bluuebunny/crossref_metadata_2025 huggingface dataset:
Patchiness in distribution of rodents and mustelids in New Zealand forests
Authors: Watkins Alison Fern , McWhirter Judith L. , King Carolyn M.
Published: March 2010

Context. Relative density indices assuming uniform distribution of the target species are often the only cost-effective method for monitoring a population over the long term and at landscape scale, and the only source of valuable historical data. Yet, theoretical models emphasise the dangers of ignoring spatial heterogeneity, especially in short-term field data.
Aims. To test whether Brown’s index of patchiness (BIP) can offer a simple means of checking rodent and mustelid survey data for violations of the assumption of uniform distribution.
Methods. We use BIP to interrogate long-term legacy data collected by index trapping of mice (Mus musculus), rats (Rattus rattus and R. norvegicus) and stoats (Mustela erminea) in New Zealand forests.
Key results. We found evidence of moderately patchy distributions that were independent of abundance in all three species. In two South Island beech (Nothofagus) forest valleys, 19% (6 of 31) of mouse samples and 8% (3 of 36) of stoat samples were significantly patchy, correlated with a seedfall event; in mixed forest at Pureora in the North Island, significant patchiness in distribution of ship rats was recorded in 19% (16 of 84) of Fenn trap samples and 5% (2 of 42) of rodent trap samples.
Conclusions. Moderate patchiness is common. The consequences for any given study depend on the purpose of the work, but may be more important for practical management than for population modeling.
Controlling Underwater Robots with Electronic Nervous Systems
Authors: Ayers Joseph , Rulkov Nikolai , Knudsen Dan , Kim Yong-Bin , Volkovskii Alexander , Selverston Allen
Published: March 2010

We are developing robot controllers based on biomimetic design principles. The goal is to realise the adaptive capabilities of the animal models in natural environments. We report feasibility studies of a hybrid architecture that instantiates a command and coordinating level with computed discrete‐time map‐based (DTM) neuronal networks and the central pattern generators with analogue VLSI (Very Large Scale Integration) electronic neuron (aVLSI) networks. DTM networks are realised using neurons based on a 1‐D or 2‐D Map with two additional parameters that define silent, spiking and bursting regimes. Electronic neurons (ENs) based on Hindmarsh–Rose (HR) dynamics can be instantiated in analogue VLSI and exhibit similar behaviour to those based on discrete components. We have constructed locomotor central pattern generators (CPGs) with aVLSI networks that can be modulated to select different behaviours on the basis of selective command input. The two technologies can be fused by interfacing the signals from the DTM circuits directly to the aVLSI CPGs. Using DTMs, we have been able to simulate complex sensory fusion for rheotaxic behaviour based on both hydrodynamic and optical flow senses. We will illustrate aspects of controllers for ambulatory biomimetic robots. These studies indicate that it is feasible to fabricate an electronic nervous system controller integrating both aVLSI CPGs and layered DTM exteroceptive reflexes.
A Biologically Derived Pectoral Fin for Yaw Turn Manoeuvres
Authors: Gottlieb Jonah R. , Tangorra James L. , Esposito Christopher J. , Lauder George V.
Published: March 2010

A bio‐robotic fin has been developed that models the pectoral fin of the bluegill sunfish as the fish turned to avoid an obstacle. This work involved biological studies of the sunfish fin, the development of kinematic models of the motions of the fin′s rays, CFD based predictions of the 3D forces and flows created by the fin, and the implementation of simplified models of the fin′s kinematics and mechanical properties in a physical model. The resulting robotic fin produced the forces and flows that drove the manoeuvre and had a sufficiently high number of degrees of freedom to create a variety of non‐biologically derived motions. The results indicate that for robotic fins to produce a level of performance on par with biological fins, both the kinematics and the mechanical properties of the biological fin must be modelled well.
ACTTS3 Encoding a Polyketide Synthase Is Essential for the Biosynthesis of ACT-Toxin and Pathogenicity in the Tangerine Pathotype of Alternaria alternata
Authors: Miyamoto Y. , Masunaka A. , Tsuge T. , Yamamoto M. , Ohtani K. , Fukumoto T. , Gomi K. , Peever T. L. , Tada Y. , Ichimura K. , Akimitsu K.
Published: March 2010

The tangerine pathotype of Alternaria alternata produces host-selective ACT-toxin and causes Alternaria brown spot disease of tangerine and tangerine hybrids. Sequence analysis of a genomic BAC clone identified part of the ACT-toxin TOX (ACTT) gene cluster, and knockout experiments have implicated several open reading frames (ORF) contained within the cluster in the biosynthesis of ACT-toxin. One of the ORF, designated ACTTS3, encoding a putative polyketide synthase, was isolated by rapid amplification of cDNA ends and genomic/reverse transcription-polymerase chain reactions using the specific primers designed from the BAC sequences. The 7,374-bp ORF encodes a polyketide synthase with putative β-ketoacyl synthase, acyltransferase, methyltransferase, β-ketoacyl reductase, and phosphopantetheine attachment site domains. Genomic Southern blots demonstrated that ACTTS3 is present on the smallest chromosome in the tangerine pathotype of A. alternata, and the presence of ACTTS3 is highly correlated with ACT-toxin production and pathogenicity. Targeted gene disruption of two copies of ACTTS3 led to a complete loss of ACT-toxin production and pathogenicity. These results indicate that ACTTS3 is an essential gene for ACT-toxin biosynthesis in the tangerine pathotype of A. alternata and is required for pathogenicity of this fungus.
Maize Leaf Epiphytic Bacteria Diversity Patterns Are Genetically Correlated with Resistance to Fungal Pathogen Infection
Authors: Balint-Kurti Peter , Simmons Susan J. , Blum James E. , Ballaré Carlos L. , Stapleton Ann E.
Published: March 2010

Plant leaves host a specific set of microbial epiphytes. Plant genetic and solar UV-B radiation effects on the diversity of the phyllosphere were examined by measuring epiphytic bacterial ribosomal DNA diversity in a maize recombinant inbred (RI) mapping population. Several chromosomal quantitative trait loci (QTL) with significant effects on bacterial diversity were identified, some of which had effects only in the presence of UV-B radiation and others that had effects both with and without UV-B. Candidate genes with allele-specific effects were mapped to the bacterial diversity chromosomal regions. A glutamate decarboxylase candidate gene was located at a UV-B–specific chromosomal locus, and in a comparison between two RI lines with contrasting bacterial diversity phenotypes, high bacterial diversity was associated with high levels of glutamate decarboxylase enzyme activity, a component of the gamma-aminobutyric acid (GABA) pathway. The bacterial diversity loci exhibited a significant overlap with loci connected with Southern leaf blight (SLB) susceptibility in the field. A SLB-resistant inbred genotype had less beta bacterial diversity, and antibiotic treatment of inbreds increased this diversity. These results suggest that the GABA pathway is genetically associated with phyllosphere bacterial diversity. Furthermore, the colocalization of QTL between low bacterial diversity and fungal blight–resistance and the increase in beta diversity in antibiotic-treated leaves suggest that occupation of leaf habitats by a particular set of suppressive bacteria may restrict phyllosphere bacterial variability and increase resistance to fungal infection.
Diversity at theMlaPowdery Mildew Resistance Locus from Cultivated Barley Reveals Sites of Positive Selection
Authors: Seeholzer Sabine , Tsuchimatsu Takashi , Jordan Tina , Bieri Stéphane , Pajonk Simone , Yang Wenxiang , Jahoor Ahmed , Shimizu Kentaro K. , Keller Beat , Schulze-Lefert Paul
Published: March 2010

The Mla locus in barley (Hordeum vulgare) conditions isolate-specific immunity to the powdery mildew fungus (Blumeria graminis f. sp. hordei) and encodes intracellular coiled-coil (CC) domain, nucleotide-binding (NB) site, and leucine-rich repeat (LRR)-containing receptor proteins. Over the last decades, genetic studies in breeding material have identified a large number of functional resistance genes at the Mla locus. To study the structural and functional diversity of this locus at the molecular level, we isolated 23 candidate MLA cDNAs from barley accessions that were previously shown by genetic studies to harbor different Mla resistance specificities. Resistance activity was detected for 13 candidate MLA cDNAs in a transient gene-expression assay. Sequence alignment of the deduced MLA proteins improved secondary structure predictions, revealing four additional, previously overlooked LRR. Analysis of nucleotide diversity of the candidate and validated MLA cDNAs revealed 34 sites of positive selection. Recombination or gene conversion events were frequent in the first half of the gene but positive selection was also found when this region was excluded. The positively selected sites are all, except two, located in the LRR domain and cluster in predicted solvent-exposed residues of the repeats 7 to 15 and adjacent turns on the concave side of the predicted solenoid protein structure. This domain-restricted pattern of positively selected sites, together with the length conservation of individual LRR, suggests direct binding of effectors to MLA receptors.
The cAMP Signaling Pathway in Fusarium verticillioides Is Important for Conidiation, Plant Infection, and Stress Responses but Not Fumonisin Production
Authors: Choi Yoon-E , Xu Jin-Rong
Published: March 2010

Fusarium verticillioides is one of the most important fungal pathogens of maize. Mycotoxin, fumonisins produced by this pathogen pose a threat to human and animal health. Because cAMP signaling has been implicated in regulating diverse developmental and infection processes in fungal pathogens, in this study, we aimed to elucidate the function of the cAMP–protein kinase A (PKA) pathway in toxin production and plant infection in F. verticillioides. Targeted deletion mutants were generated for the CPK1 and FAC1 genes that encode a catalytic subunit of PKA and the adenylate cyclase, respectively. Defects in radial growth and macroconidiation were observed in both the cpk1 and fac1 deletion mutants. The fac1 mutant also was significantly reduced in virulence and microconidiation but increased in tolerance to heat and oxidative stresses. These phenotypes were not observed in the cpk1 mutant, indicating that additional catalytic subunit of PKA must exist and function downstream from FAC1. The fac1 mutant formed microconidia mainly in false heads. The expression levels of the hydrophobin genes HYD1 and HYD2, which are known to be associated with change in formation of microconidia, were significantly reduced in the fac1 mutant. Expression of F. verticillioides GSY2 and HSP26 genes, two other putative downstream targets of FAC1, was increased in the fac1 mutant and may be associated with its enhanced stress tolerance. Although fumonisin production was normal, biosynthesis of bikaverin was increased in the fac1 mutant, suggesting that FAC1 and cAMP signaling may have pathway-or metabolite-specific regulatory roles in secondary metabolism. Overall, the pleiotropic defects of the fac1 deletion mutant indicate that the cAMP-PKA pathway is involved in growth, conidiation, bikaverin production, and plant infection in F. verticillioides.
Conspecific versus heterospecific gene exchange between populations of Darwin's finches
Authors: Grant Peter R. , Grant B. Rosemary
Published: March 2010

This study addresses the extent and consequences of gene exchange between populations of Darwin's finches. Four species of ground finches (Geospiza) inhabit the small island of Daphne Major in the centre of the Galápagos archipelago. We undertook a study of microsatellite DNA variation at 16 loci in order to quantify gene flow within species owing to immigration and between species owing to hybridization. A combination of pedigrees of observed breeders and assignments of individuals to populations by the program Structureenabled us to determine the frequency of gene exchange and the island of origin of immigrants in some cases. The relatively large populations ofGeospiza fortisandG. scandensreceive conspecific immigrants at a rate of less than one per generation. They exchange genes more frequently by rare but repeated hybridization. Effects of heterospecific gene flow from hybridization are not counteracted by lower fitness of the offspring. As a result, the standing genetic variation of the two main resident populations on Daphne Major is enhanced to a greater extent by introgressive hybridization than through breeding with conspecific immigrants. ImmigrantG. fuliginosaalso breeds withG. fortis. Conspecific immigration was highest in the fourth species,G. magnirostris. This species is much larger than the other three and perhaps for this reason it has not bred with any of them. The source island of most immigrants is probably the neighbouring island of Santa Cruz. Evolutionary change may be inhibited inG. magnirostrisby continuing gene flow, but enhanced inG. fortisandG. scandensby introgressive hybridization.
The tale of the finch: adaptive radiation and behavioural flexibility
Authors: Tebbich Sabine , Sterelny Kim , Teschke Irmgard
Published: March 2010

Darwin's finches are a classic example of adaptive radiation. The ecological diversity of the Galápagos in part explains that radiation, but the fact that other founder species did not radiate suggests that other factors are also important. One hypothesis attempting to identify the extra factor is the flexible stem hypothesis, connecting individual adaptability to species richness. According to this hypothesis, the ancestral finches were flexible and therefore able to adapt to the new and harsh environment they encountered by exploiting new food types and developing new foraging techniques. Phenotypic variation was initially mediated by learning, but genetic accommodation entrenched differences and supplemented them with morphological adaptations. This process subsequently led to diversification and speciation of the Darwin's finches. Their current behaviour is consistent with this hypothesis as these birds use unusual resources by extraordinary means. In this paper, we identify cognitive capacities on which flexibility and innovation depend. The flexible stem hypothesis predicts that we will find high levels of these capacities in all species of Darwin's finches (not just those using innovative techniques). Here, we test that prediction, and find that while most of our data are in line with the flexible stem hypothesis, some are in tension with it.
Differentiation with drift: a spatio-temporal genetic analysis of Galápagos mockingbird populations (Mimusspp.)
Authors: Hoeck Paquita E. A. , Bollmer Jennifer L. , Parker Patricia G. , Keller Lukas F.
Published: March 2010

Small and isolated island populations provide ideal systems to study the effects of limited population size, genetic drift and gene flow on genetic diversity. We assessed genetic diversity within and differentiation among 19 mockingbird populations on 15 Galápagos islands, covering all four endemic species, using 16 microsatellite loci. We tested for signs of drift and gene flow, and used historic specimens to assess genetic change over the last century and to estimate effective population sizes. Within-population genetic diversity and effective population sizes varied substantially among island populations and correlated strongly with island size, suggesting that island size serves as a good predictor for effective population size. Genetic differentiation among populations was pronounced and increased with geographical distance. A century of genetic drift did not change genetic diversity on an archipelago-wide scale, but genetic drift led to loss of genetic diversity in small populations, especially in one of the two remaining populations of the endangered Floreana mockingbird. Unlike in other Galápagos bird species such as the Darwin's finches, gene flow among mockingbird populations was low. The clear pattern of genetically distinct populations reflects the effects of genetic drift and suggests that Galápagos mockingbirds are evolving in relative isolation.
Darwin's Galápagos finches in modern biology
Authors: Abzhanov Arhat
Published: March 2010

One of the classic examples of adaptive radiation under natural selection is the evolution of 15 closely related species of Darwin's finches (Passeriformes), whose primary diversity lies in the size and shape of their beaks. Since Charles Darwin and other members of the
Beagle
expedition collected these birds on the Galápagos Islands in 1835 and introduced them to science, they have been the subjects of intense research. Many biology textbooks use Darwin's finches to illustrate a variety of topics of evolutionary theory, such as speciation, natural selection and niche partitioning. Today, as this Theme Issue illustrates, Darwin's finches continue to be a very valuable source of biological discovery. Certain advantages of studying this group allow further breakthroughs in our understanding of changes in recent island biodiversity, mechanisms of speciation and hybridization, evolution of cognitive behaviours, principles of beak/jaw biomechanics as well as the underlying developmental genetic mechanisms in generating morphological diversity. Our objective was to bring together some of the key workers in the field of ecology and evolutionary biology who study Darwin's finches or whose studies were inspired by research on Darwin's finches. Insights provided by papers collected in this Theme Issue will be of interest to a wide audience.
miR-125b-2 is a potential oncomiR on human chromosome 21 in megakaryoblastic leukemia
Authors: Klusmann Jan-Henning , Li Zhe , Böhmer Katarina , Maroz Aliaksandra , Koch Mia Lee , Emmrich Stephan , Godinho Frank J. , Orkin Stuart H. , Reinhardt Dirk
Published: March 2010

Children with trisomy 21/Down syndrome (DS) are at high risk to develop acute megakaryoblastic leukemia (DS-AMKL) and the related transient leukemia (DS-TL). The factors on human chromosome 21 (Hsa21) that confer this predisposing effect, especially in synergy with consistently mutated transcription factor GATA1 (GATA1s), remain poorly understood. Here, we investigated the role of Hsa21-encoded miR-125b-2, a microRNA (miRNA) overexpressed in DS-AMKL/TL, in hematopoiesis and leukemogenesis. We identified a function of miR-125b-2 in increasing proliferation and self-renewal of human and mouse megakaryocytic progenitors (MPs) and megakaryocytic/erythroid progenitors (MEPs). miR-125b-2 overexpression did not affect megakaryocytic and erythroid differentiation, but severely perturbed myeloid differentiation. The proproliferative effect of miR-125b-2 on MEPs accentuated the Gata1s mutation, whereas growth of DS-AMKL/TL cells was impaired upon miR-125b repression, suggesting synergism during leukemic transformation in GATA1s-mutated DS-AMKL/TL. Integrative transcriptome analysis of hematopoietic cells upon modulation of miR-125b expression levels uncovered a set of miR-125b target genes, including DICER1 and ST18 as direct targets. Gene Set Enrichment Analysis revealed that this target gene set is down-regulated in DS-AMKL patients highly expressing miR-125b. Thus, we propose miR-125b-2 as a positive regulator of megakaryopoiesis and an oncomiR involved in the pathogenesis of trisomy 21-associated megakaryoblastic leukemia.
Personal genome sequencing: current approaches and challenges
Authors: Snyder Michael , Du Jiang , Gerstein Mark
Published: March 2010

The revolution in DNA sequencing technologies has now made it feasible to determine the genome sequences of many individuals; i.e., “personal genomes.” Genome sequences of cells and tissues from both normal and disease states have been determined. Using current approaches, whole human genome sequences are not typically assembled and determined de novo, but, instead, variations relative to a reference sequence are identified. We discuss the current state of personal genome sequencing, the main steps involved in determining a genome sequence (i.e., identifying single-nucleotide polymorphisms [SNPs] and structural variations [SVs], assembling new sequences, and phasing haplotypes), and the challenges and performance metrics for evaluating the accuracy of the reconstruction. Finally, we consider the possible individual and societal benefits of personal genome sequences.
KDM7 is a dual demethylase for histone H3 Lys 9 and Lys 27 and functions in brain development
Authors: Tsukada Yu-ichi , Ishitani Tohru , Nakayama Keiichi I.
Published: March 2010

Methylation of histone H3 Lys 9 and Lys 27 (H3K9 and H3K27) is associated with transcriptional silencing. Here we show that KDM7, a JmjC domain-containing protein, catalyzes demethylation of both mono- or dimethylated H3K9 and H3K27. Inhibition of KDM7 orthologs in zebrafish resulted in developmental brain defects. KDM7 interacts with the follistatin gene locus, and KDM7 depletion in mammalian neuronal cells suppressed follistatin gene transcription in association with increased levels of dimethylated H3K9 and H3K27. Our findings identify KDM7 as a dual demethylase for H3K9 and H3K27 that functions as an eraser of silencing marks on chromatin during brain development.
Spermatogenesis rescue in a mouse deficient for the ubiquitin ligase SCFβ-TrCP by single substrate depletion
Authors: Kanarek Naama , Horwitz Elad , Mayan Inbal , Leshets Michael , Cojocaru Gady , Davis Matti , Tsuberi Ben-Zion , Pikarsky Eli , Pagano Michele , Ben-Neriah Yinon
Published: March 2010

β-TrCP, the substrate recognition subunit of a Skp1–Cul1–F-box (SCF) ubiquitin ligase, is ubiquitously expressed from two distinct paralogs, targeting many regulatory proteins for proteasomal degradation. We generated inducible β-TrCP hypomorphic mice and found that they are surprisingly healthy, yet have a severe testicular defect. We show that the two β-TrCP paralogs have a nonredundant role in spermatogenesis. The testicular defect is tightly associated with cell adhesion failure within the seminiferous tubules and is fully reversible upon β-TrCP restoration. Remarkably, testicular depletion of a single β-TrCP substrate, Snail1, rescued the adhesion defect and restored spermatogenesis. Our studies highlight an unexpected functional reserve of this central E3, as well as a bottleneck in a specific tissue: a single substrate whose stabilization is incompatible with testicular differentiation.
Fluorescent In Situ Hybridization (FISH) of Mitotic Chromosomes fromDrosophilaLarval Brain
Authors: Pimpinelli Sergio , Bonaccorsi Silvia , Fanti Laura , Gatti Maurizio
Published: March 2010

INTRODUCTION

The fluorescent in situ hybridization (FISH) technique permits fine mapping of both middle and highly repetitive DNA sequences alongDrosophila melanogasterheterochromatin. Best results are obtained when this technique is coupled with DAPI staining and digital recording of fluorescent signals. For example, if digital images of the FISH signals and DAPI fluorescence are detected separately using a charge-coupled device (CCD) camera, they can then be pseudocolored and merged using suitable computer programs. This allows precise overlapping of the DAPI banding (which is identical to the Hoechst 33258 banding) and the FISH signals, facilitating the assignment of the repetitive sequence under study to specific regions of the cytological map ofD. melanogasterheterochromatin. This article describes FISH procedures that are routinely used with larval brain squashes, including preparation of slides, preparation of biotin- and digoxigenin-labeled probes, hybridization, and detection.
Creation of Baculovirus Display Libraries: Figure 1.
Authors: Mäkelä Anna R. , Ernst Wolfgang , Grabherr Reingard , Oker-Blom Christian
Published: March 2010

INTRODUCTION

The baculovirus expression vector system has been used extensively to produce numerous proteins originating from both prokaryotic and eukaryotic sources. In addition to easy cloning techniques and abundant viral propagation, the system’s insect cell environment provides eukaryotic post-translational modification machinery. The baculovirus display vector system provides a number of advantages over prokaryotic systems, allowing the combination of genotype with phenotype, enabling presentation of foreign peptides or even complex proteins on the baculoviral envelope or capsid. Baculoviruses permit larger gene insertions, are easily propagated, and can be grown to high titers. Furthermore, surface modifications of the viral capsid enable specific targeting. This strategy can be used to enhance viral binding and entry to a wide variety of both dividing and nondividing mammalian cells as well as to produce antibodies against the displayed antigen. In addition, the technology should enable modifications of intracellular behavior, i.e., trafficking of recombinant “nanoparticles,” a highly relevant feature for studies of targeted gene or protein delivery. It is important to note that, although the viruses do not replicate in mammalian cells, they are not entirely transcriptionally silent. They can also be highly antigenic when used in vivo, limiting their therapeutic use. This protocol describes methods for generating display libraries.
Immunofluorescence Analysis of Baculovirus-Displayed Viral Proteins on Infected Insect Cells
Authors: Mäkelä Anna R. , Ernst Wolfgang , Grabherr Reingard , Oker-Blom Christian
Published: March 2010

INTRODUCTION

The baculovirus expression vector system has been used extensively to produce numerous proteins originating from both prokaryotic and eukaryotic sources. In addition to easy cloning techniques and abundant viral propagation, the system’s insect cell environment provides eukaryotic post-translational modification machinery. The baculovirus display vector system provides a number of advantages over prokaryotic systems, allowing the combination of genotype with phenotype, enabling presentation of foreign peptides or even complex proteins on the baculoviral envelope or capsid. Baculoviruses permit larger gene insertions, are easily propagated, and can be grown to high titers. Furthermore, the eukaryotic system allows for post-translational modifications, and surface modifications of the viral capsid enable specific targeting. This strategy can be used to enhance viral binding and entry to a wide variety of both dividing and nondividing mammalian cells, as well as to produce antibodies against the displayed antigen. In addition, the technology should enable modifications of intracellular behavior, i.e., trafficking of recombinant “nanoparticles,” a highly relevant feature for studies of targeted gene or protein delivery. After generating the display viral stock, it is important to confirm the presence and functionality of the displayed peptides or proteins on the viral particles before proceeding to further experiments. Accordingly, infected insect cells and budded virions can be analyzed by a variety of methods using appropriate antibodies. This protocol describes a standard immunfluorescence technique in detail.
How Calcium Indicators Work: Figure 1.
Authors: Adams Stephen R.
Published: March 2010

INTRODUCTION

In the last two decades, imaging of fluorescent indicators specific for Ca2+ has revealed its often spectacular spatial dynamics, such as rhythmic oscillations or standing gradients, within single groups or individual cells, in unprecedented detail. This short review describes how the more widely used indicators work. The currently used Ca2+ indicators have a modular design consisting of a metal-binding site (or sensor) coupled in some way to a fluorescent dye. Combining different sensors with different dyes results in numerous indicators suited to a wide range of experiments and equipment.
Imaging Single Molecules Using Total Internal Reflection Fluorescence Microscopy (TIRFM)
Authors: Reck-Peterson Samara L. , Derr Nathan D. , Stuurman Nico
Published: March 2010

INTRODUCTION

Total internal reflection fluorescence microscopy (TIRFM) allows fluorescent molecules to be visualized with an unparalleled signal-to-noise ratio. This is achieved by illuminating only the molecules that are within a thin volume near the coverslip surface but not those that are deeper in solution. Using this technique, fluorescent molecules within ~100 nm of the coverslip can be visualized, and single molecules that are separated by a distance greater than the diffraction limit (~200 nm) can be individually resolved. The application of centroid-tracking methods allows subdiffraction-limited localization precision as low as 1 nm. Additionally, by combining centroid-tracking methods with recent advances in fluorophore technology and imaging methods, even those molecules that are present at high concentrations and closer to one another than the diffraction limit can be individually imaged. TIRF is ideally suited for studying protein dynamics on or near the plasma membrane. Although TIRFM was pioneered in the 1980s, it was not until the mid-1990s that single biological molecules were imaged directly. The explosion of new fluorescent proteins, new organic dyes, and quantum dots (Qdots), along with commercially available TIRFMs, has made this technique increasingly useful and accessible to biologists. In this review, we first describe the theory of TIRFM. We then give a detailed description of important considerations for setting up a TIRFM, based on commercially available systems, and review considerations for purification and labeling of proteins. Finally, we discuss new techniques that allow single molecules to be imaged at cellular concentrations and with super-resolution localization.
Optimizing high-pressure pair distribution function measurements in diamond anvil cells
Authors: Chapman Karena W. , Chupas Peter J. , Halder Gregory J. , Hriljac Joseph A. , Kurtz Charles , Greve Benjamin K. , Ruschman Chad J. , Wilkinson Angus P.
Published: March 2010

Pair distribution function (PDF) methods have great potential for the study of diverse high-pressure phenomena. However, the measurement of high-quality, high-resolution X-ray PDF data (toQmax > 20 Å−1) remains a technical challenge. An optimized approach to measuring high-pressure total scattering data for samples contained within a diamond anvil cell (DAC) is presented here. This method takes into account the coupled influences of instrument parameters (photon energy, detector type and positioning, beam size/shape, focusing), pressure-cell parameters (target pressure range, DAC type, diamonds, pressure-transmitting media, backing plates, pressure calibration) and data reduction on the resulting PDF. The efficacy of our approach is demonstrated by the high-quality, high-pressure PDFs obtained for representative materials spanning strongly and weakly scattering systems, and crystalline and amorphous samples. These are the highest-resolution high-pressure PDFs reported to date and include those for α-alumina (toQmax  =  20 Å−1), BaTiO3(toQmax= 30 Å−1) and pressure-amorphized zeolite (toQmax  =  20 Å−1).
Characteristics of the SAS correlation function of long cylinders with oval right section
Authors: Gille Wilfried
Published: March 2010

An approximation for the small-angle scattering (SAS) correlation function (CF) β0(r) of a plane oval domainXis discussed. The approach is based on two parameters, the perimeteruand the surface areaSRS, ofX. The function β0(r) fixes the correlation function γ0(r) of the oval homogeneous rod with constant right sectionX. The mean chord lengthl1of such a rod is the root of the equation γ0(l1) = 1 − 8/(3π). For a dilute rod arrangement, the Porod lengthlpand γ′(l1), the value of the derivative of the sample CF atr=l1, are related by γ′(l1) = −4/(3πlp).
Final analysis of the UKLG LY02 trial comparing 6–8 cycles of CHOP with 3 cycles of CHOP followed by a BEAM autograft in patients <65 years with poor prognosis histologically aggressive NHL
Authors: Linch David C. , Yung Lynny , Smith Paul , Maclennan Ken , Jack Andrew , Hancock Barry , Cunningham David , Hoskin Peter , Qian Wendi , Holte Harald , Boesen Anne‐Marie , Grigg Andrew , Browett Peter , Trneny Marek
Published: March 2010

This trial involved 457 patients and sought to assess the value of early intensification with autologous transplantation in patients with poor prognosis histologically aggressive non‐Hodgkin lymphoma (NHL) showing a response to initial CHOP (cyclosphosphamide, doxorubicin, vincristine, prednisolone) chemotherapy. Randomization was made at the time of diagnosis with 223 assigned to continuing CHOP and 234 to 3 cycles of CHOP followed by a BEAM (carmustine, etoposide, cytarabine, melphalan) autograft. Analysis was on an intention to treat basis. After the initial three cycles of CHOP 19% of the whole group were in complete response (CR) and 53% in partial remission (PR). At the end of treatment 86% of patients in the CHOP arm had responded with 58% in CR. In the high‐dose therapy arm the overall response rate was 83% with 64% in CR (difference between arms not significant). The progression‐free survival (PFS) and overall survival at 5 years for the continuing CHOP arm were 38% and 50% respectively, and for the autograft arm were 44% and 50% (differences not significant). Of the patients who attained CR and subsequently relapsed, there were no long‐term survivors in the autograft recipients compared to 46% of the continuing CHOP recipients (P = 0·0008). In conclusion, no survival benefit was demonstrated for an early autograft in first response.
The novel inhibitor of histone deacetylase resminostat (RAS2410) inhibits proliferation and induces apoptosis in multiple myeloma (MM) cells
Authors: Mandl‐Weber Sonja , Meinel Felix G. , Jankowsky Rüdiger , Oduncu Fuat , Schmidmaier Ralf , Baumann Philipp
Published: March 2010

Inhibition of histone deacetylase (HDAC) is a promising mechanism for novel, anti‐myeloma agents. We investigated the effects of the novel HDAC inhibitor resminostat on multiple myeloma (MM) cells in vitro. Resminostat is a potent inhibitor of HDACs 1, 3 and 6 [50% inhibitory concentration (IC50) = 43–72 nmol/l] representing HDAC classes I and II and induces hyperacetylation of histone H4 in MM cells. Low micromolar concentrations of resminostat abrogated cell growth and strongly induced apoptosis (IC50 = 2·5–3 μmol/l in 3 out of 4 MM cell lines) in MM cell lines as well as primary MM cells. At 1 μmol/l, resminostat inhibited proliferation and induced G0/G1 cell cycle arrest in 3 out of 4 MM cell lines accompanied with decreased levels of cyclin D1, cdc25a, Cdk4 and pRb as well as upregulation of p21. Resminostat decreased phosphorylation of 4E‐BP1 and p70S6k indicating an interference with Akt pathway signalling. Treatment with resminostat resulted in increased protein levels of Bim and Bax and decreased levels of Bcl‐xL. Caspases 3, 8 and 9 were activated by resminostat. Furthermore, synergistic effects were observed for combinations of resminostat with melphalan and the proteasome inhibitors bortezomib and S‐2209. In conclusion, we have identified potent anti‐myeloma activity for this novel HDAC inhibitor.
Staphylococcus aureus enterotoxin B facilitates allergic sensitization in experimental asthma
Authors: Huvenne W. , Callebaut I. , Plantinga M. , Vanoirbeek J. A. J. , Krysko O. , Bullens D. M. A. , Gevaert P. , Van Cauwenberge P. , Lambrecht B. N. , Ceuppens J. L. , Bachert C. , Hellings P. W.
Published: March 2010

Background
Staphylococcus aureus Enterotoxin B (SEB) has immunomodulatory effects in allergic airway disease. The potential contribution of SEB to the sensitization process to allergens remains obscure.

Objective
In order to study the effects of staphylococcal‐derived toxins on the sensitization to ovalbumin (OVA) and induction of allergic airway inflammation, we have combined the nasal application of OVA with different toxins.

Methods
Nasal applications of OVA and saline, SEA, SEB, toxic shock syndrome toxin (TSST)‐1, protein A or lipopolysaccharide (LPS) were performed on alternate days from day 0 till 12. On day 14, mice were killed for the evaluation of OVA‐specific IgE, cytokine production by mediastinal lymph node (MLN) cells and bronchial hyperreactivity (BHR) to inhaled metacholine. The effect of SEB on dendritic cell (DC) migration and maturation, and on T cell proliferation was evaluated.

Results
Concomitant endonasal application of OVA and SEB resulted in OVA‐specific IgE production, whereas this was not found with SEA, TSST‐1, protein A, LPS or OVA alone. Increased DC maturation and migration to the draining lymph nodes were observed in OVA/SEB mice, as well as an increased T cell proliferation. Bronchial inflammation with an influx of eosinophils and lymphocytes was demonstrated in OVA/SEB mice, together with hyperresponsiveness and the production of IL‐4, IL‐5, IL‐10 and IL‐13 by MLN stimulated with OVA.

Conclusions
Our data demonstrate that SEB facilitates sensitization to OVA and consecutive bronchial inflammation with features of allergic asthma. This is likely due to augmentation of DC migration and maturation, as well as the allergen‐specific T cell proliferation upon concomitant OVA and SEB application.

Cite this as: W. Huvenne, I. Callebaut, M. Plantinga, J. A. J. Vanoirbeek, O. Krysko, D. M. A. Bullens, P.Gevaert, P. Van Cauwenberge, B. N. Lambrecht, J. L. Ceuppens, C. Bachert and P. W. Hellings, Clinical & Experimental Allergy, 2010 (40) 1079–1080.
Antigen dose‐dependent suppression of murine IgE responses is mediated by CD4−CD8− double‐negative T cells
Authors: Barwig C. , Raker V. , Montermann E. , Grabbe S. , Reske‐Kunz A. B. , Sudowe S.
Published: March 2010

Background
The IgE response against protein antigens is profoundly influenced by the dose used for sensitization.

Objective
The aim of the study was to identify immune cells that are involved in antigen dose‐dependent regulation of IgE formation.

Methods
Wild‐type mice as well as T helper (Th)1‐deficient IL‐12p40−/− and IFN‐γ−/− mice were immunized by repeated intraperitoneal injection of either low doses (K01 mice) or high doses (K100 mice) of keyhole limpet haemocyanin adsorbed to aluminium hydroxide. Splenocytes of immunized mice were restimulated in vitro and antigen‐dependent T cell proliferation and cytokine production were measured. The frequency of regulatory T cell subsets among splenocytes from K01 and K100 mice was compared using fluorocytometry and RT‐PCR analysis. Splenocytes or T cell subpopulations were transferred into naïve mice and the effect of lymphocyte transfer on IgE production after priming of recipients with low antigen doses was determined.

Results
Specific IgE production was considerably impaired in K100 mice. Antigenic restimulation revealed hypoproliferation of K100 splenocytes and reduced production of Th2 cytokines IL‐4, IL‐5 and IL‐13, but no induction of IFN‐γ production. Moreover, lymphocytes from K01 and K100 mice did not show significant differences in the expression of molecules associated with the phenotype or activity of conventional regulatory T cells. Transfer of splenocytes or purified T cells from K100 mice substantially suppressed the induction of IgE production in the recipients in an antigen‐ and isotype‐specific manner. Neither CD4+ nor CD8+ T cells from K100 mice were able to inhibit IgE formation; instead, we identified CD4−CD8− double‐negative T cells (dnT cells) as the principal T cell population, which potently suppressed IgE production.

Conclusion
Our data demonstrate that CD4−CD8− dnT cells play a major role in the regulation of IgE responses induced by high antigen doses.
Should allergic reactions to radio‐contrast media be investigated by an allergist?
Authors: Nasser S.
Published: March 2010

Cite this as: S. Nasser, Clinical & Experimental Allergy, 2010 (40) 697–699.
Senescent leaf exudate increases mosquito survival and microbial activity
Authors: PELZ‐STELINSKI KIRSTEN S. , WALKER EDWARD D. , KAUFMAN MICHAEL G.
Published: March 2010

1. Experiments were conducted to evaluate the effects of soluble components in senescent leaf material on the growth and development of the eastern tree hole mosquito,Aedes triseriatus(Say). Oak leaves that were either leached for 3 days to remove the labile nutrient fraction, or were not leached, served as basal nutrient inputs in each experiment.

2. Mosquito performance in microcosms containing leachate only, was significantly worse compared with microcosms containing leaf material in combination with either leachate or water, indicating the importance of leaf substrates to mosquito production.

3. Adult mosquito biomass, emergence, and development time were significantly higher in microcosms containing unleached leaves compared with leached leaf material. Additions of leachate to leached leaf treatments enhanced adult production, but not to the level observed in unleached leaf treatments.

4. Filtered and unfiltered leachate added substantial nitrogen and phosphorus to microcosms and significantly affected mosquito growth responses. Bacterial productivity and abundance were also significantly affected by leachate additions and filtering.

5. Taken together, these results suggest that while leaves decline with respect to nutritional value during decomposition, they remain important components of the habitat as substrates for microbial growth and mosquito feeding, particularly when nutrients (here, leachate) enter the system. Our results also illustrate the importance of soluble leaf material, which enhances mosquito production through effects on microbial community dynamics.
Does microhabitat structure affect foliar mite assemblages?
Authors: O'CONNELL DEAN M. , LEE WILLIAM G. , MONKS ADRIAN , DICKINSON KATHARINE J. M.
Published: March 2010

1. Habitat structure is an important factor influencing population dynamics and trophic organisation of terrestrial invertebrates. The phylloplane zone on vascular plant leaves is topographically complex, containing a multitude of microhabitats such as leaf hairs, lesions, and structural refugia such as domatia, which may modify interactions between resident invertebrate communities, colonisers, and subsequent trophic relationships. Leaf domatia are small indentations on the underside of leaves and are often inhabited by potentially beneficial mites and other arthropods.

2. This study investigated the relationship between domatia availability and foliar mite assemblages in contrasting habitats (native forest, plantation forest, and pasture) using a standard test plant (the endemic New Zealand shrubCoprosma lucida, J.R. & G. Forst.).

3. Diverse woody native vegetation types supported higher numbers of mite species than either plantation forest or pastoral grasses. The highest number of mite species occurred in the native forest (63%), plantation forest (38%), and pastoral grasses (25%). In the native vegetation type, experimentalC. lucidaleaves with domatia supported higher mite densities, greater colonisation success, and more diverse mite assemblages than those without domatia. Mite assemblages within the pastoral site were significantly different from the other two vegetation types. Only one fungivorous mite species,Orthotydeus californicus, occurred compared to five mite species in native and plantation forests.

4. This study indicated that foliar mite assemblages in native vegetation on experimentalC. lucidashrubs are influenced by domatia availability, resident foliar mites, and local mite assemblages.
Intra‐specific body size variation inPolistespaper wasps as a response to social parasite pressure
Authors: ORTOLANI IRENE , CERVO RITA
Published: March 2010

1. Like avian brood parasites, obligate insect social parasites exploit the parental care of a host species to rear their brood, causing an evident loss of host reproductive success. This fitness cost imposes selective pressure on the host to reduce the parasite effect. A possible outcome of an evolutionary arms race is the selection of host morphological counter‐adaptations to resist parasite attacks.

2. We studied host–parasite pairs ofPolisteswasps in which the fighting equipment of the parasite's body allows it to enter the host colony.

3. We searched for host morphological traits related to fighting ability that could be considered counter‐adaptations. As a host–parasite co‐evolutionary arms race can only occur where the two lineages co‐exist, we compared morphological traits of hosts belonging to populations with or without parasite pressure. We report that host foundresses belonging to populations under strong parasite pressure have a larger body size than those belonging to populations without parasite pressure.

4. Behavioural experiments carried out to test if an increase in host body size is useful to oppose parasite usurpation show that large body size foundresses exhibit a greater ability of nest defence.
Climate change affects the duration of the reproductive season in birds
Authors: Møller A. P. , Flensted‐Jensen E. , Klarborg K. , Mardal W. , Nielsen J. T.
Published: March 2010

1. The duration of the reproductive season may depend on the duration of the growing season, with recent amelioration in spring temperatures allowing earlier start of reproduction. Earlier start of reproduction may allow a longer breeding season because of more broods a longer interval between broods for multi‐brooded species.

2. We analysed extensive long‐term data sets on timing of breeding in 20 species of birds from Denmark, based on records of over 100 000 individual offspring, showing considerable heterogeneity among species in temporal change in duration of the breeding season.

3. Multi‐brooded species increased the duration of their breeding season by 0·43 days year−1while single‐brooded species decreased the duration of their breeding season by 0·44 days year−1. This implies that recent climate change has allowed more broods or better temporal spacing of broods in multi‐brooded species, while the time window for reproduction has become narrower in single‐brooded species.

4. The single‐most important predictor of change in duration of the breeding season was change in the date breeding started; there was no change in the date of end of breeding. Species advancing their breeding date the most also expanded the duration of the breeding season. In contrast, long‐distance migration and generation time did not predict change in duration of the breeding season.
Executive function in adolescents with Down Syndrome
Authors: Lanfranchi S. , Jerman O. , Dal Pont E. , Alberti A. , Vianello R.
Published: March 2010

Background  The present work is aimed at analysing executive function (EF) in adolescents with Down Syndrome (DS). So far, EF has been analysed mainly in adults with DS, showing a pattern of impairment. However, less is known about children and adolescents with this syndrome. Studying adolescents with DS might help us better understand whether performances on EF tasks of individuals with DS are determined by age or by Alzheimer disease, as some studies suggest, or whether their performances are directly related to DS cognitive profile.

Method  A battery of EF tasks assessing set shifting, planning/problem‐solving, working memory, inhibition/perseveration and fluency, as well as a tasks assessing sustained attention has been administered to a group of 15 adolescents with DS and 15 typically developing children matched for mental age. All EF tasks were selected from previous studies with individuals with intellectual disabilities or from developmental literature and are thought to be useful for the samples considered.

Results  The present results revealed that the group of individuals with DS performed at a significantly lower level on tasks assessing set shifting, planning/problem‐solving, working memory and inhibition/perseveration, but not on the tasks assessing fluency. In addition, individuals with DS demonstrated a greater number of errors and less strategy use for the sustained attention task.

Conclusions  The results suggest a broad impairment in EF in adolescents with DS, and are consistent with several similar studies conducted with adults with DS. We assume that EF deficit is a characteristic of DS.