bluuebunny/crossref_metadata_2025 huggingface dataset:
Geographic variation in seed mass within and among nine species of Pedicularis (Orobanchaceae): effects of elevation, plant size and seed number per fruit
Authors: Guo Hui , Mazer Susan J. , Du Guozhen
Published: July 2010

1. We examined geographic variation in mean individual seed mass (MISM) among 38 populations within and across nine Pedicularis species in the eastern Tibetan Plateau, measuring the effects of one extrinsic factor (elevation) and two intrinsic factors (plant size and mean seed number per fruit).

2. Across all populations, elevation is negatively correlated with MISM; within eight of nine species, this pattern is also observed among populations. This relationship, however, is not significant when controlling for variation in plant size or seeds per fruit. High‐elevation populations produce smaller plants with more seeds per fruit than low‐elevation populations; controlling for these variables eliminates the negative correlation between elevation and MISM.

3. Across all populations, the predicted trade‐off between MISM and seeds per fruit is consistently strong, with or without controlling for the effects of plant size. By contrast, the trade‐off between MISM and total seasonal fecundity can be detected only when controlling for plant size.

4. Independent of plant size, populations that produce small seeds do not support individuals with particularly low reproductive yield (fecundity × MISM). Accordingly, high‐elevation populations exhibit neither lower reproductive yield nor smaller seeds than expected given their lower biomass.

5. Synthesis. In Pedicularis, elevation, plant size and seeds per fruit are all correlated with MISM among populations across species. Elevation is less important, however, than intrinsic factors in determining the MISM of a population; the effect of elevation on MISM disappears when the effects of intrinsic factors are controlled statistically. The observed decline in MISM with increasing elevation is therefore partly mediated by the decline in plant size and partly by an increase in mean seed number per fruit with elevation. Altitudinal variation in MISM across populations or species has been described before, but this is the first study to control for the effect of intrinsic factors simultaneously. This result calls into question the conclusions of studies that have detected geographic variation in MISM without controlling for variation in intrinsic factors.
Ultramafic soils and species sorting in the flora of New Caledonia
Authors: Pillon Yohan , Munzinger Jérôme , Amir Hamid , Lebrun Michel
Published: July 2010

1. Island floras are generally characterized by disharmony due to uneven representations of plant groups. This has usually been explained by the unequal capacity of plants to disperse and colonize islands, but it has been suggested that the ecology of the recipient islands may also be important.

2. We investigated the phylogenetic structure of the flora of New Caledonia, a biodiversity hotspot in the South‐West Pacific, to examine the phylogenetic pattern of a disharmonic flora and to test two competing hypotheses: disharmony due to uneven dispersability versus disharmony due to uneven ability to adapt to the ultramafic soils that are widespread on the archipelago and constrain plant growth.

3. Dispersal did not seem to be a significant factor as plant families with low levels of endemism and thus high effective dispersal capacities tended to be under‐represented.

4. We identified several clusters of over‐represented families, such as the COM clade (Celastrales, Oxalidales and Malpighiales), in which nickel hyperaccumulation (a syndrome associated with ultramafic soils) was particularly common. We indeed found a positive association between hyperaccumulation and over‐representation. Therefore, ultramafic soils may have been a major force for species sorting in the flora of New Caledonia.

5. Because we think that most colonizers were naïve to ultramafic soils before they reached the archipelago, the over‐represented groups in New Caledonia may have possessed an exaptation to ultramafic soils, which has facilitated their settlement and diversification.

6. Synthesis. This study supports that beyond dispersal, ecology is an important factor in determining the success of different plant groups to colonize an island. In the case of New Caledonia, exaptation to ultramafic soils is likely a primary cause of ecological filtering.
Can optimal defence theory be used to predict the distribution of plant chemical defences?
Authors: McCall Andrew C. , Fordyce James A.
Published: July 2010

1. The optimal defence theory (ODT) of chemical defence provides a predictive framework for the distribution of anti‐herbivore defences in plants. One of its predictions is that chemical defences will be allocated within a plant as a function of tissue value, where value is correlated with the cost of having that tissue removed. While many studies have examined intra‐plant variation in defence chemistry, these results have rarely been compiled quantitatively to assess whether defence allocation is consistent with the prediction of ODT that more valuable tissues should be more defended than less valuable tissues.

2. We performed a formal meta‐analysis of published and unpublished studies to examine the predictive utility of ODT. Specifically, we examined whether defence chemicals occur at higher concentrations in flowers versus leaves and in younger leaves compared to older leaves, under the assumption that younger leaves are more valuable than older leaves. We also examined whether the expansion status of younger leaves, nodal position of the leaves, growing conditions and chemical class of defence compounds affected the mean effect sizes.

3. We found that tissues with higher assumed value had significantly higher concentrations of defence chemicals than tissues with lower value. In particular, we found that younger leaves had higher concentrations of defence chemicals than older leaves, consistent with the predictions of ODT. The magnitude of this difference was higher in the younger leaf/older leaf comparison than in the flower/leaf comparison, with no evidence that flowers were more defended than leaves. The overall results were not affected by chemical class, young leaf expansion status, growing conditions or leaf position on the plant.

4. Synthesis. We found general agreement between the predictions of ODT and the intraplant distribution of chemical defence and conclude it is a useful model. The effect size varied depending on the tissue compared. Explicit measures of tissue value, in particular as it relates to relative fitness, are required to further validate the predictive utility and general applicability of ODT.
Ant‐mediated seed dispersal does not facilitate niche expansion
Authors: Warren Robert J. , Giladi Itamar , Bradford Mark A.
Published: July 2010

1. Whereas classic niche theory is based on the contraction of the niche via negative interactions, facilitative niche theory suggests that mutualisms can expand the niche via positive interactions. Specifically, animal‐mediated seed dispersal can expand the utilization of physical space by plants and allow greater access to resources and other environmental requirements. Ant‐mediated dispersal of plant propagules (myrmecochory) is a common mutualism throughout the world, particularly in the deciduous forests of the eastern United States where this research is conducted.

2. We examine two facets of niche expansion via ant‐mediated seed dispersal: (1) increased utilization of resources along resource gradients and (2) escape from unfavourable density‐dependent conditions.

3. We test these assumptions by introducing Hexastylis arifolia seeds in cafeteria‐style bait stations along abiotic gradients (moisture, temperature, light) for removal by key seed dispersers from the ant genus Aphaenogaster. We also examine plant aggregation along the same gradients.

4. Ant‐mediated dispersal services decrease significantly with increasing soil moisture and ultimately fail at levels that are demonstratively within the plant’s niche optima; further, the decline in dispersal services is correlated with increasing plant aggregation, suggesting that enemy escape also falters at relatively high levels of soil moisture.

5. Synthesis. Facilitated propagule dispersal fails to expand the Hexastylis arifolia niche in either enhanced resource utilization or decreased density dependence as the niche requirements for the ant disperser are nested within those for the plant. The strength of this interaction varies across space and time, and in doing so may undermine attempts to predict future distributions. Further, given that myrmecochores are typically poor dispersers, the incomplete niche overlap between the plant and its facilitator makes this plant guild particularly susceptible to climatic change if each participant responds individually to shifting environmental conditions.
Plant–soil feedback: experimental approaches, statistical analyses and ecological interpretations
Authors: Pernilla Brinkman E. , Van der Putten Wim H. , Bakker Evert‐Jan , Verhoeven Koen J.F.
Published: July 2010

1. Feedback between plants and soil organisms has become widely recognized as a driving force of community composition and ecosystem functioning. However, there is little uniformity in quantification and analysis of plant–soil feedback effects. Meta‐analysis suggested that the various experimental methods tend to result in different feedback values. Yet, a direct comparison of the different experimental approaches and their statistical analyses is lacking.

2. We used currently applied methods to calculate plant–soil feedback value ranges and compared their statistical analyses to those based on actual biomass data. Then, we re‐analysed a case study to compare plant–soil feedback values obtained under the same environmental conditions, but using different experimental approaches: soil sterilization, addition of soil inoculum, and soil conditioning by ‘own’ vs. ‘foreign’ plant species.

3. Different measures to calculate plant–soil feedback values were more variable in positive than in negative feedback values. Analysis of calculated feedback values that are based on treatment averages can lead to a serious inflation of type I errors.

4. In our case study, both the strength and the direction of the feedback effects depended on the experimental approach that was chosen, leading to diverging conclusions on whether feedback to a certain soil was positive or negative. Soil sterilization and addition of soil organisms yielded larger feedback than comparison of own and foreign soil.

5. Synthesis. The ecological interpretation of plant–soil feedback effects strongly depends on the experimental procedure. When the research question focuses on the strength and the sign of plant–soil feedback, soil sterilization (presumed that the side effect of increased nutrient availability can be controlled) or addition of soil inoculum is to be preferred. When the research question concerns the specificity of soil feedback effects, plant performance can be better compared between own and foreign soil. We recommend that when using calculated feedback values, the original data need to be presented as well in order to trace the cause of the effect.
Complex responses to climate drivers in onset of spring flowering across a semi‐arid elevation gradient
Authors: Crimmins Theresa M. , Crimmins Michael A. , David Bertelsen C.
Published: July 2010

1. Many studies have documented advancement in spring plant phenology; however, studies in dry climates, where water, rather than temperature, is the limiting factor, are rare. To better understand how plants of a water‐limited environment may respond to predicted changes in climate, we used a species‐rich 20‐year data set collected in a semi‐arid ecosystem to determine species’ relationships with precipitation and temperature for seasons coincident with and previous to flowering. Our data were collected across a 1200‐m elevation gradient, allowing us to explore the consistency in relationships with climatic variables from desert scrub to pine forest. A second objective was to document evidence of changes in the onset of spring flowering over this 20‐year period.

2. Onset of spring flowering for species at the lowest elevations was most commonly driven by temperature and precipitation conditions of the previous autumn. In contrast, onset of spring flowering for species in high‐elevation communities was more often associated with spring temperatures, a pattern consistent with communities of higher latitudes. Despite these coarse patterns, species’ relationships to climate variables were highly variable and individualistic.

3. Approximately 10% of species showed a significant trend in changes in first flowering date over the period 1984–2003; most trends were in the direction of later onset. The decrease in autumn precipitation observed over the study period appears to explain the delay in onset observed for many of the species across the elevation gradient. Other species’ delays in spring flowering appear to be related to the slight decrease in spring temperature observed over the study period.

4. Synthesis. The south‐western USA is expected to become warmer and drier. Climate relationships documented in this study suggest divergent, individualistic changes in the onset of spring flowering. Low‐elevation plants may exhibit delayed spring flowering due to changes in the timing or amount of precipitation or insufficient chilling. High‐elevation species may show advancement in spring flowering due to warming temperatures. The highly individualistic responses to climate change may result in significant changes in the diversity, composition and abundance of plants in flower. Variable changes in phenology such as these have major implications for species population dynamics and ecosystem functioning.
Factors influencing inappropriate use of ED visits among type 2 diabetics in an evidence‐based management programme
Authors: Chiou Shang‐Jyh , Campbell Claudia , Myers Leann , Culbertson Richard , Horswell Ronald
Published: July 2010

Object  This study analyses inappropriate use of emergency department (ED) services among type 2 diabetics under an evidence‐based management programme.

Methods  Using 1999‐2006 databases of Louisiana Health Care Services Division (HCSD) eight public hospitals ED visits among the uninsured and other patients in Louisiana, we termed urgent ED visits appropriate and less‐urgent visits inappropriate. Eliminating weekend ED visits, 17 458 urgent and 22 395 less‐urgent visits by 8596 patients were analysed, using generalized estimating equation methods.

Results  Caucasians were 0.82 times (95% CI: 0.751–0.889) less likely to use the ED inappropriately compared with African Americans. Patients with commercial insurance, Medicaid and Medicare used the ED more inappropriately than uninsured, with odds ratios of 1.28, 1.32 and 1.28, respectively. Patients hospitalized the prior year were 0.84 times (95% CI: 1.08–1.31) less likely for inappropriate. Patients in larger hospitals used the ED more inappropriately, with an odds ratio of 1.44 (95% CI: 1.32–1.56).

Conclusions  The study suggests that inappropriate use of the ED among diabetic patients in an evidence‐based management programme is more likely to occur among African American, patients with insurance coverage and those seeking care in larger hospitals. Reinforcing the regular use of clinic services for diabetes management, providing clinic access in off‐hours, and engaging the health plans in providing incentives for more appropriate use of the ED might reduce inappropriate ED visits. Notably, uninsured patients with diabetes from HCSD were more efficient users of the ED.
A review of cost‐effectiveness, cost‐containment and economics curricula in graduate medical education
Authors: Varkey Prathibha , Murad Mohammad H. , Braun Chad , Grall Kristi J.H. , Saoji Vivek
Published: July 2010

Objective  Numerous studies performed over the last 30 years suggest that doctors have poor knowledge of the costs of medical care. In most graduate medical education programmes, trainees do not receive formal training in cost‐effective medical practice.

Methods  Comprehensive literature search of electronic bibliographic databases for articles that describe health economics, cost‐containment and cost‐effectiveness curricula in graduate medical education. Critical appraisal of the literature and qualitative description is presented. Heterogeneity of curricula precluded quantitative summary of data.

Results  We identified 40 articles that met the inclusion criteria for this review. Internal medicine residents were the targeted learners in 27 studies (68%); Family Medicine and Surgery residents were each targeted in five studies (13%); Rehabilitation, Paediatrics and Emergency Medicine residents were each targeted in one study. In general, the methodological quality of the included studies was poor to moderate and mostly targeted knowledge of health economics or cost‐containment as opposed to targeting cost‐effectiveness. In terms of describing the standard curricular components, studies sufficiently described the different educational strategies (e.g. didactics, interactive, experiential, self‐directed) and the component of learner assessment, but lacked the description of other elements such as needs assessment and curriculum evaluation.

Conclusion  Cost‐effectiveness curricula in graduate medical education are lacking and clearly needed.
Acute myocardial infarction – from territory to definitive treatment in an Italian province
Authors: Giuliani Enrico , Lazzerotti Sara , Fantini Giuseppe , Guerri Elisa , Serantoni Carlo , Modena Maria Grazia , Barbieri Alberto
Published: July 2010

Rationale, aims and objectives  Early reperfusion is the key to therapeutic success in acute myocardial infarction (AMI). The duration of the process is influenced by various factors which in most of the cases are not easily modifiable. The aim of this study is to analyse AMI treatment process duration to identify determining factors. The objective is to better exploit time intervals imposed by spatial distance from the hospital.

Method  One‐year data regarding acute coronary syndromes with elevated ST segment for patients presenting to Policlinico teaching hospital (Modena, Italy) have been studied. Patients were divided into two groups for hospital access: A – ambulance access to Policlinico emergency room (ER); B – self‐referral to ER.

Results  A total of 141 patients have undergone percutaneous transluminal coronary angioplasty for AMI at Policlinico, 106 males, 35 females (58.1% males in group A, 82.7% in B, P 0.002), with an average age of 66.09 ± 14.30 years in group A and 60.90 ± 13.47 in B (P 0.047). Mean pre‐hospital time for group A was 122.54 ± 130.69 minutes and B 171.49 ± 353.60 (P 0.25), mean hospital time in group A was 196.03 ± 67.66 and B 255.14 ± 113.16 (P < 0.001), mean total time in group A was 318.56 ± 146.91 and B 426.63 ± 382.01 (P 0.02).

Discussion  Data show that group B suffered on average a 108‐minute delay from symptoms insurgence to definitive treatment. The duration of hospital time plays more important role in this finding than distance from the medical facility. In fact, on the ambulance a medical crew starts the diagnostic and therapeutic process relieving ER from initial evaluation.
Clinical effectiveness in cardiovascular trials in relation to the importance to the patient of the end‐points measured
Authors: Bowater Russell J. , Lilford Richard J.
Published: July 2010

Background  In order to increase the statistical power of a trial design, it is common practice for trialists to place a strong emphasis on end‐points other than mortality. To assess the validity of this practice, the aim of this study was to investigate the relationship between the effectiveness of cardiovascular interventions in clinical trials and the importance to the patient of the end‐point used to measure this effectiveness.

Methods  A reanalysis of a database of cardiovascular trials used in an earlier study. This database consists of all randomized controlled trials published in six leading journals for cardiovascular research between January 2002 and June 2003 that involve the exposure of humans to any therapeutic or primary preventive intervention for cardiovascular disease and report at least one composite end‐point.

Results  On the basis of analysing the study data using a statistical modelling approach, the best estimate of the percentage of trials that have a true (not estimated) relative risk of less than 0.8 for the end‐point of moderate outcome, major outcome and death are 63%, 39% and 0% respectively, and the upper 95% confidence limits on these three percentages are 73%, 43% and 15% respectively.

Conclusions  The proportion of interventions tested in the cardiovascular trials considered in this study that have a substantial beneficial effect relative to the control decreases as the end‐point used to measure this effect becomes more important to the patient, that is, as the end‐point severity increases from minor outcome to major outcome to death. Also, the analysis presented in this study strongly suggests that most of these interventions are likely to have close to no genuine effect on mortality relative to the control. Overall, this study substantially strengthens the empirical basis for the belief that the actions of trialists in choosing to study and heavily emphasize end‐points other than mortality in cardiovascular trials and in particular end‐points that are of only moderate or major importance to patients, may mislead practitioners and policy‐makers about the overall effectiveness of the intervention concerned.
Blunting Occam's razor: aligning medical education with studies of complexity
Authors: Bleakley Alan
Published: July 2010

Clinical effectiveness and efficiency in medicine for patient benefit should be grounded in the quality of medical education. In turn, the quality of medical education should be informed by contemporary learning theory that offers high explanatory, exploratory and predictive power. Multiple team‐based health care interventions and associated policy are now routinely explored and explained through complexity theory. Yet medical education – how medical students learn to become doctors and how doctors learn to become clinical specialists or primary care generalists – continues to refuse contemporary, work‐based social learning theories that have deep resonance with models of complexity. This can be explained ideologically, where medicine is grounded in a tradition of heroic individualism and knowledge is treated as private capital. In contrast, social learning theories resonating with complexity theory emphasize adaptation through collaboration, where knowledge is commonly owned. The new era of clinical teamwork demands, however, that we challenge the tradition of autonomy, bringing social learning theories in from the cold, to reveal their affinities with complexity science and demonstrate their powers of illumination. Social learning theories informed by complexity science can act as a democratizing force in medical education, helping practitioners to work more effectively in non‐linear, complex, dynamic systems through inter‐professionalism, shared tolerance of ambiguity and distributed cognition. Taking complexity science seriously and applying its insights demands a shift in cultural mindset in medical education. Inevitably, patterns of resistance will arise to frustrate such potential innovation.
‘If things were simple . . .’: complexity in education
Authors: Davis Brent , Sumara Dennis
Published: July 2010

Rationale, aims and objectives In this speculative essay, we explore some of the implications and possibilities of complexity thinking for formal education.

Methods We begin by developing the working definition that complexity research is the study of learning systems. Drawing on hard (rigorously empirical) complexity research, we critique some of the untenable assumptions and constructs that are typically used to frame those social enterprises that are attentive to adaptive, learning forms – including education, social work and health care. Looking to soft (holistic and more action‐oriented) complexity research, we review some of the insights and advice that have arisen among educational researchers. This part of the discussion is framed by a brief description of an ongoing study of teachers' disciplinary knowledge of mathematics – specifically how complexity theory compels and enables us to grapple with the unique qualities of our ‘object’ of study, its emergence, its relationship to student understanding, and how it is implicated in such grander systems as culture and global ecology.

Conclusions We conclude by arguing that complexity theory might be properly construed as a theory of education, in contrast to the many theories that have been imported into and imposed on discussions of education over the past few centuries.
Complexity and health professions education: a basic glossary
Authors: Mennin Stewart
Published: July 2010

Rationale and aims The study of health professions education in the context of complexity science and complex adaptive systems involves different concepts and terminology that are likely to be unfamiliar to many health professions educators. A list of selected key terms and definitions from the literature of complexity science is provided to assist readers to navigate familiar territory from a different perspective.

Terms and concepts include agent, attractor, bifurcation, chaos, co‐evolution, collective variable, complex adaptive systems, complexity science, deterministic systems, dynamical system, edge of chaos, emergence, equilibrium, far from equilibrium, fuzzy boundaries, linear system, non‐linear system, random, self‐organization and self‐similarity.
High‐resolution cryo‐SEM allows direct identification of F‐actin at the inner nuclear membrane of Xenopus oocytes by virtue of its structural features
Authors: WALTHER P.
Published: July 2010

The nuclear envelope of Xenopus laevis stage VI oocytes was studied in a high‐resolution field emission cryo‐scanning electron microscope to compare the level of structural preservation obtainable by different procedures of specimen preparation. All approaches generally allowed frequent detection of long filaments of about 10 nm in diameter that were attached to the nuclear envelope's inner membrane facing the nuclear interior. Structural details of these 10‐nm filaments, however, could not be unveiled by standard procedures of specimen preparation and analysis, including critical point drying and imaging at room temperature. In contrast, after freeze‐drying and imaging at −100°C, the 10‐nm filament type was found to be composed of distinct globular subunits of approximately 5 nm in diameter that were arranged in a helical manner with right‐handed periodicity. Stereoscopic images showed that some of these filaments were lying directly on the membrane whereas others appeared to hover at a certain distance above the nuclear envelope. The appearance of these filaments was highly similar to that of in vitro polymerized F‐actin analysed in parallel, and closely resembled the structural characteristics of F‐actin filaments described earlier. By virtue of their structural features we therefore conclude that these filaments at the nuclear periphery represent F‐actin. The high level of structural resolution obtainable by field emission cryo‐SEM illustrates the potential of this method for studying details of biological structures in a subcellular context.
A new pathway for the synthesis of α‐ribazole‐phosphate in Listeria innocua
Authors: Gray Michael J. , Escalante‐Semerena Jorge C.
Published: July 2010

The genomes of Listeria spp. encode all but one of 25 enzymes required for the biosynthesis of adenosylcobalamin (AdoCbl; coenzyme B12). Notably, all Listeria genomes lack CobT, the nicotinamide mononucleotide:5,6‐dimethylbenzimidazole (DMB) phosphoribosyltransferase (EC 2.4.2.21) enzyme that synthesizes the unique α‐linked nucleotide N1‐(5‐phospho‐α‐d‐ribosyl)‐DMB (α‐ribazole‐5′‐P, α‐RP), a precursor of AdoCbl. We have uncovered a new pathway for the synthesis of α‐RP in Listeria innocua that circumvents the lack of CobT. The cblT and cblS genes (locus tags lin1153 and lin1110) of L. innocua encode an α‐ribazole (α‐R) transporter and an α‐R kinase respectively. Results from in vivo experiments indicate that L. innocua depends on CblT and CblS activities to salvage exogenous α‐R, allowing conversion of the incomplete corrinoid cobinamide (Cbi) into AdoCbl. Expression of the L. innocua cblT and cblS genes restored AdoCbl synthesis from Cbi and α‐R in a Salmonella enterica cobT strain. LinCblT transported α‐R across the cell membrane, but not α‐RP or DMB. UV‐visible spectroscopy and mass spectrometry data identified α‐RP as the product of the ATP‐dependent α‐R kinase activity of LinCblS. Bioinformatics analyses suggest that α‐R salvaging occurs in important Gram‐positive human pathogens.
The Bps polysaccharide of Bordetella pertussis promotes colonization and biofilm formation in the nose by functioning as an adhesin
Authors: Conover Matt S. , Sloan Gina Parise , Love Cheraton F. , Sukumar Neelima , Deora Rajendar
Published: July 2010

Many respiratory pathogens establish persistent infection or a carrier state in the human nasopharynx without overt disease symptoms but the presence of these in the lungs usually results in disease. Although the anatomy and microenvironments between nasopharynx and lungs are different, a virulence factor with an organ‐specific function in the colonization of the nasopharynx is unknown. In contrast to the severity of pertussis and mortality in non‐vaccinated young children, Bordetella pertussis results in milder and prolonged cough in vaccinated adolescents and adults. Individuals harbouring bacteria in the nasopharynx serve as reservoirs for intrafamilial and nosocomial transmission. We show that the Bps polysaccharide of B. pertussis is critical for initial colonization of the mouse nose and the trachea but not of the lungs. Our data reveal a biofilm lifestyle for B. pertussis in the nose and the requirement of Bps in this developmental process. Bps functions as an adhesin by promoting adherence of B. pertussis and Escherichia coli to human nasal but not to human lung epithelia. Patient serum specifically recognized Bps suggesting its expression during natural human infections. We describe the first bacterial factor that exhibits a differential role in colonization and adherence between the nasopharynx and the lungs.
Characterization of a DNA damage‐inducible membrane protein kinase from Deinococcus radiodurans and its role in bacterial radioresistance and DNA strand break repair
Authors: Rajpurohit Yogendra S. , Misra Hari S.
Published: July 2010

Deinococcus radiodurans mutant lacking pyrroloquinoline–quinone (PQQ) synthesis shows sensitivity to γ‐rays and impairment of DNA double strand break repair. The genome of this bacterium encodes five putative proteins having multiple PQQ binding motifs. The deletion mutants of corresponding genes were generated, and their response to DNA damage was monitored. Only the Δdr2518 mutant exhibited higher sensitivity to DNA damage. Survival of these cells decreased by 3‐log cycle both at 6 kGy γ‐rays and 1200 J m−2 UV (254 nm) radiation, and 2.5‐log cycle upon 14 days desiccation at 5% humidity. The Δdr2518 mutant showed complete inhibition of DSB repair until 24 h PIR and disappearance of a few phosphoproteins. The Δdr2518pqqE:cat double mutant showed γ‐ray sensitivity similar to Δdr2518 indicating functional interaction of these genes in D. radiodurans. DR2518 contains a eukaryotic type Ser/Thr kinase domain and structural topology suggesting stress responsive transmembrane protein. Its autokinase activity in solution was stimulated by nearly threefold with PQQ and twofold with linear DNA, but not with circular plasmid DNA. More than 15‐fold increase in dr2518 transcription and several‐fold enhanced in vivo phosphorylation of DR2518 were observed in response to γ irradiation. These results suggest that DR2518 as a DNA damage‐responsive protein kinase plays an important role in radiation resistance and DNA strand break repair in D. radiodurans.
Caspase‐12 deficiency enhances cytokine responses but does not protect against lethal Plasmodium yoelii 17XL infection
Authors: MIU J. , SALEH M. , STEVENSON M. M.
Published: July 2010

To investigate the effect of caspase‐12 deficiency on IFN‐γ‐independent control of blood‐stage malaria, we compared lethal Plasmodium yoelii 17XL infection in wild‐type C57BL/6J and caspase‐12−/− mice. Infected caspase‐12−/− mice exhibited higher parasitaemia than WT mice on days 8 and 9 post‐inoculation, but all WT and caspase‐12−/− mice succumbed by day 10. In addition, infected caspase‐12−/− mice had significantly elevated levels of IFN‐γ, TNF, IL‐18, and IL‐10 in sera compared to infected WT mice. At the terminal stage of disease, there were no differences in cytokine levels in the tissues of infected WT and caspase‐12−/− mice. However, liver pathology was more severe in infected caspase‐12−/− mice compared to infected WT mice. Together, these findings indicate that although caspase‐12 deficiency results in enhanced pro‐inflammatory and immunoregulatory cytokine levels in sera during P. yoelii 17XL infection, these responses are not essential for protection against lethal malaria infection.
Chute channels in the Holocene high‐sinuosity river deposits of the Firenze plain, Tuscany, Italy
Authors: GHINASSI MASSIMILIANO
Published: July 2010

This paper focuses on Holocene deposits of the Firenze alluvial plain (Northern Apennines, Italy) and deals with the sedimentary features of chute channels draining the down‐river edges of the meander neck formed by 70 to 100 m wide and 1 to 1·5 m deep sinuous channels. Two main types of chute channels have been recognized. Type 1 is represented by 3 to 6 m wide and 0·5 to 1 m deep straight channels filled with mud aggregates overlying a basal gravel lag made of reworked caliches. These channels drained the point bar top during floods, and are thought to have been initiated as small rills when a shallow flow overpassed the downstream side of the point bar. Type 2 channels, 3 to 6 m wide and 1 to 1·5 m deep, are moderately to highly sinuous and filled with well‐stratified sand and gravels sourced from nearby rocky highlands. Type 2 channels were connected to the main river channel also during the base flow stage. The transition from Type 1 to Type 2 channels is documented and is interpreted as the result of the meander cut‐off process. Type 1 chute channels represent the early stage of the cut‐off phase, when a headcut is incised on the down‐river edges of the meander neck. The headcut migrates up‐river across the meander neck during floods, when fast currents shape the chute channels into a straight route. The transition from Type 1 into Type 2 channels is linked to the connection of the up‐river migrating headcut with the main channel and the termination of the cut‐off process. At this stage, the cut‐off channel is drained permanently and receives bedload from the main channel. The progressive shaping of the newly formed channel will convert it into the main channel and lead to the formation of an oxbow lake in the abandoned meander branch. Development of chute channels in the Firenze alluvial plain is thought to have heralded a decrease in sinuosity of the main channels, triggered by a climate‐driven increase in water discharge.
Histological Features in the Mammary Glands of Female Dogs throughout Lactation
Authors: Orfanou D. C. , Pourlis A. , Ververidis H. N. , Mavrogianni V. S. , Taitzoglou I. A. , Boscos C. M. , Fthenakis G. C.
Published: July 2010

With 3 tables and 2 figures

The objective of this study was to describe the histology of the mammary glands of female dogs throughout lactation. Twelve lactating female dogs were operated 4, 7, 10, 14, 21, 28, 35, 42, 56, 70 and 84 days post‐partum; four mammary glands of each animal were excised for histological, ultrastructural and morphometric examination. During early lactation and mid‐lactation, all lobes and lobules within the same gland had similar features; alveoli were well developed and distended and had a spherical to slightly ovoid structure, with muscular fibres grasping them around; inflammatory cells were seen in the inter‐ and intra‐alveolar space; mammary lobules were separated with a scant amount of connective tissue. In late lactation, connective tissue was abundant and dense, with large numbers of inflammatory cells; alveoli appeared to be irregularly shaped and collapsing, shrunken or fully collapsed. Number of alveoli per lobule and number of epithelial cells per alveolus, as well as diameter of alveoli and height of epithelial cells decreased as lactation progressed. The third mammary glands (from caudal to cranial) had a significantly smaller number of alveoli, but not of epithelial cells per alveolus, than each of the two mammary glands caudally to that. The results suggest that progressive involution of the normal mammary gland starts around the end of the 2nd month of lactation and continues until the end of the 3rd month.
Comparison of genomic and traditional BLUP‐estimated breeding value accuracy and selection response under alternative trait and genomic parameters
Authors: Muir W.M.
Published: July 2010

Accuracy of prediction of estimated breeding values based on genome‐wide markers (GEBV) and selection based on GEBV as compared with traditional Best Linear Unbiased Prediction (BLUP) was examined for a number of alternatives, including low heritability, number of generations of training, marker density, initial distributions, and effective population size (Ne). Results show that the more the generations of data in which both genotypes and phenotypes were collected, termed training generations (TG), the better the accuracy and persistency of accuracy based on GEBV. GEBV excelled for traits of low heritability regardless of initial equilibrium conditions, as opposed to traditional marker‐assisted selection, which is not useful for traits of low heritability. Effective population size is critical for populations starting in Hardy‐Weinberg equilibrium but not for populations started from mutation‐drift equilibrium. In comparison with traditional BLUP, GEBV can exceed the accuracy of BLUP provided enough TG are included. Unfortunately selection rapidly reduces the accuracy of GEBV. In all cases examined, classic BLUP selection exceeds what was possible for GEBV selection. Even still, GEBV could have an advantage over traditional BLUP in cases such as sex‐limited traits, traits that are expensive to measure, or can only be measured on relatives. A combined approach, utilizing a mixed model with a second random effect to account for quantitative trait loci in linkage equilibrium (the polygenic effect) was suggested as a way to capitalize on both methodologies.
Environmental drivers of ophiuroid species richness on seamounts
Authors: O’Hara Timothy D. , Tittensor Derek P.
Published: July 2010

Benthic communities on seamounts are frequently characterised as being species rich, yet there is considerable variation in observed species richness. Although large‐scale patterns of species richness have been described from many marine and terrestrial habitats, their environmental drivers often remain poorly understood. We compared species richness of ophiuroids (brittle‐stars) on 60 seamounts throughout the South West Pacific Ocean, and used an information‐theoretic approach and generalized linear models to determine the relative importance of predictor variables. Due to high correlation among many environmental variables, we used a reduced set of predictors in an a priori model framework. Temperature was the only environmental predictor of any importance in these models over the bathymetric range of the study. Post‐hoc analyses of other potential environmental predictor variables showed that depth, calcite saturation state, temperature range, modelled current velocity and latitude all had some predictive value, but were also highly correlated with temperature or other environmental variables included in the a priori model. Longitude, large‐area species richness, habitat suitability for stony corals, and modelled POC flux did not have high predictive value. We hypothesise that temperature affects richness by constraining species distributions; in particular fewer species can tolerate the conditions on relatively warm shallow seamount summits.
Squat lobster assemblages on seamounts differ from some, but not all, deep‐sea habitats of comparable depth
Authors: Rowden Ashley A. , Schnabel Kareen E. , Schlacher Thomas A. , Macpherson Enrique , Ahyong Shane T. , Richer de Forges Bertrand
Published: July 2010

This study was carried out to test the hypothesis that benthic communities on seamounts are distinct from those of other deep‐sea habitats at comparable depths. Analysis of the squat lobster fauna of deep‐sea habitats in the Southwestern Pacific revealed that the species composition of assemblages on seamounts was not statistically dissimilar from assemblages on slope and plateau habitat at comparable depths. However, compositional differences were observed between seamount and rise and ridge habitat. Differences in assemblage composition between seamount and ridge habitat were statistically significant for two of the four ridge systems examined. Assemblages on seamounts that were distinct from non‐seamount ridge habitat were typically dominated by small‐bodied species with an abbreviated larval stage. Various environmental variables were correlated with the observed assemblage patterns observed; depth‐related variables may account for differences between seamount and rise assemblages, whilst differences in POC flux likely play a role in determining the assemblage compositional patterns between seamount and non‐seamount ridge habitat. Extensive pre‐analysis data treatment was required to ensure that multivariate analyses of assemblage data from seamount and non‐seamount habitats were robust. Our results confirm the findings of recent studies that found no compositional differences in assemblages from seamount and slope habitats, and support the idea that dissimilarity between seamount assemblages on different ridge systems increases with geographic distance. Further research will be required before the generality of these findings can be confirmed.
Bone morphogenetic protein 4 signaling regulates development of the anterior visceral endoderm in the mouse embryo
Authors: Soares Miguel L. , Torres‐Padilla Maria‐Elena , Zernicka‐Goetz Magdalena
Published: July 2010

The extraembryonic ectoderm (ExE) of the mouse conceptus is known to play a role in embryo patterning by signaling to the underlying epiblast and surrounding visceral endoderm. Bmp4 is one of the key ExE signaling molecules and has been recently implicated to participate in regulating development and migration of the anterior visceral endoderm (AVE). However, it remains unclear when exactly BMP4 signaling starts to regulate AVE positioning. To examine this, we have chosen to affect BMP4 function at two different time points, at embryonic day 5.25 (E5.25), thus before AVE migration, and E5.75, just after AVE migration. To this end, an RNAi technique was used, which consisted of the injection of Bmp4 dsRNA into the proamniotic cavity of the egg cylinder followed by its targeted electroporation into the ExE. This resulted in specific knockdown of Bmp4. It was found that Bmp4 RNAi at E5.25, but not at E5.75, led to an abnormal pattern of expression of the AVE marker Cerberus‐like. Thus, BMP4 signaling appears to affect the expression of Cer1 at a specific time window. This RNAi approach provides a convenient means to study spatial and temporal function of genes shortly after embryo implantation.
Visualization of stochastic Ca2+signals in the formed somites during the early segmentation period in intact, normally developing zebrafish embryos
Authors: Leung Christina F. , Miller Andrew L. , Korzh Vladimir , Chong Shang‐Wei , Sleptsova‐Freidrich Inna , Webb Sarah E.
Published: July 2010

Localized Ca2+signals were consistently visualized in the formed somites of intact zebrafish embryos during the early segmentation period. Unlike the regular process of somitogenesis, these signals were stochastic in nature with respect to time and location. They did, however, occur predominantly at the medial and lateral boundaries within the formed somites. Embryos were treated with modulators of [Ca2+]ito explore the signal generation mechanism and possible developmental function of the stochastic transients. Blocking elements in the phosphoinositol pathway eliminated the stochastic signals but had no obvious effect, stochastic or otherwise, on the formed somites. Such treatments did, however, result in the subsequently formed somites being longer in the mediolateral dimension. Targeted uncaging of buffer (diazo‐2) or Ca2+(NP‐ethyleneglycoltetraacetic acid [EGTA]) in the presomitic mesoderm, resulted in a regular mediolateral lengthening and shortening, respectively, of subsequently formed somites. These data suggest a requirement for IP3receptor‐mediated Ca2+release during convergence cell movements in the presomitic mesoderm, which appears to have a distinct function from that of the IP3receptor‐mediated stochastic Ca2+signaling in the formed somites.
Infrared laser‐mediated local gene induction in medaka, zebrafish and Arabidopsis thaliana
Authors: Deguchi Tomonori , Itoh Mariko , Urawa Hiroko , Matsumoto Tomohiro , Nakayama Sohei , Kawasaki Takashi , Kitano Takeshi , Oda Shoji , Mitani Hiroshi , Takahashi Taku , Todo Takeshi , Sato Junichi , Okada Kiyotaka , Hatta Kohei , Yuba Shunsuke , Kamei Yasuhiro
Published: July 2010

Heat shock promoters are powerful tools for the precise control of exogenous gene induction in living organisms. In addition to the temporal control of gene expression, the analysis of gene function can also require spatial restriction. Recently, we reported a new method for in vivo, single‐cell gene induction using an infrared laser‐evoked gene operator (IR‐LEGO) system in living nematodes (Caenorhabditis elegans). It was demonstrated that infrared (IR) irradiation could induce gene expression in single cells without incurring cellular damage. Here, we report the application of IR‐LEGO to the small fish, medaka (Japanese killifish; Oryzias latipes) and zebrafish (Danio rerio), and a higher plant (Arabidopsis thaliana). Using easily observable reporter genes, we successfully induced gene expression in various tissues in these living organisms. IR‐LEGO has the potential to be a useful tool in extensive research fields for cell/tissue marking or targeted gene expression in local tissues of small fish and plants.