bluuebunny/crossref_metadata_2025 huggingface dataset:
A new focus in the science of networks: towards methods for design
Authors: Wan Yan , Roy Sandip , Saberi Ali
Published: December 2007

In recent years, a realization that networks are ubiquitous in the natural and engineered worlds has led to a burgeoning interest in finding commonalities in their structures and dynamics. Here, we introduce a new design focus in this science of networks by proposing generic methods forsynthesizing network controllers that exploit the topological structure. That is, we motivate a canonical controller synthesis problem for networks that has applications in such diverse areas as virus-spreading control and air traffic flow management. We address this design problem by using new techniques fromdecentralized control theory. Specifically, we mesh optimization machinery together with eigenvalue sensitivity and graph theory notions to identify general structural features of optimally actuated networks. From these features, we are in turn able to explicitly construct high-performance controllers, i.e. the ones that best exploit the network's topological structure. Our general approach for controller design is important because it both provides a broad insight into the structure of well-designed networks and contributes engineering solutions in numerous application areas (e.g. reduction in management delays and human-controller workload in air traffic systems).
Instability in two-phase flows of steam
Authors: Bakhtar F , Otto S.R , Zamri M.Y , Sarkies J.M
Published: December 2007

In two-phase flows of steam, when the velocity is between the equilibrium and frozen speeds of sound, the system is fundamentally unstable. Because any disturbance of the system, e.g. imposition of a small supercooling on the fluid, will cause condensation, the resulting heat release will accelerate the flow and increase the supercooling and thus move the system further from thermodynamic equilibrium. But in high-speed flows of a two-phase mixture, dynamic changes affect the thermodynamic equilibrium within the fluid, leading to phase change, and the heat release resulting from condensation disturbs the flow further and can also cause the disturbances to be amplified at other Mach numbers. To investigate the existence of instabilities in such flows, the behaviour of small perturbations of the system has been examined using stability theory. It is found that, although the amplification rate is highest between the equilibrium and frozen speeds of sound, such flows are temporally unstable at all Mach numbers.
Old men running: mechanical work and elastic bounce
Authors: Cavagna G.A , Legramandi M.A , Peyré-Tartaruga L.A
Published: December 2007

It is known that muscular force is reduced in old age. We investigate what are the effects of this phenomenon on the mechanics of running. We hypothesized that the deficit in force would result in a lower push, causing reduced amplitude of the vertical oscillation, with smaller elastic energy storage and increased step frequency. To test this hypothesis, we measured the mechanical energy of the centre of mass of the body during running in old and young subjects. The amplitude of the oscillation is indeed reduced in the old subjects, resulting in an approximately 20% smaller elastic recovery and a greater step frequency (3.7 versus 2.8 Hz,p=1.9×10−5, at 15–17 km h−1). Interestingly, the greater step frequency is due to a lower aerial time, and not to a greater natural frequency of the system, which is similar in old and young subjects (3.6 versus 3.4 Hz,p=0.2). Moreover, we find that in the old subjects, the step frequency is always similar to the natural frequency, even at the highest speeds. This is at variance with young subjects who adopt a step frequency lower than the natural frequency at high speeds, to contain the aerobic energy expenditure. Finally, the external work to maintain the motion of the centre of mass is reduced in the old subjects (0.9 versus 1.2 J kg−1 m−1,p=5.1×10−6) due to the lower work done against gravity, but the higher step frequency involves a greater internal work to reset the limbs at each step. The net result is that the total work increases with speed more steeply in the old subjects than in young subjects.
Seasonality, cohort-dependence and the development of immunity in a natural host–nematode system
Authors: Cornell Stephen J , Bjornstad Ottar N , Cattadori Isabella M , Boag Brian , Hudson Peter J
Published: December 2007

Acquired immunity is known to be a key modulator of the dynamics of many helminth parasites in domestic and human host populations, but its relative importance in natural populations is more controversial. A detailed long-term dataset on the gastrointestinal nematodeTrichostrongylus retortaeformisin a wild population of European rabbits (Oryctolagus cuniculus) shows clear evidence of seasonal acquired immunity in the age-structured infection profiles. By fitting a hierarchy of demographic infection–immunity models to the observed age-structured infection patterns, we are able to quantify the importance of different components (seasonality, immunity and host age structure) of the parasite dynamics. We find strong evidence that the hosts' immunocompetence waxes and wanes with the seasons, but also contains a lifelong cohort factor, possibly acting through a maternal effect dependent on the host's month of birth. These observations have important and broad implications for the ecology of parasite infection in seasonal natural herbivore systems.
Intrasexual competition among females and the stabilization of a conspicuous colour polymorphism in a Lake Victoria cichlid fish
Authors: Dijkstra Peter D , Seehausen Ole , Groothuis Ton G.G
Published: December 2007

The maintenance of colour polymorphisms within populations has been a long-standing interest in evolutionary ecology. African cichlid fish contain some of the most striking known cases of this phenomenon. Intrasexual selection can be negative frequency dependent when males bias aggression towards phenotypically similar rivals, stabilizing male colour polymorphisms. We propose that where females are territorial and competitive, aggression biases in females may also promote coexistence of female morphs. We studied a polymorphic population of the cichlid fish
Neochromis omnicaeruleus
from Lake Victoria, in which three distinct female colour morphs coexist: one plain brown and two blotched morphs. Using simulated intruder choice tests in the laboratory, we show that wild-caught females of each morph bias aggression towards females of their own morph, suggesting that females of all three morphs may have an advantage when their morph is locally the least abundant. This mechanism may contribute to the establishment and stabilization of colour polymorphisms. Next, by crossing the morphs, we generated sisters belonging to different colour morphs. We find no sign of aggression bias in these sisters, making pleiotropy unlikely to explain the association between colour and aggression bias in wild fish, which is maintained in the face of gene flow. We conclude that female–female aggression may be one important force for stabilizing colour polymorphism in cichlid fish.
Human cerebral response to animal affective vocalizations
Authors: Belin Pascal , Fecteau Shirley , Charest Ian , Nicastro Nicholas , Hauser Marc D , Armony Jorge L
Published: December 2007

It is presently unknown whether our response to affective vocalizations is specific to those generated by humans or more universal, triggered by emotionally matched vocalizations generated by other species. Here, we used functional magnetic resonance imaging in normal participants to measure cerebral activity during auditory stimulation with affectively valenced animal vocalizations, some familiar (cats) and others not (rhesus monkeys). Positively versus negatively valenced vocalizations from cats and monkeys elicited different cerebral responses despite the participants' inability to differentiate the valence of these animal vocalizations by overt behavioural responses. Moreover, the comparison with human non-speech affective vocalizations revealed a common response to the valence in orbitofrontal cortex, a key component on the limbic system. These findings suggest that the neural mechanisms involved in processing human affective vocalizations may be recruited by heterospecific affective vocalizations at an unconscious level, supporting claims of shared emotional systems across species.
Dispersing brush mice prefer habitat like home
Authors: Mabry Karen E , Stamps Judy A
Published: December 2007

During natal dispersal, young animals leave their natal area and search for a new area to live. In species in which individuals inhabit different types of habitat, experience with a natal habitat may increase the probability that a disperser will select the same type of habitat post-dispersal (natal habitat preference induction or NHPI). Despite considerable interest in the ecological and the evolutionary implications of NHPI, we lack empirical evidence that it occurs in nature. Here we show that dispersing brush mice (Peromyscus boylii) are more likely to search and settle within their natal habitat type than expected based on habitat availability. These results document the occurrence of NHPI in nature and highlight the relevance of experience-generated habitat preferences for ecological and evolutionary processes.
Reinduction of ErbB2 in astrocytes promotes radial glial progenitor identity in adult cerebral cortex
Authors: Ghashghaei H.T. , Weimer Jill M. , Schmid Ralf S. , Yokota Yukako , McCarthy Ken D. , Popko Brian , Anton E.S.
Published: December 2007

Radial glial cells play a critical role in the construction of mammalian brain by functioning as a source of new neurons and by providing a scaffold for radial migration of new neurons to their target locations. Radial glia transform into astrocytes at the end of embryonic development. Strategies to promote functional recovery in the injured adult brain depend on the generation of new neurons and the appropriate guidance of these neurons to where they are needed, two critical functions of radial glia. Thus, the competence to regain radial glial identity in the adult brain is of significance for the ability to promote functional repair via neurogenesis and targeted neuronal migration in the mature brain. Here we show that the in vivo induction of the tyrosine kinase receptor, ErbB2, in mature astrocytes enables a subset of them to regain radial glial identity in the mature cerebral cortex. These new radial glial progenitors are capable of giving rise to new neurons and can support neuronal migration. These studies indicate that ErbB2 signaling critically modulates the functional state of radial glia, and induction of ErbB2 in distinct adult astrocytes can promote radial glial identity in the mature cerebral cortex.
Retrosequence formation restructures the yeast genome
Authors: Maxwell Patrick H. , Curcio M. Joan
Published: December 2007

Retrosequences generated by reverse transcription of mRNA transcripts have a substantial influence on gene expression patterns, generation of novel gene functions, and genome organization. The Ty1 retrotransposon is a major source of RT activity in the yeast, Saccharomyces cerevisiae, and Ty1 retromobility is greatly elevated in strains lacking telomerase. We report that Ty1-dependent formation of retrosequences derived from single-copy gene transcripts is progressively elevated as yeast cells senesce in the absence of telomerase. Retrosequences are frequently fused to Ty1 sequences, and occasionally to sequences from other mRNA transcripts, forming chimeric pseudogenes. Efficient retrosequence formation requires the homologous recombination gene RAD52. Selection for retrosequence formation is correlated with a high frequency of chromosome rearrangements in telomerase-negative yeast. Ty1-associated retrosequences were present at the breakpoint junctions of four chromosomes analyzed in detail. Our results support a role for reverse transcripts in promoting chromosome rearrangements.
Intersubunit signaling in RecBCD enzyme, a complex protein machine regulated by Chi hot spots
Authors: Amundsen Susan K. , Taylor Andrew F. , Reddy Manjula , Smith Gerald R.
Published: December 2007

The Escherichia coli RecBCD helicase–nuclease, a paradigm of complex protein machines, initiates homologous genetic recombination and the repair of broken DNA. Starting at a duplex end, RecBCD unwinds DNA with its fast RecD helicase and slower RecB helicase on complementary strands. Upon encountering a Chi hot spot (5′-GCTGGTGG-3′), the enzyme produces a new 3′ single-strand end and loads RecA protein onto it, but how Chi regulates RecBCD is unknown. We report a new class of mutant RecBCD enzymes that cut DNA at novel positions that depend on the DNA substrate length and that are strictly correlated with the RecB:RecD helicase rates. We conclude that in the mutant enzymes when RecD reaches the DNA end, it signals RecB’s nuclease domain to cut the DNA. As predicted by this interpretation, the mutant enzymes cut closer to the entry point on DNA when unwinding is blocked by another RecBCD molecule traveling in the opposite direction. Furthermore, when RecD is slowed by a mutation altering its ATPase site such that RecB reaches the DNA end before RecD does, the length-dependent cuts are abolished. These observations lead us to hypothesize that, in wild-type RecBCD enzyme, Chi is recognized by RecC, which then signals RecD to stop, which in turn signals RecB to cut the DNA and load RecA. We discuss support for this “signal cascade” hypothesis and tests of it. Intersubunit signaling may regulate other complex protein machines.
Protein kinase A and casein kinases mediate sequential phosphorylation events in the circadian negative feedback loop
Authors: Huang Guocun , Chen She , Li Shaojie , Cha Joonseok , Long Chengzu , Li Lily , He Qiyang , Liu Yi
Published: December 2007

Regulation of circadian clock components by phosphorylation plays essential roles in clock functions and is conserved from fungi to mammals. In the Neurospora circadian negative feedback loop, FREQUENCY (FRQ) protein inhibits WHITE COLLAR (WC) complex activity by recruiting the casein kinases CKI and CKII to phosphorylate the WC proteins, resulting in the repression of frq transcription. On the other hand, CKI and CKII progressively phosphorylate FRQ to promote FRQ degradation, a process that is a major determinant of circadian period length. Here, by using whole-cell isotope labeling and quantitative mass spectrometry methods, we show that the WC-1 phosphorylation events critical for the negative feedback process occur sequentially—first by a priming kinase, then by the FRQ-recruited casein kinases. We further show that the cyclic AMP-dependent protein kinase A (PKA) is essential for clock function and inhibits WC activity by serving as a priming kinase for the casein kinases. In addition, PKA also regulates FRQ phosphorylation, but unlike CKI and CKII, PKA stabilizes FRQ, similar to the stabilization of human PERIOD2 (hPER2) due to the phosphorylation at the familial advanced sleep phase syndrome (FASPS) site. Thus, PKA is a key clock component that regulates several critical processes in the circadian negative feedback loop.
A role for microRNAs in maintenance of mouse mammary epithelial progenitor cells
Authors: Ibarra Ingrid , Erlich Yaniv , Muthuswamy Senthil K. , Sachidanandam Ravi , Hannon Gregory J.
Published: December 2007

microRNA (miRNA) expression profiles are often characteristic of specific cell types. The mouse mammary epithelial cell line, Comma-Dβ, contains a population of self-renewing progenitor cells that can reconstitute the mammary gland. We purified this population and determined its miRNA signature. Several microRNAs, including miR-205 and miR-22, are highly expressed in mammary progenitor cells, while others, including let-7 and miR-93, are depleted. Let-7 sensors can be used to prospectively enrich self-renewing populations, and enforced let-7 expression induces loss of self-renewing cells from mixed cultures.
PRMT6-mediated methylation of R2 in histone H3 antagonizes H3 K4 trimethylation
Authors: Hyllus Dawin , Stein Claudia , Schnabel Kristin , Schiltz Emile , Imhof Axel , Dou Yali , Hsieh James , Bauer Uta-Maria
Published: December 2007

The arginine methyltransferase PRMT6 (protein arginine methyltransferase 6) has been shown recently to regulate DNA repair and gene expression. As arginine methylation of histones is an important mechanism in transcriptional regulation, we asked whether PRMT6 possesses activity toward histones. We show here that PRMT6 methylates histone H3 at R2 and histones H4/H2A at R3 in vitro. Overexpression and knockdown analysis identify PRMT6 as the major H3 R2 methyltransferase in vivo. We find that H3 R2 methylation inhibits H3 K4 trimethylation and recruitment of WDR5, a subunit of the MLL (mixed lineage leukemia) K4 methyltransferase complex, to histone H3 in vitro. Upon PRMT6 overexpression, transcription of Hox genes and Myc-dependent genes, both well-known targets of H3 K4 trimethylation, decreases. This transcriptional repression coincides with enhanced occurrence of H3 R2 methylation and PRMT6 as well as reduced levels of H3 K4 trimethylation and MLL1/WDR5 recruitment at the HoxA2 gene. Upon retinoic acid-induced transcriptional activation of HoxA2 in a cell model of neuronal differentiation, PRMT6 recruitment and H3 R2 methylation are diminished and H3 K4 trimethylation increases at the gene. Our findings identify PRMT6 as the mammalian methyltransferase for H3 R2 and establish the enzyme as a crucial negative regulator of H3 K4 trimethylation and transcriptional activation.
The deacetylase HDAC6 is a novel critical component of stress granules involved in the stress response
Authors: Kwon SoHee , Zhang Yu , Matthias Patrick
Published: December 2007

An essential part of the cellular response to environmental stress is a reversible translational suppression, taking place in dynamic cytoplasmic structures called stress granules (SGs). We discovered that HDAC6, a cytoplasmic deacetylase that acts on tubulin and HSP90 and also binds ubiquitinated proteins with high affinity, is a novel critical SG component. We found that HDAC6 interacts with another SG protein, G3BP (Ras-GTPase-activating protein SH3 domain-binding protein 1), and localizes to SGs under all stress conditions tested. We show that pharmacological inhibition or genetic ablation of HDAC6 abolishes SG formation. Intriguingly, we found that the ubiquitin-binding domain of HDAC6 is essential and that SGs are strongly positive for ubiquitin. Moreover, disruption of microtubule arrays or impairment of motor proteins also prevents formation of SGs. These findings identify HDAC6 as a central component of the stress response, and suggest that it coordinates the formation of SGs by mediating the motor-protein-driven movement of individual SG components along microtubules.
Regulatory reform of the UK gas market: The sase of the storage auction
Authors: Hawdon David , Stevens Nicola
Published: December 2007

The UK gas industry has undergone major changes since it was privatised in 1986 as a fully integrated monopoly. The most significant of these has occurred not as a result of the privatisation legislation but by the intervention of the ordinary competition authorities in support of an active industry regulator. While price capping continues to be used as the primary instrument for welfare protection against the still substantial monopolistic powers of the incumbent, new competition (which has been positively encouraged) has had the greater impact on prices and choice. Recently, however, the regulator has encouraged the use of auctions for the sale of storage capacity. This paper considers the merits of auctions and makes a tentative evaluation of their effectiveness. Further use of auctions is recommended but reserve prices are considered inappropriate where monopoly power still remains.
Yardstick and incentive issues in UK electricity distribution price controls
Authors: Weyman‐Jones Thomas
Published: December 2007

Electricity distribution is a primary candidate for regulation since it is a natural monopoly whose costs it would be inefficient to duplicate in a competitive market. In the UK since privatisation of the electricity industry in 1990, this regulation has emphasised incentives for cost efficiency through the use of RPI‐X price capping applied to 14 regional distribution businesses. The paper examines the issues that have arisen in implementation, including the practice of bench‐marking the operating and capital expenditures of different companies. It analyses how the price set at the beginning of each review period depends on the determination of cost yardsticks, the weighted average cost of capital and the regulatory asset base of the companies. The analytical model is used to evaluate Ofgem's 1999 Distribution Price Control Review and compares it with other European distribution price regulations.
Application of labour and employment law beyond the contract of employment
Authors: FREEDLAND Mark
Published: December 2007

The personal scope of employment law is the subject of much ongoing debate. Arguing that an exclusively contractual analysis of this domain is unsatisfactory, the author constructs a European‐based empirical typology distinguishing the personal work relations of “standard employees”, public officials, “liberal professions”, individual entrepreneurial workers, marginal workers, and labour market entrants. These categories and their inter‐relationships are then analysed dynamically in terms of “personal work nexuses” ‐ a concept encompassing complex legal ramifications beyond the contractual framework. The conclusions highlight the value of this analytical approach to recent efforts by the ILO and the European Commission to “modernize” labour law.
Beyond corporate codes of conduct: Work organization and labour standards at Nike's suppliers
Authors: LOCKE Richard , KOCHAN Thomas , ROMIS Monica , QIN Fei
Published: December 2007

What role can corporate codes of conduct play in monitoring compliance with international labour standards and improving working conditions in global supply chains? Addressing this question, the authors first summarize the results of research on factory audits of working conditions in 800 of Nike's suppliers in 51 countries and two intensive case studies. They then discuss how the codes fit into the broader array of institutions, policies and practices aimed at regulating and improving working conditions, suggesting an evolutionary and complementary approach to regulating working conditions in global supply chains. They outline additional research and institutional innovations needed to test these ideas.
The distribution of earnings in OECD countries
Authors: ATKINSON Anthony B.
Published: December 2007

Earnings inequality in the OECD countries is commonly seen to have widened considerably since 1980 ‐ and this is generally explained by the steady increase in relative demand for skilled labour due to skill‐biased technical change and the growing exposure of unskilled workers to international competition through globalization. But this single explanation now looks questionable: the increase in inequality has been uneven across countries, and greater earnings dispersion has mostly been occurring at the top of the distribution. This article takes a fresh look at the evidence and considers alternative explanations to supplement that provided by the race between technology and education.
The informal economy, insecurity and social cohesion in Latin America
Authors: TOKMAN Víctor E.
Published: December 2007

Most Latin American countries adopted the welfare state as a model, though developing it in very different ways and, often, imperfectly because of structural differences between them and the industrialized countries. Social protection coverage is still patchy, with many informal‐sector workers not covered and widespread public feelings of insecurity. The author examines the complicated structural and labour situation and the latest ideas in Latin America and the European Union to strengthen social cohesion. He analyses approaches to incorporating the informal sector into the modern sector, addressing social exclusion, combining flexibility for employers with security for workers, and achieving near‐universal social protection.
Transcribing RNA Polymerase II Is Phosphorylated at CTD Residue Serine-7
Authors: Chapman Rob D. , Heidemann Martin , Albert Thomas K. , Mailhammer Reinhard , Flatley Andrew , Meisterernst Michael , Kremmer Elisabeth , Eick Dirk
Published: December 2007

RNA polymerase II is distinguished by its large carboxyl-terminal repeat domain (CTD), composed of repeats of the consensus heptapeptide Tyr
1
-Ser
2
-Pro
3
-Thr
4
-Ser
5
-Pro
6
-Ser
7
. Differential phosphorylation of serine-2 and serine-5 at the 5′ and 3′ regions of genes appears to coordinate the localization of transcription and RNA processing factors to the elongating polymerase complex. Using monoclonal antibodies, we reveal serine-7 phosphorylation on transcribed genes. This position does not appear to be phosphorylated in CTDs of less than 20 consensus repeats. The position of repeats where serine-7 is substituted influenced the appearance of distinct phosphorylated forms, suggesting functional differences between CTD regions. Our results indicate that restriction of serine-7 epitopes to the Linker-proximal region limits CTD phosphorylation patterns and is a requirement for optimal gene expression.
Deep Ocean Impact of a Madden-Julian Oscillation Observed by Argo Floats
Authors: Matthews Adrian J. , Singhruck Patama , Heywood Karen J.
Published: December 2007

Using the new Argo array of profiling floats that gives unprecedented space-time coverage of the upper 2000 meters of the global ocean, we present definitive evidence of a deep tropical ocean component of the Madden-Julian Oscillation (MJO). The surface wind stress anomalies associated with the MJO force eastward-propagating oceanic equatorial Kelvin waves that extend downward to 1500 meters. The amplitude of the deep ocean anomalies is up to six times the amplitude of the observed annual cycle. This deep ocean sink of energy input from the wind is potentially important for understanding phenomena such as El Niño–Southern Oscillation and for interpreting deep ocean measurements made from ships.
A Madden-Julian Oscillation Event Realistically Simulated by a Global Cloud-Resolving Model
Authors: Miura Hiroaki , Satoh Masaki , Nasuno Tomoe , Noda Akira T. , Oouchi Kazuyoshi
Published: December 2007

A Madden-Julian Oscillation (MJO) is a massive weather event consisting of deep convection coupled with atmospheric circulation, moving slowly eastward over the Indian and Pacific Oceans. Despite its enormous influence on many weather and climate systems worldwide, it has proven very difficult to simulate an MJO because of assumptions about cumulus clouds in global meteorological models. Using a model that allows direct coupling of the atmospheric circulation and clouds, we successfully simulated the slow eastward migration of an MJO event. Topography, the zonal sea surface temperature gradient, and interplay between eastward- and westward-propagating signals controlled the timing of the eastward transition of the convective center. Our results demonstrate the potential making of month-long MJO predictions when global cloud-resolving models with realistic initial conditions are used.
Declining Wild Salmon Populations in Relation to Parasites from Farm Salmon
Authors: Krkošek Martin , Ford Jennifer S. , Morton Alexandra , Lele Subhash , Myers Ransom A. , Lewis Mark A.
Published: December 2007

Rather than benefiting wild fish, industrial aquaculture may contribute to declines in ocean fisheries and ecosystems. Farm salmon are commonly infected with salmon lice (
Lepeophtheirus salmonis
), which are native ectoparasitic copepods. We show that recurrent louse infestations of wild juvenile pink salmon (
Oncorhynchus gorbuscha
), all associated with salmon farms, have depressed wild pink salmon populations and placed them on a trajectory toward rapid local extinction. The louse-induced mortality of pink salmon is commonly over 80% and exceeds previous fishing mortality. If outbreaks continue, then local extinction is certain, and a 99% collapse in pink salmon population abundance is expected in four salmon generations. These results suggest that salmon farms can cause parasite outbreaks that erode the capacity of a coastal ecosystem to support wild salmon populations.
Stored Light in an Optical Fiber via Stimulated Brillouin Scattering
Authors: Zhu Zhaoming , Gauthier Daniel J. , Boyd Robert W.
Published: December 2007

We describe a method for storing sequences of optical data pulses by converting them into long-lived acoustic excitations in an optical fiber through the process of stimulated Brillouin scattering. These stored pulses can be retrieved later, after a time interval limited by the lifetime of the acoustic excitation. In the experiment reported here, smooth 2-nanosecond-long pulses are stored for up to 12 nanoseconds with good readout efficiency: 29% at 4-nanosecond storage time and 2% at 12 nanoseconds. This method thus can potentially store data packets that are many bits long. It can be implemented at any wavelength where the fiber is transparent and can be incorporated into existing telecommunication networks because it operates using only commercially available components at room temperature.
Comment on "Tumor Growth Need Not Be Driven by Rare Cancer Stem Cells"
Authors: Kennedy James A. , Barabé Frédéric , Poeppl Armando G. , Wang Jean C. Y. , Dick John E.
Published: December 2007

Kelly et al. (Brevia, 20 July 2007, p. 337) questioned xenotransplant experiments supporting the cancer stem cell (CSC) hypothesis because they found a high frequency of leukemia-initiating cells (L-IC) in some transgenic mouse models. However, the CSC hypothesis depends on prospective purification of cells with tumor-initiating capacity, irrespective of frequency. Moreover, we found similar L-IC frequencies in genetically comparable leukemias using syngeneic or xenogeneic models.
Response to Comment on "Tumor Growth Need Not Be Driven by Rare Cancer Stem Cells"
Authors: Adams Jerry M. , Kelly Priscilla N. , Dakic Aleksandar , Nutt Stephen L. , Strasser Andreas
Published: December 2007

A critical issue for cancer biology and therapy is whether most tumor cells or only rare “cancer stem cells” sustain tumor growth. Although the latter model seems supported by the minute proportion of human leukemia cells that can grow in immunodeficient mice, evidence that more than 10% of cells in many mouse leukemias and lymphomas are transplantable challenges its generality.
The Structure of a Human p110α/p85α Complex Elucidates the Effects of Oncogenic PI3Kα Mutations
Authors: Huang Chuan-Hsiang , Mandelker Diana , Schmidt-Kittler Oleg , Samuels Yardena , Velculescu Victor E. , Kinzler Kenneth W. , Vogelstein Bert , Gabelli Sandra B. , Amzel L. Mario
Published: December 2007

PIK3CA
, one of the two most frequently mutated oncogenes in human tumors, codes for p110α, the catalytic subunit of a phosphatidylinositol 3-kinase, isoform α (PI3Kα, p110α/p85). Here, we report a 3.0 angstrom resolution structure of a complex between p110α and a polypeptide containing the p110α-binding domains of p85α, a protein required for its enzymatic activity. The structure shows that many of the mutations occur at residues lying at the interfaces between p110α and p85α or between the kinase domain of p110α and other domains within the catalytic subunit. Disruptions of these interactions are likely to affect the regulation of kinase activity by p85 or the catalytic activity of the enzyme, respectively. In addition to providing new insights about the structure of PI3Kα, these results suggest specific mechanisms for the effect of oncogenic mutations in p110α and p85α.
The Gonzonaut Goes to Mars
Authors: Bohannon John
Published: December 2007

In this installment, our intrepid Gonzo Scientist slips the surly bonds of Earth (well, sort of) and learns that a space suit may not be the best choice of attire when attempting to sneak uninvited into a scientific meeting.
Implications of
Streptococcus pneumoniae
Penicillin Resistance and Serotype Distribution in Kuwait for Disease Treatment and Prevention
Authors: Mokaddas Eiman M. , Rotimi Vincent O. , Albert M. John
Published: December 2007

Streptococcus pneumoniae
causes serious infections. Treatment is difficult because of the emergence of penicillin resistance in
S. pneumoniae
. Pneumococcal vaccines offer the promise of control and prevention of pneumococcal infections. Serotype prevalence and penicillin susceptibility data for a country will predict the usefulness of the vaccines in that country. In Kuwait, the 23-valent polysaccharide and the 7-valent conjugate vaccines are being used without knowledge of the prevalent serotypes in the country. To obtain the necessary background information, data on penicillin susceptibility and serogroups were obtained from 397 consecutive clinical isolates collected during 2004 and 2005. Two hundred fifty-three isolates (64%) were penicillin resistant, and resistance was significantly higher in patients ≤15 years old and among the upper respiratory tract and eye isolates. The most common serotypes were 23F, 19F, 6A, 6B, 14, and 19A. Among the penicillin-resistant strains, the most common serotypes were 23F, 19F, 6B, 14, and 9A. Among the invasive strains, the most common serotypes were 14, 23F, 19A, and 9V. The polysaccharide vaccine gave 82% coverage against invasive infections in all age groups >2 years. The coverage of the 7-valent conjugate vaccine against invasive serotypes in children ≤2 years old was 55%. This moderate coverage by the conjugate vaccine against invasive infections in children necessitates a revised strategy on the use of the present conjugate vaccine and shows the need for formulation of an improved vaccine for superior coverage for Kuwait and possibly other countries of the Arabian Gulf.
Peptide Impurities in Commercial Synthetic Peptides and Their Implications for Vaccine Trial Assessment
Authors: Currier Jeffrey R. , Galley Lynee M. , Wenschuh Holger , Morafo Vivian , Ratto-Kim Silvia , Gray Clive M. , Maboko Leonard , Hoelscher Michael , Marovich Mary A. , Cox Josephine H.
Published: December 2007

The advent of T-cell assay methodologies that are amenable to high throughput coupled with the availability of large libraries of overlapping peptides have revolutionized the fields of vaccine efficacy testing and cellular immune response assessment. Since T-cell assay performance is critically dependent upon the quality and specificity of the stimulating peptides, assurance of high-quality and reliable input peptides is an important aspect of assay validation. Herein, we demonstrate that individual peptides from large human immunodeficiency virus (HIV)-based peptide library sets obtained directly from two independent custom peptide suppliers contained contaminating peptides capable of giving false-positive results, which were consistent with nominal antigen-specific CD8
+
T-cell responses. In-depth investigation of the cellular response in terms of responding CD8
+
T-cell frequency and human leukocyte antigen (HLA) restriction led to the conclusion that one set of HIV type 1 (HIV-1)-derived peptides was contaminated with a peptide from human cytomegalovirus (HCMV), which is commonly used in cellular immunology research applications. Analytical characterization of the original stock of the suspect HIV-1 peptide confirmed the presence of ∼1% by weight of the HCMV peptide. These observations have critical implications for quality assurance (QA) and quality control (QC) of peptides used in clinical trials where cellular immune-based assays are important end-point determinants. We propose a simple schema of biological QA/QC protocols to augment the standard biochemical QA/QC analyses as a means to circumvent this and other problems that can affect cellular immune-based assay outcome and interpretation.
A Double-Blind, Randomized, Controlled, Multicenter Safety and Immunogenicity Study of a Refrigerator-Stable Formulation of Zostavax
Authors: Gilderman Larry I. , Lawless James F. , Nolen Thomas M. , Sterling Tina , Rutledge Ruth Z. , Fernsler Doreen A. , Azrolan Neal , Sutradhar Santosh C. , Wang William W. , Chan Ivan S. F. , Schlienger Katia , Schödel Florian , Silber Jeffrey L.
Published: December 2007

The vaccine Zostavax has been shown to prevent herpes zoster (HZ) and postherpetic neuralgia and is recommended for individuals ≥60 years of age. This study compared the safety and the immunogenicity of a refrigerator-stable formulation (Zostavax refrigerated) with those of the current formulation (Zostavax frozen) in subjects ≥50 years of age. Subjects with a negative history for HZ were randomized 1:1 to receive one dose of either formulation. Enrollment was stratified 1:2 by age (50 to 59 years and ≥60 years). Safety was evaluated for 28 days postvaccination. Varicella-zoster virus (VZV) antibody responses were measured by a glycoprotein enzyme-linked immunosorbent assay (gpELISA). The primary endpoints were the VZV antibody geometric mean titer (GMT; day 28), the VZV antibody geometric mean rise (GMR; days 1 to 28), and the incidence of vaccine-related serious adverse experiences (AEs) over 28 days. The refrigerated (
n
= 182) and frozen (
n
= 185) formulations induced similar GMTs (727.4 and 834.4 gpELISA units/ml, respectively); the estimated GMT ratio (refrigerated formulation/frozen formulation) was 0.87 (95% confidence interval, 0.71 to 1.07). The GMRs were 2.6- and 2.9-fold, respectively. No vaccine-related serious AEs were reported in either group, and the safety profiles of the formulations were generally similar. The frequencies of injection-site AEs during follow-up were 35.6% and 46.4% in the refrigerated and the frozen formulation groups, respectively, and were generally mild. The frequencies of systemic AEs were similar in the two groups, and those of vaccine-related AEs were ∼6% in both groups. The refrigerator-stable formulation of Zostavax has an acceptable safety profile and is as immunogenic as the frozen formulation; thus, the vaccine may be used in clinical settings where freezer availability is limited.
Detection of
Mycobacterium avium
subsp.
paratuberculosis
by a Sonicate Immunoassay Based on Surface-Enhanced Raman Scattering
Authors: Yakes Betsy Jean , Lipert Robert J. , Bannantine John P. , Porter Marc D.
Published: December 2007

A sandwich immunoassay for the rapid, low-level detection of
Mycobacterium avium
subsp.
paratuberculosis
has been developed.
M. avium
subsp.
paratuberculosis
is the causative agent of Johne's disease in cattle, and one of the major obstacles in controlling the spread of this disease is the inability to rapidly detect small amounts of bacteria or other diagnostic markers shed during the subclinical stage of infection. This paper details the development and performance of an assay for sonicated
M. avium
subsp.
paratuberculosis
lysate that is based on surface-enhanced Raman scattering (SERS). There are two key components of the assay: (i) an immobilized layer of monoclonal antibodies that target a surface protein on the microorganism; and (ii) extrinsic Raman labels (ERLs) that are designed to selectively bind to captured proteins and produce large SERS signals. By correlating the number of
M. avium
subsp.
paratuberculosis
bacilli present prior to sonication to the amount of total protein in the resulting sonicate, the detection limit determined for total protein can be translated to the microorganism concentration. These findings yield detection limits of 100 and 200 ng/ml (estimated to be 500 and 1,000
M. avium
subsp.
paratuberculosis
bacilli/ml) for sonicate spiked in phosphate buffer and sonicate spiked in whole milk, respectively. Moreover, the time required to complete the assay, which includes sample preparation, antigen extraction, ERL incubation, and readout, is less than 24 h. The potential for incorporation of this novel assay into diagnostic laboratories is also briefly discussed.
Profiling Antibodies to
Mycobacterium tuberculosis
by Multiplex Microbead Suspension Arrays for Serodiagnosis of Tuberculosis
Authors: Khan Imran H. , Ravindran Resmi , Yee JoAnn , Ziman Melanie , Lewinsohn David M. , Gennaro Marila L. , Flynn JoAnne L. , Goulding Celia W. , DeRiemer Kathryn , Lerche Nickolas W. , Luciw Paul A.
Published: December 2007

Tuberculosis (TB) is a serious global disease. The fatality rate attributed to TB is among the highest of infectious diseases, with approximately 2 million deaths occurring per year worldwide. Identification of individuals infected with
Mycobacterium tuberculosis
and screening of their immediate contacts is crucial for controlling the spread of TB. Current methods for detection of
M. tuberculosis
infection are not efficient, in particular, for testing large numbers of samples. We report a novel and efficient multiplex microbead immunoassay (MMIA), based on Luminex technology, for profiling antibodies to
M. tuberculosis.
Microbead sets identifiable by unique fluorescence were individually coated with each of several
M. tuberculosis
antigens and tested in multiplex format for antibody detection in the experimental nonhuman primate model of TB. Certain
M. tuberculosis
antigens, e.g., ESAT-6, CFP-10, and HspX, were included to enhance the specificity of the MMIA, because these antigens are absent in nontuberculous mycobacteria and the vaccine strain
Mycobacterium bovis
bacillus Calmette-Guérin. The MMIA enabled simultaneous detection of multiple
M. tuberculosis
plasma antibodies in several cohorts of macaques representing different stages of infection and/or disease. Antibody profiles were defined in early and latent/chronic infection. These proof-of-concept findings demonstrate the potential clinical use of the MMIA. In addition, the MMIA serodetection system has a potential for mining
M. tuberculosis
open reading frames (about 4,000) to discover novel target proteins for the development of more-comprehensive TB serodiagnostic tests.
VirB12 Is a Serological Marker ofBrucellaInfection in Experimental and Natural Hosts
Authors: Rolán Hortensia G. , den Hartigh Andreas B. , Kahl-McDonagh Melissa , Ficht Thomas , Adams L. Garry , Tsolis Renée M.
Published: December 2007

TheBrucellaspecies type IV secretion system, encoded by thevirB1-12locus, is required for intracellular replication and persistent infection in vivo. The requirement of VirB proteins for infection suggests that they are expressed in vivo and may therefore represent serological markers of infection. To test this idea, we purified recombinant VirB1, VirB5, VirB11, and VirB12 and tested for their recognition by antibodies in sera from experimentally infected mice and goats by using an indirect enzyme-linked immunosorbent assay. Antibody responses to VirB12 but not to VirB1, VirB5, or VirB11 were detected in 20/20 mice experimentally inoculated withBrucella abortusand 12/12 goats experimentally infected withBrucella melitensis. The potential use of VirB12 as a serological tool for the diagnosis of brucellosis was evaluated in the natural bovine host. Serum samples from 145 cattle of known serology (29% negative and 71% positive) were analyzed for the production of antibody responses to VirB12. One hundred two cattle samples (70.3%) were positive for antibodies to VirB12, while 43 samples were negative (29.7%). A positive serological response to VirB12 correlated with positive serology to wholeB. abortusantigen in 99% of samples tested. These results show that VirB12 is expressed during infection of both experimental and natural hosts ofBrucellaspecies, and they suggest that VirB12 may be a useful serodiagnostic marker for brucellosis.
Humoral Immune Responses of Type 1 Diabetes Patients to
Mycobacterium avium
subsp.
paratuberculosis
Lend Support to the Infectious Trigger Hypothesis
Authors: Sechi Leonardo A. , Rosu Valentina , Pacifico Adolfo , Fadda Giovanni , Ahmed Niyaz , Zanetti Stefania
Published: December 2007

Mycobacterium avium
subsp.
paratuberculosis
is a zoonotic pathogen whose association with Crohn's disease in humans is under scrutiny. The objective of this work was to investigate its association with other chronic diseases such as type 1 diabetes mellitus (T1DM), where the involvement of a persistent pathogen such as
M. avium
subsp.
paratuberculosis
could be the trigger. For this purpose, 59 diabetic patients and 59 healthy controls were investigated for the presence of antibodies against two recombinant proteins of
M. avium
subsp.
paratuberculosis
and the whole-cell lysate. Extremely significant humoral immune responses to recombinant heparin binding hemagglutinin and glycosyl transferase proteins and the whole-cell lysates of
M. avium
subsp.
paratuberculosis
bacilli were observed in T1DM patients and compared to those of healthy controls. Finding evidence of
M. avium
subsp.
paratuberculosis
involvement in T1DM is perhaps a novel finding that might serve as a foundation stone in establishing an infectious etiology for T1DM.
Cryptococcal Glucoxylomannan Does Not Exhibit Cross-Reactivity in the MVista
Histoplasma
Antigen Enzyme Immunoassay
Authors: Zhuang David , Hage Chadi , De Jesus Magdia , Hackett Emily , Durkin Michelle , Davis Thomas E. , Casadevall Arturo , Wheat L. Joseph
Published: December 2007

The potential for cross-reaction between
Cryptococcus neoformans
and
Histoplasma capsulatum
in antigen assays was evaluated. We tested patient samples, spleens from infected mice, and purified polysaccharides in the MVista
Histoplasma
antigen enzyme immunoassay and cryptococcal antigen latex agglutination system for cross-reactivity, and none was observed.
Performance Characteristics of Microparticle Enzyme and Chemiluminescence Immunoassays for Measurement of Anti-HBc Immunoglobulin M in Sera of Patients with HBeAg-Negative Chronic Hepatitis B Virus Infection
Authors: Hadziyannis Emilia , Manesis Emanuel , Vassilopoulos Dimitrios , Georgiou Anastasia , Archimandritis Athanasios
Published: December 2007

The IMx, AxSym, and Architect immunoglobulin M anti-HBc assay systems for detecting hepatitis B virus e antigen-negative chronic hepatitis B virus infection were compared. Despite good intra- and interassay coefficients of variation, significantly different values and low correlation (overestimation by AxSym and underestimation by Architect) were observed. Association and cutoff values for distinguishing patients with viral replication should be established for all methods.