a, d, and e) into the V0complex, Voa1p dissociates from the now fully assembled V0–Vma21p complex. Our results suggest Voa1p functions with Vma21p early in V0assembly in the ER, but then it dissociates before exit of the V0–Vma21p complex from the ER for transport to the Golgi compartment.
The Cardiolipin Transacylase, Tafazzin, Associates with Two Distinct Respiratory Components Providing Insight into Barth Syndrome
Authors: Claypool Steven M. , Boontheung Pinmanee , McCaffery J. Michael , Loo Joseph A. , Koehler Carla M.
Published: September 2008

Mutations in the mitochondrial cardiolipin (CL) transacylase, tafazzin (Taz1p), result in the X-linked cardioskeletal myopathy, Barth syndrome (BTHS). The mitochondria of BTHS patients exhibit variable respiratory defects and abnormal cristae ultrastructure. The biochemical basis for these observations is unknown. In the absence of its target phospholipid, CL, a very large Taz1p complex is missing, whereas several discrete smaller complexes are still observed. None of the identified Taz1p complexes represents Taz1p homodimers. Instead, yeast Taz1p physically assembles in several protein complexes of distinct size and composition. The ATP synthase and AAC2, both required for oxidative phosphorylation, are identified in separate stable Taz1p complexes. In the absence of CL, each interaction is still detected albeit in reduced abundance compared with when CL is present. Taz1p is not necessary for the normal expression of AAC2 or ATP synthase subunits or assembly of their respective complexes. In contrast, the largest Taz1p complex requires assembled ATP synthase and CL. Mitochondria in Δtaz1 yeast, similar to ATP synthase oligomer mutants, exhibit altered cristae morphology even though ATP synthase oligomer formation is unaffected. Thus, the Taz1p interactome defined here provides novel insight into the variable respiratory defects and morphological abnormalities observed in mitochondria of BTHS patients.
Gene set enrichment analysis using linear models and diagnostics
Authors: Oron Assaf P. , Jiang Zhen , Gentleman Robert
Published: September 2008

Motivation: Gene-set enrichment analysis (GSEA) can be greatly enhanced by linear model (regression) diagnostic techniques. Diagnostics can be used to identify outlying or influential samples, and also to evaluate model fit and explore model expansion.

Results: We demonstrate this methodology on an adult acute lymphoblastic leukemia (ALL) dataset, using GSEA based on chromosome-band mapping of genes. Individual residuals, grouped or aggregated by chromosomal loci, indicate problematic samples and potential data-entry errors, and help identify hyperdiploidy as a factor playing a key role in expression for this dataset. Subsequent analysis pinpoints suspected DNA copy number abnormalities of specific samples and chromosomes (most prevalent are chromosomes X, 21 and 14), and also reveals significant expression differences between the hyperdiploid and diploid groups on other chromosomes (most prominently 19, 22, 3 and 13)—differences which are apparently not associated with copy number.

Availability: Software for the statistical tools demonstrated in this article is available as Bioconductor package GSEAlm.

Contact:  assaf.oron@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
In Response to Comment on ‘Network-constrained regularization and variable selection for analysis of genomic data’
Authors: Li Caiyan , Li Hongzhe
Published: September 2008

Contact: hongzhe@mail.med.upenn.edu
Debtor Nation: How Consumer Credit Built Postwar America
Authors: Hyman Louis
Published: September 2008

It is difficult to consider debt as having a history, because it seems like debt might be, as one popular historian of money in 1917 described it, a “semi-slavery . . . [which] existed before the dawn of history, and it exists to-day.” People, in a certain sense, have always lent money to one another: to a wayward brother, across a saloon bar, to a coworker. But even by 1917, as that popular history was written in the midst of world war, the ancient personal relationship of personal debt was changing into a modern impersonal one. My dissertation is about how what we call personal debt, that is debt incurred by individuals and not by businesses, went from being owed to other people to being owed to institutions, and what this has meant at the largest level about American capitalism.
Evolutionary conservation of mechanisms for neural regionalization, proliferation and interconnection in brain development
Authors: Reichert Heinrich
Published: September 2008

Comparative studies of brain development in vertebrate and invertebrate model systems demonstrate remarkable similarities in expression and action of developmental control genes during embryonic patterning, neural proliferation and circuit formation in the brain. Thus, comparable sets of developmental control genes are involved in specifying the early brain primordium as well as in regionalized patterning along its anteroposterior and dorsoventral axes. Furthermore, similar cellular and molecular mechanisms underlie the formation and proliferation of neural stem cell-like progenitors that generate the neurons in the central nervous systems. Finally, neural identity and some complex circuit interconnections in specific brain domains appear to be comparable in vertebrates and invertebrates and may depend on similar developmental control genes.
Exposure to infant scent lowers serum testosterone in father common marmosets (
Callithrix jacchus
)
Authors: Prudom Shelley L , Broz Carrie Ann , Schultz-Darken Nancy , Ferris Craig T , Snowdon Charles , Ziegler Toni Elaine
Published: September 2008

Common marmoset (
Callithrix jacchus
) males are bi-parental non-human primates that show extensive paternal behaviour. Fathers are in direct sensory contact with their infants during the natal period. We found that fathers exposed to isolated scents of their infant displayed a significant drop in serum testosterone levels within 20 min after exposure, whereas parentally naive males did not. These data suggest that infant's scent may have a causal role in regulating paternal testosterone in their fathers. This is the first study to demonstrate that olfactory cues have an acute effect on paternal care.
Natural beaches confer fitness benefits to nesting marine turtles
Authors: Pike David A
Published: September 2008

Coastal ecosystems provide vital linkages between aquatic and terrestrial habitats and thus support extremely high levels of biodiversity. However, coastlines also contain the highest densities of human development anywhere on the planet and are favoured destinations for tourists, creating a situation where the potential for negative effects on coastal species is extremely high. I gathered data on marine turtle reproductive output from the literature to determine whether coastal development negatively influences offspring production. Female loggerhead (
Caretta caretta
) and green turtles (
Chelonia mydas
) nesting on natural beaches (as opposed to beaches with permanent development) produce significantly more hatchling turtles per nest; all else being equal, females that successfully produce more offspring will have higher fitness than conspecifics producing fewer offspring. Thus, female marine turtles nesting on natural beaches probably have higher fitness than turtles nesting on developed beaches. Consequently, populations nesting on natural beaches may be able to recover more quickly from the historic population declines that have plagued marine turtles, and some species may recover more quickly than others.
Human plague in the USA: the importance of regional and local climate
Authors: Ben Ari Tamara , Gershunov Alexander , Gage Kenneth L , Snäll Tord , Ettestad Paul , Kausrud Kyrre L , Stenseth Nils Chr
Published: September 2008

A 56-year time series of human plague cases (
Yersinia pestis
) in the western United States was used to explore the effects of climatic patterns on plague levels. We found that the Pacific Decadal Oscillation (PDO), together with previous plague levels and above-normal temperatures, explained much of the plague variability. We propose that the PDO's impact on plague is conveyed via its effect on precipitation and temperature and the effect of precipitation and temperature on plague hosts and vectors: warmer and wetter climate leading to increased plague activity and thus an increased number of human cases. Our analysis furthermore provides insights into the consistency of plague mechanisms at larger scales.
Reproductive suppression in female cooperatively breeding cichlids
Authors: Heg Dik
Published: September 2008

Suppression by dominants of female subordinate reproduction has been found in many vertebrate social groups, but has rarely been shown experimentally. Here experimental evidence is provided for reproductive suppression in the group-living Lake Tanganyika cichlid
Neolamprologus pulcher
. Within groups of three unrelated females, suppression was due to medium- and small-sized females laying less frequently compared with large females, and compared with medium females in control pairs. Clutch size and average egg mass of all females depended on body size, but not on rank. In a second step, a large female was removed from the group and a very small female was added to keep the group size constant. The medium females immediately seized the dominant breeding position in the group and started to reproduce as frequently as control pairs, whereas clutch size and egg mass did not change. These results show that female subordinate cichlids are reproductively capable, but apparently suppressed with respect to egg laying. Nevertheless, some reproduction is tolerated, possibly to ensure continued alloparental care by subordinate females.
Methane emissions by alpine plant communities in the Qinghai–Tibet Plateau
Authors: Cao Guangmin , Xu Xingliang , Long Ruijun , Wang Qilan , Wang Changting , Du Yangong , Zhao Xinquan
Published: September 2008

For the first time to our knowledge, we report here methane emissions by plant communities in alpine ecosystems in the Qinghai–Tibet Plateau. This has been achieved through long-term field observations from June 2003 to July 2006 using a closed chamber technique. Strong methane emission at the rate of 26.2±1.2 and 7.8±1.1 μg CH
4
m
−2
 h
−1
was observed for a grass community in a
Kobresia humilis
meadow and a
Potentilla fruticosa
meadow, respectively. A shrub community in the
Potentilla
meadow consumed atmospheric methane at the rate of 5.8±1.3 μg CH
4
m
−2
 h
−1
on a regional basis; plants from alpine meadows contribute at least 0.13 Tg CH
4
yr
−1
in the Tibetan Plateau. This finding has important implications with regard to the regional methane budget and species-level difference should be considered when assessing methane emissions by plants.
Elevated levels of expression associated with regions of theDrosophilagenome that lack crossing over
Authors: Haddrill Penelope R , Waldron Fergal M , Charlesworth Brian
Published: September 2008

The recombinational environment influences patterns of molecular evolution through the effects of Hill–Robertson interference. Here, we examine genome-wide patterns of gene expression with respect to recombinational environment inDrosophila melanogaster. We find that regions of the genome lacking crossing over exhibit elevated levels of expression, and this is most pronounced for genes on the entirely non-crossing over fourth chromosome. We find no evidence for differences in the patterns of gene expression between regions of high, intermediate and low crossover frequencies. These results suggest that, in the absence of crossing over, selection to maintain control of expression may be compromised, perhaps due to the accumulation of deleterious mutations in regulatory regions. Alternatively, higher gene expression may be evolving to compensate for defective protein products or reduced translational efficiency.
Convict cichlids benefit from close proximity to another species of cichlid fish
Authors: Lehtonen Topi K
Published: September 2008

The coexistence of species with overlapping resource use is often thought to involve only negative fitness effects as a consequence of interspecific competition. Furthermore, the scarce empirical research on positive species interactions has predominantly focused on sessile organisms. Here, I experimentally assessed the effect of close proximity of a potential brood predator and competitor on reproductive success of a neotropical cichlid fish. I demonstrate that convict cichlid (
Archocentrus nigrofasciatus
) broods have a higher survival rate near territories of the Nicaragua cichlid (
Hypsophrys nicaraguensis
), and that escape from predation and nest takeovers is the most likely explanation for the decreased offspring mortality.
Ants under crowded conditions consume more energy
Authors: Cao Tuan T , Dornhaus Anna
Published: September 2008

Social insects live in colonies consisting of many workers, where worker interactions play an important role in regulating colony activities. Workers interact within the social space of the nest; therefore, constraints on nest space may alter worker behaviour and affect colony activities and energetics. Here we show in the antTemnothorax rugatulusthat changes in nest space have a significant effect on colony energetics. Colonies with restricted nest space showed a 14.2 per cent increase in metabolic rate when compared with the same colonies in large uncrowded nests. Our study highlights the importance of social space and shows that constraints on social space can significantly affect colony behaviour and energy use in ants. We discuss the implications of our findings regarding social insects in general.
Genetic covariation between effectiveness and cost of defence in aphids
Authors: Vorburger Christoph , Gouskov Alexandre , von Burg Simone
Published: September 2008

Ecological immunology distinguishes between the long-term evolutionary costs of possessing defences against parasites and the short-term costs of using them. Evolutionary biologists have typically focused on the former in the search for constraints on the evolution of resistance. Here, we show in the peach-potato aphid,
Myzus persicae
, that short-term costs may be of equal evolutionary importance. Survivors of more resistant aphid clones suffered a higher reduction of fecundity upon parasitoid attack than survivors of more susceptible clones. This genetically based trade-off between benefits and costs of defence may limit the evolution of increased resistance and explain the maintenance of genetic variation for resistance under environmental variation in parasitism risk.
Network scaling reveals consistent fractal pattern in hierarchical mammalian societies
Authors: Hill Russell A , Bentley R. Alexander , Dunbar Robin I.M
Published: September 2008

Recent studies have demonstrated that human societies are hierarchically structured with a consistent scaling ratio across successive layers of the social network; each layer of the network is between three and four times the size of the preceding (smaller) grouping level. Here we show that similar relationships hold for four mammalian taxa living in multi-level social systems. For elephant (Loxodonta africana), gelada (Theropithecus gelada) and hamadryas (Papio hamadryas hamadryas) baboon, successive layers of social organization have a scaling ratio of almost exactly 3, indicating that such branching ratios may be a consistent feature of all hierarchically structured societies. Interestingly, the scaling ratio for orca (Orcinus orca) was 3.8, which might mean that aquatic environments place different constraints on the organization of social hierarchies. However, circumstantial evidence from a range of other species suggests that scaling ratios close to 3 may apply widely, even in species where hierarchical social structures have not traditionally been identified. These results identify the origin of the hierarchical, fractal-like organization of mammalian social systems as a fundamental question.
First fossil gravid turtle provides insight into the evolution of reproductive traits in turtles
Authors: Zelenitsky Darla K , Therrien François , Joyce Walter G , B. Brinkman Donald
Published: September 2008

Here we report on the first discovery of shelled eggs inside the body cavity of a fossil turtle and on an isolated egg clutch, both referable to the Cretaceous turtle
Adocus
. These discoveries provide a unique opportunity to gain insight into the reproductive traits of an extinct turtle and to understand the evolution of such traits among living turtles. The gravid adult and egg clutch indicate that
Adocus
laid large clutches of rigid-shelled spherical eggs and established their nests near rivers, traits that are shared by its closest living relatives, the soft-shelled turtles.
Adocus
eggshell, however, was probably more rigid than that of living turtles, based on its great thickness and structure, features that may represent unique adaptations to intense predation or to arid nest environments. In light of the reproductive traits observed in
Adocus
, the distribution of reproductive traits among turtles reveals that large clutches of rigid-shelled eggs are primitive for hidden-necked turtles (cryptodirans) and that spherical eggs may have evolved independently within this group.
Optimality in a partitioned task performed by social insects
Authors: Burd Martin , Howard Jerome J
Published: September 2008

Biologists have long been aware that adaptations should not be analysed in isolation from the function of the whole organism. Here, we address the equivalent issue at the scale of a social insect colony: the optimality of component behaviours in a partitioned sequence of tasks. In colonies ofAtta colombica, a leaf-cutting ant, harvested leaf tissue is passed from foragers to nest workers that distribute, clean, shred and implant the tissue in fungal gardens. In four laboratory colonies ofA. colombica, we found that the highest colony-wide rate of leaf tissue processing in the nest was achieved when leaf fragment sizes were suboptimal for individual delivery rate by foragers. Leaf-cutting ant colonies appear to compromise the efficiency of collecting leaf tissue in order to increase their ability to handle the material when it arrives in the nest. Such compromise reinforces the idea that behavioural adaptations, like adaptations in general, must be considered within the context of the larger entity of which they are a part.
Being abundant is not enough: a decrease in effective population size over eight generations in a Norwegian population of the seaweed,Fucus serratus
Authors: Coyer James A , Hoarau Galice , Sjøtun Kjersti , Olsen Jeanine L
Published: September 2008

The brown algaFucus serratusis a key foundation species on rocky intertidal shores of northern Europe. We sampled the same population off the coast of southern Norway in 2000 and 2008, and using 26 microsatellite loci, we estimated the changes in genetic diversity and effective population size (Ne). The unexpectedly lowNe(73–386) andNe/Nratio (10−3–10−4), in combination with a significant decrease (14%) in allelic richness over the 8-year period, suggests an increased local extinction risk. If smallNeproves to be a common feature ofF. serratus, then being abundant may not be enough for the species to weather future environmental changes.
Effects of naturally acidified seawater on seagrass calcareous epibionts
Authors: Martin Sophie , Rodolfo-Metalpa Riccardo , Ransome Emma , Rowley Sonia , Buia Maria-Christina , Gattuso Jean-Pierre , Hall-Spencer Jason
Published: September 2008

Surface ocean pH is likely to decrease by up to 0.4 units by 2100 due to the uptake of anthropogenic CO
2
from the atmosphere. Short-term experiments have revealed that this degree of seawater acidification can alter calcification rates in certain planktonic and benthic organisms, although the effects recorded may be shock responses and the long-term ecological effects are unknown. Here, we show the response of calcareous seagrass epibionts to elevated CO
2
partial pressure in aquaria and at a volcanic vent area where seagrass habitat has been exposed to high CO
2
levels for decades. Coralline algae were the dominant contributors to calcium carbonate mass on seagrass blades at normal pH but were absent from the system at mean pH 7.7 and were dissolved in aquaria enriched with CO
2
. In the field, bryozoans were the only calcifiers present on seagrass blades at mean pH 7.7 where the total mass of epiphytic calcium carbonate was 90 per cent lower than that at pH 8.2. These findings suggest that ocean acidification may have dramatic effects on the diversity of seagrass habitats and lead to a shift in the biogeochemical cycling of both carbon and carbonate in coastal ecosystems dominated by seagrass beds.
Implications of multiple mating for offspring relatedness and shoaling behaviour in juvenile guppies
Authors: Evans Jonathan P , Kelley Jennifer L
Published: September 2008

Polyandry (female multiple mating) can confer important benefits to females, but few studies have considered its potential costs. One such cost may arise through differences in the relatedness of offspring born to females with different mating histories; offspring born to monandrous females are always full siblings, while those produced by polyandrous females may be full or half siblings. These differences may have important consequences for social interactions among offspring. We used artificial insemination in the guppy (
Poecilia reticulata
), a promiscuous live-bearing fish, to evaluate shoaling behaviour in polyandrous and monandrous broods. We combined this information with known parentage data for the polyandrous broods to determine whether sibling relatedness influenced offspring shoaling behaviour. While we detected no effect of mating treatment (polyandry/monandry) on shoaling behaviour, we found that pairs of full siblings spent significantly more time shoaling (and in close proximity) than pairs of half siblings. This latter finding confirms the ability of newborn guppies to distinguish brood mates on the basis of kinship, but also suggests an important and hitherto unrealized potential cost of polyandry: a reduction in within-brood relatedness with potentially important implications for offspring social behaviour.
The dangers of ignoring stock complexity in fishery management: the case of the North Sea cod
Authors: Hutchinson William F
Published: September 2008

The plight of the marine fisheries is attracting increasing attention as unsustainably high exploitation levels, exacerbated by more extreme climatic conditions, are driving stocks to the point of collapse. The North Atlantic cod (
Gadus morhua
), a species which until recently formed a major component of the demersal fisheries, has undergone significant declines across its range. The North Sea stock is typical of many, with a spawning stock biomass that has remained below the
safe biological limit
since 2000 and recruitment levels near the lowest on record. Cod within the North Sea are currently managed as a single stock, and yet mounting empirical evidence supports the existence of a metapopulation of regionally variable, genetically distinct, sub-stocks. Applying the same management strategies to multiple stocks that differ in their resilience to exploitation inevitably results in the overfishing and likely collapse of the weaker components. Indeed, recent studies have identified two North Sea spawning stocks that have undergone disproportionally large collapses with very substantial reductions in egg production. Similarly affected cod stocks in the northwest Atlantic have shown little evidence of recovery, despite fishery closures. The possible implications of ignoring sub-structuring within management units for biocomplexity, local adaptation and ecosystem stability are considered.
Gertrude Belle Elion. 23 January 1918 — 21 February 1999
Authors: Avery Mary Ellen
Published: September 2008

In the spring of 1933 Gertrude Elion graduated from high school and that summer she had to select a major subject before she could begin her freshman year at Hunter College. This posed a quandary for the future Nobel Prize recipient, as well as holder of 45 patents, 23 honorary degrees, and a long list of other honours: she had liked all her school subjects, making it difficult to select just one. ‘Iloved to learn everything, everything in sight and I was never satisfied that I knew everything there was to know in each of my courses.'Fatefully, that summer her grandfather, whom she loved dearly, died of cancer. ‘I watched him go over a period of months in a very painfulway, and it suddenly occurred to me that what I really needed to do was to become a scientist, and particularly a chemist, so that I would goout there and make a cure for cancer.' (All quotations in this memoir are from the author's taped 1997 interview with G. B. Elion.)
Thomas Edward Allibone. 11 November 1903 — 9 September 2003
Authors: Lawrenson Peter J.
Published: September 2008

Thomas Edward Allibone was a man who was small in physical stature but enormous in intellect, energy, enthusiasm and breadth of interests, and stimulating, supportive and generous to all who worked with him. They actively demonstrated respect and affection for him to theends of their lives (or his). For the Royal Society his publications spanned the years from 1926 (aged 23) to 1999, and he was a stalwart in other ways.
Robert Henry Symons. 20 March 1934 — 4 October 2006
Authors: Rogers George E. , Elliott William H.
Published: September 2008

Bob Symons died in Adelaide on 4 October 2006 after a long illness. He was distinguished through his contributions to our knowledge of the structure, function and replication of plant viruses, viroids and virusoids. His research culminated in the discovery of the hammer head folding of the RNA chain and its role as a ribozyme in self–cleavage of the RNA in some of these plant pathogens. He was a leader in his field and was responsible for commercial applications of his research and the establishment in Adelaide of the first Australian company to produce and market molecular biologicals for research.
Gordon Richard Wray. 30 January 1928 — 17 August 2005
Authors: Acar Mem¡Ş
Published: September 2008

Gordon Wray made major contributions to engineering research and development in the textile industry, particularly in the fields of machinery design and textile processing. He was widely regarded as one of the leading researchers in textile engineering. His major contributions include the air–jet texturing process, the Locstitch machine, an unconventional pile fabric machine, automatic garment linking machinery and an automatic rib transfer machine, to name just a few. He became a household name in textile circles not only in the UK but also across the world. He was a major driving force behind the setting up of Loughborough University's Engineering Design Institute (EDI) asits founding director, and was the Royal Academy of Engineering's Professor in the Principles of Engineering Design. As a professor, hetrained many researchers from many countries who currently serve in high–level positions in the industries and public sectors of their respective countries. He also played a significant advisory role in the development of the Universidade do Minho, Portugal.
Editorial
Authors: Meade T. W.
Published: September 2008

The annual volumes of
Biographical Memoirs
are one of the Society's most popular and widely read publications, mostly by Fellows themselves and others with scientific interests, but also including some lay readers. Bringing together 20 or more good quality memoirs each year has been a time–consuming job for the Physical Secretary and for those involved in editing and producing each volume. In addition, the Society has wanted to take full advantage of all the technical developments available for attractive, speedy and accurate accounts. One such obvious development was the colour dust–cover to the 2007 publication (volume 53) with mini–photographs of some of the Society's most distinguished Fellows, including the Nobel prize winners Dorothy Hodgkin and Maurice Wilkins, as well as Isaac Newton, James Cook and Christopher Wren. Another important development is that individual memoirs are now published online throughout the year as theyare received, to the same high standards as the printed versions, so that readers no longer need to wait for print publication. There is alsothe facility to search and browse the
Biographical Memoirs
online digital archive dating back to 1932.
DNA and lipid bilayers: self-assembly and insertion
Authors: Khalid Syma , Bond Peter J , Holyoake John , Hawtin Robert W , Sansom Mark S.P
Published: September 2008

DNA–lipid complexes are of biomedical importance as delivery vectors for gene therapy. To gain insight into the interactions of DNA with zwitterionic and cationic (dimyristoyltrimethylammonium propane (DMTAP)) lipids, we have used coarse-grained molecular dynamics simulations to study the self-assembly of DPPC and DPPC/DMTAP lipid bilayers in the presence of a DNA dodecamer. We observed the spontaneous formation of lipid bilayers from initial systems containing randomly placed lipids, water–counterions and DNA. In both the DPPC and DPPC/DMTAP simulations, the DNA molecule is located at the water–lipid headgroup interface, lying approximately parallel to the plane of the bilayer. We have also calculated the potential of mean force for transferring a DNA dodecamer through a DPPC/DMTAP bilayer. A high energetic barrier to DNA insertion into the hydrophobic core of the bilayer is observed. The DNA adopts a transmembrane orientation only in this region. Local bilayer deformation in the vicinity of the DNA molecule is observed, largely as a result of the DNA–DMTAP headgroup attraction.
Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds
Authors: Senthilkumar Kittusamy , Mujika Jon I , Ranaghan Kara E , Manby Frederick R , Mulholland Adrian J , Harvey Jeremy N
Published: September 2008

Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly important for the study of chemical reactions and systems in condensed phases. Here, we have tested the accuracy of a density functional theory-based QM/MM implementation (B3LYP/6-311+G(d,p)/CHARMM27) on a set of biologically relevant interactions by comparison with full QM calculations. Intermolecular charge transfer due to hydrogen bond formation is studied to assess the severity of spurious polarization of QM atoms by MM point charges close to the QM/MM boundary. The changes in total electron density and natural bond orbital atomic charges due to hydrogen bond formation in selected complexes obtained at the QM/MM level are compared with full QM results. It is found that charge leakage from the QM atoms to MM atomic point charges close to the QM/MM boundary is not a serious problem, at least with limited basis sets. The results are encouraging in showing that important properties of key biomolecular interactions can be treated well at the QM/MM level employing good-quality levels of QM theory.
Connectivity sustains disease transmission in environments with low potential for endemicity: modelling schistosomiasis with hydrologic and social connectivities
Authors: Gurarie David , Seto Edmund Y.W.
Published: September 2008

Social interaction and physical interconnections between populations can influence the spread of parasites. The role that these pathways play in sustaining the transmission of parasitic diseases is unclear, although increasingly realistic metapopulation models are being used to study how diseases persist in connected environments. We use a mathematical model of schistosomiasis transmission for a distributed set of heterogeneous villages to show that the transport of parasites via social (host movement) and environmental (parasite larvae movement) pathways has consequences for parasite control, spread and persistence. We find that transmission can be sustained regionally throughout a group of connected villages even when individual village conditions appear not to support endemicity. Optimum transmission is determined by an interplay between different transport pathways, and not necessarily by those that are the most dispersive (e.g. disperse social contacts may not be optimal for transmission). We show that the traditional targeting of villages with high infection, without regard to village interconnections, may not lead to optimum control. These findings have major implications for effective disease control, which needs to go beyond considering local variations in disease intensity, to also consider the degree to which populations are interconnected.
Incorporation of vitamin E in poly(3hydroxybutyrate)/Bioglass composite films: effect on surface properties and cell attachment
Authors: Misra Superb K , Philip Sheryl E , Chrzanowski Wojciech , Nazhat Showan N , Roy Ipsita , Knowles Jonathan C , Salih Vehid , Boccaccini Aldo R
Published: September 2008

This study investigated the possibility of incorporating α-tocopherol (vitamin E) into poly(3hydroxybutyrate) (P(3HB))/Bioglass composites, which are being developed for bone tissue engineering matrices. P(3HB) films with 20 wt% Bioglass and 10 wt% vitamin E were prepared using the solvent casting technique. Addition of vitamin E significantly improved the hydrophilicity of the composites along with increasing the total protein adsorption. The presence of protein adsorbed on the composite surface was further confirmed using X-ray photoelectron spectroscopy analysis. Preliminary cell culture studies using MG-63 human osteoblasts showed that the addition of vitamin E in the P(3HB)/20 wt% Bioglass films significantly increased cell proliferation. The results achieved in this study confirmed the possibility of incorporating vitamin E as a suitable additive in P(3HB)/Bioglass composites to engineer the surface of the composites by promoting higher protein adsorption and increasing the hydrophilicity.
Imaging scatterometry and microspectrophotometry of lycaenid butterfly wing scales with perforated multilayers
Authors: Wilts Bodo D , Leertouwer Hein L , Stavenga Doekele G
Published: September 2008

We studied the structural as well as spatial and spectral reflectance characteristics of the wing scales of lycaenid butterfly species, where the scale bodies consist of perforated multilayers. The extent of the spatial scattering profiles was measured with a newly built scatterometer. The width of the reflectance spectra, measured with a microspectrophotometer, decreased with the degree of perforation, in agreement with the calculations based on multilayer theory.
Destabilization of DNA duplexes by oxidative damage at guanine: implications for lesion recognition and repair
Authors: Jiranusornkul Supat , Laughton Charles A
Published: September 2008

We have used molecular dynamics simulations to study the structure and dynamics of a range of DNA duplexes containing the 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapydG) lesion that can result from oxidative damage at guanine. Compared to the corresponding undamaged DNA duplexes, FapydG-containing duplexes show little gross structural changes—the damaged base remains stacked in to the DNA double helix and retains hydrogen bonds to its cytosine partner. However, the experimentally observed reduction in DNA stability that accompanies lesion formation can be explained by a careful energetic analysis of the simulation data. Irrespective of the nature of the base pairs on either side of the lesion site, conversion of a guanine to a FapydG base results in increased dynamical flexibility in the base (but not in the DNA as a whole) that significantly weakens its hydrogen-bonding interactions. Surprisingly, the stacking interactions with its neighbours are not greatly altered. The formamido group adopts a non-planar conformation that can interact significantly and in a sequence-dependent manner with its 3′-neighbour. We conclude that the recognition of FapydG lesions by the repair protein formamidopyrimidine-DNA glycosylase probably does not involve the protein capturing an already-extrahelical FapydG base, but rather it relies on detecting alterations to the DNA structure and flexibility created by the lesion site.
Electro–magneto-encephalography for a three-shell model: distributed current in arbitrary, spherical and ellipsoidal geometries
Authors: Fokas A.S
Published: September 2008

The problem of determining a continuously distributed neuronal current inside the brain under the assumption of a three-shell model is analysed. It is shown that for an arbitrary geometry, electroencephalography (EEG) provides information about one of the three functions specifying the three components of the current, whereas magnetoencephalography (MEG) provides information about a combination of this function and of one of the remaining two functions. Hence, the simultaneous use of EEG and MEG yields information about two of the three functions needed for the reconstruction of the current. In particular, for spherical and ellipsoidal geometries, it is possible to determine the angular parts of these two functions as well as to obtain an explicit constraint satisfied by their radial parts. The complete determination of the radial parts, as well as the determination of the third function, requires some additionala prioriassumption about the current. One such assumption involving harmonicity is briefly discussed.