bluuebunny/crossref_metadata_2025 huggingface dataset:
Species richness enhances both algal biomass and rates of oxygen production in aquatic microcosms
Authors: Power Lillian D. , Cardinale Bradley J.
Published: July 2009

Accelerating rates of species extinction have generated much recent interest in understanding how biodiversity affects the functioning of ecosystems. Experiments to date have shown communities composed of fewer species generally capture a smaller fraction of available resources, and achieve lower standing stock biomass than more diverse communities. However, it is uncertain how changes in biodiversity and the resulting alterations in biomass affect the rates of important ecological processes like primary production, which regulates fluxes of CO2 and O2 between the biotic and abiotic components of the environment. Here we show that species richness influences not only the standing stock biomass of primary producers, but also rates of gross primary production measured by changes in O2 concentrations in aquatic systems. We manipulated the richness of five widespread species of algae in laboratory microcosms and then quantified how richness impacts algal biomass, rates of gross primary production (GPP), and the ratio of production to respiration. Algal biomass increased by a factor of 1.82 for each level of species richness, and GPP by a factor of 1.20, for each additional species. Production to respiration ratios increased about 10% for each additional species, indicating that systems with more species were increasingly autotrophic – that is, they produced more O2 than they consumed, and accumulated CO2 faster than they released it. These trends were driven by two highly productive species that became co‐dominant in species rich polycultures at the expense of other taxa. Our experiment suggests that changes in biodiversity may influence not only the rates at which O2 and CO2 are produced and released in ecosystems, but also the total amount of carbon that is sequestered and stored as biomass.
Sinks without borders: snowshoe hare dynamics in a complex landscape
Authors: Griffin Paul C. , Scott Mills L.
Published: July 2009

A full understanding of population dynamics of wide‐ranging animals should account for the effects that movement and habitat use have on individual contributions to population growth or decline. Quantifying the per‐capita, habitat‐specific contribution to population growth can clarify the value of different patch types, and help to differentiate population sources from population sinks. Snowshoe hares,Lepus americanus, routinely use various habitat types in the landscapes they inhabit in the contiguous US, where managing forests for high snowshoe hare density is a priority for conservation of Canada lynx,Lynx canadensis. We estimated density and demographic rates via mark–recapture live trapping and radio‐telemetry within four forest stand structure (FSS) types at three study areas within heterogeneous managed forests in western Montana. We found support for known fate survival models with time‐varying individual covariates representing the proportion of locations in each of the FSS types, with survival rates decreasing as use of open young and open mature FSS types increased. The per‐capita contribution to overall population growth increased with use of the dense mature or dense young FSS types and decreased with use of the open young or open mature FSS types, and relatively high levels of immigration appear to be necessary to sustain hares in the open FSS types. Our results support a conceptual model for snowshoe hares in the southern range in which sink habitats (open areas) prevent the buildup of high hare densities. More broadly, we use this system to develop a novel approach to quantify demographic sources and sinks for animals making routine movements through complex fragmented landscapes.
Portfolio theory and how parent birds manage investment risk
Authors: Forbes Scott
Published: July 2009

Investment theory is founded on the premise that higher returns are generally associated with greater risk, and that portfolio diversification reduces risk. Here I examine parental investment decisions in birds from this perspective, using data from a model system, a 16‐year study of breeding red‐winged blackbirdsAgelaius phoeniceus. Like many altricial birds, blackbirds structure their brood into core (first‐hatched) and marginal (later‐hatched) elements that differ in risk profile. I measured risk in two ways: as the coefficient of variation in growth and survival of core and marginal offspring from a given brood structure; and using financial beta derived from the capital asset pricing model of modern portfolio theory. Financial beta correlates changes in asset value with changes in the value of a broader market, defined here as individual reproductive success vs. population reproductive success. Both measures of risk increased with larger core (but not marginal) brood size; and variation in growth and survival was significantly greater during ecologically adverse conditions. Core offspring showed low beta values relative to marginal progeny. The most common brood structures in the population exhibited the highest beta values for both core and marginal offspring: many parent blackbirds embraced rather than avoided risk. But they did so prudently with an investment strategy that resembled a financial instrument, the call option. A call option is a contingent claim on the future value of the asset, and is exercised only if asset value increases beyond a point fixed in advance. Otherwise the option lapses and the investor loses only the initial option price. Parents created high risk marginal progeny that were forfeited during ecological adversity (the option lapses) but raised otherwise (the option called); at the same time parents maintained a constant investment and return in low risk core progeny that varied little with changes in brood size or ecological conditions.
Comparative chewing efficiency in mammalian herbivores
Authors: Fritz Julia , Hummel Jürgen , Kienzle Ellen , Arnold Christian , Nunn Charles , Clauss Marcus
Published: July 2009

Although the relevance of particle size reduction in herbivore digestion is widely appreciated, few studies have investigated digesta particle size across species in relation to body mass or digestive strategy. We investigated faecal particle size, which reflects the size of ingesta particles after both mastication and specialized processes such as rumination. Particle size was measured by wet sieving samples from more than 700 captive individuals representing 193 mammalian species. Using phylogenetic generalized least squares, faecal particle size scaled to body mass with an exponent of 0.22 (95% confidence interval: 0.16–0.28). In comparisons among different digestive strategies, we found that (1) equids had smaller faecal particles than other hindgut fermenters, (2) non‐ruminant foregut fermenters and hindgut fermenters had similar‐sized faecal particles (not significantly different), and (3) ruminants had finer faecal particles than non‐ruminants. These results confirm that the relationship between chewing efficiency and body mass is modified by morphological adaptations in dental design and physiological adaptations to chewing, such as rumination. This allometric relationship should be considered when investigating the effect of body size on digestive physiology, and digestion studies should include a measure of faecal particle size.
The effects of spatially correlated perturbations and habitat configuration on metapopulation persistence
Authors: Robert Alexandre
Published: July 2009

All natural populations are confronted with the temporal variability of their environment, and most of them occur in fragmented habitats. I use spatially explicit modeling to examine the interactive effects of habitat configuration, habitat deterioration and spatially correlated environmental perturbations on the viability of fragmented populations. When considering a fixed amount of habitat, viability is maximized for an intermediate (optimal) density of habitat patches, allowing effective dispersal without strong environmental correlation among patches. Starting from this optimal density, I show that the scale of habitat change (density reduction vs range contraction) interacts with the direction of change (reduction vs improvement of habitat availability). An improvement in habitat availability is always more beneficial if occurring through an increase of the species range, while a reduction in habitat availability is always more critical if occurring through a reduction of patch density (even in the presence of environmental correlation). In the context of the ‘single large or several small’ debate in reserve design, results indicate that a large number of small patches may be optimal to long‐term species persistence if the species range increases with the number of patches.
The genetics of isolated orofacial clefts: from genotypes to subphenotypes
Authors: Jugessur A , Farlie PG , Kilpatrick N
Published: July 2009

Orofacial clefts are the most common craniofacial birth defects and one of the most common congenital malformations in humans. They require complex multidisciplinary treatment and are associated with elevated infant mortality and significant lifelong morbidity. The development of craniofacial structures is an exquisitely orchestrated process involving the coordinated growth of multiple, independently derived primordia. Perturbations impacting on the genesis or growth of these primordia may interfere with the proper morphogenesis of facial structures, resulting in clefting of the lip, the primary or secondary palate, or a combination of these sites. A variety of genetic approaches involving both human populations and animal models have greatly facilitated the search for genes involved in human clefting. In this article, we review the most prominent genes for orofacial clefts in the context of developmental pathways that shape the craniofacial complex. We highlight several Mendelian clefting syndromes that have provided valuable clues in identifying genes for the more common, isolated forms of clefting. Finally, we elaborate on a number of potential subclinical features (subphenotypes) associated with what have previously been diagnosed as ‘isolated’ clefts that may serve as additional markers for identifying individuals or families in whom there may be a greater risk of inheriting a cleft.
A Sticky Affair: Resin Collection by Bornean Stingless Bees
Authors: Leonhardt Sara Diana , Blüthgen Nico
Published: July 2009

Plant resins are used by stingless bees for nest construction and maintenance. To reveal factors that influence the bees' decision about where and when to collect resin, resin collection was studied in ten stingless bee species (Apidae, Meliponini) collecting resin at natural and artificially induced wounds of nine tree species in Borneo. Artificially induced wounds were found by bees within 1–2 d. The number of foragers at artificial wounds increased during the subsequent 5 d until resin secretion stopped or the resin hardened. At natural resin wounds, species identity and number of foragers remained constant during the observation period. Bees collected resin from some trees and ignored others. Agathis borneensis (Araucariaceae) was the most attractive resin source. The bees' visitation rate did not correlate significantly with resin wound size. Inter‐ and intraspecific aggression occurred at ten resin wounds. In Tetragonilla collina and Tetragonula melanocephala, we additionally recorded resin intake at colony entrances. The proportion of workers retuning with resin varied considerably between colonies. We observed attacks by ants at three of our eight focal colonies, which resulted in a significant increase in resin intake while the nest was under attack and until 1–2 d after the attack had stopped. The increase in resin collection triggered by ant attacks was even stronger than the increase following a manual destruction of the nest entrance tube.
Leaf Gas Exchange in Canopy Species of a Venezuelan Cloud Forest
Authors: Rada Fermín , García‐Núñez Carlos , Ataroff Michele
Published: July 2009

Tropical cloud forests are considered humid ecosystems with frequent cloud cover down to the ground surface. However, seasonal variation in precipitation may induce short‐term water stress. For canopy leaves, this water stress may also be a consequence of large atmospheric vapor pressure deficits. The objective of this work was to study five canopy cloud forest species to determine if there are restrictions to leaf gas exchange as a consequence of seasonality in precipitation and to daily water deficit due to air evaporative demand mainly during maximum incoming radiation hours. Seasonal daily courses of microclimatic variables (air temperature, relative humidity, photosynthetic photon flux density) and plant responses (leaf water potential, stomatal conductance, CO2 assimilation rates, leaf nitrogen concentration) were measured at 2400 m asl in Monterrey, an intermontane valley of the Venezuelan Andes. A gradient in terms of responses to water stress conditions was observed between the species, with Clusia multiflora (a 46% reduction in stomatal conductance between seasons) as the most affected and Miconia resimoides (increased stomatal conductance) responding more favorably to slight water stress conditions. If we consider the limitations of water stress and/or light conditions on CO2 assimilation we may arrange the species into those in which water stress conditions have a greater impact on leaf carbon gain, those where light conditions are determinant and one in which both water stress and light conditions may affect leaf carbon assimilation.
Implications of Behavior and Gut Passage for Seed Dispersal Quality: The Case of Black and Gold Howler Monkeys
Authors: Bravo Susana P.
Published: July 2009

The most generalized mechanism of seed dispersal in tropical and subtropical forests is dispersal by vertebrates. The pattern of seed dispersal and germination capacity of dispersed seeds can determine the seed disperser quality because both affect the postdispersal fate of dispersed seeds. Animals' behavior is an important determinant of seed deposition pattern. One of most abundant frugivores of Neotropical forests are howler monkeys Alouatta spp., so my aim was to evaluate the potential quality of Alouatta caraya as a seed disperser, obtaining details of: (1) seed deposition pattern, (2) behavioral context of defecations, and (3) germination capacity of dispersed seeds. During 2 years the seed shadow created by howlers and the behavioral context of depositions was examined in the Paraná flooded forest, and germination tests were conducted in the laboratory. Black and gold howler monkeys consumed fruits of five canopy trees, three understory trees, one shrub, and two vines. Howlers dispersed seeds in a complex pattern: 35 percent (337 scats) of scats were deposited individually, and 65 percent were deposited in big latrines associated with the main sleeping trees and in small latrines associated with secondary sleeping trees and confrontations at territory edges. From 261 dispersal distances recorded, 20 and 40 m were the mode, but 57 percent of distances were >50 m and 31 percent were >100 m. Germination speed increased significantly in ingested seeds of Banara arguta, Ocotea diospyrifolia and Eugenia punicifolia. The seed deposition pattern generated by A. caraya may produce a diversification of environmental conditions for dispersed seeds that should be considered in future evaluations.
New species and unexpected diversity of socially parasitic bees in the genus Inquilina Michener (Hymenoptera: Apoidea: Apidae)
Authors: Smith Jaclyn A. , Schwarz Michael P.
Published: July 2009

Abstract  Allodapine bees present particular problems for taxonomy due to a high level of morphological conservatism in adults, even between genera. However, this tribe of bees also presents a unique opportunity to explore the evolution of social parasitism because of the comparatively large number of origins of socially parasitic species. Morphological differences presented here, along with DNA sequence data and molecular phylogenetic analyses, indicate a much larger number of Australian social parasite species in the genus Inquilina than previously anticipated, and suggest that the final number of socially parasitic species may be considerable. We describe five new species and present sequence data that will help elucidate the delineation of further new species. Inquilina provides a unique opportunity to study the evolution of social parasitism in social insects, but further studies will need to encompass both population genetic and phylogenetic approaches.
Angiotensin and the brain
Authors: ANDERSSON B. , ERIDSSON S. , RUNDGREN M.
Published: July 2009

A brief account for the renal renin‐angiotensin system (RAS), its inhibitors and receptors, as for the presence of an intrinsic cerebral RAS is initially provided. The review is then focused upon the circumventricular organs as cerebral targets for blood‐borne angiotensin II (Ang II) and on centrally mediated Ang II effects. These concern influences upon the cardiovascular system, water balance, sodium balance, and ACTH‐cortisol secretion.
Biopreservation of Refrigerated and Vacuum‐Packed Dicentrarchus labrax by Lactic Acid Bacteria
Authors: El Bassi Leila , Hassouna Mnasser , Shinzato Naoya , Matsui Toru
Published: July 2009

ABSTRACT:  Two lactic acid bacteria (LAB) were selected from 100 LAB isolated from various sea products to examine their use in Dicentrarchus labrax preservation. The isolates, tentatively named strain nr 3 and 7, were identified as Lactobacillus plantarum and L. pentosus, respectively. They showed antagonistic activity against psychrotroph, pathogenic, and coliform bacteria. The antagonistic activity of strain 3 was suggested to be by bacteriocins since activity was abolished by protease treatment, while that of strain 7 was due to the effect of pH decrease caused by the produced organic acids. Their use prevented total volatile basic nitrogen contents (TVB‐N) and trimethylamine (TMA) to some extent, suggesting that inoculation could extend the period of storage.
Residence Time Distribution (RTD) of Particulate Foods in a Continuous Flow Pilot‐Scale Ohmic Heater
Authors: Sarang Sanjay , Heskitt Brian , Tulsiyan Priyank , Sastry Sudhir K.
Published: July 2009

ABSTRACT:  The residence time distribution (RTD) of a model particulate–fluid mixture (potato in starch solution) in the ohmic heater in a continuous sterilization process was measured using a radio frequency identification (RFID) methodology. The effect of solid concentration and the rotational speed of the agitators on the RTD were studied. The velocity of the fastest particle was 1.62 times the mean product velocity. In general, particle velocity was found to be greater than the product bulk average velocity. Mean particle residence time (MPRT) increased with an increase in the rotational speed of the agitators (P < 0.05), and no particular trend was observed between the MPRT and the solid concentration. The distribution curves E (θ) were skewed to the right suggesting slow moving zones in the system.
Effects of Dense Phase Carbon Dioxide Pasteurization on the Physical and Quality Attributes of a Red Grapefruit Juice
Authors: Ferrentino G. , Plaza M.L. , Ramirez‐Rodrigues M. , Ferrari G. , Balaban M.O.
Published: July 2009

ABSTRACT:  Red grapefruit juice was treated with continuous dense phase carbon dioxide (DPCD) equipment to inactivate yeasts and molds and total aerobic microorganisms. A central composite design was used with pressure (13.8, 24.1, and 34.5 MPa) and residence time (5, 7, and 9 min) as variables at constant temperature (40 °C), and CO2 level (5.7%) after experimentally measuring CO2 solubility in the juice. Five log reduction for yeasts and molds and total aerobic microorganisms occurred at 34.5 MPa and 7 min of treatment. A storage study was performed on the fresh juice DPCD treated at these conditions. °Brix, pH, titratable acidity (TA), pectinesterase (PE) inactivation, cloud, color, hue tint and color density, total phenolics, antioxidant capacity, and ascorbic acid were measured after the treatment and during 6 wk storage at 4 °C. During storage, the DPCD‐treated juice showed no growth of total aerobic microorganisms and yeasts and molds. Cloud increased (91%) while percent PE inactivation was partial (69.17%). No significant (α= 0.05) differences were detected between treated and untreated samples for °Brix, pH, and TA. Treated juice had higher lightness and redness and lower yellowness. No significant differences (α= 0.05) were detected for the hue tint values while the color density value was higher for the treated samples compared to the untreated. The treatment and the storage did not affect the total phenolic content of the juice. Slight differences were detected for the ascorbic acid content and the antioxidant capacity. The experimental results showed evidence that the treatment can maintain the physical and quality attributes of the juice, extending its shelf life and safety.
Ethnic difference in patients with type 2 diabetes mellitus in inter‐East Asian populations: A systematic review and meta‐analysis focusing on gene polymorphism
Authors: TAKEUCHI Masakazu , OKAMOTO Kousuke , TAKAGI Tatsuya , ISHII Hitoshi
Published: July 2009

Background:  We previously reported that the fasting serum insulin level was significantly lower in Japanese patients than in Korean and Chinese patients, and showed evidence that a difference in the dietary component would be one of the most influential factors for the ethnic difference. However, it is well known that type 2 diabetes mellitus (T2DM) results from the interaction between genetic predispositions and environmental risk factors. Therefore, we investigated ethnic differences by focusing on gene polymorphism, possibly related to T2DM in Japanese, Korean, and Chinese subjects.

Methods:  Data sources included MEDLINE and EMBASE between January 2001 and October 2008. We conducted a search for articles containing minor allele frequency (MAF) in the gene polymorphisms of peroxisome proliferator‐activated receptor‐γ (PPARG), inward‐rectifying potassium channel Kir6.2 (KCNJ11), Calpain 10 (CAPN10), and transcription factor 7‐like 2 (TCF7L2). The pooled odds ratio was calculated by using a fixed‐effects model with the Mantel–Haenszel method after confirming statistical evidence of homogeneity across the ethnicities using the Breslow–Day test.

Results:  The Breslow–Day test revealed that there were no statistically significant differences between ethnicities in pooled odds ratios for the gene polymorphisms in PPARG (P = 0.828), KCNJ11 (P = 0.194), CAPN10 (P = 0.090), and TCF7L2 (P = 0.376). Also, pooled odds ratios of each gene polymorphism in East Asians were 0.645 for PPARG (P = 0.000), 1.168 for KCNJ11 (P = 0.000), 0.967 for CAPN10 (P = 0.759), and 1.386 for TCF7L2 (P = 0.000).

Conclusion:  The results of this study and our previous studies suggest that behavioral and environmental risk factors have a more significant impact on ethnic difference in East Asian patients with T2DM compared with genetic predispositions.
Molecular methods for differentiating grey seal (Halichoerus grypus) and harbour seal (Phoca vitulina) scat
Authors: MASLAND E. D. P. , SWEEZY M. A. , ONO K. A.
Published: June 2009

Pinniped dietary information is crucial for understanding marine ecosystems; however, in the North Atlantic, grey and harbour seals haulout concomitantly and their faeces are visually indistinguishable. Therefore, we developed molecular methods to differentiate the species’ scat. PCR primers were created that amplify a portion of mitochondrial 16S ribosomal DNA in grey and harbour seals. The samples were amplified and the resulting products were digested using the restriction enzyme Tsp509I, producing diagnostic banding patterns. These tools provide a mechanism by which separate dietary analysis can be achieved for grey and harbour seals at mixed haulouts in New England.
Quorum sensing negatively regulates chitinase in Vibrio harveyi
Authors: Defoirdt Tom , Darshanee Ruwandeepika H.A. , Karunasagar Indrani , Boon Nico , Bossier Peter
Published: July 2009

Quorum sensing, bacterial cell‐to‐cell communication, regulates the virulence of Vibrio harveyi towards different hosts. Chitinase can be considered as a virulence factor because it helps pathogenic bacteria to attach to the host and to penetrate its tissues (e.g. in case of shrimp). Here, we show that quorum sensing negatively regulates chitinase in V. harveyi. Chitinolytic activity towards natural chitin from crab shells, the synthetic chitin derivative chitin azure, and fluorogenic chitin oligomers was significantly higher in a mutant in which the quorum‐sensing system is completely inactivated when compared with a mutant in which the system is maximally active. Furthermore, the addition of signal molecule containing cell‐free culture fluids decreased chitinase activity in a Harveyi Autoinducer 1 and Autoinducer 2‐deficient double mutant. Finally, chitinase A mRNA levels were fivefold lower in the mutant in which the quorum‐sensing system is maximally active when compared with the mutant in which the system is completely inactivated. [Correction added on 25 September 2009, after first online publication: the preceding sentence was corrected from ‘Finally, chitinase A mRNA levels were fivefold lower in the mutant in which the quorum‐sensing system is completely inactivated when compared with the mutant in which the system is maximally active.’] We argue that this regulation might help the vibrios to switch between host‐associated and free‐living life styles.
Substrate temperature effects on amorphous carbon film growth, investigated by infrared spectroscopy in multiple internal reflection geometry
Authors: Shinohara Masanori , Cho Ken , Matsuda Yoshinobu , Inayoshi Takanori , Kawazoe Hiroki , Fujiyama Hiroshi , Nitta Yuuki , Nakatani Tatsuyuki
Published: June 2009

The substrate temperature effects on the amorphous carbon film growth were investigated, by using the deposition rates and in situ and “real-time” infrared spectroscopy in multiple internal reflection geometry. The deposition rates were decreased, in contrast with the increases of substrate temperature. The growth mode was also changed with substrate temperatures: the film growth depends on the gas phase reaction at low substrate temperature; on the other hand, at high temperature the film grows with the decomposition of the CH3 species.
How to Think, Say, or Do Precisely the Worst Thing for Any Occasion
Authors: Wegner Daniel M.
Published: July 2009

Did I Really Do That?

Most of us believe that our daily actions occur because we exert conscious effort to make them happen; nevertheless, we sometimes seem to end up doing the precise thing we had hoped to avoid.
Wegner
(p.
48
) reviews the recent psychological research on ironic processes. The findings support the view that the unwanted outcomes are held in working memory and that the monitoring centers that usually ensure correct behavior can be distracted or exhausted, allowing the taboo idea to escape.
Ligand-Gated Chloride Channels Are Receptors for Biogenic Amines in
C. elegans
Authors: Ringstad Niels , Abe Namiko , Horvitz H. Robert
Published: July 2009

Biogenic Amine Receptors

Biogenic amines have important effects on behavior in humans and other animals. These agents can act by binding to heterotrimeric guanine nucleotide–binding protein (G protein)–coupled receptors, but can also activate ligand-gated ion channels.

Ringstad
et al.

(p.
96
) explored the family of ion channels that respond to biogenic amines in the worm
Caenorhabditis elegans
and characterized two family members that appear to function as chloride channels. One was a receptor activated by dopamine that could bind drugs used in humans as antipsychotics. The other was activated by tyramine and was shown in genetic studies to modulate behavior. Thus, the worm family of biogenic amine–activated channels is larger than previously recognized. If the same is true in humans, related channels may account, in part, for effects of currently used drugs or could be beneficial targets for development of therapeutics.
How Did Earth Accrete?
Authors: Halliday Alex N. , Wood Bernard J.
Published: July 2009

Isotope studies are providing clues to how Earth assembled and how its core formed.
The Illusive Gold Standard in Genetic Ancestry Testing
Authors: Lee Sandra Soo-Jin , Bolnick Deborah A. , Duster Troy , Ossorio Pilar , TallBear Kimberly
Published: July 2009

New regulations on disclosure, authority, and responsibility would shape how genetic ancestry tests are used.
Impact of Shifting Patterns of Pacific Ocean Warming on North Atlantic Tropical Cyclones
Authors: Kim Hye-Mi , Webster, Peter J. , Curry Judith A.
Published: July 2009

El Niño's Cousin

The most energetic and well-known quasi-periodic, air-sea temperature disturbance is ENSO, the mother of the warming of equatorial eastern Pacific surface waters known as El Niño. El Niño, and its cold sister La Niña, can produce dramatic effects on weather across the globe and so it is of great interest and importance to understand it better. Warming in the eastern tropical Pacific is not the only recurring pattern of sea-surface temperature variability in the Pacific, however.

Kim
et al.

(p.
77
; see the Perspective by

Holland

) report that a pattern of extensive warming in the central Pacific also occurs on a quasi-periodic basis, that it has a large effect on atmospheric circulation, and that it is more predictable than El Niño. These central Pacific warming events have become increasingly more frequent in the last few decades, making it even more vital that we understand them.
An Opportunity We Cannot Waste
Authors: Pickering Thomas R.
Published: July 2009

The struggles against world poverty are more challenging than ever, given the global financial crisis. At the London G-20 summit in April, leaders of the world's largest economies acknowledged that financial recovery could be sustained only if progress is made in alleviating world poverty. Thus, the path to stable worldwide recovery requires that the issues of economic growth, development, and poverty be seen as linked with the key drivers of food, water, and health, just as climate change is now linked to the key drivers of energy and environment.
The Ecological Theater

Speciation and Patterns of Diversity
Roger K. Butlin, Jon R. Bridle, and Dolph Schluter, Eds.

Cambridge University Press, Cambridge, 2009. 345 pp. $140, £75. ISBN 9780521883184. Paper, $63, £35. ISBN 9780521709637. Ecological Reviews.
Authors: Magurran Anne E.
Published: July 2009

The contributors explore such issues as the nature of species, how species are counted, limits on diversity, mechanisms of speciation and adaptation, and speciation rates.
Sweet Silencing
Authors: Simon Jeffrey A.
Published: July 2009

A sugar molecule plays an unexpected role in controlling gene silencing by modifying repressor proteins.
Proposal to Slash Salaries Riles California Researchers
Authors: Miller Greg
Published: July 2009

Proposed salary cuts and/or furloughs for all faculty and staff members are causing consternation at the University of California, one of the nation's largest public universities, with approximately 170,000 employees.
On the Origin of The Nervous System
Authors: Miller Greg
Published: July 2009

What did the first neurons and nervous systems look like, and what advantages did they confer on the animals that possessed them? In the seventh essay in
Science
's series in honor of the Year of Darwin, Greg Miller discusses some tantalizing clues that scientists have recently gained about the evolutionary origins of nervous systems.
Optimization of a Whole-Blood Gamma Interferon Assay for Detection of
Mycobacterium bovis
-Infected Cattle
Authors: Schiller Irene , Waters W. Ray , Vordermeier H. Martin , Nonnecke Brian , Welsh Michael , Keck Nicolas , Whelan Adam , Sigafoose Teresa , Stamm Christoph , Palmer Mitchell , Thacker Tyler , Hardegger Roland , Marg-Haufe Beatrice , Raeber Alex , Oesch Bruno
Published: July 2009

Antigens of
Mycobacterium bovis
elicit a cell-mediated immune response upon intradermal injection in cattle. In vitro, such antigens stimulate the production of gamma interferon (IFN-γ) by bovine T cells in whole-blood culture (IFN-γ assay). We have analyzed various parameters of the in vitro IFN-γ assay, ranging from blood sampling to execution of the IFN-γ test, in view of potential simplifications of the assay. Here, we show that IFN-γ responses may be reduced under certain animal handling/holding conditions and that a delayed time from blood collection to culture may lead to a reduced in vitro IFN-γ response. Delayed initiation of culture in a purified-protein-derivative-based assay (24 h compared to 8 h after blood collection), however, resulted in a significant improvement of specificity (97% compared to 85%), whereas there was only a modest reduction of sensitivity (from 96% to 90%), which was statistically not significant. Furthermore, we show that the stimulation temperature needs to be 33°C or higher; that carbon dioxide is not required for stimulation; and that various plate formats, ranging from 24 to 96 wells per plate, can be utilized. The produced IFN-γ is stable at 4°C for 28 days as well as after repeated freeze-thaw cycles. Thus, stimulation of samples may be initiated in the field without the need for a carbon dioxide source, and bovine IFN-γ is stable under various routine laboratory temperature scenarios. These findings demonstrate opportunities for improvements in the bovine IFN-γ test platform and flexibilities in test application.
Transcriptional Errors in Human Immunodeficiency Virus Type 1 Generate Targets for T-Cell Responses
Authors: Garrison Keith E. , Champiat Stephane , York Vanessa A. , Agrawal Ashish T. , Kallas Esper G. , Martin Jeffrey N. , Hecht Frederick M. , Deeks Steven G. , Nixon Douglas F.
Published: July 2009

We measured T-cell responses to human immunodeficiency virus type 1 (HIV-1) cryptic epitopes encoded by regions of the viral genome not normally translated into viral proteins. T-cell responses to cryptic epitopes and to regions normally spliced out of the HIV-1 viral proteins Rev and Tat were detected in HIV-1-infected subjects.
Genotypic Comparison of Invasive
Neisseria meningitidis
Serogroup Y Isolates from the United States, South Africa, and Israel, Isolated from 1999 through 2002
Authors: Whitney Anne M. , Coulson Garry B. , von Gottberg Anne , Block Colin , Keller Nathan , Mayer Leonard W. , Messonnier Nancy E. , Klugman Keith P.
Published: July 2009

The proportion of meningococcal disease in the United States, South Africa, and Israel caused by
Neisseria meningitidis
serogroup Y (NmY) was greater than the worldwide average during the period 1999-2002. Genotypic characterization of 300 NmY isolates by multilocus sequence typing, 16S rRNA gene sequencing, and PorA variable region typing was conducted to determine the relationships of the isolates from these three countries. Seventy different genotypes were found. Two groups of ST-23 clonal complex isolates accounted for 88% of the U.S. isolates, 12% of the South African isolates, and 96% of the isolates from Israel. The single common clone (ST-23/16S-19/P1.5-2,10-1) represented 57, 5, and 35% of the NmY isolates from the United States, South Africa, and Israel. The predominant clone in South Africa (ST-175/16S-21/P1.5-1,2-2), and 11 other closely related clones made up 77% of the South African study isolates and were not found among the isolates from the United States or Israel. ST-175 was the predicted founder of the ST-175 clonal complex, and isolates of ST-175 and related sequence types have been described previously in other African countries. Continued active surveillance and genetic characterization of NmY isolates causing disease in the United States, South Africa, and Israel will provide valuable data for local and global epidemiology and allow monitoring for any expansion of existing clonal complexes and detection of the emergence of new virulent clones in the population.
Severe Cytomegalovirus-Associated Esophagitis in an Immunocompetent Patient after Short-Term Steroid Therapy
Authors: Weile Jan , Streeck Benjamin , Muck Johannes , Krebs Gerd , Jakobus Karl-Heinz , Knabbe Cornelius , Weber Friedhelm
Published: July 2009

A case of severe human cytomegalovirus esophagitis after short-term corticosteroid therapy in a patient with no other apparent cause of immunodeficiency, such as human immunodeficiency virus infection, neoplasia, or previous organ transplantation, is described herein. The cytomegalovirus esophagus infection was successfully treated with ganciclovir.
Cost Analysis of Multiplex PCR Testing for Diagnosing Respiratory Virus Infections
Authors: Mahony James B. , Blackhouse Gord , Babwah Jesse , Smieja Marek , Buracond Sonya , Chong Sylvia , Ciccotelli William , O'Shea Tim , Alnakhli Daifallah , Griffiths-Turner May , Goeree Ron
Published: July 2009

We performed a cost analysis study using decision tree modeling to determine whether the use of multiplex PCR testing for respiratory viruses (xTAG RVP test) is a more or less costly strategy than the status quo testing methods used for the diagnosis of respiratory virus infections in pediatric patients. The decision tree model was constructed by using four testing strategies for respiratory virus detection, viz., direct fluorescent-antibody staining (DFA) alone, DFA plus shell vial culture (SVC), the xTAG RVP test alone, or DFA plus the xTAG RVP test. A review of the charts of 661 pediatric patients was used to determine the length of hospital stay, the number of days in isolation, antibiotic usage, and all other medical procedures performed. The cost of hospitalization by diagnostic status was determined on the basis of the average cost per patient and the number of patients in each arm of the decision tree. The cost per case was the highest for DFA plus SVC at $3,914 (in Canadian dollars), and the lowest was for the xTAG RVP test alone at $3,623, while the costs of DFA alone ($3,911) and DFA plus RVP ($3,849) were intermediate. When all four diagnostic strategies were compared, the least costly strategy was the xTAG RVP test alone when the prevalence of infection was 11% or higher and DFA alone when the prevalence was under 11%. These data indicate a savings of $291 per case investigated if the strategy of using the xTAG RVP test alone was used to replace the status quo test of DFA plus SVC, resulting in a savings of $529,620 per year in direct costs for the four Hamilton, Ontario, Canada, hospitals on the basis of the testing of specimens from 1,820 pediatric inpatients. We conclude that the use of the xTAG RVP test is the least costly strategy for the diagnosis of respiratory virus infections in children and would generate a significant savings for hospitals.
Diagnosis of Bacteremia in Whole-Blood Samples by Use of a Commercial Universal 16S rRNA Gene-Based PCR and Sequence Analysis
Authors: Wellinghausen Nele , Kochem Anna-Julia , Disqué Claudia , Mühl Helge , Gebert Susanne , Winter Juliane , Matten Jens , Sakka Samir G.
Published: July 2009

In a prospective, multicenter study of 342 blood samples from 187 patients with systemic inflammatory response syndrome, sepsis, or neutropenic fever, a new commercial PCR test (SepsiTest; Molzym) was evaluated for rapid diagnosis of bacteremia. The test comprises a universal PCR from the 16S rRNA gene, with subsequent identification of bacteria from positive samples by sequence analysis of amplicons. Compared to blood culture (BC), the diagnostic sensitivity and specificity of the PCR were 87.0 and 85.8%, respectively. Considering the 34 BC-positive patients, 28 were also PCR positive in at least one of the samples, resulting in a patient-related sensitivity of 82.4%. The concordance of PCR and BC for both positive and negative samples was (47 + 247)/342, i.e., 86.0%. In total, 31 patients were PCR/sequencing positive and BC negative, in whom the PCR result was judged as possible or probable to true bacteremia in 25. In conclusion, the PCR approach facilitates the detection of bacteremia in blood samples within a few hours. Despite the indispensability of BC diagnostics, the rapid detection of bacteria by SepsiTest appears to be a valuable tool, allowing earlier pathogen-adapted antimicrobial therapy in critically ill patients.
Comparison of 24-Hour and 48-Hour Voriconazole MICs as Determined by the Clinical and Laboratory Standards Institute Broth Microdilution Method (M27-A3 Document) in Three Laboratories: Results Obtained with 2,162 Clinical Isolates of
Candida
spp. and Other Yeasts
Authors: Espinel-Ingroff Ana , Canton E. , Peman J. , Rinaldi M. G. , Fothergill A. W.
Published: July 2009

We evaluated the performance of the 24-h broth microdilution voriconazole MIC by obtaining MICs for 2,162 clinical isolates of
Candida
spp. and other yeasts; the 24-h results were compared to 48-h reference MICs to assess essential, as well as categorical, agreement. Although the overall essential agreement was 88.6%, it ranged from 96.4 to 100% for 6 of the 11 species or groups of yeasts tested. The overall categorical agreement was 93.2%, and it was above 90% for eight species. However, unacceptable percentages of very major errors (false susceptibility) were observed for
Candida albicans
(2.7%),
C. glabrata
(4.1%),
C. tropicalis
(9.7%), and other less common yeast species (9.8%). Since it is essential to identify potentially resistant isolates and breakpoints are based on 48-h MICs, it appears that the 24-h MIC is not as clinically useful as the 48-h reference MIC. However, further characterization of these falsely susceptible MICs for three of the four common
Candida
spp. is needed to understand whether these errors are due to trailing misinterpretation or if the 48-h incubation is required to detect voriconazole resistance. Either in vivo versus in vitro correlations or the determination of resistance mechanisms should be investigated.
Thumb Infection Caused by
Streptococcus pseudoporcinus
Authors: Mahlen Steven D. , Clarridge Jill E.
Published: July 2009

Streptococcus pseudoporcinus
, a recently described organism found in the genitourinary tract of women, was isolated from a thumb wound in a male patient subsequent to trauma. This case describes a rarely reported non-genitourinary tract clinical isolate of
S. pseudoporcinus
.
Clostridium difficile
Strains from Community-Associated Infections
Authors: Limbago Brandi M. , Long Cherie M. , Thompson Angela D. , Killgore George E. , Hannett George E. , Havill Nancy L. , Mickelson Stephanie , Lathrop Sarah , Jones Timothy F. , Park Mahin M. , Harriman Kathleen H. , Gould L. Hannah , McDonald L. Clifford , Angulo Frederick J.
Published: July 2009

Clostridium difficile
isolates from presumed community-associated infections (
n
= 92) were characterized by toxinotyping, pulsed-field gel electrophoresis,
tcdC
and
cdtB
PCR, and antimicrobial susceptibility. Nine toxinotypes (TOX) and 31 PFGE patterns were identified. TOX 0 (48, 52%), TOX III (18, 20%), and TOX V (9, 10%) were the most common; three isolates were nontoxigenic.
Population-Based Molecular Epidemiology of Leprosy in Cebu, Philippines
Authors: Sakamuri Rama Murthy , Kimura Miyako , Li Wei , Kim Hyun-Chul , Lee Hyeyoung , Kiran Madanahally D. , Black William C. , Balagon Marivic , Gelber Robert , Cho Sang-Nae , Brennan Patrick J. , Vissa Varalakshmi
Published: July 2009

To address the persisting problem of leprosy in Cebu, Philippines, we compiled a database of more than 200 patients who attend an established referral skin clinic. We described the patient characteristics in conventional demographic parameters and also applied multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) and single nucleotide polymorphism (SNP) typing for
Mycobacterium leprae
in biopsied skin lesion samples. These combined approaches revealed that transmission is ongoing, with the affected including the young Cebuano population under 40 years of age in both crowded cities and rural areas of the island. The emergence of multicase families (MCF) is indicative of infection unconstrained by standard care measures. For the SNPs, we designed a low-cost PCR-restriction fragment length polymorphism typing method. MLVA in
M. leprae
was highly discriminatory in this population yet could retain broad groups, as defined by the more stable SNPs, implying temporal marker stability suitable for interpreting population structures and evolution. The majority of isolates belong to an Asian lineage (SNP type 1), and the rest belong to a putative postcolonial lineage (SNP type 3). Specific alleles at two VNTR loci, (GGT)5 and 21-3, were highly associated with SNP type 3 in this population. MLVA identified
M. leprae
genotype associations for patients with known epidemiological links such as in MCFs and in some villages. These methods provide a molecular database and a rational framework for targeted approaches to search and confirm leprosy transmission in various scenarios.
Functional Analysis of N-Terminal Residues of Ty1 Integrase
Authors: Moore Sharon P. , Garfinkel David J.
Published: July 2009

The Ty1 retrotransposon of
Saccharomyces cerevisiae
is comprised of structural and enzymatic proteins that are functionally similar to those of retroviruses. Despite overall sequence divergence, certain motifs are highly conserved. We have examined the Ty1 integrase (IN) zinc binding domain by mutating the definitive histidine and cysteine residues and thirteen residues in the intervening (X
32
) sequence between IN-H22 and IN-C55. Mutation of the zinc-coordinating histidine or cysteine residues reduced transposition by more than 4,000-fold and led to IN and reverse transcriptase (RT) instability as well as inefficient proteolytic processing. Alanine substitution of the hydrophobic residues I28, L32, I37 and V45 in the X
32
region reduced transposition 85- to 688-fold. Three of these residues, L32, I37, and V45, are highly conserved among retroviruses, although their effects on integration or viral infectivity have not been characterized. In contrast to the HHCC mutants, all the X
32
mutants exhibited stable IN and RT, and protein processing and cDNA production were unaffected. However, glutathione
S
-transferase pulldowns and intragenic complementation analysis of selected transposition-defective X
32
mutants revealed decreased IN-IN interactions. Furthermore, virus-like particles with
in-L32A
and
in-V45A
mutations did not exhibit substantial levels of concerted integration products in vitro. Our results suggest that the histidine/cysteine residues are important for steps in transposition prior to integration, while the hydrophobic residues function in IN multimerization.