bluuebunny/crossref_metadata_2025 huggingface dataset:
An electrical switching device controlled by a magnetic field-dependent impact ionization process
Authors: Lee Jinseo , Joo Sungjung , Kim Taeyueb , Kim Ki Hyun , Rhie Kungwon , Hong Jinki , Shin Kyung-Ho
Published: December 2010

An abrupt change of conductance at a threshold magnetic field was observed in a device consisting of a nonmagnetic narrow-gap semiconductor. The conductance varies more than 25 times as the magnetic field increases. The threshold magnetic field can be tuned using a bias voltage from zero to several hundred Gauss. This large magnetoconductance effect is caused by the magnetic field-dependent impact ionization process. A theoretical model is proposed, and calculations based on this model simulate the experimental results closely. This device may be a good candidate for an electrical switching device controlled by a magnetic field.
Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA
Authors: Melero Roberto , Rajagopalan Sridharan , Lázaro Melisa , Joerger Andreas C. , Brandt Tobias , Veprintsev Dmitry B. , Lasso Gorka , Gil David , Scheres Sjors H. W. , Carazo José María , Fersht Alan R. , Valle Mikel
Published: December 2010

The multidomain homotetrameric tumor suppressor p53 has two modes of binding dsDNA that are thought to be responsible for scanning and recognizing specific response elements (REs). The C termini bind nonspecifically to dsDNA. The four DNA-binding domains (DBDs) bind REs that have two symmetric 10 base-pair sequences. p53 bound to a 20-bp RE has the DBDs enveloping the DNA, which is in the center of the molecule surrounded by linker sequences to the tetramerization domain (Tet). We investigated by electron microscopy structures of p53 bound to DNA sequences consisting of a 20-bp RE with either 12 or 20 bp nonspecific extensions on either end. We found a variety of structures that give clues to recognition and scanning mechanisms. The 44- and 60-bp sequences gave rise to three and four classes of structures, respectively. One was similar to the known 20-bp structure, but the DBDs in the other classes were loosely arranged and incompatible with specific DNA recognition. Some of the complexes had density consistent with the C termini extending from Tet to the DNA, adjacent to the DBDs. Single-molecule fluorescence resonance energy transfer experiments detected the approach of the C termini towards the DBDs on addition of DNA. The structural data are consistent with p53 sliding along DNA via its C termini and the DNA-binding domains hopping on and off during searches for REs. The loose structures and posttranslational modifications account for the affinity of nonspecific DNA for p53 and point to a mechanism of enhancement of specificity by its binding to effector proteins.
A single-molecule characterization of p53 search on DNA
Authors: Tafvizi Anahita , Huang Fang , Fersht Alan R. , Mirny Leonid A. , van Oijen Antoine M.
Published: December 2010

The tumor suppressor p53 slides along DNA while searching for its cognate site. Central to this process is the basic C-terminal domain, whose regulatory role and its coordination with the core DNA-binding domain is highly debated. Here we use single-molecule techniques to characterize the search process and disentangle the roles played by these two DNA-binding domains in the search process. We demonstrate that the C-terminal domain is capable of rapid translocation, while the core domain is unable to slide and instead hops along DNA. These findings are integrated into a model, in which the C-terminal domain mediates fast sliding of p53, while the core domain samples DNA by frequent dissociation and reassociation, allowing for rapid scanning of long DNA regions. The model further proposes how modifications of the C-terminal domain can activate “latent” p53 and reconciles seemingly contradictory data on the action of different domains and their coordination.
Dioxygenases in
Burkholderia ambifaria
and
Yersinia pestis
that hydroxylate the outer Kdo unit of lipopolysaccharide
Authors: Chung Hak Suk , Raetz Christian R. H.
Published: December 2010

Several Gram-negative pathogens, including
Yersinia pestis, Burkholderia cepacia
, and
Acinetobacter haemolyticus
, synthesize an isosteric analog of 3-deoxy-
d
-
manno
-oct-2-ulosonic acid (Kdo), known as
d
-glycero-
d
-
talo
-oct-2-ulosonic acid (Ko), in which the axial hydrogen atom at the Kdo 3-position is replaced with OH. Here we report a unique Kdo 3-hydroxylase (KdoO) from
Burkholderia ambifaria
and
Yersinia pestis
, encoded by the
bamb_0774
(
BakdoO
) and the
y1812
(
YpkdoO
) genes, respectively. When expressed in heptosyl transferase-deficient
Escherichia coli
, these genes result in conversion of the outer Kdo unit of Kdo
2
-lipid A to Ko in an O
2
-dependent manner. KdoO contains the putative iron-binding motif, HXDX

n
>40

H. Reconstitution of KdoO activity in vitro with Kdo
2
-lipid A as the substrate required addition of Fe
2+
, α-ketoglutarate, and ascorbic acid, confirming that KdoO is a Fe
2+
/α-ketoglutarate/O
2
-dependent dioxygenase. Conversion of Kdo to Ko in Kdo
2
-lipid A conferred reduced susceptibility to mild acid hydrolysis. Although two enzymes that catalyze Fe
2+
/α-ketoglutarate/O
2
-dependent hydroxylation of deoxyuridine in fungal extracts have been reported previously,
kdoO
is the first example of a gene encoding a deoxy-sugar hydroxylase. Homologues of KdoO are found exclusively in Gram-negative bacteria, including the human pathogens
Burkholderia mallei
,
Yersinia pestis
,
Klebsiella pneumoniae
,
Legionella longbeachae
, and
Coxiella burnetii
, as well as the plant pathogen
Ralstonia solanacearum
.
Adhesion and delamination of interfaces
Authors: S J Bull  , L J Balk
Published: December 2010

Thin films and coatings are used for a variety of purposes and their adhesion to the underlying substrate is essential in nearly all applications. Consequently, the need for reliable techniques to quantitatively measure adhesion is paramount. As coating systems become more complex, with, for instance, multilayered and graded architectures now commonplace in MEMS devices, there is a need to improve on existing techniques in order to assess the adhesion of the coating stack to the substrate, but also the delamination of individual interfaces within a coating stack. This requires methods to cause failure, to characterise the locus and extent of any interfacial disbond, and the models necessary to extract quantitative adhesion data from these observations. Similar challenges are faced in bulk composite materials where the adhesion between matrix and reinforcement phase or the delamination behaviour of interfaces between plies will dictate the overall mechanical response of the system

There has been considerable activity in devising ways to assess adhesion in the past few decades. In fact, a survey of the literature in 1995 indicated that over 350 different techniques were available ranging from the mundane to the very sophisticated. In spite of this proliferation of techniques there has often been considerable discord amongst people working in the area as to what exactly is being measured in an adhesion test and how reliable the quantification is. In reality, the reason that there are so many techniques is that no one technique is universally applicable, and the adhesion measurements obtained on the same system using different techniques are not always directly comparable. The best adhesion test method is often that which most closely matches the intended application and therefore it will depend on the conditions to which the coated material is exposed.

Given the plethora of available measurement and interpretation techniques and recent developments in techniques for characterisation of interfacial failure, we felt that it was timely to assemble a cluster of papers in the area showcasing the latest research and offering some insights in the selection of an appropriate adhesion test. The papers in this issue were solicited from major researchers in the area and represent a snapshot of the current state-of-the-art–we hope they will provide an excellent introduction to the topic for a more general audience.
Variation of adhesive force at the interface of Pd and SrTiO3 as a consequence of residual stresses
Authors: Nazarpour Soroush , Cirera Albert
Published: December 2010

Initially, Pd thin films were deposited over a hard substrate using electron beam physical vapour deposition. The growth and the surface roughness of the films were analysed and their effects upon the conventional indentation test were discussed. Afterwards, an experimental method is described which can measure the critical fracture force in thin films using oscillating indentation. Initially, repetitive contacts at a single point with the purpose of identifying the fracture time provide the fracture force versus fracture time plot. Non-linear curve fitting of the data reveals the theoretical fracture force by a single indentation, which is called the critical fracture force. Arguments are put forward to show the relation between piling up height and applied force. Discrepancies were observed in the plot of the ratio between total indentation depth and piling up height versus applied force when higher loads than a critical fracture force were applied. Discrepancies appear as a result of indenting the substrate. A nanoscratch test facilitated the possibility of measuring adhesion strength and adhesion energy of the films considering the measured critical fracture force as the maximum applied force. The relation between residual compressive stresses, adhesion strength, plastic deformation and piling up area was discussed using dislocation theories. Indentation with high applied loads leaves behind large plastic deformation and reduces the accuracy and reliability of the test results. Hence, lower loads (in the order of nanonewtons) were applied using atomic force microscopy in the friction mode. A pulling off force was mapped in each thickness of Pd films. The results confirm that the area around a hillock exhibits a higher pulling off force due to the local stress relaxation as a consequence of hillock formation. By repeating the mapping process over different areas with various applying forces, the plot of the pulling off force versus applied load was drawn representing discrepancies in the results at higher loads. This phenomenon is associated with the plastic deformation in the films.
An improved miniature mixed-mode delamination setup for in situ microscopic interface failure analyses
Authors: Kolluri M , Hoefnagels J P M , van Dommelen J A W , Geers M G D
Published: December 2010

Precise characterization of interface delamination in miniature interface structures is an ongoing challenge with the advent of miniaturization and multi-functionality in the electronics industry. Accurate numerical prediction of the interface behaviour is necessary to minimize delamination failures. Successful prediction requires (i) accurate determination of the interface properties like the critical energy release rate (CERR) over the full range of mode mixities and (ii) simultaneous in situ microscopic visualization of the delamination mechanism. These requirements were recently addressed by the development of the miniature mixed-mode bending (MMMB) setup (Kolluri et al 2009 Int. J. Fract.). In this paper an improved MMMB setup is presented, which overcomes the main limitations of the original design. Specifically, the improved design (i) can access a significantly larger range of interface systems due to its increased limits of maximum accessible load and stroke in all mode mixities, (ii) has significantly higher accuracy in load–displacement measurement due to its reduced clearance at the connectors, which is particularly relevant for miniature samples, and (iii) has a high reproducibility due to a newly added setup alignment tool. The measurement concept is validated on (industrially relevant) copper lead frame–moulding compound epoxy interface structures. The load–displacement curves and corresponding CERR values obtained from experiments over the full range of mode mixities are discussed in relation to the delamination mechanism observed during real-time in situ visualization. Specifically, the measured increase in the CERR towards mode II is related to a more discrete or jerky crack growth behaviour observed in the mode II dominant tests. Finally, the potential of the methodology for interface parameter characterization is illustrated.
Investigation of moisture-induced delamination failure in a semiconductor package via multi-scale mechanics
Authors: Kim Hak-Sung , Huh Jeehyang , Ryu Jongeun
Published: December 2010

In this work, moisture-induced interfacial delamination in a semiconductor package was investigated by experiment and multi-scale numerical analysis. The interfacial adhesion strength between a silicon wafer and an epoxy adhesive layer was characterized by a die-shear test with respect to moisture concentration and temperature. Molecular dynamics simulation was performed to study the effect of moisture and temperature on the interfacial adhesion energy and strength at the Si/epoxy adhesive interface. Based on the molecular dynamics predicted interfacial adhesion strength, a numerical stress analysis was performed considering hygro-swelling stress and the thermo-mechanical stress during a solder reflow process to predict the moisture-induced delamination failure of the semiconductor package. The multi-scale simulation result was compared with the actual reliability test result. From this study, it was concluded that the proposed multi-scale simulation technique can be used successfully for the prediction of moisture-induced package failure.
Investigation of delamination mechanisms in polymer coatings by scanning acoustic microscopy
Authors: Alig I , Bargmann M , Oehler H , Lellinger D , Wanner M , Koch D
Published: December 2010

Scanning acoustic microscopy (SAM) was used to investigate disbonding, delamination and blister formation in polymer coatings for different layer structures and initial defect depths during exposure to a corrosive environment. The time evolution of disbonding and blister initiation and their growth was investigated by analysing the SAM images, taken after defined times of exposure to an electrolyte solution (Harrison solution).

From investigations of a model system of coatings on steel substrates, it was possible to differentiate between water and/or ion transport (i) through the coating and (ii) along the coating–steel interface. For samples without clear coat randomly distributed blisters appeared at the coating–steel interface after exposure to the electrolyte solution, irrespective of the location of initial defects. The random distribution of growing blisters is related to diffusion of water and/or ions through the coating and ‘nucleation’ at weak points of the substrate or within the polymer. For samples with clear coat a propagating migration front along the coating–steel interface of 3–4 µm height—starting from initial defects—was detected. The linear propagation of this front cannot be explained by Fickian diffusion. Therefore, it is discussed in terms of an accelerated diffusion or crack growth kinetics. Since blistering starts only at sites, where the migration front has passed, the presence of a thin water layer at the coating–steel interface, the loss of adhesion and the following corrosive processes are prerequisites for the nucleation of blisters. The blister growth shows a square-root time dependence.
Interfacial design and structure of protein/polymer films on oxidized AlGaN surfaces
Authors: Gupta Samit K , Wu Hao-Hsuan , Kwak Kwang J , Casal Patricia , Nicholson III Theodore R , Wen Xuejin , Anisha R , Bhushan Bharat , Berger Paul R , Lu Wu , Brillson Leonard J , Lee Stephen Craig
Published: December 2010

Protein detection using biologically or immunologically modified field-effect transistors (bio/immunoFETs) depends on the nanoscale structure of the polymer/protein film at sensor interfaces (Bhushan 2010 Springer Handbook of Nanotechnology 3rd edn (Heidelberg: Springer); Gupta et al 2010 The effect of interface modification on bioFET sensitivity, submitted). AlGaN-based HFETs (heterojunction FETs) are attractive platforms for many protein sensing applications due to their electrical stability in high osmolarity aqueous environments and favourable current drive capabilities. However, interfacial polymer/protein films on AlGaN, though critical to HFET protein sensor function, have not yet been fully characterized. These interfacial films are typically comprised of protein–polymer films, in which analyte-specific receptors are tethered to the sensing surface with a heterobifunctional linker molecule (often a silane molecule). Here we provide insight into the structure and tribology of silane interfaces composed of one of two different silane monomers deposited on oxidized AlGaN, and other metal oxide surfaces. We demonstrate distinct morphologies and wear properties for the interfacial films, attributable to the specific chemistries of the silane monomers used in the films. For each specific silane monomer, film morphologies and wear are broadly consistent on multiple oxide surfaces. Differences in interfacial film morphology also drive improvements in sensitivity of the underlying HFET (coincident with, though not necessarily caused by, differences in interfacial film thickness). We present a testable model of the hypothetical differential interfacial depth distribution of protein analytes on FET sensor interfaces with distinct morphologies. Empirical validation of this model may rationalize the actual behaviour of planar immunoFETs, which has been shown to be contrary to expectations of bio/immunoFET behaviour prevalent in the literature for the last 20 years. Improved interfacial properties of bio/immunoHFETs have improved bio/immunoHFET performance: better understanding of interfaces may lead to mechanistic understanding of FET sensor properties and to clinical translation of the immunoFET platform.
Effect of surface cleanliness of aluminium substrates on silicone rubber adhesion
Authors: Petersson L , Meier P , Kornmann X , Hillborg H
Published: December 2010

The aim of this work was to determine the minimum surface cleanliness of aluminium substrates required for good and reproducible silicone rubber adhesion. Aluminium substrates were prepared, ranging from ‘contaminated’ to different degrees of ‘cleaned’. The surface energy of the substrates was determined by contact angle measurements. The surfaces were also compared using simplified methods, such as a wettability test or by the use of inks with known surface tension. Silicone rubber was then compression moulded onto the cleaned and primed substrates. The silicone rubber adhesion was then evaluated by lap-shear testing, before and after ageing. The ageing step consisted of immersion of samples in boiling water for 100 h to evaluate the hydrolytic stability of the interfaces. The failure modes after lap-shear testing were determined using optical microscopy and scanning electron microscopy and were divided into three different categories: cohesive failure, adhesive failure or a mixture thereof. Energy dispersive x-ray mapping was useful in clarifying the failure modes by determining the position of the primer, which contained Ti. It was concluded that in order to obtain a strong and stable interface, exhibiting mainly cohesive failure between the aluminium substrate and silicone rubber, the surface energy of the substrate before priming should be >45 mJ m−2, including a polar component of >10 mJ m−2. This corresponded to a hydrophobicity class of the substrate of ⩾6, according to IEC 62073.
Sonic IR Imaging of delaminations and disbonds in composites
Authors: Han Xiaoyan , Favro L D , Thomas R L
Published: December 2010

Sonic IR is a nondestructive evaluation (NDE) technique that makes images of defects in objects using an infrared camera with an ultrasonic transducer as an active stimulation source. The advantages of the method are its speed, taking only seconds, or, more usually, only a fraction of a second to make a dark-field image that shows the location and size of the defect, and its ability to cover a wide area, typically a square meter, or a significant fraction of a square meter, in a single image. This NDE method has principally been used for finding cracks in metals, but its application to polymeric composites has been lagging, in part because of artefacts that mask the indications of defects. In this paper we discuss the application of sonic IR to disbonds and delaminations in composites, and describe the use of broadband chaotic sound to eliminate artefacts resulting from acoustic interference. An additional benefit arises from the simultaneous stimulation of defects with different resonant frequencies.
In-situ study of molecular dynamics in a water environment by using imaging ellipsometry
Authors: Hwang Soon Yong , Kim Tae Jung , Diware Mangesh S , Kim Young Dong
Published: December 2010

We report on the dynamics of bio molecules and a high polymer in a water environment by using imaging ellipsometry (IE). The morphology of collapsed films of arachidic acid (AA) and poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV) Langmuir monolayers in a liquid solution is investigated. The IE images clearly show that the multilayer domains and thickness of the collapsed region change sensitively depending on Langmuir compression. Also, the adsorption of bovine serum albumin is observed by using total internal reflection resonance IE (TIRIE), which has the advantage of IE and surface plasmon resonance. We believe that IE is a powerful technique for analysis and applications of bio materials.
Habit Formation and Demand for Sugar‐Sweetened Beverages
Authors: Zhen Chen , Wohlgenant Michael K. , Karns Shawn , Kaufman Phillip
Published: December 2010

Using scanner data, we estimated demand for nine nonalcoholic beverages under habit formation. We found strong evidence for habit formation. Although demand for sugar‐sweetened beverages by low‐income households is less elastic to own‐price changes compared with high‐income households, there is evidence that high‐income households consider beverages to be more substitutable than low‐income households do. A half‐cent per ounce tax on store‐purchased sugar‐sweetened beverages will result in a moderate reduction in consumption of sugar‐sweetened beverages for both income strata. Because of habit formation, long‐run national tax revenue from a sugar‐sweetened beverage tax is about 15 to 20% lower than short‐run revenue.
The response of shrimp fisheries to climate variability off Baja California, México
Authors: Santamaría-del-Ángel Eduardo , Millán-Núñez Roberto , González-Silvera Adriana , Callejas-Jiménez Mariana , Cajal-Medrano Ramón , Galindo-Bect Manuel S.
Published: December 2010

Santamaría-del-Ángel, E., Millán-Núñez, R., González-Silvera, A., Callejas-Jiménez, M., Cajal-Medrano, R., and Galindo-Bect, M. S. 2011. The response of shrimp fisheries to climate variability off Baja California, México. – ICES Journal of Marine Science, 68: 766–772. The effect of climate variability on the shrimp fishery in the upper Gulf of California and the west coast of southern Baja California was investigated using artisanal and industrial catches of blue shrimp (Litopenaeus stylirostris) and brown shrimp (Farfantepenaeus californiensis). Catch data were compared with the Southern Oscillation Index (SOI) and remotely sensed environmental parameters, including sea surface temperature, chlorophyll a, coloured dissolved organic matter, and particulate organic carbon (Rrs412 and Rrs490). Overall, temperature was the best environmental indicator of commercial shrimp catches. Catches of blue shrimp varied directly and of brown shrimp indirectly with the SOI in their dominant areas, suggesting that the two species are influenced by El Niño conditions in different ways.
Preoperative Cerebral Oxygen Saturation and Clinical Outcomes in Cardiac Surgery
Authors: Heringlake Matthias , Garbers Christof , Käbler Jan-Hendrik , Anderson Ingrid , Heinze Hermann , Schön Julika , Berger Klaus-Ulrich , Dibbelt Leif , Sievers Hans-Hinrich , Hanke Thorsten
Published: December 2010

Background

The current study was designed to determine the relation between preoperative cerebral oxygen saturation (Sco2), variables of cardiopulmonary function, mortality, and morbidity in a heterogeneous cohort of cardiac surgery patients.

Methods

In this study, 1,178 consecutive patients scheduled for on-pump surgery were prospectively studied. Preoperative Sco2, demographics, N-terminal pro-B-type natriuretic peptide, high-sensitive troponin T, clinical outcomes, and 30-day and 1-yr mortality were recorded.

Results

Median additive EuroSCORE was 5 (range: 0-19). Thirty-day and 1-yr mortality and major morbidity (at least two major complications and/or a high-dependency unit stay of at least 10 days) were 3.5%, 7.7%, and 13.3%, respectively. Median minimal preoperative oxygen supplemented Sco2 (Sco2min-ox) was 64% (range: 15-92%). Sco2min-ox was correlated (all: P value <0.0001) with N-terminal pro-B-type natriuretic peptide (ρ: -0.35), high-sensitive troponin T (ρ: -0.28), hematocrit (ρ: 0.34), glomerular filtration rate (ρ: 0.19), EuroSCORE (τ: 0.20), and left ventricular ejection fraction class (τ: 0.12). Thirty-day nonsurvivors had a lower Sco2min-ox than survivors (median 58% [95% CI, 50.7-62%] vs. 64% [95% CI, 64-65%]; P < 0.0001). Receiver-operating curve analysis of Sco2min-ox and 30-day mortality revealed an area-under-the-curve of 0.71 (95% CI, 0.68-0.73%; P < 0.0001) in the total cohort and an area-under-the-curve of 0.77 (95% CI, 0.69-0.86%; P < 0.0001) in patients with a EuroSCORE more than 10. Logistic regression based on different EuroSCORE categories (0-2; 3-5, 6-10, >10), Sco2min-ox, and duration of cardiopulmonary bypass showed that a Sco2min-ox equal or less than 50% is an independent risk factor for 30-day and 1-yr mortality.

Conclusions

Preoperative Sco2 levels are reflective of the severity of cardiopulmonary dysfunction, associated with short- and long-term mortality and morbidity, and may add to preoperative risk stratification in patients undergoing cardiac surgery.
High Incidence of Burnout in Academic Chairpersons of Anesthesiology
Authors: De Oliveira Gildàsio S. , Ahmad Shireen , Stock M. Christine , Harter Ronald L. , Almeida Marcela D. , Fitzgerald Paul C. , McCarthy Robert J.
Published: December 2010

Background

Burnout is a work-related psychologic syndrome characterized by emotional exhaustion, low personal accomplishment, and depersonalization.

Methods

By using an instrument that included the MBI-HHS Burnout Inventory, we surveyed academic anesthesiology chairpersons in the United States. Current level of job satisfaction compared with 1 and 5 yr before the survey, likelihood of stepping down as chair in the next 2 yr, and a high risk of burnout were the primary outcomes.

Results

Of the 117 chairs surveyed, 102 (87%) responded. Nine surveys had insufficient responses for assessment of burnout. Of 93 chairs, 32 (34%) reported high current job satisfaction, which represented a significant decline compared with that reported for 1 yr (P = 0.009) and 5 yr (P = 0.001) before the survey. Of 93 chairs, 26 (28%) reported extreme likelihood of stepping down as a chair in 1-2 yr. There was no association of age (P = 0.16), sex (P = 0.82), or self-reported effectiveness (P = 0.63) with anticipated likelihood of stepping down, but there was a negative association between the modified efficacy scale scoρrgr; = -0.303, P = 0.003) and likelihood of stepping down. Of 93 chairs, 26 (28%) met the criteria for high burnout and an additional 29 (31%) met the criteria for moderately high burnout. Decreased current job satisfaction and low self-reported spousal/significant other support were independent predictors of high burnout risk.

Conclusion

Fifty-one percent of academic anesthesiology chairs exhibit a high incidence/risk of burnout. Age, sex, time as a chair, hours worked, and perceived effectiveness were not associated with high burnout; however, low job satisfaction and reduced self-reported spousal/significant other support significantly increased the risk.
Alternative life histories in the Atlantic salmon: genetic covariances within the sneaker sexual tactic in males
Authors: Páez David James , Bernatchez Louis , Dodson Julian J.
Published: December 2010

Alternative reproductive tactics are ubiquitous in many species. Tactic expression often depends on whether an individual's condition surpasses thresholds that are responsible for activating particular developmental pathways. Two central goals in understanding the evolution of reproductive tactics are quantifying the extent to which thresholds are explained by additive genetic effects, and describing their covariation with condition-related traits. We monitored the development of early sexual maturation that leads to the sneaker reproductive tactic in Atlantic salmon (
Salmo salar
L.). We found evidence for additive genetic variance in the timing of sexual maturity (which is a measure of the surpassing of threshold values) and body-size traits. This suggests that selection can affect the patterns of sexual development by changing the timing of this event and/or body size. Significant levels of covariation between these traits also occurred, implying a potential for correlated responses to selection. Closer examination of genetic covariances suggests that the detected genetic variation is distributed along at least five directions of phenotypic variation. Our results show that the potential for evolution of the life-history traits constituting this reproductive phenotype is greatly influenced by their patterns of genetic covariance.
Asymmetric reproductive character displacement in male aggregation behaviour
Authors: Pfennig Karin S. , Stewart Alyssa B.
Published: December 2010

Reproductive character displacement—the evolution of traits that minimize reproductive interactions between species—can promote striking divergence in male signals or female mate preferences between populations that do and do not occur with heterospecifics. However, reproductive character displacement can affect other aspects of mating behaviour. Indeed, avoidance of heterospecific interactions might contribute to spatial (or temporal) aggregation of conspecifics. We examined this possibility in two species of hybridizing spadefoot toad (genusSpea). We found that inSpea bombifronssympatric males were more likely than allopatric males to associate with calling males. Moreover, contrary to allopatric males, sympatricS. bombifronsmales preferentially associated with conspecific male calls. By contrast,Spea multiplicatashowed no differences between sympatry and allopatry in likelihood to associate with calling males. Further, sympatric and allopatric males did not differ in preference for conspecifics. However, allopatricS. multiplicatawere more variable than sympatric males in their responses. Thus, inS. multiplicata, character displacement may have refined pre-existing aggregation behaviour. Our results suggest that heterospecific interactions can foster aggregative behaviour that might ultimately contribute to clustering of conspecifics. Such clustering can generate spatial or temporal segregation of reproductive activities among species and ultimately promote reproductive isolation.
Shifting sources of productivity in the coastal marine tropics during the Cenozoic era
Authors: Vermeij Geerat J.
Published: December 2010

Changes in the rates and sources of marine primary production over time are difficult to document owing to the absence of direct estimates of past productivity. Here, I use the maximum body sizes of the largest species in each of 23 tropical shallow-water marine molluscan guilds (groups of species with similar habits and trophic roles) to trace the relative importance of planktonic and benthic primary productivity from the Eocene (55 Ma) onwards. The largest members of guilds are least constrained in exploiting resources and therefore reflect the availability and accessibility of those resources most accurately. Maximum sizes of suspension-feeders and predators increased by a factor of 2.3 and 4.0, respectively, whereas those in four out of five herbivorous guilds declined. I interpret these patterns, which are discernible throughout the coastal tropics, to mean that primary production in the Eocene marine tropics was concentrated on the seafloor, as is the case today on offshore reefs and islands, and that the Miocene to the recent interval witnessed a dramatic increase in planktonic productivity along continental margins. The rise in planktonic fertility is best explained by an increase in nutrient supply from the land associated with intense global tectonic activity and more vigorous ocean mixing owing to cooling.
A worm's best friend: recruitment of neutrophils by
Wolbachia
confounds eosinophil degranulation against the filarial nematode
Onchocerca ochengi
Authors: Hansen Rowena D. E. , Trees Alexander J. , Bah Germanus S. , Hetzel Udo , Martin Coralie , Bain Odile , Tanya Vincent N. , Makepeace Benjamin L.
Published: December 2010

Onchocerca ochengi
, a filarial parasite of cattle, represents the closest relative of the human pathogen,
Onchocerca volvulus
. Both species harbour
Wolbachia
endosymbionts and are remarkable in that adult female worms remain viable but sessile for many years while surrounded by host cells and antibodies. The basis of the symbiosis between filariae and
Wolbachia
is thought to be metabolic, although a role for
Wolbachia
in immune evasion has received little attention. Neutrophils are attracted to
Wolbachia
, but following antibiotic chemotherapy they are replaced by eosinophils that degranulate on the worm cuticle. However, it is unclear whether the eosinophils are involved in parasite killing or if they are attracted secondarily to dying worms. In this study, cattle infected with
Onchocerca ochengi
received adulticidal regimens of oxytetracycline or melarsomine. In contrast to oxytetracycline, melarsomine did not directly affect
Wolbachia
viability. Eosinophil degranulation increased significantly only in the oxytetracycline group; whereas nodular gene expression of bovine neutrophilic chemokines was lowest in this group. Moreover, intense eosinophil degranulation was initially associated with worm vitality, not degeneration. Taken together, these data offer strong support for the hypothesis that
Wolbachia
confers longevity on
O. ochengi
through a defensive mutualism, which diverts a potentially lethal effector cell response.
Emergent neutrality drives phytoplankton species coexistence
Authors: Segura Angel M. , Calliari Danilo , Kruk Carla , Conde Daniel , Bonilla Sylvia , Fort Hugo
Published: December 2010

The mechanisms that drive species coexistence and community dynamics have long puzzled ecologists. Here, we explain species coexistence, size structure and diversity patterns in a phytoplankton community using a combination of four fundamental factors: organism traits, size-based constraints, hydrology and species competition. Using a ‘microscopic’ Lotka–Volterra competition (MLVC) model (i.e. with explicit recipes to compute its parameters), we provide a mechanistic explanation of species coexistence along a niche axis (i.e. organismic volume). We based our model on empirically measured quantities, minimal ecological assumptions and stochastic processes. In nature, we found aggregated patterns of species biovolume (i.e. clumps) along the volume axis and a peak in species richness. Both patterns were reproduced by the MLVC model. Observed clumps corresponded to niche zones (volumes) where species fitness was highest, or where fitness was equal among competing species. The latter implies the action of equalizing processes, which would suggest emergent neutrality as a plausible mechanism to explain community patterns.
Phenological variation in annual timing of hibernation and breeding in nearby populations of Arctic ground squirrels
Authors: Sheriff Michael J. , Kenagy G. Jim , Richter Melanie , Lee Trixie , Tøien Øivind , Kohl Franziska , Buck C. Loren , Barnes Brian M.
Published: December 2010

Ecologists need an empirical understanding of physiological and behavioural adjustments that animals can make in response to seasonal and long-term variations in environmental conditions. Because many species experience trade-offs between timing and duration of one seasonal event versus another and because interacting species may also shift phenologies at different rates, it is possible that, in aggregate, phenological shifts could result in mismatches that disrupt ecological communities. We investigated the timing of seasonal events over 14 years in two Arctic ground squirrel populations living 20 km apart in Northern Alaska. At Atigun River, snow melt occurred 27 days earlier and snow cover began 17 days later than at Toolik Lake. This spatial differential was reflected in significant variation in the timing of most seasonal events in ground squirrels living at the two sites. Although reproductive males ended seasonal torpor on the same date at both sites, Atigun males emerged from hibernation 9 days earlier and entered hibernation 5 days later than Toolik males. Atigun females emerged and bred 13 days earlier and entered hibernation 9 days earlier than those at Toolik. We propose that this variation in phenology over a small spatial scale is likely generated by plasticity of physiological mechanisms that may also provide individuals the ability to respond to variation in environmental conditions over time.
Cyanide degradation by Pseudomonas pseudoalcaligenes CECT5344 involves a malate : quinone oxidoreductase and an associated cyanide-insensitive electron transfer chain
Authors: Luque-Almagro Victor M. , Merchán Faustino , Blasco Rafael , Igeño M. Isabel , Martínez-Luque Manuel , Moreno-Vivián Conrado , Castillo Francisco , Roldán M. Dolores
Published: December 2010

The alkaliphilic bacteriumPseudomonas pseudoalcaligenesCECT5344 is able to grow with cyanide as the sole nitrogen source. Membrane fractions from cells grown under cyanotrophic conditions catalysed the production of oxaloacetate froml-malate. Several enzymic activities of the tricarboxylic acid and glyoxylate cycles in association with the cyanide-insensitive respiratory pathway seem to be responsible for the oxaloacetate formationin vivo. Thus, in cyanide-grown cells, citrate synthase and isocitrate lyase activities were significantly higher than those observed with other nitrogen sources. Malate dehydrogenase activity was undetectable, but a malate : quinone oxidoreductase activity coupled to the cyanide-insensitive alternative oxidase was found in membrane fractions from cyanide-grown cells. Therefore, oxaloacetate production was linked to the cyanide-insensitive respiration inP. pseudoalcaligenesCECT5344. Cyanide and oxaloacetate reacted chemically inside the cells to produce a cyanohydrin (2-hydroxynitrile), which was further converted to ammonium. In addition to cyanide, strain CECT5344 was able to grow with several cyano derivatives, such as 2- and 3-hydroxynitriles. The specific system required for uptake and metabolization of cyanohydrins was induced by cyanide and by 2-hydroxynitriles, such as the cyanohydrins of oxaloacetate and 2-oxoglutarate.
Enhanced recovery of Salmonella Typhimurium DT104 from exposure to stress at low temperature
Authors: Humphrey Suzanne , Clark Leann F. , Humphrey Tom J. , Jepson Mark A.
Published: December 2010

Salmonella enterica serovar Typhimurium (S. Typhimurium) remains an important cause of food-borne infection in the developed world. In order to establish infection within a host, Salmonella must survive and recover from a range of environmental stresses. S. Typhimurium strain SL1344 is among the most extensively studied pathogenic Salmonella strains, while S. Typhimurium phage type DT104 is an important type that has been associated with pandemic spread and a high number of food-borne disease outbreaks over the last two decades. In this study, we have compared the abilities of these two S. Typhimurium types to recover from stress exposures commonly encountered in food production, including 685 mM NaCl, pH 3.8, low temperature (6 °C) and combinations thereof. Following removal from prolonged (8 days) stress, DT104 cultures that had been exposed to low temperature, with or without additional stress, resumed exponential growth more rapidly than SL1344 cultures exposed to the same conditions. SL1344 showed higher levels of filamentation than DT104 in response to NaCl exposure at low temperature. Further, SL1344 incurred higher levels of membrane damage in response to elevated NaCl and pH 3.8 at both temperatures compared with DT104. However, both strains recovered normal cell division and membrane integrity within 6 h when all stresses were removed. Expression of the Salmonella pathogenicity island 1 gene prgH, the first gene in the prg/org operon, was monitored using a chromosomal reporter in which gfp+
expression was driven by the prgH promoter. Recovery of prgH expression was comparable for SL1344 and DT104 exposed to stress at 22 °C. However, DT104 cultures exposed to pH 3.8 or combined NaCl and low-pH stress at low temperature resumed prgH expression more rapidly than SL1344. Both strains recovered maximal levels of prgH expression after 6 h recovery from all stresses and, interestingly, maximal levels of prgH expression were significantly higher in SL1344, consistent with prgH expression in late-exponential, non-stressed SL1344 and DT104 cultures. Together, these data show that S. Typhimurium is capable of rapid recovery from environmental and food-related stresses, and give insight into the enhanced ability of DT104 compared with SL1344 to adapt to such stresses, which may contribute to the success of this globally disseminated pathogenic phage type.
Effects of high-pressure carbon dioxide on proteins and DNA in Escherichia coli
Authors: Liao Hongmei , Zhang Fusheng , Hu Xiaosong , Liao Xiaojun
Published: December 2010

Protein changes in Escherichia coli, when subjected to high-pressure carbon dioxide (HPCD) at 10 MPa and 3 °C for 5–75 min, were assessed using the Bradford method, 2D electrophoresis (2-DE) and liquid chromatography-electrospray ionization-MS-MS (LC-ESI-MS-MS). The changes in DNA in E. coli under the same conditions were also investigated by using flow cytometry with propidium iodide and acridine orange, agarose gel electrophoresis (AGE) and the comet assay. The results showed that HPCD induced leakage loss of the proteins and DNA of E. coli as a function of treatment time. With regard to the protein changes, 182 proteins in the 2-DE profile were not found in the HPCD-treated E. coli. Among 20 selected protein spots exhibiting significant changes in intensity, 18 protein spots were identified as 15 known proteins and two as hypothetical proteins. These proteins were involved in cell composition, energy metabolism pathways, nucleic acid metabolism, global stress regulation and general metabolism. The DNA denaturation of E. coli induced by HPCD was demonstrated in this study for the first time to our knowledge, and the denaturation was enhanced by increasing treatment time. However, HPCD did not cause DNA degradation, as suggested by both AGE analysis and the comet assay.
A global analysis of C. elegans trans-splicing
Authors: Allen Mary Ann , Hillier LaDeana W. , Waterston Robert H. , Blumenthal Thomas
Published: December 2010

Trans-splicing of one of two short leader RNAs, SL1 or SL2, occurs at the 5′ ends of pre-mRNAs of many C. elegans genes. We have exploited RNA-sequencing data from the modENCODE project to analyze the transcriptome of C. elegans for patterns of trans-splicing. Transcripts of ∼70% of genes are trans-spliced, similar to earlier estimates based on analysis of far fewer genes. The mRNAs of most trans-spliced genes are spliced to either SL1 or SL2, but most genes are not trans-spliced to both, indicating that SL1 and SL2 trans-splicing use different underlying mechanisms. SL2 trans-splicing occurs in order to separate the products of genes in operons genome wide. Shorter intercistronic distance is associated with greater use of SL2. Finally, increased use of SL1 trans-splicing to downstream operon genes can indicate the presence of an extra promoter in the intercistronic region, creating what has been termed a “hybrid” operon. Within hybrid operons the presence of the two promoters results in the use of the two SL classes: Transcription that originates at the promoter upstream of another gene creates a polycistronic pre-mRNA that receives SL2, whereas transcription that originates at the internal promoter creates transcripts that receive SL1. Overall, our data demonstrate that >17% of all C. elegans genes are in operons.
Polycomb preferentially targets stalled promoters of coding and noncoding transcripts
Authors: Enderle Daniel , Beisel Christian , Stadler Michael B. , Gerstung Moritz , Athri Prashanth , Paro Renato
Published: December 2010

The Polycomb group (PcG) and Trithorax group (TrxG) of proteins are required for stable and heritable maintenance of repressed and active gene expression states. Their antagonistic function on gene control, repression for PcG and activity for TrxG, is mediated by binding to chromatin and subsequent epigenetic modification of target loci. Despite our broad knowledge about composition and enzymatic activities of the protein complexes involved, our understanding still lacks important mechanistic detail and a comprehensive view on target genes. In this study we use an extensive data set of ChIP-seq, RNA-seq, and genome-wide detection of transcription start sites (TSSs) to identify and analyze thousands of binding sites for the PcG proteins and Trithorax from a Drosophila S2 cell line. In addition of finding a preference for stalled promoter regions of annotated genes, we uncover many intergenic PcG binding sites coinciding with nonannotated TSSs. Interestingly, this set includes previously unknown promoters for primary transcripts of microRNA genes, thereby expanding the scope of Polycomb control to noncoding RNAs essential for development, apoptosis, and growth.
Developmental control of the DNA replication and transcription programs
Authors: Nordman Jared , Li Sharon , Eng Thomas , MacAlpine David , Orr-Weaver Terry L.
Published: December 2010

Polyploid or polytene cells, which have more than 2C DNA content, are widespread throughout nature and present in most differentiated Drosophila tissues. These cells also can display differential replication, that is, genomic regions of increased or decreased DNA copy number relative to overall genomic ploidy. How frequently differential replication is used as a developmental strategy remains unclear. Here, we use genome-wide array-based comparative genomic hybridization (aCGH) to profile differential DNA replication in isolated and purified larval fat body and midgut tissues of Drosophila, and we compare them with recent aCGH profiles of the larval salivary gland. We identify sites of euchromatic underreplication that are common to all three tissues and others that are tissue specific. We demonstrate that both common and tissue-specific underreplicated sites are dependent on the Suppressor of Underreplication protein, SUUR. mRNA-seq profiling shows that whereas underreplicated regions are generally transcriptionally silent in the larval midgut and salivary gland, transcriptional silencing and underreplication have been uncoupled in the larval fat body. In addition to revealing the prevalence of differential replication, our results show that transcriptional silencing and underreplication can be mechanistically uncoupled.