bluuebunny/crossref_metadata_2025 huggingface dataset:
Randomized Controlled Trial of Feeding a Concentrated Formula to Infants Born to Women Infected by Human Immunodeficiency Virus
Authors: Winter Harland S , Oleske James M , Hughes Michael D , McKinney Ross E , Elgie Carol , Powell Christine , Purdue Lynette , Puga Ana M , Jimenez Eleanor , Scott Gwendolyn B , Cruz Maria Leticia Santos , Moye Jack ,   Pediatric AIDS Clinical Trials Group Protocol 247 Study Team
Published: July 2009

Objective:

We tested the hypothesis that concentrated formula (CF) begun within the first 2 weeks of life increases growth in infants born to human immunodeficiency virus (HIV)–infected mothers.

Materials and Methods:

HIV‐exposed infants from the United States, the Bahamas, and Brazil were randomized in a double‐blind, controlled trial to receive either a CF (87 kcal/100 mL [26 kcal/oz]) or a standard formula (SF; 67 kcal/100 mL [20 kcal/oz]) for 8 weeks. This article presents results for infants who were not determined to be HIV infected based on testing at 4 weeks. Primary outcomes were safety, tolerability, and growth in weight and length.

Results:

Two thousand ninety‐seven infants were enrolled, of whom 1998 were uninfected and had study formula dispensed. At weeks 4 and 8, uninfected infants receiving CF showed higher energy intake than those who were receiving SF (P < 0.001). By week 8, uninfected infants assigned to CF weighed more than infants receiving SF. There were no consistent differences in measures of tolerability, and rates of discontinuation or perceived formula intolerance were similar between treatment groups.

Conclusions:

A CF is well tolerated and results in increased weight gain compared with SF. Until the HIV status of an infant is reliably determined, early introduction of a CF in HIV‐exposed children may have beneficial effects on growth. The role of early nutritional intervention remains to be determined for individuals living in countries with endemic malnutrition for whom formula feeding is a viable option.
Moving From Tube to Oral Feeding in Medically Fragile Nonverbal Toddlers
Authors: Davis Ann McGrath , Bruce Amanda Schurle , Mangiaracina Cathy , Schulz Trina , Hyman Paul
Published: July 2009

The current article describes a 14‐week outpatient protocol for transitioning from gastrostomy tube to oral feeding in toddlers with medical complications. The team ensured that eating skills were mastered before treating patients for 8 weeks with continuous gastrojejunal drip tube feedings and low‐dose tricyclic antidepressant and/or gabapentin. We prescribed 6 weeks of megestrol for hunger provocation while withdrawing tube feedings. A chart review after treatment demonstrated 9 subjects were eating exclusively orally and 1 was eating 50% orally.
Infliximab Therapy in Children With Concurrent Perianal Crohn Disease: Observations From REACH
Authors: Crandall Wallace , Hyams Jeffrey , Kugathasan Subra , Griffiths Anne , Zrubek Julie , Olson Allan , Liu Grace , Heuschkel Robert , Markowitz James , Cohen Stanley , Winter Harland , Veereman‐Wauters Gigi , Ferry George , Baldassano Robert N
Published: July 2009

Objective:

Post hoc analyses evaluated the effect of infliximab upon concurrent perianal Crohn disease (CD) in a subpopulation of 31 patients from REACH, a randomized trial of 112 children with moderately to severely active luminal CD.

Materials and Methods:

The Pediatric Crohn Disease Activity Index perirectal subscore was used to assess perianal symptom activity and therapeutic response. Patients with no symptoms or asymptomatic tags received a score of 0; those with “1–2 indolent fistula, scant drainage, no tenderness” received a score of 5; and those with “active fistula, drainage, tenderness or abscess” received a score of 10. Initial perirectal subscores of 10 or 5 decreasing to 0 were considered complete response. Subscores of 10 decreasing to 5 were considered partial response. All patients were followed for efficacy and safety through week 54.

Results:

Twenty‐two patients with baseline perianal disease were randomized at week 10 following a 3‐dose infliximab induction regimen. At week 2, 40.9% (9/22) of patients with signs and symptoms of perianal disease at baseline attained response (4 partial and 5 complete). At week 54, 72.7% (16/22) of patients with signs and symptoms of perianal disease attained response (1 partial and 15 complete). Nine patients developed perianal signs and symptoms during treatment; 7 had complete response and 2 had no response at week 54. The incidence of adverse events for patients with perianal symptoms at baseline and for those in the overall REACH population was similar (95.7% vs 94.6%).

Conclusions:

Infliximab rapidly reduced concurrent perianal disease signs and symptoms in this REACH cohort.
Western scrub-jays conceal auditory information when competitors can hear but cannot see
Authors: Stulp Gert , Emery Nathan J. , Verhulst Simon , Clayton Nicola S.
Published: July 2009

Western scrub-jays (
Aphelocoma californica
) engage in a variety of cache-protection strategies to reduce the chances of cache theft by conspecifics. Many of these strategies revolve around reducing visual information to potential thieves. This study aimed to determine whether the jays also reduce auditory information during caching. Each jay was given the opportunity to cache food in two trays, one of which was filled with small pebbles that made considerable noise when cached in (‘noisy’ tray), whereas the other one contained soil that made little detectable noise when cached in (‘quiet’ tray). When the jays could be heard, but not seen, by a competitor, they cached proportionally less food items in the ‘noisy’ substrate than when they cached alone in the room, or when they could be seen and heard by competitors. These results suggest that western scrub-jays know when to conceal auditory information, namely when a competitor cannot see but can hear the caching event.
The evolution of growth rates on an expanding range edge
Authors: Phillips Ben L.
Published: July 2009

Individuals in the vanguard of a species invasion face altered selective conditions when compared with conspecifics behind the invasion front. Assortment by dispersal ability on the expanding front, for example, drives the evolution of increased dispersal, which, in turn, leads to accelerated rates of invasion. Here I propose an additional evolutionary mechanism to explain accelerating invasions: shifts in population growth rate (
r
). Because individuals in the vanguard face lower population density than those in established populations, they should (relative to individuals in established populations) experience greater
r
-selection. To test this possibility, I used the ongoing invasion of cane toads (
Bufo marinus
) across northern Australia. Life-history theory shows that the most efficient way to increase the rate of population growth is to reproduce earlier. Thus, I predict that toads on the invasion front will exhibit faster individual growth rates (and thus will reach breeding size earlier) than those from older populations. Using a common garden design, I show that this is indeed the case: both tadpoles and juvenile toads from frontal populations grow around 30 per cent faster than those from older, long established populations. These results support theoretical predictions that
r
increases during range advance and highlight the importance of understanding the evolution of life history during range advance.
Stress, song and survival in sparrows
Authors: MacDougall-Shackleton S. A. , Dindia L. , Newman A. E. M. , Potvin D. A. , Stewart K. A. , MacDougall-Shackleton E. A.
Published: July 2009

The stress response—increases in circulating glucocorticoids following a stressor—is typically considered adaptive, but few studies address the fitness consequences of individual variation in stress response. Generally, due to negative consequences of prolonged elevation of glucocorticoids, animals should have a transient stress response just sufficient to cope with the stressor. In rodents, stress responsiveness is affected by early developmental experience, and hyper-responsiveness to stress is linked to morbidity and mortality. We assessed individual variation in stress responses in free-living song sparrows,
Melospiza melodia
, in relation to fitness-related measures including song and overwinter survival. Birds with greater increases in corticosterone 30 min following restraint stress were less likely to return to breed the following year. Stress responsiveness was also correlated with song complexity: males with fewer syllables in their song repertoires had greater stress reactivity. Our findings support the hypothesis that developmental stressors both impair song development and affect the adult stress response. Thus, individual variation in the stress response may relate to variation in fitness.
‘Tales ofSymphonia’: extinction dynamics in response to past climate change in Madagascan rainforests
Authors: Virah-Sawmy Malika , Bonsall Michael B. , Willis Katherine J.
Published: July 2009

Madagascar's rainforests are among the most biodiverse in the world. Understanding the population dynamics of important species within these forests in response to past climatic variability provides valuable insight into current and future species composition. Here, we use a population-level approach to analyse palaeoecological records over the last 5300 years to understand how populations ofSymphoniacf.verrucosabecame locally extinct in some rainforest fragments along the southeast coast of Madagascar in response to rapid climate change, yet persisted in others. Our results indicate that regional (climate) variability contributed to synchronous decline ofS. cf.verrucosapopulations in these forests. Superimposed on regional fluctuations were local processes that could have contributed or mitigated extinction. Specifically, in the forest with low soil nutrients, population model predictions indicated that there was coexistence betweenS. cf.verrucosaandEricaspp., but in the nutrient-rich forest, interspecific effects betweenSymphoniaandEricaspp. may have pushedSymphoniato extinction at the peak of climatic change. We also demonstrate thatSymphoniais a good indicator of a threshold event, exhibiting erratic fluctuations prior to and long after the critical climatic point has passed.
Host–parasite interactions: resist or tolerate but never stop running
Authors: Evans Jay D.
Published: July 2009

A conference exploring ‘The impact of the environment on innate immunity: the threat of diseases’ was held on 4–9 May 2009 in Obergurgl, Austria, thanks to the support from the European Science Foundation, Innsbruck University and the Austrian Science Foundation. The goals of the conference were to explore how the outcomes of host–parasite interactions depend on variation across individuals, their parasites and the environment in which they both find themselves. Central themes were the inherent costs of mounting an immune response, the ability of some organisms to pre-empt infection by ‘priming’ their immune systems, the fact that parasites learn to evade immune responses over time and the use of theory to predict when diseases will get out of hand. Many of the systems presented had clear impacts on human health, agriculture or the maintenance of complex ecosystems. There was common ground throughout in developing methodologies and embracing what one of the organizers termed the ‘interactome’ between hosts and those which would exploit them.
Bio-metals imaging and speciation in cells using proton and synchrotron radiation X-ray microspectroscopy
Authors: Ortega Richard , Devès Guillaume , Carmona Asunción
Published: July 2009

The direct detection of biologically relevant metals in single cells and of their speciation is a challenging task that requires sophisticated analytical developments. The aim of this article is to present the recent achievements in the field of cellular chemical element imaging, and direct speciation analysis, using proton and synchrotron radiation X-ray micro- and nano-analysis. The recent improvements in focusing optics for MeV-accelerated particles and keV X-rays allow application to chemical element analysis in subcellular compartments. The imaging and quantification of trace elements in single cells can be obtained using particle-induced X-ray emission (PIXE). The combination of PIXE with backscattering spectrometry and scanning transmission ion microscopy provides a high accuracy in elemental quantification of cellular organelles. On the other hand, synchrotron radiation X-ray fluorescence provides chemical element imaging with less than 100 nm spatial resolution. Moreover, synchrotron radiation offers the unique capability of spatially resolved chemical speciation using micro-X-ray absorption spectroscopy. The potential of these methods in biomedical investigations will be illustrated with examples of application in the fields of cellular toxicology, and pharmacology, bio-metals and metal-based nano-particles.
Calcium ions induce collapse of charged O-side chains of lipopolysaccharides from
Pseudomonas aeruginosa
Authors: Schneck Emanuel , Papp-Szabo Erzsebet , Quinn Bonnie E. , Konovalov Oleg V. , Beveridge Terry J. , Pink David A. , Tanaka Motomu
Published: July 2009

Lipopolysaccharide (LPS) monolayers deposited on planar, hydrophobic substrates were used as a defined model of outer membranes of
Pseudomonas aeruginosa
strain dps 89. To investigate the influence of ions on the (out-of-plane) monolayer structure, we measured specular X-ray reflectivity at high energy (22 keV) to ensure transmission through water. Electron density profiles were reconstructed from the reflectivity curves, and they indicate that the presence of Ca
2+
ions induces a significant change in the conformation of the charged polysaccharide head groups (O-side chains). Monte Carlo simulations based on a minimal computer model of LPS molecules allow for the modelling of 100 or more molecules over 10
−3
s and theoretically explained the tendency found by experiments.
On spatially explicit models of cholera epidemics
Authors: Bertuzzo E. , Casagrandi R. , Gatto M. , Rodriguez-Iturbe I. , Rinaldo A.
Published: July 2009

We generalize a recently proposed model for cholera epidemics that accounts for local communities of susceptibles and infectives in a spatially explicit arrangement of nodes linked by networks having different topologies. The vehicle of infection (Vibrio cholerae) is transported through the network links that are thought of as hydrological connections among susceptible communities. The mathematical tools used are borrowed from general schemes of reactive transport on river networks acting as the environmental matrix for the circulation and mixing of waterborne pathogens. Using the diffusion approximation, we analytically derive the speed of propagation for travelling fronts of epidemics on regular lattices (either one-dimensional or two-dimensional) endowed with uniform population density. Power laws are found that relate the propagation speed to the diffusion coefficient and the basic reproduction number. We numerically obtain the related, slower speed of epidemic spreading for more complex, yet realistic river structures such as Peano networks and optimal channel networks. The analysis of the limit case of uniformly distributed population sizes proves instrumental in establishing the overall conditions for the relevance of spatially explicit models. To that extent, the ratio between spreading and disease outbreak time scales proves the crucial parameter. The relevance of our results lies in the major differences potentially arising between the predictions of spatially explicit models and traditional compartmental models of the susceptible–infected–recovered (SIR)-like type. Our results suggest that in many cases of real-life epidemiological interest, time scales of disease dynamics may trigger outbreaks that significantly depart from the predictions of compartmental models.
Towards a systems biology approach to understanding seed dormancy and germination
Authors: Penfield Steven , King John
Published: July 2009

Seed germination is the first adaptive decision in the development of many land plants. Advances in genetics and molecular physiology have taught us much about the control of germination using the model plantArabidopsis thaliana. Here we review the current state of the art with an emphasis on mechanistic considerations and explore the potential impact of a systems biology approach to the problem.
Viscous medium promotes cooperation in the pathogenic bacteriumPseudomonas aeruginosa
Authors: Kümmerli Rolf , Griffin Ashleigh S. , West Stuart A. , Buckling Angus , Harrison Freya
Published: July 2009

There has been extensive theoretical debate over whether population viscosity (limited dispersal) can favour cooperation. While limited dispersal increases the probability of interactions occurring between relatives, which can favour cooperation, it can also lead to an increase in competition between relatives and this can reduce or completely negate selection for cooperation. Despite much theoretical attention, there is a lack of empirical research investigating these issues. We culturedPseudomonas aeruginosabacteria in medium with different degrees of viscosity and examined the fitness consequences for a cooperative trait—the production of iron-scavenging siderophore molecules. We found that increasing viscosity of the growth medium (i) significantly limited bacterial dispersal and the diffusion of siderophore molecules and (ii) increased the fitness of individuals that produced siderophores relative to mutants that did not. We propose that viscosity favours siderophore-producing individuals in this system, because the benefits of siderophore production are more likely to accrue to relatives (i.e. greater indirect benefits), and, at the same time, bacteria are more likely to gain direct fitness benefits by taking up siderophore molecules produced by themselves (i.e. the trait becomes less cooperative). Our results suggest that viscosity of the microbial growth environment is a crucial factor determining the dynamics of wild-type bacteria and siderophore-deficient mutants in natural habitats, such as the viscous mucus in cystic fibrosis lung.
Does stress response predict return rate in a migratory bird species? A study of American redstarts and their non-breeding habitat
Authors: Angelier Frédéric , Holberton Rebecca L. , Marra Peter P.
Published: July 2009

In vertebrates, the adrenocortical stress response activates an emergency life-history stage, which is thought to promote survival by helping individuals escape life-threatening situations. Although the adrenocortical stress response promotes many behavioural and physiological changes, it remains unclear whether this stress response actually translates into higher survival in wild vertebrates. We measured the adrenocortical stress response of non-breeding American redstarts (
Setophaga ruticilla
), a migratory bird that wintered in habitats of either high (mangroves) or low suitability (scrubs), and subsequently monitored their return rate during the following non-breeding seasons. The intensity of the adrenocortical stress response was consistent within individuals across the non-breeding season and was positively correlated with return rates in redstarts that wintered in scrubs, but not in redstarts that wintered in mangroves. Thus, in a context-dependent manner, the ability of an individual to physiologically react to stress determines its ability of returning to its non-breeding territory the following winters. For an individual, the ability to mount an important adrenocortical stress response probably benefits to survival. However, this beneficial effect probably depends on an individual's environment and phenotypic characteristics because these two variables are likely to affect its probability of being confronted with life-threatening stressors during its annual life cycle.
Historical distribution patterns of trigonioidids (non-marine Cretaceous bivalves) in Asia and their palaeogeographic significance
Authors: Sha Jingeng
Published: July 2009

The non-marine trigonioidid bivalves show five phases of radiation in the Cretaceous of Pal-Asia: pre-Aptian (?Valanginian/Hauterivian–Barremian), Aptian, Albian, Cenomanian and Turonian–Maastrichtian. Their distribution patterns show two distinct palaeo-river systems feeding trigonioidids. Before the Cenomanian, the river system occupied the southwestern–southern–southeastern Pal-Asian continental margin areas. During the Turonian–Maastrichtian, it extended along the line of southcentral China−eastern China−northeastern China−northern China and Mongolia−northwestern China–eastern Fergana Basin of Kyrgyzstan−western Tajikistan Basin of Tajikistan–Tashkent area of Kazakhstan−central Kyzylkum of northern Uzbekistan–Aral Sea area of Kazakhstan. Furthermore, the general trigonioidid distribution pattern demonstrates that Japan was probably attached to part of eastern China and/or Korea during the ?Valanginian/Hauterivian–Cenomanian stages.
Where sociality and relatedness diverge: the genetic basis for hierarchical social organization in African elephants
Authors: Wittemyer George , Okello John B. A. , Rasmussen Henrik B. , Arctander Peter , Nyakaana Silvester , Douglas-Hamilton Iain , Siegismund Hans R.
Published: July 2009

Hierarchical properties characterize elephant fission–fusion social organization whereby stable groups of individuals coalesce into higher order groups or split in a predictable manner. This hierarchical complexity is rare among animals and, as such, an examination of the factors driving its emergence offers unique insight into the evolution of social behaviour. Investigation of the genetic basis for such social affiliation demonstrates that while the majority of core social groups (second-tier affiliates) are significantly related, this is not exclusively the case. As such, direct benefits received through membership of these groups appear to be salient to their formation and maintenance. Further analysis revealed that the majority of groups in the two higher social echelons (third and fourth tiers) are typically not significantly related. The majority of third-tier members are matrilocal, carrying the same mtDNA control region haplotype, while matrilocality among fourth-tier groups was slightly less than expected at random. Comparison of results to those from a less disturbed population suggests that human depredation, leading to social disruption, altered the genetic underpinning of social relations in the study population. These results suggest that inclusive fitness benefits may crystallize elephant hierarchical social structuring along genetic lines when populations are undisturbed. However, indirect benefits are not critical to the formation and maintenance of second-, third- or fourth-tier level bonds, indicating the importance of direct benefits in the emergence of complex, hierarchical social relations among elephants. Future directions and conservation implications are discussed.
Collective decision-making in white-faced capuchin monkeys
Authors: Petit O. , Gautrais J. , Leca J.-B. , Theraulaz G. , Deneubourg J.-L.
Published: July 2009

In group-living animals, collective movements are a widespread phenomenon and occur through consensus decision. When one animal proposes a direction for group movement, the others decide to follow or not and hence take part in the decision-making process. This paper examines the temporal spread of individual responses after the departure of a first individual (the initiator) in a semi-free ranging group of white-faced capuchins (Cebus capucinus). We analysed 294 start attempts, 111 succeeding and 183 failing. Using a modelling approach, we have demonstrated that consensus decision-making for group movements is based on two complementary phenomena in this species: firstly, the joining together of group members thanks to a mimetic process; and secondly, a modulation of this phenomenon through the propensity of the initiator to give up (i.e. cancellation rate). This cancellation rate seems to be directly dependent upon the number of followers: the greater this number is, the lower the cancellation rate is seen to be. The coupling between joining and cancellation rates leads to a quorum: when three individuals join the initiator, the group collectively moves. If the initiator abandons the movement, this influences the joining behaviour of the other group members, which in return influences the initiator's behaviour. This study demonstrates the synergy between the initiator's behaviour and the self-organized mechanisms underlying group movements.
Hookworm infection, anaemia and genetic variability of the New Zealand sea lion
Authors: Acevedo-Whitehouse Karina , Petetti Laura , Duignan Padraig , Castinel Aurelie
Published: July 2009

Hookworms are intestinal blood-feeding nematodes that parasitize and cause high levels of mortality in a wide range of mammals, including otariid pinnipeds. Recently, an empirical study showed that inbreeding (assessed by individual measures of multi-locus heterozygosity) is associated with hookworm-related mortality of California sea lions. If inbreeding increases susceptibility to hookworms, effects would expectedly be stronger in small, fragmented populations. We tested this assumption in the New Zealand sea lion, a threatened otariid that has low levels of genetic variability and high hookworm infection rates. Using a panel of 22 microsatellites, we found that average allelic diversity (5.9) and mean heterozygosity (0.72) were higher than expected for a small population with restricted breeding, and we found no evidence of an association between genetic variability and hookworm resistance. However, similar to what was observed for the California sea lion, homozygosity at a single locus explained the occurrence of anaemia and thrombocytopenia in hookworm-infected pups (generalized linear model,F= 11.81,p< 0.001) and the effect was apparently driven by a particular allele (odds ratio = 34.95%; CI: 7.12–162.41;p< 0.00001). Our study offers further evidence that these haematophagus parasites exert selective pressure on otariid blood-clotting processes.
A new North American therizinosaurid and the role of herbivory in ‘predatory’ dinosaur evolution
Authors: Zanno Lindsay E. , Gillette David D. , Albright L. Barry , Titus Alan L.
Published: July 2009

Historically, ecomorphological inferences regarding theropod (i.e. ‘predatory’) dinosaurs were guided by an assumption that they were singularly hypercarnivorous. A recent plethora of maniraptoran discoveries has produced evidence challenging this notion. Here, we report on a new species of maniraptoran theropod,
Nothronychus graffami
sp. nov. Relative completeness of this specimen permits a phylogenetic reassessment of Therizinosauria—the theropod clade exhibiting the most substantial anatomical evidence of herbivory. In the most comprehensive phylogenetic study of the clade conducted to date, we recover Therizinosauria as the basalmost maniraptoran lineage. Using concentrated changes tests, we present evidence for correlated character evolution among herbivorous and hypercarnivorous taxa and propose ecomorphological indicators for future interpretations of diet among maniraptoran clades. Maximum parsimony optimizations of character evolution within our study indicate an ancestral origin for dietary plasticity and facultative herbivory (omnivory) within the clade. These findings suggest that hypercarnivory in paravian dinosaurs is a secondarily derived dietary specialization and provide a potential mechanism for the invasion of novel morpho- and ecospace early in coelurosaurian evolution—the loss of obligate carnivory and origin of dietary opportunism.
Molecular and Chromosomal Evidence for Allopolyploidy in Soybean
Authors: Gill Navdeep , Findley Seth , Walling Jason G. , Hans Christian , Ma Jianxin , Doyle Jeff , Stacey Gary , Jackson Scott A.
Published: July 2009

Recent studies have documented that the soybean (Glycine max) genome has undergone two rounds of large-scale genome and/or segmental duplication. To shed light on the timing and nature of these duplication events, we characterized and analyzed two subfamilies of high-copy centromeric satellite repeats, CentGm-1 and CentGm-2, using a combination of computational and molecular cytogenetic approaches. These two subfamilies of satellite repeats mark distinct subsets of soybean centromeres and, in at least one case, a pair of homologs, suggesting their origins from an allopolyploid event. The satellite monomers of each subfamily are arranged in large tandem arrays, and intermingled monomers of the two subfamilies were not detected by fluorescence in situ hybridization on extended DNA fibers nor at the sequence level. This indicates that there has been little recombination and homogenization of satellite DNA between these two sets of centromeres. These satellite repeats are also present in Glycine soja, the proposed wild progenitor of soybean, but could not be detected in any other relatives of soybean examined in this study, suggesting the rapid divergence of the centromeric satellite DNA within the Glycine genus. Together, these observations provide direct evidence, at molecular and chromosomal levels, in support of the hypothesis that the soybean genome has experienced a recent allopolyploidization event.
Polyphenoloxidase Silencing Affects Latex Coagulation in Taraxacum Species
Authors: Wahler Daniela , Gronover Christian Schulze , Richter Carolin , Foucu Florence , Twyman Richard M. , Moerschbacher Bruno M. , Fischer Rainer , Muth Jost , Prüfer Dirk
Published: July 2009

Latex is the milky sap that is found in many different plants. It is produced by specialized cells known as laticifers and can comprise a mixture of proteins, carbohydrates, oils, secondary metabolites, and rubber that may help to prevent herbivory and protect wound sites against infection. The wound-induced browning of latex suggests that it contains one or more phenol-oxidizing enzymes. Here, we present a comprehensive analysis of the major latex proteins from two dandelion species, Taraxacum officinale and Taraxacum kok-saghyz, and enzymatic studies showing that polyphenoloxidase (PPO) is responsible for latex browning. Electrophoretic analysis and amino-terminal sequencing of the most abundant proteins in the aqueous latex fraction revealed the presence of three PPO-related proteins generated by the proteolytic cleavage of a single precursor (pre-PPO). The laticifer-specific pre-PPO protein contains a transit peptide that can target reporter proteins into chloroplasts when constitutively expressed in dandelion protoplasts, perhaps indicating the presence of structures similar to plastids in laticifers, which lack genuine chloroplasts. Silencing the PPO gene by constitutive RNA interference in transgenic plants reduced PPO activity compared with wild-type controls, allowing T. kok-saghyz RNA interference lines to expel four to five times more latex than controls. Latex fluidity analysis in silenced plants showed a strong correlation between residual PPO activity and the coagulation rate, indicating that laticifer-specific PPO plays a major role in latex coagulation and wound sealing in dandelions. In contrast, very little PPO activity is found in the latex of the rubber tree Hevea brasiliensis, suggesting functional divergence of latex proteins during plant evolution.
RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice
Authors: Lee Tae-Ho , Kim Yeon-Ki , Pham Thu Thi Minh , Song Sang Ik , Kim Ju-Kon , Kang Kyu Young , An Gynheung , Jung Ki-Hong , Galbraith David W. , Kim Minkyun , Yoon Ung-Han , Nahm Baek Hie
Published: July 2009

Microarray data can be used to derive understanding of the relationships between the genes involved in various biological systems of an organism, given the availability of databases of gene expression measurements from the complete spectrum of experimental conditions and materials. However, there have been no reports, to date, of such a database being constructed for rice (Oryza sativa). Here, we describe the construction of such a database, called RiceArrayNet (RAN; http://www.ggbio.com/arraynet/), which provides information on coexpression between genes in terms of correlation coefficients (r values). The average number of coexpressed genes is 214, with sd of 440 at r ≥ 0.5. Given the correlation between genes in a gene pair, the degrees of closeness between genes can be visualized in a relational tree and a relational network. The distribution of correlated genes according to degree of stringency shows how each gene is related to other genes. As an application of RAN, the 16-member L7Ae ribosomal protein family was explored for coexpressed genes and gene expression values within and between rice and Arabidopsis (Arabidopsis thaliana), and common and unique features in coexpression partners and expression patterns were observed for these family members. We observed a correlation pattern between Os01g0968800, a drought-responsive element-binding transcription factor, Os02g0790500, a trehalose-6-phosphate synthase, and Os06g0219500, a small heat shock factor, reflecting the fact that genes responding to the same biological stresses are regulated together. The RAN database can be used as a tool to gain insight into a particular gene by examining its coexpression partners.
Physiological and Transcriptome Analysis of Iron and Phosphorus Interaction in Rice Seedlings
Authors: Zheng Luqing , Huang Fangliang , Narsai Reena , Wu Jiaojiao , Giraud Estelle , He Fei , Cheng Longjun , Wang Fang , Wu Ping , Whelan James , Shou Huixia
Published: July 2009

The antagonistic interaction between iron (Fe) and phosphorus (P) has been noted in the area of plant nutrition. To understand the physiology and molecular mechanisms of this interaction, we studied the growth performance, nutrient concentration, and gene expression profiles of root and shoot segments derived from 10-d-old rice (Oryza sativa) seedlings under four different nutrient conditions: (1) full strength of Fe and P (+Fe+P); (2) full strength of P and no Fe (−Fe+P); (3) full strength of Fe and no P (+Fe−P); and (4) without both Fe and P (−Fe−P). While removal of Fe in the growth medium resulted in very low shoot and root Fe concentrations, the chlorotic symptoms and retarded seedling growth were only observed on seedlings grown in the presence of P. Microarray data showed that in roots, 7,628 transcripts were significantly changed in abundance in the absence of Fe alone. Interestingly, many of these changes were reversed if P was also absent (−Fe−P), with only approximately 15% overlapping with –Fe alone (–Fe+P). Analysis of the soluble Fe concentration in rice seedling shoots showed that P deficiency resulted in significantly increased Fe availability within the plants. The soluble Fe concentration under –Fe–P conditions was similar to that under +Fe+P conditions. These results provide evidence that the presence of P can affect Fe availability and in turn can influence the regulation of Fe-responsive genes.
The Role of Oxophytodienoate Reductases in the Detoxification of the Explosive 2,4,6-Trinitrotoluene by Arabidopsis
Authors: Beynon Emily R. , Symons Zoe C. , Jackson Rosamond G. , Lorenz Astrid , Rylott Elizabeth L. , Bruce Neil C.
Published: July 2009

The explosive 2,4,6-trinitrotoluene (TNT) is a significant environmental pollutant that is both toxic and recalcitrant to degradation. Phytoremediation is being increasingly proposed as a viable alternative to conventional remediation technologies to clean up explosives-contaminated sites. Despite the potential of this technology, relatively little is known about the innate enzymology of TNT detoxification in plants. To further elucidate this, we used microarray analysis to identify Arabidopsis (Arabidopsis thaliana) genes up-regulated by exposure to TNT and found that the expression of oxophytodienoate reductases (OPRs) increased in response to TNT. The OPRs share similarity with the Old Yellow Enzyme family, bacterial members of which have been shown to transform explosives. The three predominantly expressed forms, OPR1, OPR2, and OPR3, were recombinantly expressed and affinity purified. Subsequent biochemical characterization revealed that all three OPRs are able to transform TNT to yield nitro-reduced TNT derivatives, with OPR1 additionally producing the aromatic ring-reduced products hydride and dihydride Meisenheimer complexes. Arabidopsis plants overexpressing OPR1 removed TNT more quickly from liquid culture, produced increased levels of transformation products, and maintained higher fresh weight biomasses than wild-type plants. In contrast, OPR1,2 RNA interference lines removed less TNT, produced fewer transformation products, and had lower biomasses. When grown on solid medium, two of the three OPR1 lines and all of the OPR2-overexpressing lines exhibited significantly enhanced tolerance to TNT. These data suggest that, in concert with other detoxification mechanisms, OPRs play a physiological role in xenobiotic detoxification.
Structures of strontium diformate and strontium fumarate. A synchrotron powder diffraction study
Authors: Ståhl Kenny , Andersen Jens E. T. , Shim Irene , Christgau Stephan
Published: July 2009

The crystal structures of strontium diformate in space groups P212121 (α form, 295 K), P41212 (β form, 334 and 540 K) and I41/amd (δ form, 605 K), and strontium fumarate in space groups Fddd (β form, 105 K) and I41/amd (α form, 293 K) have been determined from synchrotron X-ray powder diffraction data. Except for the α-strontium diformate, all the structures are based on a diamond-like Sr-ion arrangement, as in strontium acetylene dicarboxylate. The formate ions are disordered in the δ phase owing to steric hindrance. The fumarate ions are disordered over four (α) or two (β) symmetry-equivalent orientations. α-Strontium fumarate crystallizes with a unique 90° carboxylate dihedral angle, and is stable up to 773 K.
Structural elucidation of the Bi2(n + 2)Mo
n
O6(n + 1) (n = 3, 4, 5 and 6) family of fluorite superstructures by transmission electron microscopy
Authors: Landa-Cánovas Ángel R. , Vila Eladio , Hernández-Velasco Jorge , Galy Jean , Castro Alicia
Published: July 2009

The cationic framework structure of a whole new family of compounds with the general formula Bi2(n + 2)Mo
n
O6(n + 1) (n = 3, 4, 5 and 6) has been elucidated by transmission electron microscopy (TEM) methods. High-resolution transmission electron microscopy (HRTEM) has been used to postulate heavy-atom models based on the known structure of the n = 3 phase, Bi10Mo3O24. These models were tested by HRTEM image simulation, electron diffraction and powder X-ray diffraction simulation methods which agreed with the experimental results. The four known phases of this family correspond to n = 3, 4, 5 and 6 members and all show fluorite superstructures. They consist of a common δ-Bi2O3 fluorite-type framework, inside of which are distributed ribbons of {MoO4} tetrahedra which are infinite along b, one tetrahedron thick along c, and of variable widths of 3, 4, 5 or 6 {MoO4} tetrahedra along a depending on the family member (n value). These {MoO4} tetrahedra are isolated, i.e. without sharing any corner as in the [Bi12O14] columnar structural-type phase Bi[Bi12O14][MoO4]4[VO4]. The structure of all these family members can be described as crystallographic shear derivatives from Aurivillius-type phases such as Bi2MoO6, the n = ∞ end member. All these compounds are good oxygen-ion conductors.
Trigonal structures of ABe2BO3F2 (A = Rb, Cs, Tl) crystals
Authors: McMillen Colin D. , Hu Jia , VanDerveer Donald , Kolis Joseph W.
Published: July 2009

Several interesting fluoroberyllium borates were synthesized hydrothermally and characterized by single-crystal X-ray diffraction. The crystal structures of RbBe2BO3F2 (RBBF; rubidium fluoroberyllium borate) and CsBe2BO3F2 (CBBF; caesium fluoroberyllium borate), previously determined in the space group C2, were reinvestigated for higher symmetry and found to have more suitable solutions in the space group R32. TlBe2BO3F2 (TBBF; thallium fluoroberyllium borate) was synthesized as a novel compound also having this trigonal structure type. Details of the space-group determination and unique structural features are discussed. These crystal structures were compared with that of KBe2BO3F2, revealing interesting structural trends within this family of compounds that are also discussed. A crystallographic explanation of the physical morphology is postulated.
Crystal structures and cation ordering in Cs2MgSi5O12, Rb2MgSi5O12 and Cs2ZnSi5O12 leucites
Authors: Bell A. M. T. , Henderson C. M. B.
Published: July 2009

The crystal structures of the leucite analogues Cs2MgSi5O12, Cs2ZnSi5O12 and Rb2MgSi5O12 have been determined by synchrotron X-ray powder diffraction using Rietveld refinement in conjunction with 29Si MAS NMR spectroscopy. These leucites are framework structures with distinct tetrahedral sites (T sites) occupied by Si and a divalent cation (either Mg or Zn in these samples); there is also a monovalent extra-framework cation (either Cs or Rb in these samples). The refined crystal structures were based on the Pbca leucite structure of Cs2CdSi5O12, thus a framework with five ordered Si T sites and one ordered Cd T site was used as the starting model for refinement. 29Si MAS NMR shows five distinct Si T sites for Cs2MgSi5O12 and Rb2MgSi5O12, but six Si T sites for Cs2ZnSi5O12. The refined structures for Cs2MgSi5O12 and Rb2MgSi5O12 were determined with complete T-site ordering, but the refined structure for Cs2ZnSi5O12 was determined with partial disorder of Mg and Si over two of the T sites.
Microwave‐Assisted Combustion Synthesis of Tantalum Nitride in a Fluidized Bed
Authors: Jain Akhil , Brezinsky Kenneth
Published: July 2009

Combustion synthesis experiments in a fluidized bed have been conducted using nitrogen as the fluidizing gas for the formation of transition‐metal nitrides that are potential replacements for traditional hydrodenitrogenation and hydrodesulfurization catalysts. The microwave‐assisted ignition of reaction has been investigated for its potential to produce nitride overlayers on two different sizes of tantalum particle substrates. Various characterization techniques—X‐ray diffractometry, energy dispersive spectroscopy, scanning electron microscopy, and high‐resolution transmission electron microscopy—have been used to study the presence of nitride overlayers. The results indicate that microwave assistance can permit controlled formation of tantalum nitride (Ta2N) overlayers.
Modeling of the Pressure Distribution in Three‐Dimensional Porous Green Bodies during Binder Removal
Authors: Feng Kai , Lombardo Stephen J.
Published: July 2009

A model is developed to describe flow in porous media from the thermal decomposition of binder in three‐dimensional bodies with anisotropic permeability. The model is able to describe the pressure within the body as a function of position, time, and temperature during the heating cycle. The results from numerical solution of the un‐steady‐state partial differential equation are compared to those obtained from an analytical solution to the steady‐state equation. Under many conditions that are representative of binder removal, the analytical solution provides a reasonable representation of the numerical solution. A criterion is also developed to determine when the analytical solution is valid. Scaling relationships for the buildup of pressure in terms of the dimensions of the body, the rate of reaction, and the permeability are also derived.
Bulk, Dense, Nanocrystalline Yttrium Aluminum Garnet by Consolidation of Amorphous Powders at Low Temperatures and High Pressures
Authors: Choudhury Samrat , Gandhi Ashutosh S. , Jayaram Vikram
Published: July 2009

Amorphous Al2O3–37.5% Y2O3 powders, prepared using spray pyrolysis followed by partial or complete thermal decomposition, were hot‐pressed at 315°–640°C and 500 or 750 MPa uniaxial pressure. Hot pressing of fully decomposed amorphous powder at 450°–640°C at pressures up to 750 MPa led to densification (up to 96%) as well as nanocrystallization of yttrium aluminum garnet (YAG). When the pressure was applied during heating, instead of after reaching the final temperature, higher relative densities resulted. Fully crystalline starting powder did not densify. The low true density of the amorphous phase (3.1 g·cm−3) was believed to be responsible for the densification through enhanced ionic mobilities.
Evolution of Average Microstructural Properties in the Final Stage Sintering of Alumina
Authors: Nettleship Ian , Patterson Burton R. , Slaughter William S.
Published: July 2009

Models of simultaneous coarsening and densification in final stage sintering commonly assume that the coarsening process results in microstructures that evolve self‐similarly from a fixed microstructural geometry, differing only in scale. This assumption is experimentally tested for alumina in the solid volume fraction range of 0.97–1 using nondimensional microstructural parameters. The results clearly show that such models based on assumed geometries often underestimate the pore size relative to the grain size. The largest differences between the model and the experiments occur for lower firing temperatures and higher doping levels. It is concluded that the coarsening reflected in the effect of temperature and dopant level is not a self‐similar process from a common microstructural geometry.
Elimination of Surface Spallation of Alumina Green Bodies Prepared by Acrylamide‐Based Gelcasting via Poly(vinylpyrrolidone)
Authors: Ma Jingtao , Xie Zhipeng , Miao Hezhuo , Zhou Longjie , Huang Yong , Cheng Yibing
Published: July 2009

Surface spallation of gelcast alumina green bodies due to the exposure of the surface to air during gelation was successfully eliminated by adding a proper amount of poly(vinylpyrrolidone) (PVP) in aqueous acrylamide premix solution. The influences of PVP on the colloidal characteristics of alumina powder in aqueous solutions, the rheological properties of alumina slurries, the gelation process, and the properties and microstructures of the gelcast green bodies and the sintered samples were systematically investigated. Even though the addition of PVP to premix solution has slightly negative effects on the viscosity of alumina slurries, gelation and strength of green bodies, it has no obvious influence on the final structure and properties of alumina ceramics. Thus, PVP was considered an effective polymer to resolve the problem of the inhibition of gelation due to the presence of oxygen, which usually occurs in gelcasting during the formation of polymer network gel by in situ polymerization of monomers in air. The mechanism of PVP in eliminating the surface spallation problems of green bodies is also discussed.
Effect of Precursor and Solvent on Morphology of Zirconia Nanoparticles Produced by Combustion Aerosol Synthesis
Authors: Limaye Amit U. , Helble Joseph J.
Published: July 2009

Zirconia nanoparticles were synthesized using a flame‐based system involving spray droplet combustion of different precursor solutions. The characteristics of the feed were varied by varying the precursor compound, precursor concentration, and solvent type, and by using droplets of different mean sizes. When large droplets were used, agglomerated particles were formed when an organometallic precursor was used and large cenospheric particles were produced when an inorganic precursor was used. Reduction of the droplet size to a number‐mean droplet diameter of 3.2 μm resulted in the production of solid spherical particles regardless of the precursor type. When an inertial impactor was used to eliminate droplets larger than 2.3 μm, the large particles in the final product were eliminated and uniformly sized solid zirconia particles having a smaller mean size were produced. The final particle size did not vary with the concentration of the precursor, indicating that multiple ceramic particles resulted from each precursor‐containing droplet.