bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative image analysis approaches for probing Rab GTPase localization and function in mammalian cells
Authors: Singan Vasanth R. , Handzic Kenan , Simpson Jeremy C.
Published: November 2012

Membrane traffic pathways play an essential role in cells, providing a mechanism for organelles of the endomembrane system to communicate and exchange material between each other. A significant number of infections and diseases are associated with trafficking pathways, and as such gaining a greater understanding of their regulation is essential. Fluorescence-based imaging techniques are widely used to probe the trafficking machinery within cells, and many of these methods have the potential to be applied in a quantitative manner. In the present mini-review, we highlight several recent examples of how image intensity, kinetic measurements, co-localization and texture feature analysis have been used to study the function of one key family of membrane traffic regulators, the Rab GTPases. We give specific emphasis to the importance of the quantitative nature of these recent studies and comment on their potential applicability to a high-throughput format.
Rab proteins of the endoplasmic reticulum: functions and interactors
Authors: Sandoval Carolina Ortiz , Simmen Thomas
Published: November 2012

Whereas most of what we know today about the Ras-related small GTPases of the Rab family stems from observations made on Golgi complex, endosome and plasma membrane trafficking, a subset of Rabs localizes in part or predominantly to the ER (endoplasmic reticulum). Here, Rabs such as Rab1, Rab2, Rab6 and Rab33 can regulate the anterograde and retrograde trafficking of vesicles between the Golgi complex, the ERGIC (ER–Golgi intermediate compartment) and the ER itself. However, among the ER-associated Rabs, some Rabs appear to perform roles not directly related to trafficking: these Rabs (e.g. Rab32 or Rab24) could aid proteins of the atlastin and reticulon families in determining the extent and direction of ER tubulation. In so doing, these Rabs regulate not only ER contacts with other organelles such as mitochondria, but also the formation of autophagosomes.
RAB3GAP1, RAB3GAP2 and RAB18: disease genes in Micro and Martsolf syndromes
Authors: Handley Mark T. , Aligianis Irene A.
Published: November 2012

Micro syndrome (OMIM 60018) and Martsolf syndrome (OMIM 21270) are related rare autosomal recessive disorders characterized by ocular and neurological abnormalities and hypothalamic hypogonadism. Micro syndrome has been associated with causative mutations in three disease genes: RAB3GAP1, RAB3GAP2 and RAB18. Martsolf syndrome has been associated with a mutation in RAB3GAP2. The present review summarizes the current literature on these genes and the proteins they encode.
Hijacking cellular functions for processing and delivery of colicins E3 and D into the cytoplasm
Authors: de Zamaroczy Miklos , Mora Liliana
Published: November 2012

The mechanisms for importing colicins from the extracellular medium into Escherichia coli target cells implicate a complex cascade of interactions with host proteins. It is known that colicins interact with membrane receptors, and they may appropriate them structurally, but not functionally, as a scaffold on the surface of the target cell so that they can be translocated across the outer membrane. During the import into the periplasm, colicins parasitize functionally membrane porins and energy-transducers by mimicking their natural substrates or interacting partners. Such structural or functional parasitism also takes place during the late molecular events responsible for the processing and translocation of nuclease colicins across the inner membrane. Two different RNase colicins (D and E3) require an endoproteolytic cleavage, dependent on the inner membrane ATPase/protease FtsH, in order to transfer their C-terminal toxic domain into the cytoplasm. Moreover, the processing of colicin D necessitates a specific interaction with the signal peptidase LepB, but without appropriating the catalytic activity of this enzyme. A comparison of the differences in structural and functional organizations of these two colicins, as well as the pore-forming colicin B, is discussed in the present paper in connection with the sequential steps of their import mechanisms and the exploitation of the machinery of the target cell.
Import of periplasmic bacteriocins targeting the murein
Authors: Braun Volkmar , Helbig Stephanie , Patzer Silke I.
Published: November 2012

Colicins are the only proteins imported by Escherichia coli and thus serve as tools to study the protein import mechanism. Most of the colicins studied degrade DNA, 16S RNA or tRNA in the cytoplasm, or form pores in the cytoplasmic membrane. Two bacteriocins, Cma (colicin M) and Pst (pesticin), affect the murein structure in the periplasm. These two bacteriocins must be imported only across the outer membrane and therefore represent the simplest system for studying protein import. Cma can be reversibly translocated across the outer membrane. Cma and Pst unfold during import. The crystal structure of Pst reveals a phage T4L (T4 lysozyme) fold of the activity domain. Both bacteriocins require energy for import which is translocated from the cytoplasmic membrane into the outer membrane by the Ton system. Cma kills cells only when the periplasmic FkpA PPIase (peptidylprolyl cis–trans isomerase)/chaperone is present.
Comparative c-type cytochrome expression analysis in Shewanella oneidensis strain MR-1 and Anaeromyxobacter dehalogenans strain 2CP-C grown with soluble and insoluble oxidized metal electron acceptors
Authors: Nissen Silke , Liu Xiaoxin , Chourey Karuna , Hettich Robert L. , Wagner Darlene D. , Pfiffner Susan M. , Löffler Frank E.
Published: November 2012

The genomes of Shewanella oneidensis strain MR-1 and Anaeromyxobacter dehalogenans strain 2CP-C encode 40 and 69 putative c-type cytochrome genes respectively. Deletion mutant and biochemical studies have assigned specific functions to a few c-type cytochromes involved in electron transfer to oxidized metals in S. oneidensis strain MR-1. Although promising, the genetic approach is limited to gene deletions that produce a distinct phenotype and to an organism for which a genetic system is available. To investigate and compare c-type cytochrome expression in S. oneidensis strain MR-1 and Anaeromyxobacter dehalogenans strain 2CP-C more comprehensively, proteomic measurements were used to characterize lysates of cells grown with soluble Fe(III) (as ferric citrate) and insoluble Mn(IV) (as MnO2) as electron acceptors. Strain MR-1 expressed 19 and 20, and strain 2CP-C expressed 27 and 25, c-type cytochromes when grown with Fe(III) and Mn(IV) respectively. The majority of c-type cytochromes (77% for strain MR-1 and 63% for strain 2CP-C) were expressed under both growth conditions; however, the analysis also revealed unique c-type cytochromes that were specifically expressed in cells grown with soluble Fe(III) or insoluble Mn(IV). Proteomic characterization proved to be a promising approach for determining the c-type cytochrome complement expressed under different growth conditions, and will help to elucidate the specific functions of more c-type cytochromes that are the basis for Shewanella and Anaeromyxobacter respiratory versatility.
Microcins in action: amazing defence strategies of Enterobacteria
Authors: Rebuffat Sylvie
Published: November 2012

Probably the oldest and most widespread antimicrobial strategy in living organisms is the use of antimicrobial peptides. Bacteria secrete such defence peptides, termed bacteriocins, that they use for microbial competitions. Microcins are bacteriocins of less than 10 kDa produced by Escherichia coli and related enterobacteria through the ribosomal pathway. They are synthesized as linear precursors, which can further undergo complex post-translational modifications resulting from dedicated maturation enzymes encoded in the microcin gene clusters, and are processed by proteolytic cleavage. Microcins exert potent bactericidal activities that use subtle and clever mechanisms to cross outer and inner membranes of Gram-negative bacteria. To cross the outer membrane, siderophore-microcins hijack receptors involved in iron acquisition. The lasso-peptide microcin J25, which is characterized by a knotted arrangement where the C-terminal tail is threaded through an N-terminal macrolactam ring, uses a hydroxamate siderophore receptor and the inner-membrane protein SbmA for import in sensitive bacteria, where it inhibits bacterial transcription through binding to RNAP (RNA polymerase). Microcin C produced as a heptapeptide adenylate, requires an outer-membrane porin and an inner-membrane ABC (ATP-binding-cassette) transporter to reach the cytoplasm of target bacteria, where it is processed by proteases into a non-hydrolysable aspartyl-adenylate analogue. Therefore, despite showing different killing mechanisms and the absence of any structural homology, microcins have the common characteristic to use Trojan horse strategies to destroy their competitors. They offer new and promising tracks for further design and engineering of novel efficient antibiotics.
Antimicrobial mechanism of lantibiotics
Authors: Islam Mohammad R. , Nagao Jun-ichi , Zendo Takeshi , Sonomoto Kenji
Published: November 2012

Lantibiotics are ribosomally synthesized antimicrobial peptides that commonly target the cell wall precursor lipid II during their antimicrobial mechanism and exert their inhibitory activity by (i) inhibition of cell wall biosynthesis, and (ii) stable pore formation in the target membrane. Type-A(I) (i.e. nisin) and two-component (i.e. lacticin 3147) lantibiotics initially interact with lipid II to stabilize the complex, which then proceeds to inhibit cell wall biosynthesis and pore formation. Type-A(II) (i.e. nukacin ISK-1) and type-B (i.e. mersacidin) lantibiotics also use lipid II as a docking molecule, but can only inhibit cell wall biosynthesis without forming pores. In the present paper, we review the antimicrobial mechanism of different types of lantibiotics, their current progress and future prospect.
Application of anti-listerial bacteriocins: monitoring enterocin expression by multiplex relative reverse transcription–PCR
Authors: Williams D. Ross , Chanos Panagiotis
Published: November 2012

Listeriosis is a deadly food-borne disease, and its incidence may be limited through the biotechnological exploitation of a number of anti-listerial biocontrol agents. The most widely used of these agents are bacteriocins and the Class II enterocins are characterized by their activity against Listeria. Enterocins are primarily produced by enterococci, particularly Enterococcus faecium and many strains have been described, often encoding multiple bacteriocins. The use of these strains in food will require that they are free of virulence functions and that they exhibit a high level expression of anti-listerial enterocins in fermentation conditions. Multiplex relative RT (reverse transcription)–PCR is a technique that is useful in the discovery of advantageous expression characteristics among enterocin-producing strains. It allows the levels of individual enterocin gene expression to be monitored and determination of how expression is altered under different growth conditions.
‘Bac’ to the future: bioengineering lantibiotics for designer purposes
Authors: Molloy Evelyn M. , Ross R. Paul , Hill Colin
Published: November 2012

Bacteriocins are bacterially produced peptides or proteins that inhibit the growth of other bacterial strains. They can have a broad (effective against multiple genera) or narrow (effective against specific species) spectrum of activity. The diversity of bacteriocins found in Nature, in terms of both spectrum of activity and physiochemical properties, offers the possibility of multiple applications in the food and pharmaceutical industries. However, traditional screening strategies may not provide a sufficient range of natural molecules with specifically desired properties. Research suggests that bioengineering of existing inhibitors has the potential to address this issue, extending the application of natural bacteriocins for use in novel settings and against different targets. In the present paper, we discuss the successful implementation of bioengineering strategies to alter and even improve the functional characteristics of a bacteriocin, using the prototypical lantibiotic nisin as an example. Additionally, we describe the recent use of the nisin-modification machinery in vivo to enhance the properties of medically significant peptides.
Killing as means of promoting biodiversity
Authors: Abrudan Monica I. , Brown Sarah , Rozen Daniel E.
Published: November 2012

Bacteriocins are usually viewed as the effective weapons of bacterial killers. However, killing competitors with bacteriocins may be not only a means of eliminating other strains, but also a crucial unappreciated mechanism promoting bacterial diversity. In the present short review, we summarize recent empirical and theoretical studies examining the role bacteriocins that may play in driving and maintaining diversity among microbes. We conclude by highlighting limitations of current models and suggest directions for future studies.
Novel functions for Rab GTPases in multiple aspects of tumour progression
Authors: Recchi Chiara , Seabra Miguel C.
Published: November 2012

Rab GTPases are master regulators of intracellular trafficking and, in recent years, their role in the control of different aspects of tumour progression has emerged. In the present review, we show that Rab GTPases are disregulated in many cancers and have central roles in tumour cell migration, invasion, proliferation, communication with stromal cells and the development of drug resistance. As a consequence, Rab proteins may be novel potential candidates for the development of anticancer drugs and, in this context, the preliminary results obtained with an inhibitor of Rab function are also discussed.
Rab27a and melanosomes: a model to investigate the membrane targeting of Rabs
Authors: Booth Antonia E.G. , Seabra Miguel C. , Hume Alistair N.
Published: November 2012

Rab proteins constitute the largest family within the Ras superfamily of small GTPases (>60 in mammals) and are essential regulators of transport between intracellular organelles. Key to this activity is their targeting to specific compartments within the cell. However, although great strides have been made over the last 25 years in assigning functions to individual Rabs and identifying their downstream effectors, the mechanism(s) regulating their targeting to specific subcellular membranes remains less well understood. In the present paper, we review the evidence supporting the proposed mechanisms of Rab targeting and highlight insights into this process provided by studies of Rab27a.
Pathways of colicin import: utilization of BtuB, OmpF porin and the TolC drug-export protein
Authors: Zakharov Stanislav D. , Sharma Onkar , Zhalnina Mariya , Yamashita Eiki , Cramer William A.
Published: November 2012

Pathway I. Group A nuclease colicins parasitize and bind tightly (Kd ≤ 10−9 M) to the vitamin B12 receptor on which they diffuse laterally in the OM (outer membrane) and use their long (≥100 Å; 1 Å=0.1 nm) receptor-binding domain as a ‘fishing pole’ to locate the OmpF porin channel for translocation. Crystal structures of OmpF imply that a disordered N-terminal segment of the colicin T-domain initiates insertion. Pathway II. Colicin N does not possess a ‘fishing pole’ receptor-binding domain. Instead, it uses OmpF as the Omp (outer membrane protein) for reception and translocation, processes in which LPS (lipopolysaccharide) may also serve. Keio collection experiments defined the LPS core that is used. Pathway III. Colicin E1 utilizes the drug-export protein TolC for import. CD spectra and thermal-melting analysis predict: (i) N-terminal translocation (T) and central receptor (BtuB) -binding (R) domains are predominantly α-helical; and (ii) helical coiled-coil conformation of the R-domain is similar to that of colicins E3 and Ia. Recombinant colicin peptides spanning the N-terminal translocation domain defined TolC-binding site(s). The N-terminal 40-residue segment lacks the ordered secondary structure. Peptide 41–190 is helical (78%), co-elutes with TolC and occluded TolC channels. Driven by a trans-negative potential, peptides 82–140 and 141–190 occluded TolC channels. The use of TolC for colicin E1 import implies that the interaction of this colicin with the other Tol proteins does not occur in the periplasmic space, but rather through Tol domains in the cytoplasmic membrane, thus explaining colicin E1 cytotoxicity towards a strain in which a 234 residue periplasmic TolA segment is deleted.
Membrane activities of colicin nuclease domains: analogies with antimicrobial peptides
Authors: Vankemmelbeke Mireille , James Richard , Penfold Christopher N.
Published: November 2012

Nuclease colicins, such as colicin E9, are a class of Escherichia coli bacteriocins that kill E. coli and closely related Gram-negative bacteria through nucleolytic action in the cytoplasm. In order to accomplish this, their cytotoxic domains require transportation across two sets of membranes and the periplasmic space. Currently, little information is available concerning how the membrane translocation processes are achieved, and the present review summarizes our recent results on the in vitro membrane activities of the colicin nuclease domains. Using model membranes, we have analysed the cytotoxic domains of a number of DNase-type colicins and one rRNase colicin for their bilayer insertion depth and for their ability to induce vesicle aggregation, lipid mixing and increased bilayer permeability. We found that, by analogy with AMPs (antimicrobial peptides), the interplay between charge and hydrophobic character of the nuclease domains governs their pleiotropic membrane activities and these results form the basis of ongoing work to unravel the molecular mechanisms underlying their membrane translocation.
Colicin-like bacteriocins as novel therapeutic agents for the treatment of chronic biofilm-mediated infection
Authors: Brown Carla L. , Smith Karen , McCaughey Laura , Walker Daniel
Published: November 2012

The emergence of pan-resistant strains of Gram-negative pathogens and the ability of many bacteria to form multidrug-resistant biofilms during chronic infection poses the grave threat of bacterial infections that are truly untreatable with our current armoury of antibiotics. Despite obvious clinical need, few new antibiotics have entered clinical practice in recent years. For ‘difficult to treat’ Gram-negative bacteria such as Pseudomonas aeruginosa and Escherichia coli, where the presence of outer membrane and multidrug-efflux pumps severely limit the effectiveness of whole classes of antibiotics, the need is particularly pressing. An alternative approach to antimicrobial treatment is to use the well-characterized species-specific colicin-like bacteriocins which are produced by a wide range of Gram-negative bacteria, including Pseudomonas aeruginosa and Escherichia coli. Our current work on colicin-like bacteriocins aims to determine whether these potent antimicrobial agents are effective at killing bacteria growing in the biofilm state and during infection.
Rab25 in cancer: a brief update
Authors: Mitra Shreya , Cheng Kwai W. , Mills Gordon B.
Published: November 2012

Derailed endocytosis is a hallmark of cancer. The endocytic pathway, as demonstrated by our laboratory, is a frequent target of genomic aberrations in cancer and plays a critical role in the maintenance of cellular polarity, stem cell function, bioenergetics, proliferation, motility, invasion, metastasis, apoptosis and autophagy. The Rab GTPases, along with their effectors, are critical regulators of this endocytic machinery and can have a huge impact on the cellular itinerary of growth and metabolism. Rab25 is an epithelial-cell-specific member of the Rab GTPase superfamily, sharing close homology with Rab11a, the endosomal recycling Rab GTPase. RAB25 has been implicated in various cancers, with reports presenting it as both an oncogene and a tumour-suppressor gene. At the cellular level, Rab25 was shown to contribute to invasiveness of cancer cells by regulating integrin trafficking. Recently, our laboratory uncovered a critical role for Rab25 in cellular energetics. Assimilating all of the existing evidence, in the present review, we give an updated overview of the complex and often context-dependent role of Rab25 in cancer.
A multisite managed environment facility for targeted trait and germplasm phenotyping
Authors: Rebetzke Greg J. , Chenu Karine , Biddulph Ben , Moeller Carina , Deery Dave M. , Rattey Allan R. , Bennett Dion , Barrett-Lennard Ed G. , Mayer Jorge E.
Published: November 2012

Field evaluation of germplasm for performance under water and heat stress is challenging. Field environments are variable and unpredictable, and genotype × environment interactions are difficult to interpret if environments are not well characterised. Numerous traits, genes and quantitative trait loci have been proposed for improving performance but few have been used in variety development. This reflects the limited capacity of commercial breeding companies to screen for these traits and the absence of validation in field environments relevant to breeding companies, and because little is known about the economic benefit of selecting one particular trait over another. The value of the proposed traits or genes is commonly not demonstrated in genetic backgrounds of value to breeding companies. To overcome this disconnection between physiological trait breeding and uptake by breeding companies, three field sites representing the main environment types encountered across the Australian wheatbelt were selected to form a set of managed environment facilities (MEFs). Each MEF manages soil moisture stress through irrigation, and the effects of heat stress through variable sowing dates. Field trials are monitored continuously for weather variables and changes in soil water and canopy temperature in selected probe genotypes, which aids in decisions guiding irrigation scheduling and sampling times. Protocols have been standardised for an essential core set of measurements so that phenotyping yield and other traits are consistent across sites and seasons. MEFs enable assessment of a large number of traits across multiple genetic backgrounds in relevant environments, determine relative trait value, and facilitate delivery of promising germplasm and high value traits into commercial breeding programs.
Heteroblasty in bromeliads - anatomical, morphological and physiological changes in ontogeny are not related to the change from atmospheric to tank form
Authors: Meisner Kerstin , Winkler Uwe , Zotz Gerhard
Published: November 2012

Heteroblasty is defined as an abrupt change in gross morphology during ontogeny, whereas homoblastic species show no or gradual changes. For Bromeliaceae, there are conflicting reports on a very limited number of species on the functional importance of this step change compared with gradual changes (ontogenetic drift). Studying a large set of species should allow more general conclusions. Seventeen homoblastic and heteroblastic species from Panama were investigated, including the entire size range of most species. Measurements included functionally relevant anatomical (water storage tissue), morphological (stomatal and trichome densities) and physiological parameters (transpiration rates, nutrient uptake rates). Size-related variation in all parameters was common, but evidence for a step change in the studied parameters could not be detected in any of the heteroblastic species. Our results caused us to question the widely held view of the course of the ontogenetic development in heteroblastic bromeliads and their functional implications. These findings suggest that the possible functional relevance of heteroblasty in bromeliads require rethinking and future investigations should employ a comparative approach with both homoblastic and heteroblastic species and including the entire size range to account for ontogenetic drift.
Artificial fertilisation in a terrestrial toadlet (Pseudophryne guentheri): effect of medium osmolality, sperm concentration and gamete storage
Authors: Silla Aimee J.
Published: November 2012

Anurans exhibit a greater reproductive diversity than any other vertebrate order. However, studies investigating the effects of the external fertilisation environment on fertilisation success are limited to aquatic-breeding species. This study investigated the effects of fertilisation medium osmolality, sperm concentration and short-term oocyte storage on fertilisation success in a terrestrial-breeding anuran, Pseudophryne guentheri. Split-clutch experimental designs were used to determine optimal fertilisation conditions. To determine the effect of short-term sperm storage, sperm viability was assessed using fluorescence microscopy and percentage sperm motility and velocity quantified with a computer-assisted sperm analysis system. Fertilisation success was highest in media ranging in osmolality from 25 mOsm kg–1 to 100 mOsm kg–1, representing a broader range and higher optimal osmolality than previously reported for aquatic breeders. High rates of fertilisation (>75%) were achieved in relatively low sperm concentrations (2.5 × 104 mL–1). Oocytes stored in isotonic solutions (200 mOsm kg–1) retained fertilisation capacity (32%) after 8 h of storage, while sperm suspensions maintained motility (≥26%) for 13 days. Additional studies on terrestrial-breeding anurans will be required to ascertain whether the optimal fertilisation conditions reported reflect adaptations to achieve fertilisation in a terrestrial environment.
Modelling the probability of Australian grassfires escaping initial attack to aid deployment decisions
Authors: Plucinski Matt P.
Published: November 2012

Most grassfires that occur in southern Australia are contained to small areas by local suppression resources. Those that are not require extra resources from neighbouring districts. Identifying these fires at the start of initial attack can prompt early resource requests so that resources arrive earlier when they can more effectively assist with containment. This study uses operational data collected from Australian grassfires that used ground tankers and aircraft for suppression. Variables were limited to those available when the first situation report is provided to incident controllers and included weather parameters, resource response times, slope, curing state, pasture condition and estimated fire area at initial attack. Logistic regression and classification trees were used to identify grassfires likely to escape initial attack by (a) becoming large (final area ≥100 ha), (b) being of long duration (containment time ≥4 h) or (c) either or both of these. These fires would benefit from having more resources deployed to them than are normally available. The best models used initial fire area and Grassland Fire Danger Index as predictor variables. Preliminary operational decision guides developed from classification trees could be used by fire managers to make quick assessments of the need for extra resources at early stages of a fire.
Modelling the determinants of ignition in the Sydney Basin, Australia: implications for future management
Authors: Penman T. D. , Bradstock R. A. , Price O.
Published: November 2012

Variations in area burnt by fire are governed by four processes: biomass growth, availability to burn, fire weather and ignitions. Insight into these how these processes are shaped by biophysical and human influences is required to underpin the development of effective management strategies. Patterns of natural and arson ignitions were examined within the densely populated Sydney region of south-eastern Australia to determine the extent to which management can alter the risk of ignition. Arson ignitions were more likely on ridges in association with human infrastructure, i.e. roads and houses. Lightning ignitions also occurred more frequently on ridges, but at greater distances from human infrastructure. These patterns are consistent with those reported in studies from forested regions in the northern hemisphere. Fuel age had a variable effect with lightning more likely in older fuels (>25 years) and arson more likely in younger fuels (<10 years). Probability of both ignition types increased under more severe fire weather. Climate change is predicted to increase the severity of fire weather and is therefore likely to result in an increase in ignition frequency in the Sydney Basin. Urban expansion is also likely to have significant effects on ignitions and resultant risks to people and property via an increase in the probability of arson ignitions.
Tuning ion correlations at an electrified soft interface
Authors: Laanait Nouamane , Mihaylov Miroslav , Hou Binyang , Yu Hao , Vanýsek Petr , Meron Mati , Lin Binhua , Benjamin Ilan , Schlossman Mark L.
Published: November 2012

Ion distributions play a central role in various settings—from biology, where they mediate the electrostatic interactions between charged biomolecules in solution, to energy storage devices, where they influence the charging properties of supercapacitors. These distributions are determined by interactions dictated by the chemical properties of the ions and their environment as well as the long-range nature of the electrostatic force. Recent theoretical and computational studies have explored the role of correlations between ions, which have been suggested to underlie a number of counterintuitive results, such as like-charge attraction. However, the interdependency between ion correlations and other interactions that ions experience in solution complicates the connection between physical models of ion correlations and the experimental investigation of ion distributions. We exploit the properties of the liquid/liquid interface to vary the coupling strength

of ion–ion correlations from weak to strong while monitoring their influence on ion distributions at the nanometer scale with X-ray reflectivity and the macroscopic scale with interfacial tension measurements. These data are in agreement with the predictions of a parameter-free density functional theory that includes ion–ion correlations and ion–solvent interactions over the entire range of experimentally tunable correlation coupling strengths (from 0.8 to 3.7). This study provides evidence for a sharply defined electrical double layer for large coupling strengths in contrast to the diffuse distributions predicted by mean field theory, thereby confirming a common prediction of many ion correlation models. The reported findings represent a significant advance in elucidating the nature and role of ion correlations in charged soft matter.
Specific and reversible DNA-directed self-assembly of oil-in-water emulsion droplets
Authors: Hadorn Maik , Boenzli Eva , Sørensen Kristian T. , Fellermann Harold , Eggenberger Hotz Peter , Hanczyc Martin M.
Published: November 2012

Higher-order structures that originate from the specific and reversible DNA-directed self-assembly of microscopic building blocks hold great promise for future technologies. Here, we functionalized biotinylated soft colloid oil-in-water emulsion droplets with biotinylated single-stranded DNA oligonucleotides using streptavidin as an intermediary linker. We show the components of this modular linking system to be stable and to induce sequence-specific aggregation of binary mixtures of emulsion droplets. Three length scales were thereby involved: nanoscale DNA base pairing linking microscopic building blocks resulted in macroscopic aggregates visible to the naked eye. The aggregation process was reversible by changing the temperature and electrolyte concentration and by the addition of competing oligonucleotides. The system was reset and reused by subsequent refunctionalization of the emulsion droplets. DNA-directed self-assembly of oil-in-water emulsion droplets, therefore, offers a solid basis for programmable and recyclable soft materials that undergo structural rearrangements on demand and that range in application from information technology to medicine.
Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations
Authors: Vargiu Attilio V. , Nikaido Hiroshi
Published: November 2012

Multidrug resistance in Gram-negative bacteria, to which multidrug efflux pumps such as the AcrB transporter makes a major contribution, is becoming a major public health problem. Unfortunately only a few compounds have been cocrystallized with AcrB, and thus computational approaches are essential in elucidating the interaction between diverse ligands and the pump protein. We used molecular dynamics simulation to examine the binding of nine substrates, two inhibitors, and two nonsubstrates to the distal binding pocket of AcrB, identified earlier by X-ray crystallography. This approach gave us more realistic views of the binding than the previously used docking approach, as the explicit water molecules contributed to the process and the flexible binding site was often seen to undergo large structural changes. We analyzed the interaction in detail in terms of the binding energy, hydrophobic surface-matching, and the residues involved in the process. We found that all substrates tested bound to the pocket, whereas the binding to this site was not preferred for the nonsubstrates. Interestingly, both inhibitors [Phe-Arg-β-naphthylamide and 1-(1-naphtylmethyl)-piperazine] tended to move out of the pocket at least partially, getting into contact with a glycine-rich loop that separates the distal pocket from the more proximal region of the protein and is thought to control the access of substrates to the distal pocket.
Sony’s redemption: the Blu-ray vs. HD-DVD standards war
Authors: Cozzarin Brian
                      Paul , Lee William , Koo Bonwoo
Published: November 2012

This paper examines the factors that affect market dominance in a standards competition by comparing the VHS–Beta war in the 1980s with that between Blu-ray and HD-DVD in the 2000s. We first look at the changing home video market in terms of technological development. Then we move on to discuss three main strategies in a standards war: first-mover advantage, indirect network effects and software provision, and strategic alliances of hardware firms. We find that technological innovation is essential. Being a first mover is helpful, but not sufficient, in building a dominant position in the market. Historical evidence shows that Sony created a network of complementary firms for Blu-ray. Consequently, an effective strategy to become a winner in a standards competition appears to be building a network of complementary products and subsequently an installed base.
Effects of confidence and anxiety on flow state in competition
Authors: Koehn Stefan
Published: November 2012

Confidence and anxiety are important variables that underlie the experience of flow in sport. Specifically, research has indicated that confidence displays a positive relationship and anxiety a negative relationship with flow. The aim of this study was to assess potential direct and indirect effects of confidence and anxiety dimensions on flow state in tennis competition. A sample of 59 junior tennis players completed measures of Competitive State Anxiety Inventory‐2d and Flow State Scale‐2. Following predictive analysis, results showed significant positive correlations between confidence (intensity and direction) and anxiety symptoms (only directional perceptions) with flow state. Standard multiple regression analysis indicated confidence as the only significant predictor of flow. The results confirmed a protective function of confidence against debilitating anxiety interpretations, but there were no significant interaction effects between confidence and anxiety on flow state.
Notch signaling from the endosome requires a conserved dileucine motif
Authors: Zheng Li , Saunders Cosmo A. , Sorensen Erika B. , Waxmonsky Nicole C. , Conner Sean D.
Published: November 2012

Notch signaling is reliant on γ-secretase–mediated processing, although the subcellular location where γ-secretase cleaves Notch to initiate signaling remains unresolved. Accumulating evidence demonstrates that Notch signaling is modulated by endocytosis and endosomal transport. In this study, we investigated the relationship between Notch transport itinerary and signaling capacity. In doing so, we discovered a highly conserved dileucine sorting signal encoded within the cytoplasmic tail that directs Notch to the limiting membrane of the lysosome for signaling. Mutating the dileucine motif led to receptor accumulation in cation-dependent mannose-phosphate receptor–positive tubular early endosomes and a reduction in Notch signaling capacity. Moreover, truncated receptor forms that mimic activated Notch were readily cleaved by γ-secretase within the endosome; however, the cleavage product was proteasome-sensitive and failed to contribute to robust signaling. Collectively these results indicate that Notch signaling from the lysosome limiting membrane is conserved and that receptor targeting to this compartment is an active process. Moreover, the data support a model in which Notch signaling in mammalian systems is initiated from either the plasma membrane or lysosome, but not the early endosome.
Reduced TOR signaling sustains hyphal development inCandida albicansby lowering Hog1 basal activity
Authors: Su Chang , Lu Yang , Liu Haoping
Published: November 2012

Candida albicans is able to undergo reversible morphological changes between yeast and hyphal forms in response to environmental cues. This morphological plasticity is essential for its pathogenesis. Hyphal development requires two temporally linked changes in promoter chromatin, which is sequentially regulated by temporarily clearing the transcription inhibitor Nrg1 upon activation of cAMP/protein kinase A and promoter recruitment of the histone deacetylase Hda1 under reduced target of rapamycin (Tor1) signaling. The GATA family transcription factor Brg1 recruits Hda1 to promoters for sustained hyphal development, and BRG1 expression is a readout of reduced Tor1 signaling. How Tor1 regulates BRG1 expression is not clear. Using a forward genetic screen for mutants that can sustain hyphal elongation in rich media, we found hog1, ssk2, and pbs2 mutants of the HOG mitogen-activated protein kinase pathway to express BRG1 irrespective of rapamycin. Furthermore, rapamycin lowers the basal activity of Hog1 through the functions of the two Hog1 tyrosine phosphatases Ptp2 and Ptp3. Active Hog1 represses the expression of BRG1 via the transcriptional repressor Sko1 as Sko1 disassociates from the promoter of BRG1 in the hog1 mutant or in rapamycin. Our data suggest that reduced Tor1 signaling lowers Hog1 basal activity via Hog1 phosphatases to activate BRG1 expression for hyphal elongation.
Altered nitric oxide production mediates matrix-specific PAK2 and NF-κB activation by flow
Authors: Yurdagul Arif , Chen Jie , Funk Steven Daniel , Albert Patrick , Kevil Christopher G. , Orr A. Wayne
Published: November 2012

Shear stress generated by distinct blood flow patterns modulates endothelial cell phenotype to spatially restrict atherosclerotic plaque development. Signaling through p21-activated kinase (PAK) mediates several of the deleterious effects of shear stress, including enhanced NF-κB activation and proinflammatory gene expression. Whereas shear stress activates PAK in endothelial cells on a fibronectin matrix, basement membrane proteins limit shear-induced PAK activation and inflammation through a protein kinase A–dependent pathway; however, the mechanisms underlying this regulation were unknown. We show that basement membrane proteins limit membrane recruitment of PAK2, the dominant isoform in endothelial cells, by blocking its interaction with the adaptor protein Nck. This uncoupling response requires protein kinase A–dependent nitric oxide production and subsequent PAK2 phosphorylation on Ser-20 in the Nck-binding domain. Of importance, shear stress does not stimulate nitric oxide production in endothelial cells on fibronectin, resulting in enhanced PAK activation, NF-κB phosphorylation, ICAM-1 expression, and monocyte adhesion. These data demonstrate that differential flow–induced nitric oxide production regulates matrix-specific PAK signaling and describe a novel mechanism of nitric oxide–dependent NF-κB inhibition.
A Lasso multi-marker mixed model for association mapping with population structure correction
Authors: Rakitsch Barbara , Lippert Christoph , Stegle Oliver , Borgwardt Karsten
Published: November 2012

Motivation: Exploring the genetic basis of heritable traits remains one of the central challenges in biomedical research. In traits with simple Mendelian architectures, single polymorphic loci explain a significant fraction of the phenotypic variability. However, many traits of interest seem to be subject to multifactorial control by groups of genetic loci. Accurate detection of such multivariate associations is non-trivial and often compromised by limited statistical power. At the same time, confounding influences, such as population structure, cause spurious association signals that result in false-positive findings.

Results: We propose linear mixed models LMM-Lasso, a mixed model that allows for both multi-locus mapping and correction for confounding effects. Our approach is simple and free of tuning parameters; it effectively controls for population structure and scales to genome-wide datasets. LMM-Lasso simultaneously discovers likely causal variants and allows for multi-marker–based phenotype prediction from genotype. We demonstrate the practical use of LMM-Lasso in genome-wide association studies in Arabidopsis thaliana and linkage mapping in mouse, where our method achieves significantly more accurate phenotype prediction for 91% of the considered phenotypes. At the same time, our model dissects the phenotypic variability into components that result from individual single nucleotide polymorphism effects and population structure. Enrichment of known candidate genes suggests that the individual associations retrieved by LMM-Lasso are likely to be genuine.

Availability: Code available under http://webdav.tuebingen.

mpg.de/u/karsten/Forschung/research.html.

Contact:  rakitsch@tuebingen.mpg.de, ippert@microsoft.com or stegle@ebi.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
An effective framework for reconstructing gene regulatory networks from genetical genomics data
Authors: Flassig R. J. , Heise S. , Sundmacher K. , Klamt S.
Published: November 2012

Motivation: Systems Genetics approaches, in particular those relying on genetical genomics data, put forward a new paradigm of large-scale genome and network analysis. These methods use naturally occurring multi-factorial perturbations (e.g. polymorphisms) in properly controlled and screened genetic crosses to elucidate causal relationships in biological networks. However, although genetical genomics data contain rich information, a clear dissection of causes and effects as required for reconstructing gene regulatory networks is not easily possible.

Results: We present a framework for reconstructing gene regulatory networks from genetical genomics data where genotype and phenotype correlation measures are used to derive an initial graph which is subsequently reduced by pruning strategies to minimize false positive predictions. Applied to realistic simulated genetic data from a recent DREAM challenge, we demonstrate that our approach is simple yet effective and outperforms more complex methods (including the best performer) with respect to (i) reconstruction quality (especially for small sample sizes) and (ii) applicability to large data sets due to relatively low computational costs. We also present reconstruction results from real genetical genomics data of yeast.

Availability: A MATLAB implementation (script) of the reconstruction framework is available at www.mpi-magdeburg.mpg.de/projects/cna/etcdownloads.html

Contact:  klamt@mpi-magdeburg.mpg.de
Characterization of naturally Epstein–Barr virus-infected gastric carcinoma cell line YCCEL1
Authors: Kim Do Nyun , Seo Min Koo , Choi Hoyun , Kim Su Yeon , Shin Hee Jong , Yoon A-Ran , Tao Qian , Rha Sun Young , Lee Suk Kyeong
Published: November 2012

Epstein–Barr virus (EBV) is a herpesvirus associated with lymphomas and carcinomas. While EBV-associated epithelial cell lines are good model systems to investigate the role of EBV in carcinoma, only a few cell lines are available as they are hard to acquire. A greater variety of naturally EBV-infected cell lines which are derived from tumour patients are needed to represent various features of EBVaGC. We characterized cell line YCCEL1, established from a Korean EBVaGC patient, to ascertain whether it can be used to study the roles of EBV in EBVaGC. The expression of EBV genes and cell surface markers was examined by in situ hybridization, RT-PCR, Western blot analysis, immunofluorescence assay and Northern blot analysis. EBV episomal status was analysed by Southern blotting and real-time PCR. This cell line expressed EBV nuclear antigen 1 (EBNA1) and latent membrane protein 2A (LMP2A), but not EBNA2, LMP2B nor LMP1. The majority of the lytic proteins were not detected in YCCEL1 cells either before or after treatment with 12-O-tetradecanoylphorbol-13-acetate. YCCEL1 cells expressed BART microRNAs (miRNAs) at high level but did not express BHRF1 miRNAs. YCCEL1 cells expressed cytokeratin, but not CD21 and CD19, suggesting CD21-independent EBV infection. The latent EBV gene and EBV miRNA expression pattern of YCCEL1 cells closely resembled that of general EBVaGC cases. Our results support the value of YCCEL1 cells as a good model system to study the role of EBV in gastric carcinogenesis.
Genetic characterization by composite sequence analysis of a new pathogenic field strain of equine infectious anemia virus from the 2006 outbreak in Ireland
Authors: Quinlivan Michelle , Cook Frank , Kenna Rachel , Callinan John J. , Cullinane Ann
Published: November 2012

Equine infectious anemia virus (EIAV), the causative agent of equine infectious anaemia (EIA), possesses the least-complex genomic organization of any known extant lentivirus. Despite this relative genetic simplicity, all of the complete genomic sequences published to date are derived from just two viruses, namely the North American EIAVWYOMING (EIAVWY) and Chinese EIAVLIAONING (EIAVLIA) strains. In 2006, an outbreak of EIA occurred in Ireland, apparently as a result of the importation of contaminated horse plasma from Italy and subsequent iatrogenic transmission to foals. This EIA outbreak was characterized by cases of severe, sometimes fatal, disease. To begin to understand the molecular mechanisms underlying this pathogenic phenotype, complete proviral genomic sequences in the form of 12 overlapping PCR-generated fragments were obtained from four of the EIAV-infected animals, including two of the index cases. Sequence analysis of multiple molecular clones produced from each fragment demonstrated the extent of diversity within individual viral genes and permitted construction of consensus whole-genome sequences for each of the four viral isolates. In addition, complete env gene sequences were obtained from 11 animals with differing clinical profiles, despite exposure to a common EIAV source. Although the overall genomic organization of the Irish EIAV isolates was typical of that seen in all other strains, the European viruses possessed ≤80 % nucleotide sequence identity with either EIAVWY or EIAVLIA. Furthermore, phylogenetic analysis suggested that the Irish EIAV isolates developed independently of the North American and Chinese viruses and that they constitute a separate monophyletic group.