bluuebunny/crossref_metadata_2025 huggingface dataset:
The Role of Dual‐Trained Conventional/Complementary Physicians as Mediators of Integration in Primary Care
Authors: Ben-Arye Eran
Published: May 2008

A growing number of physicians study complementary and alternative medicine (CAM). Limited data are available on perspectives of physicians with dual training in conventional medicine and CAM, on issues of communication and collaboration with CAM practitioners (CAMPs). Questionnaires were administered to primary care physicians employed in the largest health maintenance organization (HMO) in Israel and to MD and non‐MD CAM practitioners employed by a CAM‐related agency of the same HMO. Data for statistical analysis were available from 333 primary care physicians (PCPs) and 241 CAM practitioners. Thirty‐one of the 241 CAMPs were dual‐trained physicians employed in a CAM‐related agency as practitioners and/or triage‐consultants. Dual trained physicians and CAMPs shared similar attitudes and supported, more so than PCPs, collaborative physician–CAM practitioner teamwork in clinical practice, medical education and research. Nevertheless, dual trained physicians supported a physician‐dominant teamwork model (similar to the PCPs’ approach) in contrast to non‐MD CAM practitioners who mainly supported a co‐directed teamwork model. Compared to PCPs and non‐MD CAM practitioners, dual trained physicians supported significantly more a medical/referral letter as the preferred means of doctor–CAM practitioner communication. Dual trained physicians have a unique outlook toward CAM integration and physician–practitioner collaboration, compared to non‐MD CAM practitioners and PCPs. More studies are warranted to explore the role of dual trained physicians as mediators of integration.
Ten Years Evidence‐Based High‐Tech Acupuncture Part 3: A Short Review of Animal Experiments
Authors: Litscher Gerhard
Published: May 2008

High‐tech acupuncture research has been performed for 10 years at the Research Unit of Biomedical Engineering in Anesthesia and Intensive Care Medicine at the Medical University of Graz. This article as a part of a series comprises animal experiments in the field of needle and laser acupuncture. The investigations presented in this article were performed in pigs, dogs and sheep. In all studies sedative stimulation effects of the acupoint Yintang are described using different measurement parameters (EEG‐bispectral index, EEG spectral edge frequency and metabolic parameters).
Management of an invasive marine species: defining and testing the effectiveness of ballast-water management options using management strategy evaluation
Authors: Dunstan Piers K. , Bax Nicholas J.
Published: May 2008

Dunstan, P. K., and Bax, N. J. 2008. Management of an invasive marine species: defining and testing the effectiveness of ballast-water management options using management strategy evaluation. – ICES Journal of Marine Science, 65: 841–850. Invasive marine and fresh-water species are being spread around the world in ships' ballast water, damaging industries and natural resources. Management policies are being developed nationally and internationally in response to the threat, but these options are not being rigorously evaluated for their potential to meet management objectives. We used management strategy evaluation (MSE) simulation to compare the performance of different management rules for controlling the spread of an invasive sea star, Asterias amurensis, around the southern coast of Australia. A model incorporating population dynamics, oceanographic patterns, and vessel movement was developed to compare the performance of different ballast-water exchange rules at reducing the likelihood of new populations establishing at locations along the coast over time. Static management rules, where ballast exchange was mandated on all voyages, reduced the median likelihood of new invasions from 0.67 with no ballast control to between 0.36 and 0.42 as distance from the coast was varied. Reducing the volume of high-risk ballast water by 95% did not reduce the likelihood of invasion by 95%, but by an average of 21%. Exchanging ballast farther from the coast did not reduce the likelihood of invasion for any of the static management rules. Feedback management rules using a port monitoring programme to assess the risk of transporting larvae between ports were at least as effective as the static rules, but at a significantly reduced cost for this single-species example. MSE provides a method to compare management options against objectives in this uncertain environment, and can be used to evaluate new and expensive treatment options for their effectiveness and value.
Roadmap to New Virulence Determinants in Pseudomonas syringae: Insights from Comparative Genomics and Genome Organization
Authors: Lindeberg Magdalen , Myers Christopher R. , Collmer Alan , Schneider David J.
Published: May 2008

Systematic comparison of the current repertoire of virulence-associated genes for three Pseudomonas syringae strains with complete genome sequences, P. syringae pv. tomato DC3000, P. syringae pv. phaseolicola 1448A, and P. syringae pv. syringae B728a, is prompted by recent advances in virulence factor identification in P. syringae and other bacteria. Among these are genes linked to epiphytic fitness, plant- and insect-active toxins, secretion pathways, and virulence regulators, all reflected in the recently updated DC3000 genome annotation. Distribution of virulence genes in relation to P. syringae genome organization was analyzed to distinguish patterns of conservation among genomes and association between genes and mobile genetic elements. Variable regions were identified on the basis of deviation in sequence composition and gaps in syntenic alignment among the three genomes. Mapping gene location relative to the genome structure revealed strong segregation of the HrpL regulon with variable genome regions (VR), divergent distribution patterns for toxin genes depending on association with plant or insect pathogenesis, and patterns of distribution for other virulence genes that highlight potential sources of strain-to-strain differences in host interaction. Distribution of VR among other sequenced bacterial genomes was analyzed and future plans for characterization of this potential reservoir of virulence genes are discussed.
Early Progress in Aphid Genomics and Consequences for Plant–Aphid Interactions Studies
Authors: Tagu Denis , Klingler John P. , Moya Andrès , Simon Jean-Christophe
Published: May 2008

Aphids occupy a niche comprising two conceptual realms: a micron-scale feeding site beneath the plant surface, in which a syringe-like appendage mediates chemical exchange with a specific plant cell type; and the larger realm of a metazoan with sensory organs, a nervous system, and behavior, all responsive to the condition of the host plant and the broader environment. The biology that connects these realms is not well understood, but new details are emerging with the help of genomic tools. The power of these tools is set to increase substantially now that the first genome of an aphid is being sequenced and annotated. This has been possible because a community of aphid researchers focused their efforts to develop and share genomic resources through an international consortium. This complete genome sequence, along with other resources, should permit major advances in understanding the complex and peculiar biological traits responsible for aphids' evolutionary success and their damaging effects on agriculture. This review highlights early progress in the application of aphid genomics and identifies key issues of plant–aphid interactions likely to benefit as molecular tools are further developed. Use of this new knowledge could make significant contributions to crop protection against these and other phloem-feeding insects.
Virus-Induced Gene Silencing (VIGS) as a Reverse Genetic Tool to Study Development of Symbiotic Root Nodules
Authors: Constantin G. D. , Grønlund M. , Johansen I. E. , Stougaard J. , Lund O. S.
Published: May 2008

Virus-induced gene silencing (VIGS) can provide a shortcut to plants with altered expression of specific genes. Here, we report that VIGS of the Nodule inception gene (Nin) can alter the nodulation phenotype and Nin gene expression in Pisum sativum. PsNin was chosen as target because of the distinct non-nodulating phenotype of nin mutants in P. sativum, Lotus japonicus, and Medicago truncatula. The vector based on Pea early browning virus (PEBV) was engineered to carry one of three nonoverlapping fragments (PsNinA, PsNinB, and PsNinC) derived from the PsNin cDNA. Vector inoculation was mediated by agroinfiltration and, 2 weeks later, a Rhizobium leguminosarum bv. viceae culture was added in order to induce root nodulation. At this time point, it was estimated that systemic silencing was established because leaves of reference plants inoculated with PEBV carrying a fragment of Phytoene desaturase displayed photo bleaching. Three weeks after Rhizobium spp. application, plants inoculated with a control vector nodulated normally, whereas nodulation was almost eliminated in plants inoculated with a vector carrying PsNinA and PsNinC. For plants inoculated with a vector carrying PsNinB, nodulation was reduced by at least 45%. Down-regulation of PsNin transcripts in plants inoculated with vectors carrying PsNin cDNA fragments was confirmed and these plants displayed a relative increase in the root/shoot ratio, as expected if nitrogen fixation had been impaired.
Tomatinase from Fusarium oxysporum f. sp. lycopersici Is Required for Full Virulence on Tomato Plants
Authors: Pareja-Jaime Yolanda , Roncero M. Isabel G. , Ruiz-Roldán M. Carmen
Published: May 2008

Saponin detoxification enzymes from pathogenic fungi are involved in the infection process of their host plants. Fusarium oxysporum f. sp lycopersici, a tomato pathogen, produces the tomatinase enzyme Tom1, which degrades α-tomatine to less toxic derivates. To study the role of the tom1 gene in the virulence of F. oxysporum, we performed targeted disruption and overexpression of the gene. The infection process of tomato plants inoculated with transformants constitutively producing Tom1 resulted in an increase of symptom development. By contrast, tomato plants infected with the knockout mutants showed a delay in the disease process, indicating that Tom1, although not essential for pathogenicity, is required for the full virulence of F. oxysporum. Total tomatinase activity in the disrupted strains was reduced only 25%, leading to β2-tomatine as the main hydrolysis product of the saponin in vitro. In silico analysis of the F. oxysporum genome revealed the existence of four additional putative tomatinase genes with identities to tomatinases from family 3 of glycosyl hydrolases. These might be responsible for the remaining tomatinase activity in the Δtom1 mutants. Our results indicate that detoxification of α-tomatine in F. oxysporum is carried out by several tomatinase activities, suggesting the importance of these enzymes during the infection process.
Soil Bacteria Confer Plant Salt Tolerance by Tissue-Specific Regulation of the Sodium Transporter HKT1
Authors: Zhang Huiming , Kim Mi-Seong , Sun Yan , Dowd Scot E. , Shi Huazhong , Paré Paul W.
Published: May 2008

Elevated sodium (Na+) decreases plant growth and, thereby, agricultural productivity. The ion transporter high-affinity K+ transporter (HKT)1 controls Na+ import in roots, yet dysfunction or overexpression of HKT1 fails to increase salt tolerance, raising questions as to HKT1's role in regulating Na+ homeostasis. Here, we report that tissue-specific regulation of HKT1 by the soil bacterium Bacillus subtilis GB03 confers salt tolerance in Arabidopsis thaliana. Under salt stress (100 mM NaCl), GB03 concurrently down- and upregulates HKT1 expression in roots and shoots, respectively, resulting in lower Na+ accumulation throughout the plant compared with controls. Consistent with HKT1 participation in GB03-induced salt tolerance, GB03 fails to rescue salt-stressed athkt1 mutants from stunted foliar growth and elevated total Na+ whereas salt-stressed Na+ export mutants sos3 show GB03-induced salt tolerance with enhanced shoot and root growth as well as reduced total Na+. These results demonstrate that tissue-specific regulation of HKT1 is critical for managing Na+ homeostasis in salt-stressed plants, as well as underscore the breadth and sophistication of plant–microbe interactions.
Basic Compatibility of Albugo candida in Arabidopsis thaliana and Brassica juncea Causes Broad-Spectrum Suppression of Innate Immunity
Authors: Cooper A. J. , Latunde-Dada A. O. , Woods-Tör A. , Lynn J. , Lucas J. A. , Crute I. R. , Holub E. B.
Published: May 2008

A biotrophic parasite often depends on an intrinsic ability to suppress host defenses in a manner that will enable it to infect and successfully colonize a susceptible host. If the suppressed defenses otherwise would have been effective against alternative pathogens, it follows that primary infection by the “suppressive” biotroph potentially could enhance susceptibility of the host to secondary infection by avirulent pathogens. This phenomenon previously has been attributed to true fungi such as rust (basidiomycete) and powdery mildew (ascomycete) pathogens. In our study, we observed broad-spectrum suppression of host defense by the oomycete Albugo candida (white blister rust) in the wild crucifer Arabidopsis thaliana and a domesticated relative, Brassica juncea. A. candida subsp. arabidopsis suppressed the “runaway cell death” phenotype of the lesion mimic mutant lsd1 in Arabidopsis thaliana in a sustained manner even after subsequent inoculation with avirulent Hyaloperonospora arabidopsis (Arabidopsis thaliana downy mildew). In sequential inoculation experiments, we show that preinfection by virulent Albugo candida can suppress disease resistance in cotyledons to several downy mildew pathogens, including contrasting examples of genotype resistance to H. arabidopsis in Arabidopsis thaliana that differ in the R protein and modes of defense signaling used to confer the resistance; genotype specific resistance in B. juncea to H. parasitica (Brassica downy mildew; isolates derived from B. juncea); species level (nonhost) resistance in both crucifers to Bremia lactucae (lettuce downy mildew) and an isolate of the H. parasitica race derived from Brassica oleracea; and nonhost resistance in B. juncea to H. arabidopsis. Broad-spectrum powdery mildew resistance conferred by RPW8 also was suppressed in Arabidopsis thaliana to two morphotypes of Erysiphe spp. following pre-infection with A. candida subsp. arabidopsis.
Distinct and Combined Roles of the MAP Kinases of Cochliobolus heterostrophus in Virulence and Stress Responses
Authors: Igbaria Aeid , Lev Sophie , Rose Mark S. , Lee Bee Na , Hadar Ruthi , Degani Ofir , Horwitz Benjamin A.
Published: May 2008

Pathogenicity mitogen-activated protein kinases (MAPKs), related to yeast FUS3/KSS1, are essential for virulence in fungi, including Cochliobolus heterostrophus, a necrotrophic pathogen causing Southern corn leaf blight. We compared the phenotypes of mutants in three MAPK genes: HOG1, MPS1, and CHK1. The chk1 and mps1 mutants show autolytic appearance, light pigmentation, and dramatic reduction in virulence and conidiation. Similarity of mps1 and chk1 mutants is reflected by coregulation by these two MAPKs of several genes. Unlike chk1, mps1 mutants are female-fertile and form normal-looking appressoria. HOG1 mediates resistance to hyperosmotic and, to a lesser extent, oxidative stress, and is required for stress upregulation of glycerol-3-phosphate phosphatase, transaldolase, and a monosaccharide transporter. Hog1, but not Mps1 or Chk1, was rapidly phosphorylated in response to increased osmolarity. The hog1 mutants have smaller appressoria and cause decreased disease symptoms on maize leaves. Surprisingly, loss of MPS1 in a wild-type or hog1 background improved resistance to some stresses. All three MAPKs contribute to the regulation of central developmental functions under normal and stress conditions, and full virulence cannot be achieved without appropriate input from all three pathways.
Expression of Two Functionally Distinct Plant Endo-β-1,4-Glucanases Is Essential for the Compatible Interaction Between Potato Cyst Nematode and Its Hosts
Authors: Karczmarek Aneta , Fudali Sylwia , Lichocka Malgorzata , Sobczak Miroslaw , Kurek Wojciech , Janakowski Slawomir , Roosien Jan , Golinowski Wladyslaw , Bakker Jaap , Goverse Aska , Helder Johannes
Published: May 2008

For the proliferation of their feeding sites (syncytia), the potato cyst nematode Globodera rostochiensis is thought to recruit plant endo-β-1,4-glucanases (EGases, EC. 3.2.1.4). Reverse-transcription polymerase chain reaction experiments on tomato (Solanum lycopersicum) indicated that the expression of two out of the at least eight EGases, namely Sl-cel7 and Sl-cel9C1, is specifically upregulated during syncytium formation. In situ hybridization and immunodetection studies demonstrated that both EGases are specifically expressed inside and adjacent to proliferating syncytia. To assess the importance of Sl-cel7 and Sl-cel9C1 for nematode development, we decided to knock them out individually. Sl-cel9C1 probably is the only class C EGase in tomato, and we were unable to regenerate Sl-cel9C1–silenced plants. Potato (S. tuberosum), a close relative of tomato, harbors at least two class C EGases, and St-cel7-or St-cel9C1–silenced potato plants showed no obvious aberrant phenotype. Infection with potato cyst nematodes resulted in a severe reduction of the number of adult females (up to 60%) and a sharp increase in the fraction of females without eggs (up to 89%). Hence, the recruitment of CEL7, an enzyme that uses xyloglucan and noncrystalline cellulose as natural substrates, and CEL9C1, an enzyme that uses crystalline cellulose, is essential for growth and development of potato cyst nematodes.
NADPH Oxidases Are Involved in Differentiation and Pathogenicity in Botrytis cinerea
Authors: Segmüller Nadja , Kokkelink Leonie , Giesbert Sabine , Odinius Daniela , van Kan Jan , Tudzynski Paul
Published: May 2008

Nicotinamide adenine dinucleotide (NADPH) oxidases have been shown to be involved in various differentiation processes in fungi. We investigated the role of two NADPH oxidases in the necrotrophic phytopathogenic fungus, Botrytis cinerea. The genes bcnoxA and bcnoxB were cloned and characterized; their deduced amino acid sequences show high homology to fungal NADPH oxidases. Analyses of single and double knock-out mutants of both NADPH oxidase genes showed that both bcnoxA and bcnoxB are involved in formation of sclerotia. Both genes have a great impact on pathogenicity: whereas bcnoxB mutants showed a retarded formation of primary lesions, probably due to an impaired formation of penetration structures, bcnoxA mutants were able to penetrate host tissue in the same way as the wild type but were much slower in colonizing the host tissue. Double mutants showed an additive effect: they were aberrant in penetration and colonization of plant tissue and, therefore, almost nonpathogenic. To study the structure of the fungal Nox complex in more detail, bcnoxR (encoding a homolog of the mammalian p67phox, a regulatory subunit of the Nox complex) was functionally characterized. The phenotype of ΔbcnoxR mutants is identical to that of ΔbcnoxAB double mutants, providing evidence that BcnoxR is involved in activation of both Bcnox enzymes.
Structure of the Glucanase Inhibitor Protein (GIP) Family from Phytophthora Species Suggests Coevolution with Plant Endo-β-1,3-Glucanases
Authors: Damasceno Cynthia M. B. , Bishop John G. , Ripoll Daniel R. , Win Joe , Kamoun Sophien , Rose Jocelyn K. C.
Published: May 2008

During invasion of their plant hosts, species of the oomycete genus Phytophthora secrete glucanase inhibitor proteins (GIPs) into the plant apoplast, which bind and inhibit the activity of plant extracellular endo-β-1,3-glucanases (EGases). GIPs show structural homology to the chymotrypsin class of serine proteases (SP) but lack proteolytic activity due to the absence of an intact catalytic triad and, thus, belong to a broader class of proteins called serine protease homologs (SPH). To study the evolutionary relationship between GIPs and functional SP, database searches were used to identify 48 GIP homologs in the P. sojae, P. ramorum, and P. infestans genomes, composing GIPs, SPH, and potentially functional SP. Analyses of P. infestans–inoculated tomato leaves showed that P. infestans GIPs and tomato EGases are present in the apoplast and form stable complexes in planta. Studies of the temporal expression of a four-membered GIP family from P. infestans (PiGIP1 to PiGIP4) further revealed that the genes show distinctly different patterns during an infection timecourse. Codon evolution analyses of GIP homologs identified several positively selected peptide sites and structural modeling revealed them to be in close proximity to rapidly evolving EGase residues, suggesting that the interaction between GIPs and EGases has the hallmarks of a coevolving molecular arms race.
Duplication of Plasmid-Borne Nitrite Reductase Gene nirK in the Wheat-Associated Plant Growth–Promoting Rhizobacterium Azospirillum brasilense Sp245
Authors: Pothier Joël F. , Prigent-Combaret Claire , Haurat Jacqueline , Moënne-Loccoz Yvan , Wisniewski-Dyé Florence
Published: May 2008

In the plant growth–promoting rhizobacterium Azospirillum brasilense Sp245, nitric oxide produced by denitrification could be a signal involved in stimulation of root branching, and the dissimilatory nitrite reductase gene nirK is upregulated on wheat roots. Here, it was found that Sp245 did not contain one copy of nirK but two (named nirK1 and nirK2), localized on two different plasmids, including one plasmid prone to rearrangements. Their deduced protein sequences displayed 99.2% identity but their promoter regions and upstream genetic environment differed. Phylogenetic studies revealed that nirK1 and nirK2 clustered next to most β-proteobacterial sequences rather than in the vicinity of other Azospirillum spp. and most α-proteobacterial sequences, regardless of whether DNA or deduced protein sequences were used. This points to past horizontal gene transfers. Analysis of the number of nonsynonymous and synonymous substitutions per site indicated that nirK has been subjected to neutral selection in bacteria. The use of transcriptional fusions with egfp, encoding an enhanced green fluorescent protein variant, revealed that both nirK1 and nirK2 promoter regions were upregulated in vitro under microaerobiosis or the presence of nitrite as well as on wheat roots. The analysis of nirK1 and nirK2 mutants revealed that the two genes were functional. Overall, results suggest that nirK has been acquired horizontally by A. brasilense Sp245 from a distant relative and underwent subsequent duplication; however, both paralogs remained functional and retained their upregulation by the plant partner.
Molecular Analysis of Lipoxygenases Associated with Nodule Development in Soybean
Authors: Hayashi Satomi , Gresshoff Peter M. , Kinkema Mark
Published: May 2008

We utilized transcriptional profiling to identify genes associated with nodule development in soybean. Many of the candidate genes were predicted to be involved in processes such as defense, metabolism, transcriptional regulation, oxidation, or iron storage. Here, we describe the detailed characterization of one specific class of genes that encode the enzyme lipoxygenase (LOX). The LOX9 and LOX10 genes identified by microarray analysis represent novel soybean LOXs expressed in developing nodules. LOX expression during nodulation was relatively complex, with at least eight different LOX genes expressed in soybean nodules. Histochemical analyses utilizing LOX9 promoter∷β-glucuronidase (GUS) fusion constructs in transgenic soybean hairy roots suggest that this gene is involved in the growth and development of specific cells within the root and nodules. In soybean roots, LOX9 was expressed specifically in the developing phloem. In nodules, the expression of LOX9 was correlated with the development of cells in the vasculature and lenticels. The use of RNAi in transgenic hairy roots reduced LOX expression by approximately 95%. Despite this significant reduction in LOX expression, there was no detectable effect on the development of roots or nodules. Our findings are discussed with respect to the potential function of LOXs in nodulation.
Perceptual switch rates with ambiguous structure-from-motion figures in bipolar disorder
Authors: Krug Kristine , Brunskill Emma , Scarna Antonina , Goodwin Guy M , Parker Andrew J
Published: May 2008

Slowing of the rate at which a rivalrous percept switches from one configuration to another has been suggested as a potential trait marker for bipolar disorder. We measured perceptual alternations for a bistable, rotating, structure-from-motion cylinder in bipolar and control participants. In a control task, binocular depth rendered the direction of cylinder rotation unambiguous to monitor participants' performance and attention during the experimental task. A particular direction of rotation was perceptually stable, on average, for 33.5 s in participants without psychiatric diagnosis. Euthymic, bipolar participants showed a slightly slower rate of switching between the two percepts (percept duration 42.3 s). Under a parametric analysis of the best-fitting model for individual participants, this difference was statistically significant. However, the variability within groups was high, so this difference in average switch rates was not big enough to serve as a trait marker for bipolar disorder. We also found that low-level visual capacities, such as stereo threshold, influence perceptual switch rates. We suggest that there is no single brain location responsible for perceptual switching in all different ambiguous figures and that perceptual switching is generated by the actions of local cortical circuitry.
The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast
Authors: Musso Gabriel , Costanzo Michael , Huangfu ManQin , Smith Andrew M. , Paw Jadine , San Luis Bryan-Joseph , Boone Charles , Giaever Guri , Nislow Corey , Emili Andrew , Zhang Zhaolei
Published: May 2008

Since complete redundancy between extant duplicates (paralogs) is evolutionarily unfavorable, some degree of functional congruency is eventually lost. However, in budding yeast, experimental evidence collected for duplicated metabolic enzymes and in global physical interaction surveys had suggested widespread functional overlap between paralogs. While maintained functional overlap is thought to confer robustness against genetic mutation and facilitate environmental adaptability, it has yet to be determined what properties define paralogs that can compensate for the phenotypic consequence of deleting a sister gene, how extensive this epistasis is, and how adaptable it is toward alternate environmental states. To this end, we have performed a comprehensive experimental analysis of epistasis as indicated by aggravating genetic interactions between paralogs resulting from an ancient whole-genome duplication (WGD) event occurring in the budding yeast Saccharomyces cerevisiae, and thus were able to compare properties of large numbers of epistatic and non-epistatic paralogs with identical evolutionary times since divergence. We found that more than one-third (140) of the 399 examinable WGD paralog pairs were epistatic under standard laboratory conditions and that additional cases of epistasis became obvious only under media conditions designed to induce cellular stress. Despite a significant increase in within-species sequence co-conservation, analysis of protein interactions revealed that paralogs epistatic under standard laboratory conditions were not more functionally overlapping than those non-epistatic. As experimental conditions had an impact on the functional categorization of paralogs deemed epistatic and only a fraction of potential stress conditions have been interrogated here, we hypothesize that many epistatic relationships remain unresolved.
Transcription induces strand-specific mutations at the 5′ end of human genes
Authors: Polak Paz , Arndt Peter F.
Published: May 2008

A regional analysis of nucleotide substitution rates along human genes and their flanking regions allows us to quantify the effect of mutational mechanisms associated with transcription in germ line cells. Our analysis reveals three distinct patterns of substitution rates. First, a sharp decline in the deamination rate of methylated CpG dinucleotides, which is observed in the vicinity of the 5′ end of genes. Second, a strand asymmetry in complementary substitution rates, which extends from the 5′ end to 1 kbp downstream from the 3′ end, associated with transcription-coupled repair. Finally, a localized strand asymmetry, an excess of C→T over G→A substitution in the nontemplate strand confined to the first 1–2 kbp downstream of the 5′ end of genes. We hypothesize that higher exposure of the nontemplate strand near the 5′ end of genes leads to a higher cytosine deamination rate. Up to now, only the somatic hypermutation (SHM) pathway has been known to mediate localized and strand-specific mutagenic processes associated with transcription in mammalia. The mutational patterns in SHM are induced by cytosine deaminase, which just targets single-stranded DNA. This DNA conformation is induced by R-loops, which preferentially occur at the 5′ ends of genes. We predict that R-loops are extensively formed in the beginning of transcribed regions in germ line cells.
Origin of INSL3-mediated testicular descent in therian mammals
Authors: Park Jae-Il , Semyonov Jenia , Chang Chia Lin , Yi Wei , Warren Wesley , Hsu Sheau Yu Teddy
Published: May 2008

Testicular descent is a unique physiological adaptation found in therian mammals allowing optimal spermatogenesis below core body temperature. Recent studies show that INSL3, produced by Leydig cells, and its receptor LGR8 (RXFP2) are essential for mediating the transabdominal phase of testicular descent during early development. However, the origin and genetic basis for this physiological adaptation is not clear. Using syntenic mapping and the functional characterization of contemporary and resurrected relaxin family hormones, we show that derivation of INSL3-mediated testicular descent involved the duplication of an ancestral RLN3-like gene that encodes an indiscriminate ligand for LGR7 (RXFP1) and LGR8. This event was followed by acquisition of the LGR7-selective characteristics by a daughter gene (RLN3) prior to the evolution of the common ancestor of monotremes, marsupials, and placentals. A subsequent mutation of the other daughter gene (INSL3) occurred before the emergence of therian mammals, which then led to the derivation of the reciprocal LGR8-specific characteristics of INSL3. The stepwise evolution of these independent signaling pathways through gene duplication and subsequent divergence is consistent with Darwinian theory of selection and adaptation, and the temporal proximity suggests an association between these genetic events and the concurrent evolution of testicular descent in ancestral therian mammals.
Defensins and the convergent evolution of platypus and reptile venom genes
Authors: Whittington Camilla M. , Papenfuss Anthony T. , Bansal Paramjit , Torres Allan M. , Wong Emily S.W. , Deakin Janine E. , Graves Tina , Alsop Amber , Schatzkamer Kyriena , Kremitzki Colin , Ponting Chris P. , Temple-Smith Peter , Warren Wesley C. , Kuchel Philip W. , Belov Katherine
Published: May 2008

When the platypus (Ornithorhynchus anatinus) was first discovered, it was thought to be a taxidermist’s hoax, as it has a blend of mammalian and reptilian features. It is a most remarkable mammal, not only because it lays eggs but also because it is venomous. Rather than delivering venom through a bite, as do snakes and shrews, male platypuses have venomous spurs on each hind leg. The platypus genome sequence provides a unique opportunity to unravel the evolutionary history of many of these interesting features. While searching the platypus genome for the sequences of antimicrobial defensin genes, we identified three Ornithorhynchus venom defensin-like peptide (OvDLP) genes, which produce the major components of platypus venom. We show that gene duplication and subsequent functional diversification of beta-defensins gave rise to these platypus OvDLPs. The OvDLP genes are located adjacent to the beta-defensins and share similar gene organization and peptide structures. Intriguingly, some species of snakes and lizards also produce venoms containing similar molecules called crotamines and crotamine-like peptides. This led us to trace the evolutionary origins of other components of platypus and reptile venom. Here we show that several venom components have evolved separately in the platypus and reptiles. Convergent evolution has repeatedly selected genes coding for proteins containing specific structural motifs as templates for venom molecules.
Retroposed SNOfall—A mammalian-wide comparison of platypus snoRNAs
Authors: Schmitz Jürgen , Zemann Anja , Churakov Gennady , Kuhl Heiner , Grützner Frank , Reinhardt Richard , Brosius Jürgen
Published: May 2008

Diversification of mammalian species began more than 160 million years ago when the egg-laying monotremes diverged from live bearing mammals. The duck-billed platypus (Ornithorhynchus anatinus) and echidnas are the only potential contemporary witnesses of this period and, thereby, provide a unique insight into mammalian genome evolution. It has become clear that small RNAs are major regulatory agents in eukaryotic cells, and the significant role of non-protein-coding (npc) RNAs in transcription, processing, and translation is now well accepted. Here we show that the platypus genome contains more than 200 small nucleolar (sno) RNAs among hundreds of other diverse npcRNAs. Their comparison among key mammalian groups and other vertebrates enabled us to reconstruct a complete temporal pathway of acquisition and loss of these snoRNAs. In platypus we found cis- and trans-duplication distribution patterns for snoRNAs, which have not been described in any other vertebrates but are known to occur in nematodes. An exciting novelty in platypus is a snoRNA-derived retroposon (termed snoRTE) that facilitates a very effective dispersal of an H/ACA snoRNA via RTE-mediated retroposition. From more than 40,000 detected full-length and truncated genomic copies of this snoRTE, at least 21 are processed into mature snoRNAs. High-copy retroposition via multiple host gene-promoted transcription units is a novel pathway for combining housekeeping function and SINE-like dispersal and reveals a new dimension in the evolution of novel snoRNA function.
Salamander evolution across a latitudinal cline in gape‐limited predation risk
Authors: Urban Mark C.
Published: May 2008

General predictions of community dynamics require that insights derived from local habitats can be scaled up to explain phenomena across geographic scales. Across these larger spatial extents, adaptation can play an increasing role in determining the outcome of species interactions. If local adaptation is common, then our ability to generalize measures of species interaction strength across communities will be limited without an additional understanding of the genetic variation underlying interaction traits. In the context of predator–prey interactions, prey individuals commonly are expected to reduce risky foraging behaviors and subsequent growth under predation threat. However, rapid growth into a large body size can defend against gape‐limited predators, creating a tradeoff between increased predation risk due to elevated foraging activity and decreased predation risk due to large size. Here I combine field observations, natural selection experiments, and common garden assays to understand potential adaptations of spotted salamanderAmbystoma maculatumlarvae to gape‐limited and gape‐unconstrained predators. Field observations and natural selection trials suggested antagonistic selection on prey body size among ponds dominated by gape‐limited predator salamandersA. opacumand gape‐unconstrained beetle larvaeDytiscus. In common garden experiments, prey from sites with high gape‐limited predation risk grew larger than those from other sites, suggesting the evolution of rapid growth into a prey size refuge. Larvae from all sites grew to a large size when exposed to the gape‐limitedN. viridescenspredator's kairomones. Hence, induced rapid growth into a size refuge may be an adaptive response to gape‐limited predation risk. Results point to an important role for cross‐community generalizations based on functional classifications of predators by their gape constraints and inter‐site genetic variation in prey growth rates and behaviors.
Coexistence of succulent tree aloes: partitioning of bird pollinators by floral traits and flowering phenology
Authors: Botes Christo , Johnson Steven D. , Cowling Richard M.
Published: May 2008

Coexistence among species that lack genetic barriers to hybridization usually depends on pre‐mating isolating barriers. It has been difficult to explain coexistence among African Aloe species because they readily hybridize, often flower simultaneously and are mostly bird‐pollinated. Here we show that co‐flowering aloes in a succulent thicket community in South Africa partition the fauna of flower‐visiting birds. Aloe species with small amounts of concentrated nectar in long corolla tubes were pollinated primarily by long‐billed sunbirds. These species co‐flowered with species with large amounts of dilute nectar in short corolla tubes which were pollinated primarily by short‐billed, generalist nectarivores. Aloe species which share pollinators tend to have divergent flowering times and differences in pollen placement on birds. Without these isolating barriers, genetic dissolution of sympatric Aloe species would be likely.
Links between floral morphology and floral visitors along an elevational gradient in aPenstemonhybrid zone
Authors: Kimball Sarah
Published: May 2008

Hybrid zones can form when two species of plants hybridize along an environmental gradient. Changes in floral morphology across such a gradient and the degree of reproductive isolation can be influenced by pollinator behavior, but little is known about pollinator visitation to hybridizing species that receive visits from a diverse array of animals. I studied floral morphology, nectar rewards and pollinator visitation forPenstemon newberryi,P. davidsoniiand their hybrids along an elevational gradient in the Sierra Nevada of California. Sixty‐two floral visitor species were observed visiting plants, making this system highly generalized compared to previous studies of visitation in hybrid zones. Morphological measurements were used to construct a plant hybrid index and examine the correlation with elevation and with floral visitors. Using observations of floral visitors along the gradient, I performed an ordination to determine whether the pollinator community changed along with plant morphology. Plants varied in a clinal pattern along the elevational gradient. The visitor community varied incrementally with altitude, although visitors toPenstemon davidsoniiwere separated from those toP. newberryiand hybrids along the main ordination axis. Hummingbirds were only found at low and middle elevations, and small halictid bees were relatively more abundant at high elevations. Although there is some potential for ecological isolation in the pollinator community, 11 common pollinator species visited both parent species and could be contributing to hybrid formation.
Effects of diversity on diversity: consequences of competition and facilitation
Authors: Vellend Mark
Published: May 2008

Diversity in one group of species or genotypes is often correlated with diversity in a second group – prominent examples including native vs exotic species, and genetic diversity in a focal species vs species diversity in the rest of the community. I used simulation models to investigate the roles of competition and facilitation among species or genotypes in creating diversity–diversity relationships, with a focus on facilitation, which has received little theoretical attention. When competitive interactions dominate, increasing diversity in one group reduces diversity in the second group via filling of available niche space. Facilitation can create positive diversity–diversity relationships via a sampling effect, whereby a strong facilitator of the second group is more likely to be present as diversity increases in the first group, and also via one group acting as a source of biotic heterogeneity (i.e. diversifying selection) on the second group. However, the biotic heterogeneity effect is expected only under restricted conditions – with asymmetric facilitation, only during a transient period, or only over a small range of species diversity levels – and therefore seems unlikely to operate within trophic levels in natural communities. More generally, the simultaneous operation of competition and facilitation results in several different diversity–diversity relationships and underlying mechanisms. The results clarify the potential roles of positive and negative interactions in creating diversity–diversity relationships, and in determining the outcome of community dynamics in general. This study also highlights some important difficulties in incorporating facilitation into ecological theory for communities with many species.
Influential factors for natal dispersal in an avian island metapopulation
Authors: Wilson Amy G. , Arcese Peter
Published: May 2008

Dispersal is a key parameter in evolutionary, demographic and conservation theory, but the factors influencing dispersal between populations are rarely known, and the contribution of immigrants to population stability remains uncertain. Using dispersal data from nine island populations of song sparrows, we show that female and male immigrants responded differently to population structure: in females, immigration varied with adult sex ratio; whereas immigration by males was more influenced by population density. These patterns are consistent with the hypothesis that intra‐sexual competition for breeding resources influenced recruitment patterns. Immigrants often constituted a substantial fraction of local population size, and in six cases immigration by females prevented the extirpation of that sex from the island. Breeding vacancies and extirpations may have been more likely in females because their apparent survival was lower than in males. Local recruitment and immigration varied markedly among islands, perhaps as consequence of island size and isolation. Overall, our results suggest that immigration varied with local demography in a sex‐specific way, stabilized population numbers and reduced extinction rates in the smallest populations.
Good vibrations? Structure and function of the cloacal tip of male Australian Maluridae
Authors: Rowe Melissah , Bakst Murray R. , Pruett‐Jones Stephen
Published: May 2008

When females mate multiply, sperm competition can generate strong selection for traits that provide males with a fertilisation advantage. This study examined the cloacal tip, a unique morphological structure of males that appears to be associated with sperm competition in Australian Maluridae. Species in this group appear to experience a range of sperm competition intensities and exhibit a diversity of associated reproductive adaptations and behaviours. A prominent cloacal tip was present in the striated grasswrenAmytornis striatus striatus, and superbMalurus cyaneus cyanochlamys, splendidM. splendens melanotus, red‐backedM. melanocephalusand white‐winged fairy‐wrensM. leucopterus leuconotus, while variegatedM. lamberti assimilisand blue‐breastedM. pulcherrimusfairy‐wrens possessed a rudimentary tip, and the southern emu‐wrenStipiturus malachurus malachuruslacked a tip. The tip was a muscular hydrostatic appendage of the cloacal protuberance comprised of longitudinal striated muscle, a two‐dimensional matrix of connective tissue and a keratinised epithelium. After controlling for phylogenetic relationships, cloacal tip length was positively related to combined testes mass but not body mass. Therefore, species inferred to experience more intense sperm competition exhibited a longer cloacal tip. We discuss the potential function of the cloacal tip and suggest that it may increase a male's likelihood of paternity success and represents a novel adaptation to sperm competition.
Oxidative stress causes telomere damage in Fanconi anaemia cells – a possible predisposition for malignant transformation
Authors: Uziel Orit , Reshef Hagai , Ravid Amiram , Fabian Ina , Halperin Drora , Ram Ron , Bakhanashvili Mary , Nordenberg Jardena , Lahav Meir
Published: May 2008

Fanconi anaemia (FA) is an autosomal recessive and X‐linked disease characterized by severe genetic instability and increased incidence of cancer. One explanation for this instability may be the cellular hypersensitivity to oxidative stress leading to chromosomal breaks. This study explored the possible oxidative damage to telomeres of FA lymphocyte cell line, HSC536/N, and its possible effect on telomere function. We postulated that combination of oxidative damage with overexpression of telomerase may provide a possible model for malignant transformation in FA. The cells were grown in the presence of telomerase inhibitor and exposed for 1 month to H2O2 combined with various antioxidants. This exposure caused shortening of telomere length and damage to the telomere single stranded overhang, which was prevented by several oxidants. This shortening was associated with development of severe telomere dysfunction. Control cells did not exhibit this sensitivity to H2O2. Telomere dysfunction did not evoke damage response in FA cells, in contrast to normal P53 upregulation in control cells. Reconstitution of telomerase activity protected FA telomeres from further oxidative damage. These results suggest a scenario in which oxidative stress causes telomere shortening and ensuing telomere dysfunction may form the basis for malignant transformation in FA cells. Upregulation of telomerase activity in sporadic FA cells may perpetuate that process, thus explaining the malignant character of FA cells in vivo.
The combination of cyclophosphamide and human T cells genetically engineered to target CD19 can eradicate established B‐cell lymphoma
Authors: Cheadle Eleanor J , Gilham David E , Hawkins Robert E
Published: May 2008

T cells genetically engineered to express tumour‐targeting receptors are attractive anti‐cancer therapeutic agents. Human T cells engrafted with a chimeric receptor specific for the B‐cell lymphoma antigen CD19 fused to the CD3ζ receptor (aCD19z) are functional in vitro. Current successful clinical protocols targeting melanoma use pre‐conditioning chemotherapy in combination with T cells. This study demonstrated that interleukin‐2 expanded aCD19z T cells combined with cyclophosphamide effectively treated five‐day established Raji B‐cell lymphoma in an immunocompromised model system with 50% of mice surviving >100 days. This observation strongly supports the combination of antibody targeted T cells with chemotherapy as a novel approach for the therapy of CD19+ B‐cell malignancies.
Combination of the anti‐CD30‐auristatin‐E antibody‐drug conjugate (SGN‐35) with chemotherapy improves antitumour activity in Hodgkin lymphoma
Authors: Oflazoglu Ezogelin , Kissler Kim M. , Sievers Eric L. , Grewal Iqbal S. , Gerber Hans‐Peter
Published: May 2008

The antibody‐drug conjugate (ADC) cAC10‐vcMMAE consists of the tubulin inhibitor monomethyl auristatin E (MMAE) conjugated to the chimeric anti‐CD30 monoclonal antibody cAC10. This ADC potently interferes with the growth of CD30‐positive haematological tumours, including Hodgkin lymphoma (HL) and anaplastic large‐cell lymphoma. This study found improved antitumour activity in a preclinical model of HL when SGN‐35 was combined with chemotherapeutic regimens such as ABVD (doxorubicin, bleomycin, vinblastine and dacarbazine) or gemcitabine. Improved efficacy was also observed in high tumour burden models, indicating that combining ADCs with chemotherapeutic agents may be advantageous for the treatment of patients with relapsed or refractory HL.