bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Single or Double Exposures to Hydrogen Peroxide or Iodine on Salmonid Egg Survival and Bacterial Growth
Authors: Wagner Eric J , Oplinger Randall W , Bartley Matthew
Published: February 2012

Four disinfection tests were conducted on the eggs of cutthroat trout Oncorhynchus clarkii, rainbow trout O. mykiss, and brown trout Salmo trutta. In each egg test, the effects of treating twice were determined, which simulated treatment at both the brood source and the receiving hatchery. Cutthroat trout eggs were treated at 1 h and again at 3 or 6 h after fertilization. Survival to the eyed stage was greater for eggs treated with 100 mg/L iodine for 10 min (86.9%) than with 1.5% hydrogen peroxide (H2O2) for 2 min (82.4%); the timing of the second disinfection had no effect on egg survival. Bacterial growth was significantly greater among H2O2-treated eggs. For eyed rainbow trout eggs, 2,000 mg/L iodine for 10 min was toxic (<11% hatch), but eggs treated either once or twice with hydrogen peroxide (1% H2O2 for 2 min) survived to hatch, as did the controls. Bacterial growth was significantly greater on eggs treated with H2O2 than control eggs treated with 100 mg/L iodine for 10 min. In a subsequent test with eyed rainbow trout eggs exposed to 1,000 mg/L iodine for 15 min either once or twice, hatching rates did not significantly differ from those of controls. Bacterial growth was significantly lower after 1,000-mg/L iodine treatment than in controls treated with 100 mg/L. In the fourth test, survival to hatch of eyed brown trout eggs treated with 1,000 mg/L iodine once or twice did not differ from that of controls. For bacterial control, double treatments are safe at iodine doses of no more than 1,000 mg/L or when 1% H2O2 is used. The bacteriological results suggest that a single or double dose of 1,000 mg/L iodine provides the best control of bacterial growth.
Fluctuations with long-distance correlation in quasi-stationary and transient plasmas of LHD
Authors: Inagaki S. , Tamura N. , Tokuzawa T. , Ida K. , Kobayashi T. , Shimozuma T. , Kubo S. , Tsuchiya H. , Nagayama Y. , Kawahata K. , Sudo S. , Fujisawa A. , Itoh K. , Itoh S.-I.
Published: February 2012

Electron temperature fluctuations with long-distance correlation have been discovered in LHD. This paper reports the extended observations recently made on the spatiotemporal structure of the long-range fluctuations both in quasi-stationary and transient plasmas. The detailed characteristics or spatiotemporal characteristics of long-range temperature fluctuations are revealed successfully using correlation analysis. Particularly, the dynamics of the long-range fluctuations is investigated to find that the amplitude of the fluctuations decreased and their radial correlation lengths shortened during the transient phase induced by pellet injection. Temporal changes of radial correlation structure and amplitude of fluctuations at the onset of change in the plasma state are discussed.
Functional and haemodynamic recovery after implantation of continuous‐flow left ventricular assist devices in comparison with pulsatile left ventricular assist devices in patients with end‐stage heart failure
Authors: Pruijsten Ralph V. , Lok Sjoukje I. , Kirkels Hans H. , Klöpping Corinne , Lahpor Jaap R. , de Jonge Nicolaas
Published: February 2012

Aims

Caused by ageing of the population, better survival from ischaemic heart disease, and improved treatment of chronic heart disease, the incidence of heart failure has increased enormously. Worldwide, left ventricular assist devices (LVADs) are increasingly being used as a bridge or alternative to heart transplantation. In this study, we investigated whether there is difference in functional and haemodynamic recovery after implantation of pulsatile and continuous‐flow pumps.

Methods and results

We compared laboratory and echocardiographic data and exercise performance in patients with end‐stage heart failure, before and 3 months after implantation of pulsatile and continuous‐flow LVADs. A significant improvement in all laboratory parameters after implantation of both types of LVADs was seen, as well as a significant decrease in heart rate and LV dimensions, indicating better haemodynamics and cardiac recompensation. This improvement was better for the pulsatile device, probably due to higher plasma levels and higher LV dimensions before implantation. Exercise capacity strongly improved: 3 months after implantation of pulsatile and continuous‐flow LVADs, peak VO2 was 20.2 ± 4.8 vs. 18.3 ± 4.8 mL/kg/min (P = 0.09) (53 ± 12 vs. 49 ± 11% of predicted for age and gender) (P = 0.28).

Conclusion

Pulsatile and continuous‐flow LVADs result in extensive haemodynamic recovery and exercise performance compatible with daily life activities. Exercise performance with continuous‐flow LVADs is equal to that with pulsatile devices. This, in combination with improved survival of the newer devices, allows its use as an alternative to heart transplantation in selected patients.
Ejection fraction and outcomes in patients with atrial fibrillation and heart failure: the Loire Valley Atrial Fibrillation Project
Authors: Banerjee Amitava , Taillandier Sophie , Olesen Jonas Bjerring , Lane Deirdre A. , Lallemand Benedicte , Lip Gregory Y.H. , Fauchier Laurent
Published: February 2012

Aims

Heart failure (HF) increases the risk of stroke and thrombo‐embolism (TE) in non‐valvular atrial fibrillation (NVAF), and is incorporated in stroke risk stratification scores. We aimed to establish the role of ejection fraction (EF) in risk prediction in patients with NVAF and HF.

Methods and results

Patients with NVAF, history of HF, and measured EF were included in a retrospective analysis. Patients with HF and preserved ejection fraction (HFPEF) were defined as those with clinical HF and EF ≥50% in this study. Among 7156 patients with NVAF, 1276 (17.8%) patients with HF and measured EF were included. Of these, 747/1276 (58.5%) patients were on vitamin K antagonists. The stroke/TE event rate per 100 person‐years was 1.05 [95% confidence interval (CI) 0.87–1.25]. Patients with HFPEF were more likely to be female (P < 0.001), older (P < 0.001), and hypertensive (P < 0.001), and less likely to have prior vascular disease (P < 0.001). There were no differences in rates of stroke (P = 0.17) and stroke/TE (P = 0.11) between patients with HFPEF and those with HF and reduced EF. There were no significant differences in rates of all‐cause mortality when patients were stratified by EF. In multivariate analyses, only previous stroke (hazard ratio 2.36, 95% CI 1.45–3.86) and vascular disease (1.57, 1.07–2.30) increased the risk of stroke/TE amongst NVAF patients with HF, but EF <35% did not (0.75, 0.44–1.30).

Conclusion

In NVAF patients with HF, there were no differences in rates of stroke, TE, or death between EF categories. Only previous stroke and vascular disease (and not decreased EF) independently increased risk of stroke/TE in multivariate analyses.
Thermal habitat for 0-group fish in the Barents Sea; how climate variability impacts their density, length, and geographic distribution
Authors: Eriksen Elena , Ingvaldsen Randi , Stiansen Jan Erik , Johansen Geir Odd
Published: February 2012

Eriksen, E., Ingvaldsen, R., Stiansen, J. E., and Johansen, G. O. 2012. Thermal habitat for 0-group fish in the Barents Sea; how climate variability impacts their density, length, and geographic distribution. – ICES Journal of Marine Science, 69: 870–879. Between 1980 and 2008, the climate changed from cold to warm conditions in the Barents Sea. Warmer conditions have been indicated as favourable for cod, haddock, and herring recruitment and unfavourable for capelin, although during recent years these relationships have weakened and need to be revised. Extensive survey observations of temperature and 0-group cod, haddock, herring, and capelin are explored, a bounded temperature range occupied by ∼80–90% of 0-group fish (core thermal habitat, CTH) defined for each species, and an analysis made of how climate variability influenced density, length, and geographic distribution. Maximum fish densities were at 6.2°C for cod, 7.2°C for haddock, 7.0°C for herring, and 5.1°C for capelin. The area of CTH for cod, haddock, and herring increased from cold to warm years, as did the occupation area of each species. Capelin underwent a northeast distributional shift from cold to warm years. The 0-group fish were observed in a broad range of temperatures of −1 to 10.5°C. However, fish densities showed a dome-shaped distribution with temperature. Mean fish length was 7.1 cm for cod, 8.9 cm for haddock, 7.0 cm for herring, and 4.6 cm for capelin, with length distributions exhibiting a non-uniform response to temperature.
Remote copulation: male adaptation to female cannibalism
Authors: Li Daiqin , Oh Joelyn , Kralj-Fišer Simona , Kuntner Matjaž
Published: February 2012

Sexual cannibalism by females and associated male behaviours may be driven by sexual conflict. One such male behaviour is the eunuch phenomenon in spiders, caused by total genital emasculation, which is a seemingly maladaptive behaviour. Here, we provide the first empirical testing of an adaptive hypothesis to explain this behaviour, the remote copulation, in a highly sexually cannibalistic orb-web spider
Nephilengys malabarensis
. We demonstrate that sperm transfer continues from the severed male organ into female genitals after the male has been detached from copula. Remote copulation increases the total amount of sperm transferred, and thus probably enhances paternity. We conclude that the mechanism may have evolved in response to sexual cannibalism and female-controlled short copulation duration.
Electromagnetic characterization of millimetre-scale replicas of the gyroid photonic crystal found in the butterfly
Parides sesostris
Authors: Pouya C. , Vukusic P.
Published: February 2012

We have used three-dimensional stereolithography to synthetically replicate the gyroid photonic crystal (PC) structure that occurs naturally in the butterfly
Parides sesostris
. We have experimentally characterized the transmission response of this structure in the microwave regime at two azimuthal angles (
ϕ
) over a comprehensive range of polar angles (
θ
). We have modelled its electromagnetic response using the finite-element method (FEM) and found excellent agreement with experimental data. Both theory and experiment show a single relatively broad transmission minimum at normal incidence (
θ
= 0°) that comprises several narrow band resonances which separate into clearly identifiable stop-bands at higher polar angles. We have identified the specific effective geometric planes within the crystal, and their associated periodicities that give rise to each of these stop-bands. Through extensive theoretical FEM modelling of the gyroid PC structure, using varying filling fractions of material and air, we have shown that a gyroid PC with material volume fraction of 40 per cent is appropriate for optimizing the reflected bandwidth at normal incidence (for a refractive index contrast of 1.56). This is the same gyroid PC material volume fraction used by the butterfly
P. sesostris
itself to produce its green structurally coloured appearance. This infers further optimization of this biological PC beyond that of its lattice constant alone.
Resonance in herbaceous plant stems as a factor in vibrational communication of pentatomid bugs (Heteroptera: Pentatomidae)
Authors: Polajnar Jernej , Svenšek Daniel , Čokl Andrej
Published: February 2012

Pentatomid bugs communicate using substrate-borne vibrational signals that are transmitted along herbaceous plant stems in the form of bending waves with a regular pattern of minimal and maximal amplitude values with distance. We tested the prediction that amplitude variation is caused by resonance, by measuring amplitude profiles of different vibrational pulses transmitted along the stem of aCyperus alternifoliusplant, and comparing their patterns with calculated spatial profiles of corresponding eigenfrequencies of a model system. The measured distance between nodes of the amplitude pattern for pulses with different frequencies matches the calculated values, confirming the prediction that resonance is indeed the cause of amplitude variation in the studied system. This confirmation is supported by the resonance profile obtained by a frequency sweep, which matches theoretical predictions of the eigenfrequencies of the studied system. Signal bandwidth influences the amount of amplitude variation. The effect of both parameters on signal propagation is discussed in the context of insect vibrational communication.
The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins
Authors: Burki Fabien , Okamoto Noriko , Pombert Jean-François , Keeling Patrick J.
Published: February 2012

An important missing piece in the puzzle of how plastids spread across the eukaryotic tree of life is a robust evolutionary framework for the host lineages. Four assemblages are known to harbour plastids derived from red algae and, according to the controversial chromalveolate hypothesis, these all share a common ancestry. Phylogenomic analyses have consistently shown that stramenopiles and alveolates are closely related, but haptophytes and cryptophytes remain contentious; they have been proposed to branch together with several heterotrophic groups in the newly erected Hacrobia. Here, we tested this question by producing a large expressed sequence tag dataset for the katablepharid
Roombia truncata
, one of the last hacrobian lineages for which genome-level data are unavailable, and combined this dataset with the recently completed genome of the cryptophyte
Guillardia theta
to build an alignment composed of 258 genes. Our analyses strongly support haptophytes as sister to the SAR group, possibly together with telonemids and centrohelids. We also confirmed the common origin of katablepharids and cryptophytes, but these lineages were not related to other hacrobians; instead, they branch with plants. Our study resolves the evolutionary position of haptophytes, an ecologically critical component of the oceans, and proposes a new hypothesis for the origin of cryptophytes.
Investigating sex-biased migration during the Neolithic transition in Europe, using an explicit spatial simulation framework
Authors: Rasteiro Rita , Bouttier Pierre-Antoine , Sousa Vítor C. , Chikhi Lounès
Published: February 2012

Cultural practices can deeply influence genetic diversity patterns. The Neolithic transitions that took place at different times and locations around the world led to major cultural and demographic changes that influenced and therefore left their marks on human genetic diversity patterns. Several studies on the European Neolithic transition suggest that mitochondrial DNA (mtDNA) and Y-chromosome data can exhibit different patterns, which could be owing to different demographic histories for females and males. Archaeological and anthropological data suggest that the transition from hunter–gatherers (HGs) to farmers' societies is probably associated with changes in social organization, particularly in post-marital residence (PMR) rules (i.e. patrilocality, matrilocality or bilocality). The movements of humans and genes associated with these rules can be seen as sex-biased short-range migrations. We developed a new individual-based simulation approach to explore the genetic consequences of 45 different scenarios, where we varied the patterns of PMR and admixture between HGs and farmers. We recorded mtDNA and Y-chromosome data and analysed their diversity patterns within and between populations, through time and space. We also collected published mtDNA and Y-chromosome data from European and Near-Eastern populations in order to identify the scenarios that would best explain them. We show that: (i) different PMR systems can lead to different patterns of genetic diversity and differentiation, (ii) asymmetries between mtDNA and Y-chromosome can be owing to different behaviours between males and females, but also to different mutations rates, and (iii) patrilocality in farmers explains the present patterns of genetic diversity better than matrilocality or bilocality. Moreover, we found that (iv) the genetic diversity of farmers change depending on the HGs PMR rules even though they are assumed to disappear more than 5000 years ago in our simulations.
Linking genes to communities and ecosystems:
Daphnia
as an ecogenomic model
Authors: Miner Brooks E. , De Meester Luc , Pfrender Michael E. , Lampert Winfried , Hairston Nelson G.
Published: February 2012

How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea
Daphnia
satisfies these criteria, and genomic approaches capitalizing on the pivotal role
Daphnia
plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity,
Daphnia
represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make
Daphnia
a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances.
Skeletal development in the African elephant and ossification timing in placental mammals
Authors: Hautier Lionel , Stansfield Fiona J. , Allen W. R. Twink , Asher Robert J.
Published: February 2012

We provide here unique data on elephant skeletal ontogeny. We focus on the sequence of cranial and post-cranial ossification events during growth in the African elephant (Loxodonta africana). Previous analyses on ossification sequences in mammals have focused on monotremes, marsupials, boreoeutherian and xenarthran placentals. Here, we add data on ossification sequences in an afrotherian. We use two different methods to quantify sequence heterochrony: the sequence method and event-paring/Parsimov. Compared with other placentals, elephants show late ossifications of the basicranium, manual and pedal phalanges, and early ossifications of the ischium and metacarpals. Moreover, ossification in elephants starts very early and progresses rapidly. Specifically, the elephant exhibits the same percentage of bones showing an ossification centre at the end of the first third of its gestation period as the mouse and hamster have close to birth. Elephants show a number of features of their ossification patterns that differ from those of other placental mammals. The pattern of the initiation of the ossification evident in the African elephant underscores a possible correlation between the timing of ossification onset and gestation time throughout mammals.
Testosterone disrupts human collaboration by increasing egocentric choices
Authors: Wright Nicholas D. , Bahrami Bahador , Johnson Emily , Di Malta Gina , Rees Geraint , Frith Christopher D. , Dolan Raymond J.
Published: February 2012

Collaboration can provide benefits to the individual and the group across a variety of contexts. Even in simple perceptual tasks, the aggregation of individuals' personal information can enable enhanced group decision-making. However, in certain circumstances such collaboration can worsen performance, or even expose an individual to exploitation in economic tasks, and therefore a balance needs to be struck between a collaborative and a more egocentric disposition. Neurohumoral agents such as oxytocin are known to promote collaborative behaviours in economic tasks, but whether there are opponent agents, and whether these might even affect information aggregation without an economic component, is unknown. Here, we show that an androgen hormone, testosterone, acts as such an agent. Testosterone causally disrupted collaborative decision-making in a perceptual decision task, markedly reducing performance benefit individuals accrued from collaboration while leaving individual decision-making ability unaffected. This effect emerged because testosterone engendered more egocentric choices, manifest in an overweighting of one's own relative to others' judgements during joint decision-making. Our findings show that the biological control of social behaviour is dynamically regulated not only by modulators promoting, but also by those diminishing a propensity to collaborate.
Visual extrapolation under risk: human observers estimate and compensate for exogenous uncertainty
Authors: Warren Paul A. , Graf Erich W. , Champion Rebecca A. , Maloney Laurence T.
Published: February 2012

Humans commonly face choices between multiple options with uncertain outcomes. Such situations occur in many contexts, from purely financial decisions (which shares should I buy?) to perceptuo-motor decisions between different actions (where should I aim my shot at goal?). Regardless of context, successful decision-making requires that the uncertainty at the heart of the decision-making problem is taken into account. Here, we ask whether humans can recover an estimate of exogenous uncertainty and then use it to make good decisions. Observers viewed a small dot that moved erratically until it disappeared behind an occluder. We varied the size of the occluder and the unpredictability of the dot's path. The observer attempted to capture the dot as it emerged from behind the occluded region by setting the location and extent of a ‘catcher’ along the edge of the occluder. The reward for successfully catching the dot was reduced as the size of the catcher increased. We compared human performance with that of an agent maximizing expected gain and found that observers consistently selected catcher size close to this theoretical solution. These results suggest that humans are finely tuned to exogenous uncertainty information and can exploit it to guide action.
Foraging costs drive female resistance to a sensory trap
Authors: Garcia Constantino Macías , Lemus Yolitzi Saldívar
Published: February 2012

Male ornaments can evolve through the exploitation of female perceptual biases such as those involved in responding to cues from food. This type of sensory exploitation may lead to confusion between the male signals and the cues that females use to find/recognize food. Such interference would be costly to females and may be one reason why females evolve resistance to the male ornaments. Using a group of species of viviparous fish where resistance to a sensory trap has evolved, we demonstrate that females exposed to an ornament that resembles food have a diminished foraging efficiency, that this effect is apparent when foraging on a food item with which the ornament shares visual attributes, and that not all species are equally affected by such confusion. Our results lend support to the model of ornamental evolution through chase-away sexual conflict.
Disturbance–diversity models: what do they really predict and how are they tested?
Authors: Svensson J. Robin , Lindegarth Mats , Jonsson Per R. , Pavia Henrik
Published: February 2012

The intermediate disturbance hypothesis (IDH) and the dynamic equilibrium model (DEM) are influential theories in ecology. The IDH predicts large species numbers at intermediate levels of disturbance and the DEM predicts that the effect of disturbance depends on the level of productivity. However, various indices of diversity are considered more commonly than the predicted number of species in tests of the hypotheses. This issue reaches beyond the scientific community as the predictions of the IDH and the DEM are used in the management of national parks and reserves. In order to compare responses with disturbance among measures of biodiversity, we used two different approaches of mathematical modelling and conducted an extensive meta-analysis. Two-thirds of the surveyed studies present different results for different diversity measures. Accordingly, the meta-analysis showed a narrow range of negative quadratic regression components for richness, but not evenness. Also, the two models support the IDH and the DEM, respectively, when biodiversity is measured as species richness, but predict evenness to increase with increasing disturbance, for all levels of productivity. Consequently, studies that use compound indices of diversity should present logical arguments,
a priori
, to why a specific index of diversity should peak in response to disturbance.
The limits of brain determinacy
Authors: Clarke Peter G. H.
Published: February 2012

The genes do not control everything that happens in a cell or an organism, because thermally induced molecular movements and conformation changes are beyond genetic control. The importance of uncontrolled events has been argued from the differences between isogenic organisms reared in virtually identical environments, but these might alternatively be attributed to subtle, undetected differences in the environment. The present review focuses on the uncontrolled events themselves in the context of the developing brain. These are considered at cellular and circuit levels because even if cellular physiology was perfectly controlled by the genes (which it is not), the interactions between different cells might still be uncoordinated. A further complication is that the brain contains mechanisms that buffer noise and others that amplify it. The final resultant of the battle between these contrary mechanisms is that developmental stochasticity is sufficiently low to make neurobehavioural defects uncommon, but a chance component of neural development remains. Thus, our brains and behaviour are not entirely determined by a combination of genes-plus-environment.
Tel1ATM and Rad3ATR phosphorylate the telomere protein Ccq1 to recruit telomerase and elongate telomeres in fission yeast
Authors: Yamazaki Harutake , Tarumoto Yusuke , Ishikawa Fuyuki
Published: February 2012

In fission yeast, the DNA damage sensor kinases Tel1ATM and Rad3ATR exist at telomeres and are required for telomere maintenance, but the biological role they play at telomeres is not known. Here we show that the telomere protein Ccq1 is phosphorylated at Thr 93 (threonine residue at amino acid 93) by Tel1ATM and Rad3ATR both in vitro and in vivo. A ccq1 mutant in which alanine was substituted for Thr 93 failed to recruit telomerase to telomeres and showed gradual shortening of telomeres. These results indicate that the direct phosphorylation of Ccq1 Thr 93 by Tel1 and Rad3 is involved in the recruitment of telomerase to elongate telomeres.
NF-κB, the first quarter-century: remarkable progress and outstanding questions
Authors: Hayden Matthew S. , Ghosh Sankar
Published: February 2012

The ability to sense and adjust to the environment is crucial to life. For multicellular organisms, the ability to respond to external changes is essential not only for survival but also for normal development and physiology. Although signaling events can directly modify cellular function, typically signaling acts to alter transcriptional responses to generate both transient and sustained changes. Rapid, but transient, changes in gene expression are mediated by inducible transcription factors such as NF-κB. For the past 25 years, NF-κB has served as a paradigm for inducible transcription factors and has provided numerous insights into how signaling events influence gene expression and physiology. Since its discovery as a regulator of expression of the κ light chain gene in B cells, research on NF-κB continues to yield new insights into fundamental cellular processes. Advances in understanding the mechanisms that regulate NF-κB have been accompanied by progress in elucidating the biological significance of this transcription factor in various physiological processes. NF-κB likely plays the most prominent role in the development and function of the immune system and, not surprisingly, when dysregulated, contributes to the pathophysiology of inflammatory disease. As our appreciation of the fundamental role of inflammation in disease pathogenesis has increased, so too has the importance of NF-κB as a key regulatory molecule gained progressively greater significance. However, despite the tremendous progress that has been made in understanding the regulation of NF-κB, there is much that remains to be understood. In this review, we highlight both the progress that has been made and the fundamental questions that remain unanswered after 25 years of study.
Translational genomics: The challenge of developing cancer biomarkers
Authors: Brooks James D.
Published: February 2012

Early detection and definitive treatment of cancer have been shown to decrease death and suffering in epidemiologic and intervention studies. Application of genomic approaches to many malignancies has produced thousands of candidate biomarkers for detection and prognostication, yet very few have become established in clinical practice. Fundamental issues related to tumor heterogeneity, cancer progression, natural history, and biomarker performance have provided challenges to biomarker development. Technical issues in biomarker assay detection limits, specificity, clinical deployment, and regulation have also slowed progress. The recent emergence of biomarkers and molecular imaging strategies for treatment selection and monitoring demonstrates the promise of cancer biomarkers. Organized efforts by interdisciplinary teams will spur progress in cancer diagnostics.
Antibody Staining of the Central Nervous System in Adult Drosophila
Authors: Sweeney Sean T. , Hidalgo Alicia , de Belle J. Steven , Keshishian Haig
Published: February 2012

The Drosophila nervous system provides a valuable model for studying various aspects of brain development and function. The postembryonic Drosophila brain is especially useful, because specific neuron types derive from specific progenitors at specific times. Elucidating the means by which diverse neuron types derive from a limited number of progenitors can contribute significantly to our understanding of the genetic and molecular mechanisms involved in developmental neurobiology. Antibody-labeling techniques are particularly useful for examining the Drosophila brain. These methods generally use primary antibodies specific to a protein or a structure of interest and a fluorescently labeled or enzyme-coupled secondary antibody to detect the primary antibodies. Immunofluorescence methods allow for simultaneous probing for multiple antigens using different fluorophores, as well as high-resolution confocal examination of deep structures. This protocol describes general procedures for antibody labeling of neural tissue from Drosophila, as well as visualization techniques for fluorescent and enzyme-linked probes.
Hydroxyurea Ablation of Mushroom Bodies inDrosophila
Authors: Sweeney Sean T. , Hidalgo Alicia , de Belle J. Steven , Keshishian Haig
Published: February 2012

Chemical ablation is an effective tool for studying nervous system development and function inDrosophila. Hydroxyurea (HU) inhibits ribonucleotide reductase, blocking DNA synthesis, and killing dividing cells. The specificity of HU ablation is thus dependent on developmental events. In this respect, HU is useful in determining temporal patterns of neuroblast proliferation and the origins of neuronal elements in flies and other insects. InDrosophila, an especially fortuitous time window occurs at the end of embryonic development. For the first 8–12 h after larval hatching, only five neuroblasts are proliferating in each brain hemisphere. Four of these are found in the dorsal protocerebrum and give rise to the intrinsic elements (Kenyon cells [KCs] and glia) of the mushroom bodies (MBs). The remaining single neuroblast has an anterolateral position in the brain and is the progenitor of local interneurons (LocI) in the antennal lobe (AL) and a subset of lateral relay interneurons (RIl) in the inner antennocerebral tract (iACT). Treating newly hatched larvae with HU results in adult flies with KCs and AL interneurons of embryonic origin only. This protocol describes methods for collecting newly hatchedDrosophilalarvae and treating them with HU.
Monitoring Membrane Excitability in Drosophila Expressing Modified Shaker Constructs: Figure 1.
Authors: Olsen Douglas P. , Keshishian Haig
Published: February 2012

The Drosophila neuromuscular junction (NMJ) ranks as one of the preeminent model systems for studying synaptic development, function, and plasticity. This protocol describes the use of the two-electrode voltage clamp (TEVC) to examine potassium (K+) currents mediated by voltage-gated ion channels, and gives several genetic and pharmacological methods that are used to study the currents. Drosophila larval muscle fibers possess three major K+ currents. One of these, a fast voltage-activating and inactivating IA current, is mediated by the Shaker channel. The Shaker channel is characterized by its sensitivity to the drug 4-aminopyridine (4-AP). Two useful transgenic tools for altering membrane excitability have been developed by making specific modifications of the Shaker channel; their use is described here.
Verification of 2A Peptide Cleavage
Authors: Szymczak-Workman Andrea L. , Vignali Kate M. , Vignali Dario A.A.
Published: February 2012

The need for reliable, multicistronic vectors for multigene delivery is at the forefront of biomedical technology. It is now possible to express multiple proteins from a single open reading frame (ORF) using 2A peptide-linked multicistronic vectors. These small sequences, when cloned between genes, allow for efficient, stoichiometric production of discrete protein products within a single vector through a novel “cleavage” event within the 2A peptide sequence. The easiest and most effective way to assess 2A cleavage is to perform transient transfection of 293T cells (human embryonic kidney cells) followed by western blot analysis, as described in this protocol. 293T cells are easy to grow and can be efficiently transfected with a variety of vectors. Cleavage can be assessed by detection with antibodies against the target proteins or anti-2A serum.
Experimental Methods for Examining Synaptic Plasticity in Drosophila
Authors: Olsen Douglas P. , Keshishian Haig
Published: February 2012

The Drosophila neuromuscular junction (NMJ) ranks as one of the preeminent model systems for studying synaptic development, function, and plasticity. In this article, we review the experimental genetic methods that include the use of mutated or reengineered ion channels to manipulate the synaptic connections made by motor neurons onto larval body-wall muscles. We also provide a consideration of environmental and rearing conditions that phenocopy some of the genetic manipulations.
Genetic Analysis: Moving between Linkage and Association
Authors: Smith Albert Vernon
Published: February 2012

The approaches to identifying genes and genomic regions associated with human disease can be grouped into two categories: linkage analysis and genetic association analysis. Linkage analysis is useful for diseases of high penetrance that run strongly within families, but is limited in its ability to detect situations where there are multiple genes with smaller effects. An alternative is genetic association studies, which were initially performed on small numbers of candidate genes. This approach identified relatively few genes that were consistently associated with disease, but it is now possible to do a genetic association for the whole genome, making this approach more powerful. In practice, the two types of analysis are often interlinked. This article provides information on the tools needed to perform both genetic linkage and genetic association analysis.
Three-Dimensional Morphology and Gene Expression Mapping for the Drosophila Blastoderm
Authors: Knowles David W.
Published: February 2012

To properly understand the transcriptional network of animals, we must have full quantitative comprehension of the spatial and temporal expression patterns of transcription factors and their targets. Visual inspection of embryos stained to reveal the patterns of genes shows levels of expression that change from cell to cell in a complex manner. With our current wealth of knowledge regarding the basic biology of animal genomes and the components of their transcriptional regulatory networks, combined with current technologies in optical microscopy, computing, and image and vision analysis, we should be able to capture quantitative, three-dimensional (3D) information about the transcriptional network (all factors and targets) for an entire animal at cellular resolution. It should also be possible to assemble these data into a single computationally analyzable database—an atlas—that could be the basis for uncovering new biology governing regulatory gene networks. This article describes progress toward realizing these goals, with the focus on Drosophila melanogaster. It describes a suite of high-throughput methods that have been used to create the first quantitative 3D description of gene expression and morphology at cellular resolution in a whole animal, and it presents some of the new biology that has been revealed by this quantitative atlas.
Loss of Abaxial Leaf Epicuticular Wax inMedicago truncatula irg1/palm1Mutants Results in Reduced Spore Differentiation of Anthracnose and Nonhost Rust Pathogens
Authors: Uppalapati Srinivasa Rao , Ishiga Yasuhiro , Doraiswamy Vanthana , Bedair Mohamed , Mittal Shipra , Chen Jianghua , Nakashima Jin , Tang Yuhong , Tadege Million , Ratet Pascal , Chen Rujin , Schultheiss Holger , Mysore Kirankumar S.
Published: February 2012

To identify genes that confer nonhost resistance to biotrophic fungal pathogens, we did a forward-genetics screen using Medicago truncatula Tnt1 retrotransposon insertion lines. From this screen, we identified an inhibitor of rust germ tube differentation1 (irg1) mutant that failed to promote preinfection structure differentiation of two rust pathogens, Phakopsora pachyrhizi and Puccinia emaculata, and one anthracnose pathogen, Colletotrichum trifolii, on the abaxial leaf surface. Cytological and chemical analyses revealed that the inhibition of rust preinfection structures in irg1 mutants is due to complete loss of the abaxial epicuticular wax crystals and reduced surface hydrophobicity. The composition of waxes on abaxial leaf surface of irg1 mutants had >90% reduction of C30 primary alcohols and a preferential increase of C29 and C31 alkanes compared with the wild type. IRG1 encodes a Cys(2)His(2) zinc finger transcription factor, PALM1, which also controls dissected leaf morphology in M. truncatula. Transcriptome analysis of irg1/palm1 mutants revealed downregulation of eceriferum4, an enzyme implicated in primary alcohol biosynthesis, and MYB96, a major transcription factor that regulates wax biosynthesis. Our results demonstrate that PALM1 plays a role in regulating epicuticular wax metabolism and transport and that epicuticular wax influences spore differentiation of host and nonhost fungal pathogens.
Assessment of exposure to drugs of abuse during pregnancy by hair analysis in a Mediterranean island
Authors: Friguls Bibiana , Joya Xavier , Garcia‐Serra Joan , Gómez‐Culebras Mario , Pichini Simona , Martinez Susana , Vall Oriol , Garcia‐Algar Oscar
Published: February 2012

Aims  This study aims to estimate the prevalence of drug use by pregnant women living in Ibiza, using structured interviews and biomarkers in maternal hair. In addition, the potentially detrimental effects of maternal drug abuse on their newborns were investigated. Ibiza has a large international night‐life resort associated with clubs, music and use of recreational drugs.

Design, setting and participants  Hair samples were collected prospectively from January to March 2010 from a cohort of consecutive mothers after giving birth in the Hospital Can Misses in Ibiza.

Measurements  Opiates, cocaine, cannabis, methadone, amphetamines, 3,4‐methylenedioxymethamphetamine (MDMA) and their metabolites were detected in a 3‐cm‐long proximal segment of maternal hair corresponding to the last trimester of pregnancy by gas chromatography coupled to mass spectrometry (n = 107). Data on socio‐demographic characteristics and on tobacco, alcohol, drugs of prescription and drugs of abuse consumption during pregnancy were collected using a structured questionnaire.

Findings  Hair analysis showed an overall 16% positivity for drugs of abuse in the third trimester of pregnancy, with a specific prevalence of cannabis, cocaine, MDMA and opiates use of 10.3, 6.4, 0.9 and 0%, respectively. In the questionnaires, only 1.9% of mothers declared using drugs of abuse during pregnancy. Gestational drug of abuse consumption was associated with active tobacco smoking, a higher number of smoked cigarettes and the mother being Spanish.

Conclusions  Illicit drug use is substantially under‐reported among pregnant women living in Ibiza, particularly among Spanish nationals. Voluntary, routine objective biological toxicology screening should be considered as part of routine examinations in antenatal clinics on this Mediterranean island.
BcAtf1, a global regulator, controls various differentiation processes and phytotoxin production inBotrytis cinerea
Authors: TEMME NORA , OESER BIRGITT , MASSAROLI MICHELLI , HELLER JENS , SIMON ADELINE , GONZÁLEZ COLLADO ISIDRO , VIAUD MURIEL , TUDZYNSKI PAUL
Published: February 2012

Atf1‐homologous basic region leucine zipper (bZIP) transcription factors are known to act downstream of the stress‐activated mitogen‐activated protein kinase (SAPK) cascade in mammals, as well as in several fungi; they regulate the transcription of genes involved in the general stress response. Functional analyses of BcAtf1 inBotrytis cinereashow that it is also connected to the SAPK BcSak1, as it shares several stress response target genes. However, Δbcatf1 mutants are not hypersensitive to osmotic or oxidative stress, as are Δbcsak1 mutants. Both BcSak1 and BcAtf1 are regulators of differentiation, but their roles in these processes are almost inverse as, in contrast with Δbcsak1, Δbcatf1 mutants are significantly impaired in conidia production and do not differentiate any sclerotia. They show extremely vigorous growth in axenic culture, with a thick layer of aerial hyphae and a marked increase in colonization efficiency on different host plants and tissues. In addition, the sensitivity to cell wall‐interfering agents is increased strongly. Microarray analyses demonstrate that the loss of BcAtf1 leads to extensive transcriptional changes: apart from stress response genes, the expression of a broad set of genes, probably involved in primary metabolism, cell wall synthesis and development, is affected by BcAtf1. Unexpectedly, BcAtf1 also controls secondary metabolism: the mutant contains significantly elevated levels of phytotoxins. These data indicate that BcAtf1 controls a diversity of cellular processes and has broad regulatory functions.
Intracerebroventricular opioids for intractable pain
Authors: Raffa Robert B. , Pergolizzi Jr Joseph V.
Published: February 2012

When pain is refractory to systemic opioid and non‐opioid analgesic therapy and palliative chemoradiation or ablative or stimulant neurosurgical procedures are not possible, palliative treatment becomes limited, particularly if the patient wishes to be at home at the end of life. Intracerebroventricular (ICV) infusion of morphine in the home setting might be presented as an option. The present article reviews the basic and clinical evidence of the efficacy and safety of ICV administration of opioids. Information was gathered from various bibliographic sources, including PubMed and others, and summarized and evaluated to assess the efficacy and safety of ICV opioids for pain relief. Results from ICV infusion of morphine into terminally ill patients refractory to other pain treatments have been reported since the early 1980s. Good efficacy has been achieved for the vast majority of patients, without serious development of analgesic tolerance. There have also been a low incidence of adverse effects, such as constipation and respiratory depression, and a significant retention of alertness associated with this route of administration. Intracerebroventricular infusion of opioid analgesics thus appears to be a safe and effective therapy for the palliative treatment of refractory pain.
Into and out of Africa – taking over from Denis Burkitt
Authors: Ziegler John L.
Published: February 2012

Denis Burkitt's description of the eponymous lymphoma in 1958 in Uganda, opened up a vast and important field of enquiry in haematology and oncology. His pioneering experiments with chemotherapy demonstrated the possibility of cure, often with a single dose. His geographical explorations showed the tumour to be delimited by climate, suggesting an infectious cause vectored by mosquitoes. His clinical observations furthered the field of cancer immunotherapy. And his collegial, inquisitive nature facilitated the development of an enduring cancer research centre in Kampala. Burkitt's legacy in Uganda has wide‐reaching effects that endure not only in Uganda but also throughout the haematology‐oncology community to this day.
ATX‐II‐induced pulmonary vein arrhythmogenesis related to atrial fibrillation and long QT syndrome
Authors: Lu Yen‐Yu , Cheng Chen‐Chuan , Chen Yao‐Chang , Chen Shih‐Ann , Chen Yi‐Jen
Published: February 2012

Eur J Clin Invest 2012;

Background  Long QT syndrome (LQTS) is associated with a high incidence of atrial fibrillation (AF), but the underlying mechanisms are unclear. Pulmonary veins (PVs) play a critical role in AF genesis. Type 3 LQTS increases late sodium current (INa,L), which may increase PV arrhythmogenesis and AF. Therefore, this study examines PV arrhythmogenesis in anemonia sulcata toxin II (ATX‐II)‐induced type 3 LQTS and evaluates whether the INa,L inhibitor ranolazine can suppress PV arrhythmogenesis.

Materials and methods  Conventional microelectrodes were used to record the action potentials (AP) and contractility in isolated rabbit PV specimens before and after ATX‐II administration with or without ranolazine.

Results  Anemonia sulcata toxin II (100 nM) increased the PV spontaneous rates from 2·0 ± 0·1 to 2·9 ± 0·2 Hz (n = 7), induced PV burst firing (100%) with the genesis of early afterdepolarization (EAD) (86%) and prolonged the AP duration. Ranolazine (0·1, 1 and 10 μM) dose dependently reduced the PV spontaneous rates from 2·5 ± 0·2 to 2·3 ± 0·2 Hz, 1·9 ± 0·2 and 1·5 ± 0·3 Hz (P < 0·05) and decreased the diastolic tension by 40 ± 19%, 87 ± 26% and 113 ± 28%. In the presence of ranolazine (10 μM), ATX‐II (100 nM) further increased the AP duration. However, ATX‐II neither increased the PV spontaneous rates (1·6 ± 0·1 vs. 1·7 ± 0·2 Hz, n = 7) nor induced PV burst firing or EAD. Moreover, ranolazine (10 μM) reduced ATX‐II‐induced PV acceleration and EAD.

Conclusions  The INa,L enhancer ATX‐II can increase PV arrhythmogenesis, which can be attenuated or blocked by ranolazine. This suggests that AF may be related to type 3 LQTS through increased INa,L.