bluuebunny/crossref_metadata_2025 huggingface dataset:
Human predators outpace other agents of trait change in the wild
Authors: Darimont Chris T. , Carlson Stephanie M. , Kinnison Michael T. , Paquet Paul C. , Reimchen Thomas E. , Wilmers Christopher C.
Published: January 2009

The observable traits of wild populations are continually shaped and reshaped by the environment and numerous agents of natural selection, including predators. In stark contrast with most predators, humans now typically exploit high proportions of prey populations and target large, reproductive-aged adults. Consequently, organisms subject to consistent and strong ‘harvest selection’ by fishers, hunters, and plant harvesters may be expected to show particularly rapid and dramatic changes in phenotype. However, a comparison of the rate at which phenotypic changes in exploited taxa occurs relative to other systems has never been undertaken. Here, we show that average phenotypic changes in 40 human-harvested systems are much more rapid than changes reported in studies examining not only natural (
n
= 20 systems) but also other human-driven (
n
= 25 systems) perturbations in the wild, outpacing them by >300% and 50%, respectively. Accordingly, harvested organisms show some of the most abrupt trait changes ever observed in wild populations, providing a new appreciation for how fast phenotypes are capable of changing. These changes, which include average declines of almost 20% in size-related traits and shifts in life history traits of nearly 25%, are most rapid in commercially exploited systems and, thus, have profound conservation and economic implications. Specifically, the widespread potential for transitively rapid and large effects on size- or life history-mediated ecological dynamics might imperil populations, industries, and ecosystems.
Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame
Authors: Khazina Elena , Weichenrieder Oliver
Published: January 2009

Non-LTR retrotransposons (NLRs) are a unique class of mobile genetic elements that have significant impact on the evolution of eukaryotic genomes. However, the molecular details and functions of their encoded proteins, in particular of the accessory ORF1p proteins, are poorly understood. Here, we identify noncanonical RNA-recognition-motifs (RRMs) in several phylogenetically unrelated NLR ORF1p proteins. This provides an explanation for their RNA-binding properties and clearly shows that they are not related to the retroviral nucleocapsid protein Gag, despite the frequent presence of CCHC zinc knuckles. In particular, we characterize the ORF1p protein of the human long interspersed nuclear element 1 (LINE-1 or L1). We show that L1ORF1p is a multidomain protein, consisting of a coiled coil (cc), RRM, and C-terminal domain (CTD). Most importantly, we solved the crystal structure of the RRM domain, which is characterized by extended loops stabilized by unique salt bridges. Furthermore, we demonstrate that L1ORF1p trimerizes via its N-terminal cc domain, and we suggest that this property is functionally important for all homologues. The formation of distinct complexes with single-stranded nucleic acids requires the presence of the RRM and CTD domains on the same polypeptide chain as well as their close cooperation. Finally, the phylogenetic analysis of mammalian L1ORF1p shows an ancient origin of the RRM domain and supports a modular evolution of NLRs.
A new feather type in a nonavian theropod and the early evolution of feathers
Authors: Xu Xing , Zheng Xiaoting , You Hailu
Published: January 2009

All described feathers in nonavian theropods are composite structures formed by multiple filaments. They closely resemble relatively advanced stages predicted by developmental models of the origin of feathers, but not the earliest stage. Here, we report a feather type in two specimens of the basal therizinosaur
Beipiaosaurus
, in which each individual feather is represented by a single broad filament. This morphotype is congruent with the stage I morphology predicted by developmental models, and all major predicted morphotypes have now been documented in the fossil record. This congruence between the full range of paleontological and developmental data strongly supports the hypothesis that feathers evolved and initially diversified in nonavian theropods before the origin of birds and the evolution of flight.
Second-to-fourth digit ratio predicts success among high-frequency financial traders
Authors: Coates John M. , Gurnell Mark , Rustichini Aldo
Published: January 2009

Prenatal androgens have important organizing effects on brain development and future behavior. The second-to-fourth digit length ratio (2D:4D) has been proposed as a marker of these prenatal androgen effects, a relatively longer fourth finger indicating higher prenatal androgen exposure. 2D:4D has been shown to predict success in highly competitive sports. Yet, little is known about the effects of prenatal androgens on an economically influential class of competitive risk taking—trading in the financial world. Here, we report the findings of a study conducted in the City of London in which we sampled 2D:4D from a group of male traders engaged in what is variously called “noise” or “high-frequency” trading. We found that 2D:4D predicted the traders' long-term profitability as well as the number of years they remained in the business. 2D:4D also predicted the sensitivity of their profitability to increases both in circulating testosterone and in market volatility. Our results suggest that prenatal androgens increase risk preferences and promote more rapid visuomotor scanning and physical reflexes. The success and longevity of traders exposed to high levels of prenatal androgens further suggests that financial markets may select for biological traits rather than rational expectations.
The physiologic aggresome mediates cellular inactivation of iNOS
Authors: Pandit Lavannya , Kolodziejska Katarzyna E. , Zeng Shenyan , Eissa N. Tony
Published: January 2009

Nitric Oxide (NO), produced by inducible nitric oxide synthase (iNOS), has been implicated in the pathogenesis of various biological and inflammatory disorders. Recent evidence suggests that aggresome formation is a physiologic stress response not limited to misfolded proteins. That stress response, termed “physiologic aggresome,” is exemplified by aggresome formation of iNOS, an important host defense protein. The functional significance of cellular formation of the iNOS aggresome is hitherto unknown. In this study, we used live cell imaging, fluorescence microscopy, and intracellular fluorescence NO probes to map the subcellular location of iNOS and NO under various conditions. We found that NO production colocalized with cytosolic iNOS but aggresomes containing iNOS were distinctly devoid of NO production. Further, cells expressing iNOS aggresomes produced significantly less NO as compared with cells not expressing aggresomes. Importantly, primary normal human bronchial epithelial cells, stimulated by cytokines to express iNOS, progressively sequestered iNOS to the aggresome, a process that correlated with marked reduction of NO production. These results suggest that bronchial epithelial cells used the physiologic aggresome mechanism for iNOS inactivation. Our studies reveal a novel cellular strategy to terminate NO production via formation of the iNOS aggresome.
Retinol saturase promotes adipogenesis and is downregulated in obesity
Authors: Schupp Michael , Lefterova Martina I. , Janke Jürgen , Leitner Kirstin , Cristancho Ana G. , Mullican Shannon E. , Qatanani Mohammed , Szwergold Nava , Steger David J. , Curtin Joshua C. , Kim Roy J. , Suh Moo-jin , Albert Martin R. , Engeli Stefan , Gudas Lorraine J. , Lazar Mitchell A.
Published: January 2009

Adipocyte differentiation is controlled by many transcription factors, but few known downstream targets of these factors are necessary for adipogenesis. Here we report that retinol saturase (RetSat), which is an enzyme implicated in the generation of dihydroretinoid metabolites, is induced during adipogenesis and is directly regulated by the transcription factor peroxisome proliferator activated receptor γ (PPARγ). Ablation of RetSat dramatically inhibited adipogenesis but, surprisingly, this block was not overcome by the putative product of RetSat enzymatic activity. On the other hand, ectopic RetSat with an intact, but not a mutated, FAD/NAD dinucleotide-binding motif increased endogenous PPARγ transcriptional activity and promoted adipogenesis. Indeed, RetSat was not required for adipogenesis when cells were provided with exogenous PPARγ ligands. In adipose tissue, RetSat is expressed in adipocytes but is unexpectedly downregulated in obesity, most likely owing to infiltration of macrophages that we demonstrate to repress RetSat expression. Thiazolidinedione treatment reversed low RetSat expression in adipose tissue of obese mice. Thus, RetSat plays an important role in the biology of adipocytes, where it favors normal differentiation, yet is reduced in the obese state. RetSat is thus a novel target for therapeutic intervention in metabolic disease.
Nanoscale magnetic resonance imaging
Authors: Degen C. L. , Poggio M. , Mamin H. J. , Rettner C. T. , Rugar D.
Published: January 2009

We have combined ultrasensitive magnetic resonance force microscopy (MRFM) with 3D image reconstruction to achieve magnetic resonance imaging (MRI) with resolution <10 nm. The image reconstruction converts measured magnetic force data into a 3D map of nuclear spin density, taking advantage of the unique characteristics of the “resonant slice” that is projected outward from a nanoscale magnetic tip. The basic principles are demonstrated by imaging the1H spin density within individual tobacco mosaic virus particles sitting on a nanometer-thick layer of adsorbed hydrocarbons. This result, which represents a 100 million-fold improvement in volume resolution over conventional MRI, demonstrates the potential of MRFM as a tool for 3D, elementally selective imaging on the nanometer scale.
Phenotypic correction of murine hemophilia A using an iPS cell-based therapy
Authors: Xu Dan , Alipio Zaida , Fink Louis M. , Adcock Dorothy M. , Yang Jianchang , Ward David C. , Ma Yupo
Published: January 2009

Hemophilia A is caused by mutations within the Factor VIII (FVIII) gene that lead to depleted protein production and inefficient blood clotting. Several attempts at gene therapy have failed for various reasons—including immune rejection. The recent generation of induced pluripotent stem (iPS) cells from somatic cells by the ectopic expression of 3 transcription factors, Oct4, Sox2, and Klf4, provides a means of circumventing the immune rejection barrier. To date, iPS cells appear to be indistinguishable from ES cells and thus provide tremendous therapeutic potential. Here we prepared murine iPS cells from tail-tip fibroblasts and differentiated them to both endothelial cells and endothelial progenitor cells by using the embryoid body differentiation method. These iPS cells express major ES cell markers such as Oct4, Nanog, SSEA-1, alkaline phosphatase, and SALL4. Endothelial/endothelial progenitor cells derived from iPS cells expressed cell-specific markers such as CD31, CD34, and Flk1 and secreted FVIII protein. These iPS-derived cells were injected directly into the liver of irradiated hemophilia A mice. At various times after transplantation (7–90 days) hemophilia A mice and their control mice counterparts were challenged by a tail-clip bleeding assay. Nontransplanted hemophilia A mice died within a few hours, whereas transplanted mice survived for more than 3 months. Plasma FVIII levels increased in transplanted hemophilia A mice during this period to 8% to 12% of wild type and corrected the hemophilia A phenotype. Our studies provide additional evidence that iPS cell therapy may be able to treat human monogenetic disorders in the future.
TAp73 regulates the spindle assembly checkpoint by modulating BubR1 activity
Authors: Tomasini Richard , Tsuchihara Katsuya , Tsuda Chiharu , Lau Suzanne K. , Wilhelm Margareta , Rufini Alessandro , Tsao Ming-sound , Iovanna Juan L. , Jurisicova Andrea , Melino Gerry , Mak Tak W.
Published: January 2009

The role of various p73 isoforms in tumorigenesis has been controversial. However, as we have recently shown, the generation of TAp73-deficient (TAp73
−/−
) mice reveals that TAp73 isoforms exert tumor-suppressive functions, indicating an emerging role for
Trp-73
in the maintenance of genomic stability. Unlike mice lacking all p73 isoforms, TAp73
−/−
mice show a high incidence of spontaneous tumors. Moreover, TAp73
−/−
mice are infertile and produce oocytes exhibiting spindle abnormalities. These data suggest a link between TAp73 activities and the common molecular machinery underlying meiosis and mitosis. Previous studies have indicated that the spindle assembly checkpoint (SAC) complex, whose activation leads to mitotic arrest, also regulates meiosis. In this study, we demonstrate in murine and human cells that TAp73 is able to interact directly with several partners of the SAC complex (Bub1, Bub3, and BubR1). We also show that TAp73 is involved in SAC protein localization and activities. Moreover, we show that decreased TAp73 expression correlates with increases of SAC protein expression in patients with lung cancer. Our results establish TAp73 as a regulator of SAC responses and indicate that TAp73 loss can lead to mitotic arrest defects. Our data suggest that SAC impairment in the absence of functional TAp73 could explain the genomic instability and increased aneuploidy observed in TAp73-deficient cells.
Detritivorous crustaceans become herbivores on jasmonate-deficient plants
Authors: Farmer Edward E. , Dubugnon Lucie
Published: January 2009

The jasmonate signal pathway is known to control defenses against herbivores, such as leaf eaters (folivores). Does the reach of the pathway extend to defense against other types of animal? Among the arthropods attracted to seed baits placed below flowering
Arabidopsis thaliana
plants are 2 largely nocturnal isopod crustaceans generally considered as detritivores:
Porcellio scaber
and
Armadillidium vulgare
. Parallel laboratory experiments identified the isopods as being capable of predation on intact plants. Isopod feeding was strongly facilitated in jasmonate-deficient
Arabidopsis
and rice plants. The feeding activity of isopods revealed potentially detritivore-sensitive, jasmonate-protected Achilles' heels in these architecturally different plants (petioles and inflorescence stems in
Arabidopsis
, and lower stem and mesocotyl in rice). The work addresses the question of what stops 2 detritivores from attacking living plants and provides evidence that it is, in part, the jasmonate signal pathway. Furthermore, senescent leaves from an
Arabidopsis
jasmonate mutant were consumed more rapidly than senescent wild-type leaves, suggesting that past activity of the jasmonate signal pathway in leaves may slow carbon recycling through detritivory.
A human B cell methylome at 100−base pair resolution
Authors: Rauch Tibor A. , Wu Xiwei , Zhong Xueyan , Riggs Arthur D. , Pfeifer Gerd P.
Published: January 2009

Using a methylated-DNA enrichment technique (methylated CpG island recovery assay, MIRA) in combination with whole-genome tiling arrays, we have characterized by MIRA-chip the entire B cell “methylome” of an individual human at 100-bp resolution. We find that at the chromosome level high CpG methylation density is correlated with subtelomeric regions and Giemsa-light bands (R bands). The majority of the most highly methylated regions that could be identified on the tiling arrays were associated with genes. Approximately 10% of all promoters in B cells were found to be methylated, and this methylation correlates with low gene expression. Notably, apparent exceptions to this correlation were the result of transcription from previously unidentified, unmethylated transcription start sites, suggesting that methylation may control alternate promoter usage. Methylation of intragenic (gene body) sequences was found to correlate with increased, not decreased, transcription, and a methylated region near the 3′ end was found in approximately 12% of all genes. The majority of broad regions (10–44 kb) of high methylation were at segmental duplications. Our data provide a valuable resource for the analysis of CpG methylation patterns in a differentiated human cell type and provide new clues regarding the function of mammalian DNA methylation.
Intracellular Proton-Transfer Mutants in a CLC Cl−/H+ Exchanger
Authors: Lim Hyun-Ho , Miller Christopher
Published: January 2009

CLC-ec1, a bacterial homologue of the CLC family’s transporter subclass, catalyzes transmembrane exchange of Cl− and H+. Mutational analysis based on the known structure reveals several key residues required for coupling H+ to the stoichiometric countermovement of Cl−. E148 (Gluex) transfers protons between extracellular water and the protein interior, and E203 (Gluin) is thought to function analogously on the intracellular face of the protein. Mutation of either residue eliminates H+ transport while preserving Cl− transport. We tested the role of Gluin by examining structural and functional properties of mutants at this position. Certain dissociable side chains (E, D, H, K, R, but not C and Y) retain H+/Cl− exchanger activity to varying degrees, while other mutations (V, I, or C) abolish H+ coupling and severely inhibit Cl− flux. Transporters substituted with other nonprotonatable side chains (Q, S, and A) show highly impaired H+ transport with substantial Cl− transport. Influence on H+ transport of side chain length and acidity was assessed using a single-cysteine mutant to introduce non-natural side chains. Crystal structures of both coupled (E203H) and uncoupled (E203V) mutants are similar to wild type. The results support the idea that Gluin is the internal proton-transfer residue that delivers protons from intracellular solution to the protein interior, where they couple to Cl− movements to bring about Cl−/H+ exchange.
Evidence-Based Infection Control Planning Based on National Healthcare-Associated Infection Prevalence Data
Authors: Reilly Jacqueline , Stewart Sally , Allardice Gwen , Cairns Shona , Ritchie Lisa , Bruce Julie
Published: January 2009

This study identifies factors associated with a high prevalence of healthcare-associated infection (HAI) in the Scottish inpatient population, on the basis of the Scotland National HAI Prevalence Survey data set. The multivariate models developed can be used to predict HAI prevalence in specific patient groups to help with planning and policy in infection control.
Cohort Study of Adherence to Correct Hand Antisepsis Before and After Performance of Clinical Procedures
Authors: Laustsen Sussie , Lund Elisabeth , Bibby Bo Martin , Kristensen Brian , Thulstrup Ane Marie , Møller Jens Kjølseth
Published: January 2009

Objective.

To investigate the rate of adherence by hospital staff members to the correct use of alcohol-based hand rub before and after performance of clinical procedures.

Design.

A cohort study conducted during the period from 2006 through 2007 and 2 cross-sectional studies conducted in 2006 and 2007.

Setting.

Århus University Hospital, Skejby, in Århus, Denmark.

Participants.

Various hospital staff members.

Methods.

Following an ongoing campaign promoting the correct use of alcohol-based hand rub, we observed rates of adherence by hospital staff to the correct use of alcohol-based hand rub. Observations were made before and after each contact with patients or patient surroundings during 5 weekdays during the period from 2006 through 2007 in 10 different hospital units. A logistic regression model was used to estimate the rate of adherence to the correct use of alcohol-based hand rub before and after performance of a clinical procedure.

Results.

A total of 496 participants were observed during 22,906 opportunities for hand hygiene (ie, 11,177 before and 11,729 after clinical procedures) that required the use of alcohol-based hand rub. The overall rates of adherence to the correct use of alcohol-based hand rub were 62.3% (6,968 ofthe 11,177 opportunities) before performance and 68.6% (8,041 ofthe 11,729 opportunities) after performance of clinical procedures. Compared with male participants, female participants were significantly better at adhering to the correct use of alcohol-based hand rub before performance (odds ratio [OR] 1.51 [95% confidence interval {CI}, 1.09–2.10]) and after performance (OR, 1.73 [95% CI, 1.27–2.36]) of clinical procedures. In general, the rate of adherence was significantly higher after the performance of clinical procedures, compared with before (OR, 1.43 [95% CI, 1.35–1.52]). For our cohort of 214 participants who were observed during 14,319 opportunities, the rates of adherence to the correct use of alcohol-based hand rub were 63.2% (4,469 of the 7,071 opportunities) before performance and 69.3% (5,021 of the 7,248 opportunities) after performance of clinical procedures, and these rates increased significantly from 2006 to 2007, except for physicians.

Conclusion.

We found a high and increasing rate of adherence to the correct use of alcohol-based hand rub before and after performance of clinical procedures following a campaign that promoted the correct use of alcohol-based hand rub. More hospital staff performed hand hygiene with alcohol-based hand rub after performance of clinical procedures, compared with before performance. Future campaigns to improve the rate of adherence to the correct use of alcohol-based hand rub ought be aware that certain groups of hospital staff (eg, male staff members) are known to exhibit a low level of adherence to the correct use of alcohol-based hand rub.
Pulsars as the sources of high energy cosmic ray positrons
Authors: Dan Hooper  , Pasquale Blasi  , Pasquale Dario Serpico
Published: January 2009

Recent results from the PAMELA satellite indicate the
presence of a large flux of positrons (relative to electrons) in the
cosmic ray spectrum between approximately 10 and 100 GeV. As
annihilating dark matter particles in many models are predicted to
contribute to the cosmic ray positron spectrum in this energy range, a
great deal of interest has resulted from this observation. Here, we
consider pulsars (rapidly spinning, magnetized neutron stars) as an
alternative source of this signal. After calculating the contribution
to the cosmic ray positron and electron spectra from pulsars, we find
that the spectrum observed by PAMELA could plausibly originate from
such sources. In particular, a significant contribution is expected
from the sum of all mature pulsars throughout the Milky Way, as well
as from the most nearby mature pulsars (such as Geminga and
B0656+14). The signal from nearby pulsars is expected to generate a
small but significant dipole anisotropy in the cosmic ray electron
spectrum, potentially providing a method by which the Fermi gamma-ray
space telescope would be capable of
discriminating between the pulsar and dark matter origins of the
observed high energy positrons.
Using a simple morphometric marker to identify spatial units for abalone fishery management
Authors: Saunders T. , Mayfield S. , Hogg A.
Published: January 2009

Saunders, T., Mayfield, S., and Hogg, A. 2009. Using a simple morphometric marker to identify spatial units for abalone fishery management. – ICES Journal of Marine Science, 66: 305–314. Managing stocks of sedentary marine invertebrates is complicated by the highly structured populations they form. Blacklip abalone (Haliotis rubra) form isolated populations with variable life-history characteristics. Many of the populations are “stunted”, attaining a lower maximum size than those in adjacent areas. To reduce the risks of overfishing and localized depletion, management units (MUs) that encompass individual populations need to be determined, then managed according to their life-history characteristics. Here, potential MUs in a South Australian abalone fishery were identified from the broad-scale, spatial distribution of stunted and “non-stunted” populations of blacklip abalone, by applying a morphometric marker to commercial shell samples. Key life-history parameters of the populations within the potential MUs were estimated using relationships between the morphometric marker and blacklip abalone biology. Data from fine-scale systematic sampling by commercial fishers were used to validate spatial patterns observed from the more broadly distributed commercial catch samples. The location, distribution, and size of potential MUs were largely inconsistent with those of current management. The locations of two MUs (in Gerloffs Bay) were consistent across the broad- and fine-scale datasets, with the fine-scale samples more informative for identifying a potential boundary between them. The disparity between these data and current management arrangements are highlighted, and approaches for modifying them are discussed. This approach is among the first to provide a practical means of more closely aligning the scales of assessment and management with biological reality for sedentary marine invertebrates.
Oestradiol level and opportunistic mating in women
Authors: Durante Kristina M , Li Norman P
Published: January 2009

The ovarian steroid hormone oestradiol plays a crucial role in female fertility, sexual motivation and behaviour. We investigated the relationship between oestradiol and the likelihood that women would engage in opportunistic mating. Two salivary samples were taken from normally cycling women within the peri-ovulatory and luteal phase of the menstrual cycle. At both testing sessions, participants also completed self-perceived desirability scales and provided subjective reports of sexual and social motivations, and satisfaction with their primary relationship partner. Oestradiol level was positively associated with a woman's self- and other-perceived physical attractiveness and with inclinations to mate outside her current relationship. Oestradiol was marginally negatively associated with a woman's satisfaction with her primary partner and relationship commitment. Results provide support for the relationship between physical beauty and fertility and suggest that physiological mechanisms play a major role in guiding a woman's mating strategies.
Sites of evolutionary divergence differ between olfactory and gustatory receptors of
Drosophila
Authors: Gardiner Anastasia , Butlin Roger K , Jordan William C , Ritchie Michael G
Published: January 2009

Drosophila
olfactory (ORs) and gustatory (GRs) receptors are evolutionarily unrelated to vertebrate ORs or nematode chemosensory receptors. Insect ORs display a reverse membrane topology compared with conventional G-protein-coupled receptors, suggesting that the mammalian scheme of chemosensory signal transduction cannot directly apply to insects. Experimental studies of GR membrane topology are lacking. We analysed the distribution of amino acid sites in GRs and ORs that show evidence for divergence under either positive selection or relaxed purifying constraints, in the genomes of 12
Drosophila
species and found significant differences between these two receptor types. This suggests that insect ORs and GRs have distinct molecular properties and mechanisms of ligand recognition and/or signal transduction.
Many variations on a few themes: a broader look at development of iridescent scales (and feathers)
Authors: Ghiradella Helen T , Butler Michael W
Published: January 2009

Iridescent structures are some of the most visually stunning phenomena in biological organisms. Insects and birds have in common the display of such colours in their non-living investiture, the scales and bristles in insects and the feathers in birds. The biological mechanisms underlying the formation of these structures, at least in insects, appear quite conservative in that the same architect, the eukaryotic cell, can produce not only the iridescent structure but, with some tweaking of the genome, other structures as well, a fact that may be of particular interest to materials scientists and industrial parties seeking to biomimic these forms. Here, we review two examples, one on the cellular and the other on the subcellular level of this developmental flexibility in insects. We then go on to review what is known about iridescent feather development in birds. We suggest that, in view of the increasing evidence that genes and pathways are conserved among taxa, the work on insects may perhaps suggest perspectives or directions of potential use in the study of birds.
A protean palette: colour materials and mixing in birds and butterflies
Authors: Shawkey Matthew D , Morehouse Nathan I , Vukusic Peter
Published: January 2009

While typically classified as either ‘structural’ or ‘pigmentary’, bio-optical tissues of terrestrial animals are rarely homogeneous and typically contain both a structural material such as keratin or chitin and one or more pigments. These base materials interact physically and chemically to create colours. Combinations of structured base materials and embedded pigment molecules often interact optically to produce unique colours and optical properties. Therefore, to understand the mechanics and evolution of bio-optical tissues it is critical to understand their material properties, both in isolation and in combination. Here, we review the optics and evolution of coloured tissues with a focus on their base materials, using birds and butterflies as exemplar taxa owing to the strength of our current knowledge of colour production in these animals. We first review what is known of their base materials, and then discuss the consequences of these interactions from an optical perspective. Finally, we suggest directions for future research on colour optics and evolution that will be invaluable as we move towards a fuller understanding of colour in the natural world.
A weighted communicability measure applied to complex brain networks
Authors: Crofts Jonathan J , Higham Desmond J
Published: January 2009

Recent advances in experimental neuroscience allow non-invasive studies of the white matter tracts in the human central nervous system, thus making available cutting-edge brain anatomical data describing these global connectivity patterns. Through magnetic resonance imaging, this non-invasive technique is able to infer a snapshot of the cortical network within the living human brain. Here, we report on the initial success of a new weighted network communicability measure in distinguishing local and global differences between diseased patients and controls. This approach builds on recent advances in network science, where an underlying connectivity structure is used as a means to measure the ease with which information can flow between nodes. One advantage of our method is that it deals directly with the real-valued connectivity data, thereby avoiding the need to discretize the corresponding adjacency matrix, i.e. to round weights up to 1 or down to 0, depending upon some threshold value. Experimental results indicate that the new approach is able to extract biologically relevant features that are not immediately apparent from the raw connectivity data.
A large cholera outbreak due to a new cholera toxin variant of the Vibrio cholerae O1 El Tor biotype in Orissa, Eastern India
Authors: Kumar P. , Jain M. , Goel A. K. , Bhadauria S. , Sharma S. K. , Kamboj D. V. , Singh L. , Ramamurthy T. , Nair G. B.
Published: January 2009

A total of 32 Vibrio cholerae isolates were collected during a recent large cholera outbreak in Eastern India. Biochemical and serological studies revealed that all of the isolates belonged to serogroup O1, biotype El Tor, serotype Ogawa. Two multiplex PCR assays confirmed the presence of various toxigenic and pathogenic genes – ace, ctxAB, hlyA, ompU, ompW, rfbO1, rtx, tcp, toxR and zot – in all of the isolates. Sequencing of the ctxB gene from the isolates revealed a novel mutation in the gene. Sequencing also confirmed the presence of altered cholera toxin B of the classical biotype in all of the El Tor isolates, suggesting infection of isolates by classical CTXΦ. The molecular diversity of V. cholerae isolates studied by enterobacterial repetitive intergenic consensus sequence PCR, BOX-PCR and randomly amplified polymorphic DNA analysis uniformly showed the clonal relationship among the outbreak V. cholerae O1 isolates. The results of this study suggest that cholera-causing V. cholerae strains are constantly evolving in epidemic areas, highlighting the potential of the emergence of more virulent strains.
Group B streptococcus colonization of pregnant women and their children observed on obstetric and neonatal wards of the University Hospital in Krakow, Poland
Authors: Strus Magdalena , Pawlik Dorota , Brzychczy-Włoch Monika , Gosiewski Tomasz , Rytlewski Krzysztof , Lauterbach Ryszard , Heczko Piotr B.
Published: January 2009

The study was arranged to assess the actual rates of colonization of pregnant women and their children with group B streptococcus (GBS) in a Polish university hospital. Resistance of these cocci to macrolides and clindamycin was also tested and routes of transmission of GBS were followed in some cases using molecular typing. Colonization with GBS was checked in 340 pregnant women living in the south-eastern region of Poland (Małopolska) in the years 2004–2006. Women with a complicated pregnancy were more often colonized than those with a normal pregnancy (20.0 % versus 17.2 %). Moreover, women with a complicated pregnancy were twice as often colonized with GBS strains with the MLSBphenotype indicating resistance to macrolides and clindamycin. Regarding neonatal colonization by GBS, we found that neonates born from the colonized mothers with a complicated pregnancy were more often colonized with GBS than those from the mothers with a normal pregnancy (35 % versus 26.7 %). By molecular typing of the GBS strains isolated from mothers and their newborns we have been able to suggest the possibility of horizontal transmission of the strains from the hospital environment to newborns. Our results clearly indicate that rates of GBS colonization among pregnant women and neonates in a Polish university hospital have reached levels comparable to those reported in other European clinical centres.
Membrane transporter proteins are involved in Trichophyton rubrum pathogenesis
Authors: Maranhão Fernanda C. A. , Paião Fernanda G. , Fachin Ana Lúcia , Martinez-Rossi Nilce M.
Published: January 2009

Trichophyton rubrum is a dermatophyte responsible for the majority of human superficial mycoses. The functional expression of proteins important for the initial step and the maintenance of the infection process were identified previously in T. rubrum by subtraction suppression hybridization after growth in the presence of keratin. In this study, sequences similar to genes encoding the multidrug-resistance ATP-binding cassette (ABC) transporter, copper ATPase, the major facilitator superfamily and a permease were isolated, and used in Northern blots to monitor the expression of the genes, which were upregulated in the presence of keratin. A sequence identical to the TruMDR2 gene, encoding an ABC transporter in T. rubrum, was isolated in these experiments, and examination of a T. rubrum ΔTruMDR2 mutant showed a reduction in infecting activity, characterized by low growth on human nails compared with the wild-type strain. The high expression levels of transporter genes by T. rubrum in mimetic infection and the reduction in virulence of the ΔTruMDR2 mutant in a disease model in vitro suggest that transporters are involved in T. rubrum pathogenicity.
The microbiology of the acute dental abscess
Authors: Robertson D. , Smith A. J.
Published: January 2009

The acute dental abscess is frequently underestimated in terms of its morbidity and mortality. The risk of potential serious consequences arising from the spread of a dental abscess is still relevant today with many hospital admissions for dental sepsis. The acute dental abscess is usually polymicrobial comprising facultative anaerobes, such as viridans group streptococci and the Streptococcus anginosus group, with predominantly strict anaerobes, such as anaerobic cocci, Prevotella and Fusobacterium species. The use of non-culture techniques has expanded our insight into the microbial diversity of the causative agents, identifying such organisms as Treponema species and anaerobic Gram-positive rods such as Bulleidia extructa, Cryptobacterium curtum and Mogibacterium timidum. Despite some reports of increasing antimicrobial resistance in isolates from acute dental infection, the vast majority of localized dental abscesses respond to surgical treatment, with antimicrobials limited to spreading and severe infections. The microbiology and treatment of the acute localized abscess and severe spreading odontogenic infections are reviewed.
T helper 1 to T helper 2 shift in cytokine expression: an autoregulatory process in superantigen-associated psoriasis progression?
Authors: Jain Sarika , Kaur Iqbal R. , Das Shukla , Bhattacharya S. N. , Singh Anjani
Published: January 2009

Psoriasis is an inflammatory skin disorder characterized by increased activation of CD4+T lymphocytes, and systemic and local overexpression of pro-inflammatory cytokines such as interleukin 2 (IL-2), gamma interferon (IFN-γ), IL-6 and tumour necrosis factor alpha, indicating that immunopathogenesis of the disease is T helper 1 (Th1) mediated. Several studies suggest a pivotal role of bacterial superantigens in the initiation and/or exacerbation of this illness. This study was conducted to assess the systemic Th1/Th2 imbalance in Indian psoriasis patients presenting with variable duration of disease by studying systemic superantigen-stimulated peripheral blood mononuclear cell (PBMC) cytokine expression. PBMCs were isolated and stimulatedin vitrowith superantigens (streptococcal pyrogenic exotoxin A and staphylococcal enterotoxin B), and the cytokines released (IFN-γfor a Th1 response, and IL-4 and IL-10 for a Th2 response) were assayed. In contrast to controls, psoriasis patients in the early course of disease were characterized by significantly increased expression of the pro-inflammatory cytokine IFN-γ, whilst a shift towards IL-10 secretion (Th2 response) was observed in those presenting with increased duration of disease. These observations suggest a possible shift from a Th1 to a Th2 cytokine response with superantigen-associated progression for the duration of psoriasis, perhaps as an adaptive process by the immune system in an attempt to downregulate abnormal inflammatory Th1 immune responses.
Molecular differentiation and antifungal susceptibilities of Candida parapsilosis isolated from patients with bloodstream infections
Authors: Tay Sun Tee , Na Shiang Ling , Chong Jennifer
Published: January 2009

The genetic heterogeneity and antifungal susceptibility patterns of Candida parapsilosis isolated from blood cultures of patients were investigated in this study. Randomly amplified polymorphic DNA (RAPD) analysis generated 5 unique profiles from 42 isolates. Based on the major DNA fragments of the RAPD profiles, the isolates were identified as RAPD type P1 (29 isolates), P2 (6 isolates), P3 (4 isolates), P4 (2 isolates) and P5 (1 isolate). Sequence analysis of the internal transcribed spacer (ITS) gene of the isolates identified RAPD type P1 as C. parapsilosis, P2 and P3 as Candida orthopsilosis, P4 as Candida metapsilosis, and P5 as Lodderomyces elongisporus. Nucleotide variations in ITS gene sequences of C. orthopsilosis and C. metapsilosis were detected. Antifungal susceptibility testing using Etests showed that all isolates tested in this study were susceptible to amphotericin B, fluconazole, ketoconazole, itraconazole and voriconazole. C. parapsilosis isolates exhibited higher MIC50 values than those of C. orthopsilosis for all of the drugs tested in this study; however, no significant difference in the MICs for these two Candida species was observed. The fact that C. orthopsilosis and C. metapsilosis were responsible for 23.8 and 4.8 % of the cases attributed to C. parapsilosis bloodstream infections, respectively, indicates the clinical relevance of these newly described yeasts. Further investigations of the ecological niche, mode of transmission and virulence of these species are thus essential.
Isolation of Brucella melitensis from an abscess on the left foot of a 3-year-old infant
Authors: Resendiz-Sánchez Jesús , Contreras-Rodríguez Araceli , López-Merino Ahidé , Bravo-Guzmán Leopoldo , Valle-Valdez Juan Gabriel
Published: January 2009

An unusual case of a 3-year-old girl with a brucellar foot abscess is reported. Although direct microscopic examination of samples from the lesion did not reveal micro-organisms of any kind, a 7 day culture of caseous material yielded small colonies of Gram-negative cocobacilli in Löwenstein–Jensen medium. These were biochemically and molecularly identified asBrucella melitensis. The possibility of foot abscess being caused byBrucellashould be considered in countries where brucellosis is endemic.
Effective use of JC virus PCR for diagnosis of progressive multifocal leukoencephalopathy
Authors: Wang Yihong , Kirby James E. , Qian Qinfang
Published: January 2009

In a retrospective review of data from 168 patients with suspected progressive multifocal leukoencephalopathy (PML) between 1996 and 2006, JC virus (JCV) PCR on cerebrospinal fluid (CSF) samples was positive only in human immunodeficiency virus (HIV)-infected patients with low CD4 cell counts and in severely immunocompromised patients with radiographic lesions consistent with PML or infectious processes generally. Of note, one HIV patient with a very low CD4 cell count had a positive JCV PCR despite a normal magnetic resonance imaging exam. We concluded that JCV PCR testing on CSF specimens should therefore be targeted to these high-risk patients.
Molecular diagnosis of Aspergillus endocarditis after cardiac surgery
Authors: Badiee Parisa , Alborzi Abdolvahab , Shakiba Elaheh , Ziyaeyan Mazyar , Pourabbas Bahman
Published: January 2009

The prevalence of Aspergillus endocarditis (AE) is increasing in the hospital population. Aspergillus species contribute to approximately 25 % of all cases of fungal endocarditis. This study is a descriptive report of the use of nested PCR to detect DNA specific for Aspergillus species in serum for the diagnosis of cardiac infections. Open heart surgery was performed on patients and collected samples were examined microscopically and cultured. Ten sera in total from five patients were extracted for Aspergillus DNA and nested PCR with Aspergillus species primers was carried out. The lowest limit of detection for the PCR assay was 1 c.f.u. (ml serum) −1. The PCR was positive in three patients. Culture of valvular tissue confirmed the growth of Aspergillus fumigatus in one patient and Aspergillus niger in two patients. In this study we have demonstrated the presence of invasive aspergillosis in patients who had undergone open heart surgery and the usefulness of a molecular assay for the diagnosis of AE.
Human bloodstream infection caused by Staphylococcus pettenkoferi
Authors: Song Sang Hoon , Park Jeong Su , Kwon Hye Rin , Kim Sung Han , Kim Hong Bin , Chang Ho Eun , Park Kyoung Un , Song Junghan , Kim Eui Chong
Published: January 2009

Staphylococcus pettenkoferi is a recently isolated human pathogen with only a few reported cases of infection. We report a case of bloodstream infection caused by S. pettenkoferi in a patient with pulmonary tuberculosis.
Neisseria meningitidis antigen NMB0088: sequence variability, protein topology and vaccine potential
Authors: Sardiñas Gretel , Yero Daniel , Climent Yanet , Caballero Evelin , Cobas Karem , Niebla Olivia
Published: January 2009

The significance ofNeisseria meningitidisserogroup B membrane proteins as vaccine candidates is continually growing. Here, we studied different aspects of antigen NMB0088, a protein that is abundant in outer-membrane vesicle preparations and is thought to be a surface protein. The gene encoding protein NMB0088 was sequenced in a panel of 34 different meningococcal strains with clinical and epidemiological relevance. After this analysis, four variants of NMB0088 were identified; the variability was confined to three specific segments, designated VR1, VR2 and VR3. Secondary structure predictions, refined with alignment analysis and homology modelling using FadL ofEscherichia coli, revealed that almost all the variable regions were located in extracellular loop domains. In addition, the NMB0088 antigen was expressed inE. coliand a procedure for obtaining purified recombinant NMB0088 is described. The humoral immune response elicited in BALB/c mice was measured by ELISA and Western blotting, while the functional activity of these antibodies was determined in a serum bactericidal assay and an animal protection model. After immunization in mice, the recombinant protein was capable of inducing a protective response when it was administered inserted into liposomes. According to our results, the recombinant NMB0088 protein may represent a novel antigen for a vaccine against meningococcal disease. However, results from the variability study should be considered for designing a cross-protective formulation in future studies.
Molecular characterization of carbapenem-resistant Acinetobacter species in an Irish university hospital: predominance of Acinetobacter genomic species 3
Authors: Boo T. W. , Walsh F. , Crowley B.
Published: January 2009

A 30 month prospective study of Acinetobacter species encountered in the Central Pathology Laboratory of St James's Hospital, Dublin, Ireland, was conducted to investigate the prevalence and molecular epidemiology of carbapenem resistance in such isolates. Acinetobacter genomic species 3 (AG3) was found to be the predominant Acinetobacter species (45/114, 39 %) in our institution. A total of 11 % of all Acinetobacter species (12/114) and 22 % of AG3 isolates (10/45) were carbapenem resistant. Carbapenem resistance was mediated by Ambler class D β-lactamase OXA-23 in all 12 isolates, with insertion sequence ISAba1 found upstream of bla
OXA-23. ISAba1 was also found upstream of bla
ADC-25, which encodes the enzyme AmpC, in an Acinetobacter baumannii isolate, and upstream of the aminoglycoside-acetyltransferase-encoding gene aacC2 in three AG3 isolates. Inter-species plasmidic transfer was most likely involved in the emergence and spread of bla
OXA-23 among the Acinetobacter isolates within our institution. The emergence of carbapenem resistance was associated not only with prior carbapenem use but also with the use of other antimicrobial agents, most notably β-lactam/β-lactamase-inhibitor combinations. The study demonstrated the emerging trend of carbapenem resistance in the wider context of the Acinetobacter genus, and reiterated the paramount importance of the prudent use of antimicrobial agents, stringent infection control measures and resistance surveillance of pathogens.