bluuebunny/crossref_metadata_2025 huggingface dataset:
Shared developmental mechanisms pattern the vertebrate gill arch and paired fin skeletons
Authors: Gillis J. Andrew , Dahn Randall D. , Shubin Neil H.
Published: March 2009

Here, we describe the molecular patterning of chondrichthyan branchial rays (gill rays) and reveal profound developmental similarities between gill rays and vertebrate appendages. Sonic hedgehog (Shh) and fibroblast growth factor 8 (Fgf8) regulate the outgrowth and patterning of the chondrichthyan gill arch skeleton, in an interdependent manner similar to their roles in gnathostome paired appendages. Additionally, we demonstrate that paired appendages and branchial rays share other conserved developmental features, includingShh-mediated mirror-image duplications of the endoskeleton after exposure to retinoic acid, andFgf8expression by a pseudostratified distal epithelial ridge directing endoskeletal outgrowth. These data suggest that the skeletal patterning role of the retinoic acid/Shh/Fgf8regulatory circuit has a deep evolutionary origin predating vertebrate paired appendages and may have functioned initially in patterning pharyngeal structures in a deuterostome ancestor of vertebrates.
Disruption of fast axonal transport is a pathogenic mechanism for intraneuronal amyloid beta
Authors: Pigino G. , Morfini G. , Atagi Y. , Deshpande A. , Yu C. , Jungbauer L. , LaDu M. , Busciglio J. , Brady S.
Published: March 2009

The pathological mechanism by which Aβ causes neuronal dysfunction and death remains largely unknown. Deficiencies in fast axonal transport (FAT) were suggested to play a crucial role in neuronal dysfunction and loss for a diverse set of dying back neuropathologies including Alzheimer's disease (AD), but the molecular basis for pathological changes in FAT were undetermined. Recent findings indicate that soluble intracellular oligomeric Aβ (oAβ) species may play a critical role in AD pathology. Real-time analysis of vesicle mobility in isolated axoplasms perfused with oAβ showed bidirectional axonal transport inhibition as a consequence of endogenous casein kinase 2 (CK2) activation. Conversely, neither unaggregated amyloid beta nor fibrillar amyloid beta affected FAT. Inhibition of FAT by oAβ was prevented by two specific pharmacological inhibitors of CK2, as well as by competition with a CK2 substrate peptide. Furthermore, perfusion of axoplasms with active CK2 mimics the inhibitory effects of oAβ on FAT. Both oAβ and CK2 treatment of axoplasm led to increased phosphorylation of kinesin-1 light chains and subsequent release of kinesin from its cargoes. Therefore pharmacological modulation of CK2 activity may represent a promising target for therapeutic intervention in AD.
Acetalated dextran is a chemically and biologically tunable material for particulate immunotherapy
Authors: Broaders Kyle E. , Cohen Joel A. , Beaudette Tristan T. , Bachelder Eric M. , Fréchet Jean M. J.
Published: March 2009

Materials that combine facile synthesis, simple tuning of degradation rate, processability, and biocompatibility are in high demand for use in biomedical applications. We report on acetalated dextran, a biocompatible material that can be formed into microparticles with degradation rates that are tunable over 2 orders of magnitude depending on the degree and type of acetal modification. Varying the degradation rate produces particles that perform better than poly(lactic-
co
-glycolic acid) and iron oxide, two commonly studied materials used for particulate immunotherapy, in major histocompatibility complex class I (MHC I) and MHC II presentation assays. Modulating the material properties leads to antigen presentation on MHC I via pathways that are dependent or independent of the transporter associated with antigen processing. To the best of our knowledge, this is the only example of a material that can be tuned to operate on different immunological pathways while maximizing immunological presentation.
Surgical Hand Antisepsis With Alcohol-Based Hand Rub Comparison of Effectiveness After 1.5 and 3 Minutes of Application
Authors: Weber Walter P. , Reck Stefan , Neff Uschi , Saccilotto Ramon , Dangel Marc , Rotter Manfred L. , Frei Reno , Oertli Daniel , Marti Walter R. , Widmer Andreas F.
Published: March 2009

Objective.

Research has shown 1.5 minutes of surgical hand antisepsis with alcohol-based hand rub to be at least as effective under experimental conditions as the 3-minute reference disinfection recommended by European Norm 12791. The aim of the present study was to validate the effectiveness of 1.5 minutes of surgical hand antisepsis in a clinical setting by comparing the effectiveness of 1.5- and 3-minute applications of alcohol-based hand rub (45% vol/vol 2-propanol, 30% vol/vol 1-propanol, and 0.2% mecetronium ethylsulphate).

Design.

Prospective crossover trial in which each surgeon served as his or her own control, with individual randomization to the 1.5-or the 3-minute group during the first part of the trial.

Setting.

Basel University Hospital, Switzerland.

Participants.

Thirty-two surgeons with different levels of postdoctoral training.

Methods.

We measured the bactericidal effectiveness of 1.5 minutes and 3 minutes of surgical hand antisepsis with alcohol-based hand rub by assessing the mean (± SD) log10 number of colony-forming units before the application of hand rub (baseline), after the application of hand rub (immediate effect), and after surgery (sustained effect) so as to follow European Norm 12791 as closely as possible.

Results.

The immediate mean (± SD) log10 reduction in colony-forming units (cfu) was 2.66 ±1.13 log10 cfu for the 1.5-minute group and 3.01 ±1.06 log10 cfu for the 3-minute group (P = .204). Similarly, there was no statistically significant difference between the 2 groups with respect to the sustained effect; the mean ( ± SD) log10 increase in bacterial density during surgery was 1.08 ± 1.13 log10 cfu for the 1.5-minute group and 0.95 ± 1.27 log10 cfu for the 3-minute group (P = .708). No adverse effects were recorded.

Conclusion.

In this clinical trial, surgical hand antisepsis with alcohol-based hand rub resulted in a similar bacterial reduction, regardless of whether it was applied for 3 or 1.5 minutes, which confirms experimental data generated with healthy volunteers.
Trf1 Is Not Required for Proliferation or Functional Telomere Maintenance in Chicken DT40 Cells
Authors: Cooley Carol , Baird Katie M. , Faure Virginie , Wenner Thomas , Stewart Jillian L. , Modino Sonie , Slijepcevic Predrag , Farr Christine J. , Morrison Ciaran G.
Published: March 2009

The telomere end-protection complex prevents the ends of linear eukaryotic chromosomes from degradation or inappropriate DNA repair. The homodimeric double-stranded DNA-binding protein, Trf1, is a component of this complex and is essential for mouse embryonic development. To define the requirement for Trf1 in somatic cells, we deleted Trf1 in chicken DT40 cells by gene targeting. Trf1-deficient cells proliferated as rapidly as control cells and showed telomeric localization of Trf2, Rap1, and Pot1. Telomeric G-strand overhang lengths were increased in late-passage Trf1-deficient cells, although telomere lengths were unaffected by Trf1 deficiency, as determined by denaturing Southern and quantitative FISH analysis. Although we observed some clonal variation in terminal telomere fragment lengths, this did not correlate with cellular Trf1 levels. Trf1 was not required for telomere seeding, indicating that de novo telomere formation can proceed without Trf1. The Pin2 isoform and a novel exon 4, 5–deleted isoform localized to telomeres in Trf1-deficient cells. Trf1-deficient cells were sensitive to DNA damage induced by ionizing radiation. Our data demonstrate that chicken DT40 B cells do not require Trf1 for functional telomere structure and suggest that Trf1 may have additional, nontelomeric roles involved in maintaining genome stability.
dCAS: a desktop application for cDNA sequence annotation
Authors: Guo Yongjian , Ribeiro Jose M. C. , Anderson Jennifer M. , Bour Stephan
Published: March 2009

Motivation: Understanding gene regulation and expression is the key to the advancement of biology. EST sequence assembly and analysis provide unique benefits in this regard. We have developed a standalone application, dCAS (Desktop cDNA Annotation System), which performs automated EST cleaning, clustering, assembly and annotation on a desktop computer. Compared with other available tools, dCAS provides a more convenient and user-friendly solution to biologists for extracting biological meaning from sequence data.

Availability: The dCAS package is distributed freely. A cross-platform installer and associated sequence databases can be downloaded at: http://exon.niaid.nih.gov/applications.html

Contact:  guoyo@mail.nih.gov
Integrating shotgun proteomics and mRNA expression data to improve protein identification
Authors: Ramakrishnan Smriti R. , Vogel Christine , Prince John T. , Wang Rong , Li Zhihua , Penalva Luiz O. , Myers Margaret , Marcotte Edward M. , Miranker Daniel P.
Published: March 2009

Motivation: Tandem mass spectrometry (MS/MS) offers fast and reliable characterization of complex protein mixtures, but suffers from low sensitivity in protein identification. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other information available, e.g. the probability of a protein's presence is likely to correlate with its mRNA concentration.

Results: We develop a Bayesian score that estimates the posterior probability of a protein's presence in the sample given its identification in an MS/MS experiment and its mRNA concentration measured under similar experimental conditions. Our method, MSpresso, substantially increases the number of proteins identified in an MS/MS experiment at the same error rate, e.g. in yeast, MSpresso increases the number of proteins identified by ∼40%. We apply MSpresso to data from different MS/MS instruments, experimental conditions and organisms (Escherichia coli, human), and predict 19–63% more proteins across the different datasets. MSpresso demonstrates that incorporating prior knowledge of protein presence into shotgun proteomics experiments can substantially improve protein identification scores.

Availability and Implementation: Software is available upon request from the authors. Mass spectrometry datasets and supplementary information are available from http://www.marcottelab.org/MSpresso/.

Contact:  marcotte@icmb.utexas.edu; miranker@cs.utexas.edu

Supplementary Information: Supplementary data website: http://www.marcottelab.org/MSpresso/.
An assessment of the functional variability of selected coastal ecosystems in the context of local environmental changes
Authors: Baird Dan
Published: March 2009

Baird, D. (2009) An assessment of the functional variability of selected coastal ecosystems in the context of local environmental changes. – ICES Journal of Marine Science, 66: 1520–1527. The functioning of coastal ecosystems is greatly dependent on a wide variety of external pulses (e.g. tides, freshwater influx, seasonal trends in temperature, nutrient input, etc.). Assessments of the effect of a selection of environmental characteristics driven by natural and/or anthropogenic forces on ecosystem function are given using selected ecosystem properties, such as total system throughput, system organization, productivity, recycling, and trophic efficiency, derived from ecological network analysis (ENA) of several coastal ecosystems on monthly, intra-seasonal, seasonal, and interdecadal scales. Each ecosystem was modelled depicting data of standing stocks, the flows between the constituent living and non-living components in the system, exports, and imports. Results from ENA revealed considerable differences of the same property (or properties) resulting from physical changes (e.g. temperature, salinity, oxygen, rate of freshwater inflow) over time. A small temperature increase in a Florida seagrass bed, for example, resulted in increases in system throughput, the P/B ratio, and in the rate of carbon recycling, but also in a significant decrease in system organization. The effect of seasonal increases in water temperature and of measured decrease/increase in river run-off to a few selected estuaries is discussed using ENA.
The comparative effects of habitat complexity on faunal assemblages of northern temperate artificial and natural reefs
Authors: Hunter W. R. , Sayer M. D. J.
Published: March 2009

Hunter, W. R., and Sayer, M. D. J. 2009. The comparative effects of habitat complexity on faunal assemblages of northern temperate artificial and natural reefs. – ICES Journal of Marine Science, 66: 691–698. Several north temperate marine species were recorded on subtidal hard-substratum reef sites selected to produce a gradient of structural complexity. The study employed an established scuba-based census method, the belt transect. The three types of reef examined, with a measured gradient of increasing structural complexity, were natural rocky reef, artificial reef constructed of solid concrete blocks, and artificial reef made of concrete blocks with voids. Surveys were undertaken monthly over a calendar year using randomly placed fixed rope transects. For a number of conspicuous species of fish and invertebrates, significant differences were found between the levels of habitat complexity and abundance. Overall abundance for many of the species examined was 2–3 times higher on the complex artificial habitats than on simple artificial or natural reef habitats. The enhanced habitat availability produced by the increased structural complexity delivered through specifically designed artificial reefs may have the potential to augment faunal abundance while promoting species diversity.
Hippocampal Erk mechanisms linking prediction error to fear extinction: Roles of shock expectancy and contextual aversive valence
Authors: Huh Kyu Hwan , Guzman Yomayra F. , Tronson Natalie C. , Guedea Anita L. , Gao Can , Radulovic Jelena
Published: March 2009

Extinction of fear requires learning that anticipated aversive events no longer occur. Animal models reveal that sustained phosphorylation of the extracellular signal-regulated kinase (Erk) in hippocampal CA1 neurons plays an important role in this process. However, the key signals triggering and regulating the activity of Erk are not known. By varying the degree of expected and delivered aversive reinforcement, we demonstrate that Erk specifically responds to prediction errors of contextual aversive events. An increase of somatonuclear phospho-Erk (pErk) within principal CA1 neurons was observed only when the expectation of contextual foot shock was violated, but not when the context was consistently nonreinforced or reinforced by foot shock. The rate of error detection, Erk signaling, and fear extinction markedly depended on shock expectancy and the aversive valence of the context, as revealed by comparison of groups trained with single, continuous, or partial reinforcement. On the basis of these findings, the hippocampal Erk response to prediction errors of aversive outcome is proposed as a unique mechanism of fear extinction. Improving the detection and processing of these errors has the potential to attenuate fear responses in patients with anxiety disorders.
Infants with late breast milk acquisition of HIV-1 generate interferon-gamma responses more rapidly than infants with early peripartum acquisition
Authors: Lohman-Payne B , Slyker J A , Richardson B A , Farquhar C , Majiwa M , Maleche-Obimbo E , Mbori-Ngacha D , Overbaugh J , Rowland-Jones S , John-Stewart G
Published: March 2009

Infants infected with HIV-1 after the first month of life have a lower viral set-point and slower disease progression than infants infected before 1 month. We investigated the kinetics of HIV-1-specific CD8+ T lymphocyte secretion of interferon (IFN)-γ in infants infected before 1 month of life compared with those infected between months 1 and 12 (late infection). HIV-1 infection was assessed at birth and at months 1, 3, 6, 9 and 12 and timing of infection was determined by HIV-1 gag DNA from dried blood spots and verified by plasma HIV-1 RNA levels. HIV-1 peptide-specific IFN-γ responses were measured by enzyme-linked immunospot at months 1, 3, 6, 9 and 12. Timing of development of IFN-γ responses was compared using the log–rank test and Kaplan–Meier survival curves. Infants infected late developed HIV-1-specific CD8+ T cell responses 2·8 months sooner than infants infected peripartum: 2·3 versus 5·1 months after HIV-1 infection (n = 52, P = 0·04). Late-infected infants had more focused epitope recognition than early-infected infants (median 1 versus 2 peptides, P = 0·03); however, there were no differences in the strength of IFN-γ responses. In infants infected with HIV-1 after the first month of life, emergence of HIV-1-specific CD8+ IFN-γ responses is coincident with the decline in viral load, nearly identical to what is observed in adults and more rapid than in early-infected infants.
Out in the cold: physiological capacity influences behaviour in deer mice
Authors: Sears Michael W. , Hayes Jack P. , Banta Marilyn R. , McCormick Donna
Published: March 2009

Understanding the links between physiological performance and fitness is key to predicting the responses of individuals to environmental change, especially that imposed by climate. Of particular interest are traits linked with metabolic performance. In particular, maximal metabolic rate (MMR; which describes the upper limit to heat production) and basal metabolic rate (BMR; which describes the lower limit to heat production for a normothermic endotherm) are important causal mechanisms that determine the physiological limits for activity under cold conditions.

Previous work with deer mice has shown important links between maximal metabolic performance and activity. Selection for elevated MMRs was detected in nature, and higher rates of above‐ground activity during periods of cold were associated with elevated MMRs. Here, we investigate further the links between activity and elevated MMRs.

We conducted a laboratory study to test whether BMR or MMR was correlated with activity and foraging behaviour of deer mice exposed to a series of cold temperatures (–5, –10 and –15 °C). Each mouse had access to a warm nest box, but needed to enter a cold environmental chamber to access food, ice chips and a running wheel. Behaviours were monitored for 2 days under these experimental conditions. Prior to the experimental trials, BMR and MMR were measured. MMR was also measured after the trials.

The amount of time that mice spent active in the cold was negatively correlated with ambient temperature. The duration of activity per bout (when mice were out of the nest box) decreased at colder temperatures, but the number of bouts did not. The total duration of activity and duration per bout increased with an individual's MMR and change in MMR over the course of the experiment. Body mass decreased at colder temperatures, and mice with higher MMR and greater increases in MMR consumed more food.

Our study suggests that mice with high MMR, or a capacity to increase MMR may be best able to tolerate cold environments. Thus, physiological capacity and behaviour can influence each other in response to environmental conditions.

Integrative studies between behaviour and physiology in an ecological context provide greater understanding of the potential responses of organisms to environmental change. With respect to climate, such responses will depend either on the ability of individuals to induce plastic (or acclamatory) responses to environmental stressors or on the structure of genetic variation for physiological traits within a particular population. Although, some effort has been directed at understanding the evolutionary significance of metabolic traits (particularly with respect to heritabilities), we suggest that priority should be given to studies that explicitly address the mechanistic links between physiology and fitness in light of ongoing climate change.
Cholesterol and desmosterol in two sperm populations separated on Sil‐Select gradient
Authors: Zalata A. , Hassan A. , Christophe A. , Comhaire F. , Mostafa T.
Published: March 2009

Sperm lipids are important for sperm viability, maturity and function. This study aimed to identify cholesterol and desmosterol composition of human spermatozoa of two sperm populations separated on Sil‐Select gradient. Forty‐eight males were divided into four groups namely healthy men (n = 13), asthenozoospermia (n = 11), asthenoteratozoospermia (n = 10) and oligoasthenoteratozoospermia (n = 14). Sperm cholesterol and desmosterol were estimated in two human sperm population separated by centrifugation in a discontinuous Sil‐Select gradient. The results showed that cholesterol and desmosterol were the major sterols in human spermatozoa. Spermatozoa recovered from upper/lower layer interface (fraction I) had low fertilization potential, while those from the base (fraction II) had high fertilization potential. Median values of cholesterol and desmosterol in fraction I were 2.55 μmol and 0.77 μmol/109 spermatozoa and in fraction II were 1.16 μmol and 0.27 μmol/109 spermatozoa. Cholesterol/desmosterol ratio was significantly higher in fraction II than I (4.8 vs. 3.2, p < 0.01). Cholesterol, desmosterol, total phospholipids and sterols/phospholipids were negatively correlated with sperm concentrations, sperm motility, linear velocity, normal sperm morphology and acrosome reaction percentage whereas cholesterol/desmosterol ratio was positively correlated with these parameters. It is concluded that the difference in sterol composition of sperm subpopulations separated on Sil‐Select gradient suggests that composition of sterols is related to sperm functions.
Combined effect of the finasteride and doxazosin on rat ventral prostate morphology and physiology
Authors: Justulin Jr Luis A. , Acquaro Carolina , Carvalho Robson F. , Silva Maeli Dal Pai , Felisbino Sérgio L.
Published: March 2009

Finasteride (Fin) and Doxazosin (Dox), alone or in combination, have been widely used in treatment of benign prostatic hyperplasia (BPH) symptoms and recently have been suggested as potential drugs for prostate cancer (PCa)prevention and treatment. However, little is known about the effects of the combination therapy on prostate tissue morphology, physiology and matrix metalloproteinases (MMPs) activity, a special set of enzymes closely related to PCa progression and metastasis. In this study, adult Wistar rats were treated with Fin + Dox (25 mg/kg per day) and the ventral prostate (VP) was excised at days 3 and 30 of treatment to evaluate morphology, cell proliferation, death, transforming growth factor‐beta1 (TGF‐β1) protein expression, MMP‐2, MMP‐9 activities and MMP‐2, MMP‐9, TIMP‐1 and TIMP‐2 mRNA expression. Fin + Dox treatment induced a transient increase in testosterone (T) plasma concentration and a permanent reduction in dihydrotestosterone (DHT). The VP and epithelial cell proliferation were reduced and the stromal collagen fibre volume fraction and apoptosis of the epithelial cell were increased. Fin + Dox treatment also increased the TGF‐β1 immunoreaction in the epithelium and in the stroma. The mRNAs for MMP‐2, TIMPs‐1 and ‐2 expressions after 30 days of treatment were decreased. The mRNA for MMP‐9 was not detected in any of the groups analysed. Fin + Dox treatment for 30 days promoted a decrease in gelatinolytic activity of MMP‐2 and an increase in MMP‐9. In conclusion, combined treatment with Fin and Dox interferes in the epithelial cell behaviour and in the MMPs activity, potentially via TGF‐β1‐mediated and androgen pathways. Our results contribute to a better understanding of the clinical data and also of the molecular mechanisms behind isolated or combined Fin and Dox long‐term treatment.
Testing island biogeography theory with visitation rates of birds to British islands
Authors: Stracey Christine M. , Pimm Stuart L.
Published: March 2009

Aim  We consider three hypotheses – MacArthur and Wilson’s island biogeography theory (IBT), Lack’s habitat diversity idea and the ‘target effect’– that explain the pattern of decreased species richness on small and distant islands.

Location  We evaluate these hypotheses using a detailed dataset on the occurrence and abundance of terrestrial birds on nine islands off the coast of Britain and the Republic of Ireland.

Methods  Unlike previous studies, we compile data on species that visit the islands, rather than just those that breed on them. We divided the species into five mutually exclusive categories based upon their migratory status and where they regularly breed: British residents, summer visitors to Britain, winter visitors to Britain, and vagrants from Europe or beyond Europe. For each species group on each island we calculated the average number of species visiting each year. We then regressed the average number of species against island area and distance to the mainland (all variables were log‐transformed). We also compared the average number of species visiting each island with the average number of species breeding on each island.

Results  Average number of visiting British residents decreased significantly with increasing island distance, but showed no relationship with island area. There was no significant relationship between island area or island distance and average number of summer or winter visitors. European and non‐European vagrants likewise showed no relationship between numbers of species visiting and island distance. However, the relationship between island area and number of visiting species was significant for both these categories; as island area increases so too does the number of visiting species.

Main conclusions  As predicted by IBT, there were fewer visiting species on more distant islands. There were substantially more visitors to each island than breeding species, supporting Lack’s argument that lower bird richness is not a result of varying immigration rates (as predicted by IBT) but rather a result of some other island property, e.g. fewer resources. Birds make a decision to either leave an island or stay and breed. The target effect was also clearly demonstrated by the increase in European and non‐European breeders with increasing island size.
Late Neogene history of the laurel tree (Laurus L., Lauraceae) based on phylogeographical analyses of Mediterranean and Macaronesian populations
Authors: Rodríguez‐Sánchez Francisco , Guzmán Beatriz , Valido Alfredo , Vargas Pablo , Arroyo Juan
Published: March 2009

Aim  The post‐glacial range dynamics of many European plant species have been widely investigated, but information rapidly diminishes as one moves further back in time. Here we infer the historical range shifts of Laurus, a paradigmatic tree of the Tethyan flora that has covered southern Eurasia since the Oligo‐Miocene, by means of phylogenetic and phylogeographical analyses.

Location  Mediterranean Basin, Black Sea and Macaronesian archipelagos (Azores, Madeira, Canary Islands).

Methods  We analysed plastid DNA (cpDNA) sequence (trnK–matK, trnD–trnT) variation in 57 populations of Laurus and three Lauraceae genera. Phylogenetic methods (maximum parsimony and Bayesian inference) and statistical parsimony networks were used to reconstruct relationships among haplotypes. These results were contrasted with the fossil record and bioclimatic niche‐based model predictions of past distributions to infer the migration routes and location of refugia.

Results  The phylogenetic tree revealed monophyly for Laurus. Overall sequence variability was low within Laurus, but six different haplotypes were distinguished and a single network retrieved, portraying three lineages primarily related to geography. A strongly divergent eastern lineage occupied Turkey and the Near East, a second clade was located in the Aegean region and, lastly, a western clade grouped all Macaronesian and central and western Mediterranean populations. A close relationship was observed between the Macaronesian populations of L. azorica and the western populations of L. nobilis.

Main conclusions  The phylogeographical structure of Laurus preserves the imprints of an ancient contraction and break‐up of the range that resulted in the evolution of separate cpDNA lineages in its western‐ and easternmost extremes. Intense range dynamics in the western Mediterranean and multiple glacial refugia contributed to the generation and long‐term conservation of this phylogeographical pattern, as shown by the fit between the haplotype ranges and past suitable areas inferred from bioclimatic models. Finally, our results challenge the taxonomic separation of Laurus into two distinct species.
Biogeography of Aphodiinae dung beetles based on the regional composition and distribution patterns of genera
Authors: Cabrero‐Sañudo Francisco J. , Lobo Jorge M.
Published: March 2009

Aim  To examine current biogeographical patterns of Aphodiinae dung beetles (Coleoptera: Scarabaeoidea: Scarabaeidae) in order to reveal relationships among regions and their potential impact on the diversification of this group.

Location  Worldwide.

Methods  Information about all Aphodiinae genera was obtained from the literature. An occurrence matrix was built for the six worldwide biogeographical regions, and their faunas were characterized through simple statistics. Regional variations and similarities were further explored using co‐occurrence and nestedness analyses, sequential agglomerative, hierarchical and nested clustering (SAHN), and a parsimony analysis of endemicity (PAE). Mantel tests were also employed to assess the relationships between several characteristics of the regions and their faunas.

Results  The Palaearctic and Palaeotropical regions showed the highest total numbers of Aphodiinae genera and the greatest generic endemism. Both these regions and the Oriental also showed higher numbers of genera than would be expected according to their size. Co‐occurrence and nestedness analyses confirmed the non‐randomness of the distribution of genera. Clustering and PAE showed that the Palaearctic and Oriental regions are the most similar, followed by the Palaeotropical region. Regional dissimilarity in genera composition was related to biological and historical traits, but not to ecoregions.

Main conclusions  A structured geographical pattern for Aphodiinae was confirmed. Land continuity and proximity in the long term could have played a unifying role in regional faunas. We suggest that the different biogeographical regions have acted as either macroevolutionary sources (basically the Palaearctic and the Palaeotropical regions) or sink regions, according to their role as diversification centres. We review the processes and events that could account for current patterns of Aphodiinae diversity.
Nocardia seriolae infection in the three striped tigerfish, Terapon jarbua (Forsskål)
Authors: Wang P‐C , Chen S‐D , Tsai M‐A , Weng Y‐J , Chu S‐Y , Chern R‐S , Chen S‐C
Published: March 2009

An epizootic in pond cultured three striped tigerfish, Terapon jarbua, in Taiwan was caused by Nocardia seriolae. Diseased fish first showed clinical signs and mortalities in February and March 2003. The cumulative mortality within 2 months was 2.4% (1200 of 50 000) and affected fish were 7 months old with total lengths from 18 to 25 cm. Most affected fish were pale and lethargic with haemorrhages and ulcers on the skin. The most significant gross pathological changes were varying degrees of ascites and enlargement of the spleen, kidney and liver. Obvious white nodules, varying in size, were found in these organs. Bacteria were either coccal or filamentous in appearance, with bead‐like forms. Isolates from diseased fish were characterized using the API ZYM (Analytical profile index; Bio Mérieux, France) systems and conventional tests and identified as Nocardia sp. The isolate was designated NS127 and was confirmed as N. seriolae by a polymerase chain reaction assay that gave the expected specific 432 bp amplicon. In addition, its 16S rDNA sequence gave 100% sequence identity with N. seriolae. A partial sequence of the 16S rRNA gene, heat shock protein gene and RNA polymerase gene (rpo B) of NS127 and the type strain of N. seriolae BCRC 13745 formed a monophyletic clade with a high sequence similarity and bootstrap value of 99.9%. White nodules induced in experimental fish were similar to naturally infected cases and N. seriolae was re‐isolated on brain heart infusion agar. This is the first report of N. seriolae‐infection in three striped tigerfish in aquaculture.
Identification of immune cells interacting with Vibrio spp. and its in vitro post‐phagocytic killing mechanism of haemocytes in the penaeid shrimp, Penaeus indicus H. Milne Edwards
Authors: Jayasree S
Published: March 2009

Immune cells were identified and their interaction towards Vibrio alginolyticus, V. parahaemolyticus and V. anguillarum was studied in vitro in the penaeid shrimp, Penaeus indicus. Haemocytes were divided into agranulocytes, semi‐dense granulocytes and dense granulocytes according to their morphology. Agranulocytes (100%) and 0.3–0.7% of granulocytes were actively involved in coagulation. Granulocytes were involved in in vitro phagocytosis and encapsulation of foreign materials. Phagocytosis was enhanced by prior opsonization of bacteria with cell‐free shrimp haemolymph. Semi‐dense granulocytes were phagocytic towards V. alginolyticus with and without opsonization at the rate of 91.1% and 83.1%, respectively (P < 0.05). Granulocyte death observed after 2 h with opsonized haemolymph was 26.1%. About 64.5% of dense granulocytes and 23.2% of semi‐dense granulocytes were actively involved in encapsulation, forming capsules. A spectrophotometric nitroblue tetrazolium (NBT) reduction assay was used to demonstrate the production of superoxide anions (O2−) by shrimp haemocytes. All the Vibrio spp. were able to induce superoxide anions (O2−) during phagocytosis. Live Vibrio sp. induced O2− production in haemocytes in a dose‐dependent manner. Significant activity was detected with a 40:1 bacteria to haemocyte ratio (P < 0.05). NBT reduction assay for measuring the post‐phagocytic killing mechanism in shrimp haemocytes might be a valuable tool for monitoring shrimp health and immunological studies.
Protein markers of Marteilia sydneyi infection in Sydney rock oysters, Saccostrea glomerata
Authors: Simonian M , Nair S V , O’Connor W A , Raftos D A
Published: March 2009

Marteilia sydneyi is the causative agent of QX disease in Sydney rock oyster, Saccostrea glomerata. It is responsible for disease outbreaks among oysters that occur during summer and can result in up to 95% mortality. QX disease has significantly decreased S. glomerata production in some areas of Australia’s eastern seaboard over the past 30 years. Marteilia sydneyi sporulates in the digestive gland of oysters leading to complete disorganization of the infected tissues. The current study used proteomics to identify potential molecular markers of sporulating M. sydneyi infection during a field trial undertaken in the Georges River, Sydney, between December 2006 and May 2007. Early stages of M. sydneyi infection were detected by polymerase chain reaction, whilst cytological examination was used to identify sporulating M. sydneyi in the gut. Protein expression in oyster haemolymph was assessed during the M. sydneyi infection period by two dimensional electrophoresis. Proteome maps identified significant differences in the expression of four proteins in oysters with sporulating M. sydneyi infections.
Modulating T‐cell homeostasis with IL‐7: preclinical and clinical studies
Authors: Capitini C. M. , Chisti A. A. , Mackall C. L.
Published: March 2009

Interleukin‐7 (IL‐7) is required for the development and survival of T cells and plays a critical role in modulating T‐cell homeostasis. This review will address current understanding of IL‐7 biology, review recent clinical experiences and discuss potential future clinical applications of IL‐7, or IL‐7 blockade, in the setting of disease.
Glacial refugia in a maritime temperate climate: Cicada (Kikihia subalpina) mtDNA phylogeography in New Zealand
Authors: MARSHALL DAVID C. , HILL KATHY B. R. , FONTAINE KATHRYN M. , BUCKLEY THOMAS R. , SIMON CHRIS
Published: March 2009

Understanding the biological significance of Pleistocene glaciations requires knowledge of the nature and extent of habitat refugia during glacial maxima. An opportunity to examine evidence of glacial forest refugia in a maritime, Southern Hemisphere setting is found in New Zealand, where the extent of Pleistocene forests remains controversial. We used the mitochondrial phylogeography of a forest‐edge cicada (Kikihia subalpina) to test the hypothesis that populations of this species survived throughout South Island during the Last Glacial Maximum. We also compared mitochondrial DNA phylogeographic patterns with male song patterns that suggest allopatric divergence across Cook Strait. Cytochrome oxidase I and II sequences were analyzed using network analysis, maximum‐likelihood phylogenetic estimation, Bayesian dating and Bayesian skyline plots. K. subalpina haplotypes from North Island and South Island form monophyletic clades that are concordant with song patterns. Song divergence corresponds to approximately 2% genetic divergence, and Bayesian dating suggests that the North Island and South Island population‐lineages became isolated around 761 000 years bp. Almost all South Island genetic variation is found in the north of the island, consistent with refugia in Marlborough Sounds, central Nelson and northwest Nelson. All central and southern South Island and Stewart Island haplotypes are extremely similar to northern South Island haplotypes, a ‘northern richness/southern purity’ pattern that mirrors genetic patterns observed in many Northern Hemisphere taxa. Proposed southern South Island forest habitat fragments may have been too small to sustain populations of K. subalpina, and/or they may have harboured ecological communities with no modern‐day analogues.
Dispersal to or from an African biodiversity hotspot?
Authors: BLACKBURN D. C. , MEASEY G. J.
Published: March 2009

Biodiversity hotspots are centres of endemism and thus contain many range‐restricted species. In addition, within these hotspots occur widespread species that might have originated within a hotspot before dispersing to neighbouring or distant regions. We test this hypothesis with a phylogeographic analysis of a miniature leaf litter frog, Arthroleptis xenodactyloides, that has a large distribution throughout the Eastern Arc biodiversity hotspot and other regions in East Africa. Maximum‐likelihood and Bayesian estimates of the mitochondrial gene phylogeny are used as a proxy for understanding the evolutionary history of diversification and the historical relationships between populations. The north–south range of this species extends for approximately 1900 km; our sampling covers approximately 85% of this range. Using phylogenetic comparative methods, we estimate the region of origin and direction of dispersal within A. xenodactyloides. We compare contrasting hypotheses of latitudinal range expansion using bayes factors. The ancestral region of origin of A. xenodactyloides is reconstructed as having occurred within the Eastern Arc before dispersing southwards into the southern Rift Mountains, probably in the Pleistocene. The phylogeographic structure within this leaf litter frog is surprisingly similar to that of forest birds, revealing that similar geographic features might have had a driving role in diversification of these very dissimilar taxa. Latitudinal expansion occurred early in the evolutionary history of A. xenodactyloides, which may indicate that physiological adaptation facilitated its wide geographic distribution.
Genomic pattern of adaptive divergence in Arabidopsis halleri, a model species for tolerance to heavy metal
Authors: MEYER CLAIRE‐LISE , VITALIS RENAUD , SAUMITOU‐LAPRADE PIERRE , CASTRIC VINCENT
Published: March 2009

Pollution by heavy metals is one of the strongest environmental constraints in human‐altered environments that only a handful of species can cope with. Identifying the genes conferring to those species the ability to grow in polluted areas is a first step towards a global understanding of the evolutionary processes involved and will eventually improve phytoremediation practices. We used a genome‐scan approach to detect loci under divergent selection among four populations of Arabidopsis halleri growing on either polluted or nonpolluted habitats. Based on a high density of amplified fragment length polymorphism (AFLP) markers (820 AFLP markers, i.e. ~1 marker per 0.3 Mb), evidence for selection was found for some markers in every sampled population. Four loci departed from neutrality in both metallicolous populations and thus constitute high‐quality candidates for general adaptation to pollution. Interestingly, some candidates differed between the two metallicolous populations, suggesting the possibility that different loci may be involved in adaptation in the different metallicolous populations.
Roles of relSpn in stringent response, global regulation and virulence of serotype 2 Streptococcus pneumoniae D39
Authors: Kazmierczak Krystyna M. , Wayne Kyle J. , Rechtsteiner Andreas , Winkler Malcolm E.
Published: March 2009

RelA/SpoT homologue (RSH) proteins have (p)ppGpp synthetase and hydrolase activities that mediate major global responses to nutrient limitation and other stresses. RSH proteins are conserved in most bacteria and play diverse roles in bacterial pathogenesis. We report here that the RSH protein of Streptococcus pneumoniae, RelSpn, can be deleted and is the primary source of (p)ppGpp synthesis in virulent strain D39 under some conditions. A D39 ΔrelSpn mutant grew well in complex medium, but did not grow in chemically defined medium unless supplemented with the metals copper and manganese. Transcriptome analysis of D39 rel+Spn and ΔrelSpn strains treated with mupirocin revealed relSpn‐independent (translation stress), relSpn‐dependent (stringent response) and ΔrelSpn‐dependent changes, suggesting that relSpn and (p)ppGpp amount play wide‐ranging homeostatic roles in pneumococcal physiology, besides adjusting macromolecular synthesis and transport in response to nutrient availability. Notably, the relSpn‐dependent response included significant upregulation of the ply operon encoding pneumolysin toxin, whereas the ΔrelSpn‐dependent response affected expression linked to the VicRK and CiaRH two‐component systems. Finally, a D39 ΔrelSpn mutant was severely attenuated and displayed a significantly altered course of disease progression in a mouse model of infection, which was restored to normal by an ectopic copy of rel+Spn.
Spatial and temporal evolution of a terminal fluvial fan system: the Permian Organ Rock Formation, South‐east Utah, USA
Authors: CAIN STEPHEN A. , MOUNTNEY NIGEL P.
Published: March 2009

The recognition of terminal fluvial systems, otherwise termed ‘terminal fans’ or ‘distributary fluvial fan systems’, preserved in the ancient rock record is based primarily on the recognition of facies characteristics indicative of a progressive downstream decrease in: (i) fluvial discharge; (ii) channel depth and width; (iii) lateral and vertical connectivity of channel‐fill elements; and (iv) evidence for channellized flow and a systematic increase in: (i) evidence for sheetflood deposition; (ii) aeolian and/or playa deposits; and (iii) channel bifurcation. However, despite these criteria having been applied previously to a variety of outcrop successions, there is still no unifying facies model that adequately accounts for the complex stratigraphic architectural relationships expected for such systems, based on the varied styles of fluvial activity and system interaction known from modern examples. Moreover, few previous studies have given significant consideration to the long‐term temporal evolution of terminal fluvial fans. These issues are addressed by this study of the Permian (Leonardian/Artinskian) Organ Rock Formation of the Paradox Basin, South‐east Utah. A detailed stratigraphic framework based on 84 sedimentary logs demonstrates proximal to distal variations in sedimentary style. Integration of these data with high‐resolution architectural panels depicting the geometry and facies characteristics of individual fluvial elements has enabled the development of a series of depositional models that account for both the spatial and temporal evolution of the system and which are representative of: (i) initial progradation of the fluvial system into the Paradox foreland basin; (ii) retreat of the fluvial system and expansion of a distal aeolian dune system; (iii) the final phase of fluvial progradation following aeolian dune deflation; and (iv) the final retrogradation of the fluvial system back towards the hinterland.
Phylogeny and classification of Corylophidae (Coleoptera: Cucujoidea) with descriptions of new genera and larvae
Authors: ŚLIPIŃSKI ADAM , TOMASZEWSKA WIOLETTA , LAWRENCE JOHN F.
Published: March 2009

AbstractPhylogenetic relationships within the family Corylophidae were investigated. Twenty ingroup taxa and six outgroups were included in a cladistic analysis, based on 48 characters derived from adult and larval morphology. Phylogenetic analysis confirms that Corylophidae are monophyletic within the superfamily Cucujoidea and may be subdivided into two subfamilies: the Australian Periptycinae and the cosmopolitan Corylophinae containing 10 tribes: Foadiinitrib.n., Cleidostethini, Aenigmaticini, Parmulini, Sericoderini, Peltinodini, Orthoperini, Corylophini, Teplinini and Rypobiini. All currently recognized family‐group taxa are thoroughly diagnosed, and keys to their identification based on adults and larvae are provided. Two new genera and three species are described:Weirusgen.n., containing onlyW.tozersp.n. (Australia: Queensland), andStanusgen.n., with the two speciesS. bowesteadisp.n. (New Zealand) andS. tasmanicussp.n.(Tasmania). The larvae ofPakalukodes bimaculatusŚlipińskiet al.from Queensland and ofStanus bowesteadisp.n.from New Zealand are described and illustrated for the first time.
Dissimilar molecular defense responses are elicited in Triticum aestivum after infestation by different Diuraphis noxia biotypes
Authors: Zaayman Dewald , Lapitan Nora L.V. , Botha Anna‐Maria
Published: March 2009

For sustainable solutions to the problem of insect infestation, the study of molecular plant‐insect interactions is integral to resistance breeding strategies. This also holds true in the case of wheat (Triticum aestivum), where the Russian wheat aphid (Diuraphis noxia, Kurdjumov, RWA) is responsible for significant crop losses in most major wheat producing countries around the world. Our study is focused on gaining a greater understanding of the resistance mechanisms activated by the RWA resistance gene Dn7 by comparing responses following infestation with three different aphid biotypes (RWA‐SA, RWA‐US1 and RWA‐US2). This consisted of analyzing the resistant wheat line 94M370 (containing Dn7) and its susceptible counterpart (Gamtoos) on a transcriptional level with complementary DNA‐amplified fragment length polymorphisms (cDNA‐AFLPs) using 17 primer combinations, as well as quantitative reverse transcription polymerase chain reaction (qRT‐PCR) of 10 differentially expressed transcripts. The results of this expression profile analysis suggest that Dn7 activates similar responses against the two US aphid biotypes, which differ noticeably from the response following infestation with a South African aphid biotype. This is consistent with recent research showing limited molecular variations between the two US aphid biotypes (∼ 0.12%), compared with a distinctly different South African biotype. We therefore conclude that Dn7 recognizes and interacts in a highly specific manner with different aphid's putative eliciting agents, which in turn activates specific defense pathways unique to that interaction.