bluuebunny/crossref_metadata_2025 huggingface dataset:
Completing the English Vocabulary Profile: C1 and C2 vocabulary
Authors: Capel Annette
Published: November 2012

The English Vocabulary Profile is an online vocabulary resource for teachers, teacher trainers, exam setters, materials writers and syllabus designers. It offers extensive information about the Common European Framework of Reference (CEFR) levels of words, phrases, phrasal verbs and idioms, and currently includes just under 7,000 headwords. This article reports on the trialling and validation phase of the A1−B2 levels of the resource, as well as outlining the research and completion of the C1 and C2 levels. The project has followed a ‘can-do’ rationale, focusing on what learners actually know rather than prescribing what they should know, and is underpinned by up-to-date corpus evidence, including the 50-million word Cambridge Learner Corpus and the 1.2-billion word Cambridge English Corpus of first language use. At C1 and C2 levels, the English Vocabulary Profile describes both General and Academic English, and the additional sources used to research this area of language learning are described in the article. Polysemous words are treated in depth and the project has sought to determine which meanings of these important words appear to be acquired first; new, less frequent meanings often continue to be learned across all six CEFR levels. Phrases form another substantial part of the resource and this aspect has been guided by expert research (see Martínez 2011).
Mtr extracellular electron-transfer pathways in Fe(III)-reducing or Fe(II)-oxidizing bacteria: a genomic perspective
Authors: Shi Liang , Rosso Kevin M. , Zachara John M. , Fredrickson James K.
Published: November 2012

Originally discovered in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 (MR-1), key components of the Mtr (i.e. metal-reducing) pathway exist in all strains of metal-reducing Shewanella characterized. The protein components identified to date for the Mtr pathway of MR-1 include four multihaem c-Cyts (c-type cytochromes), CymA, MtrA, MtrC and OmcA, and a porin-like outer membrane protein MtrB. They are strategically positioned along the width of the MR-1 cell envelope to mediate electron transfer from the quinone/quinol pool in the inner membrane to Fe(III)-containing minerals external to the bacterial cells. A survey of microbial genomes has identified homologues of the Mtr pathway in other dissimilatory Fe(III)-reducing bacteria, including Aeromonas hydrophila, Ferrimonas balearica and Rhodoferax ferrireducens, and in the Fe(II)-oxidizing bacteria Dechloromonas aromatica RCB, Gallionella capsiferriformans ES-2 and Sideroxydans lithotrophicus ES-1. The apparent widespread distribution of Mtr pathways in both Fe(III)-reducing and Fe(II)-oxidizing bacteria suggests a bidirectional electron transfer role, and emphasizes the importance of this type of extracellular electron-transfer pathway in microbial redox transformation of iron. The organizational and electron-transfer characteristics of the Mtr pathways may be shared by other pathways used by micro-organisms for exchanging electrons with their extracellular environments.
Mind the gap: diversity and reactivity relationships among multihaem cytochromes of the MtrA/DmsE family
Authors: Bewley Kathryn D. , Firer-Sherwood Mackenzie A. , Mock Jee-Young , Ando Nozomi , Drennan Catherine L. , Elliott Sean J.
Published: November 2012

Shewanella oneidensis MR-1 has the ability to use many external terminal electron acceptors during anaerobic respiration, such as DMSO. The pathway that facilitates this electron transfer includes the decahaem cytochrome DmsE, a paralogue of the MtrA family of decahaem cytochromes. Although both DmsE and MtrA are decahaem cytochromes implicated in the long-range electron transfer across a ~300 Å (1 Å=0.1 nm) wide periplasmic ‘gap’, MtrA has been shown to be only 105 Å in maximal length. In the present paper, DmsE is further characterized via protein film voltammetry, revealing that the electrochemistry of the DmsE haem cofactors display macroscopic potentials lower than those of MtrA by 100 mV. It is possible this tuning of the redox potential of DmsE is required to shuttle electrons to the outer-membrane proteins specific to DMSO reduction. Other decahaem cytochromes found in S. oneidensis, such as the outer-membrane proteins MtrC, MtrF and OmcA, have been shown to have electrochemical properties similar to those of MtrA, yet possess a different evolutionary relationship.
Spectroelectrochemical analyses of electroactive microbial biofilms
Authors: Millo Diego
Published: November 2012

Understanding the mechanism of ET (electron transfer) through electroactive microbial biofilms is a challenge in the field of fundamental and applied life sciences. To date, electrochemical techniques such as CV (cyclic voltammetry) have been applied successfully to study the ET process in intact microbial biofilms on electrodes, providing important insight into their redox properties. However, CV as such does not provide any structural information about the species involved in the redox process. This shortcoming may limit the understanding of the ET process in microbial biofilms. To overcome this restriction, spectroelectrochemical techniques have been designed consisting of a spectroscopic technique performed in combination with electrochemical methods on the same electrode sample. These analytical approaches allow in vivo measurements of microbial biofilms under physiologically relevant conditions and controlled applied potential. The present review describes these spectroelectrochemical methodologies and critically addresses their impact on the understanding of the ET through biofilms.
Biological photovoltaics: intra- and extra-cellular electron transport by cyanobacteria
Authors: Bradley Robert W. , Bombelli Paolo , Rowden Stephen J.L. , Howe Christopher J.
Published: November 2012

A large variety of new energy-generating technologies are being developed in an effort to reduce global dependence on fossil fuels, and to reduce the carbon footprint of energy generation. The term ‘biological photovoltaic system’ encompasses a broad range of technologies which all employ biological material that can harness light energy to split water, and then transfer the resulting electrons to an anode for power generation or electrosynthesis. The use of whole cyanobacterial cells is a good compromise between the requirements of the biological material to be simply organized and transfer electrons efficiently to the anode, and also to be robust and able to self-assemble and self-repair. The principle that photosynthetic bacteria can generate and transfer electrons directly or indirectly to an anode has been demonstrated by a number of groups, although the power output obtained from these devices is too low for biological photovoltaic devices to be useful outside the laboratory. Understanding how photosynthetically generated electrons are transferred through and out of the organism is key to improving power output, and investigations on this aspect of the technology are the main focus of the present review.
Electrochemical communication between microbial cells and electrodes via osmium redox systems
Authors: Hasan Kamrul , Patil Sunil A. , Leech Dónal , Hägerhäll Cecilia , Gorton Lo
Published: November 2012

Electrochemical communication between micro-organisms and electrodes is the integral and fundamental part of BESs (bioelectrochemical systems). The immobilization of bacterial cells on the electrode and ensuring efficient electron transfer to the electrode via a mediator are decisive features of mediated electrochemical biosensors. Notably, mediator-based systems are essential to extract electrons from the non-exoelectrogens, a major group of microbes in Nature. The advantage of using polymeric mediators over diffusible mediators led to the design of osmium redox polymers. Their successful use in enzyme-based biosensors and BFCs (biofuel cells) paved the way for exploring their use in microbial BESs. The present mini-review focuses on osmium-bound redox systems used to date in microbial BESs and their role in shuttling electrons from viable microbial cells to electrodes.
On conducting electron traffic across the periplasm
Authors: Gralnick Jeffrey A.
Published: November 2012

Dissimilatory metal-reducing bacteria are able to conduct electrons from their cytoplasmic membrane across the periplasm and the outer membrane to redox proteins located on the surface of their cells. The Mtr respiratory pathway in Shewanella is the best-understood metal-reducing pathway to date. The core components of this pathway are well agreed upon, but are they sufficient? Could there be other components that we have yet to uncover? The present paper specifically considers the periplasm, its physical properties and organization. Two models are presented to explain how electrons could be conducted across this compartment in Shewanella.
The molecular toolbox for chromosomal heterologous multiprotein expression in Escherichia coli
Authors: Richter Katrin , Gescher Johannes
Published: November 2012

Heterologous multiprotein expression is the tool to answer a number of questions in basic science as well as to convert strains into producers and/or consumers of certain compounds in applied sciences. Multiprotein expression can be driven by plasmids with the disadvantages that the gene dosage might, in some cases, lead to toxic effects and that the continuous addition of antibiotics is undesirable. Stable genomic expression of proteins can forgo these problems and is a helpful and promising tool in synthetic biology. In the present paper, we provide an extract of methods from the toolbox for chromosome-based heterologous expression in Escherichia coli.
The roles of CymA in support of the respiratory flexibility of Shewanella oneidensis MR-1
Authors: Marritt Sophie J. , McMillan Duncan G.G. , Shi Liang , Fredrickson James K. , Zachara John M. , Richardson David J. , Jeuken Lars J.C. , Butt Julea N.
Published: November 2012

Shewanella species are isolated from the oxic/anoxic regions of seawater and aquatic sediments where redox conditions fluctuate in time and space. Colonization of these environments is by virtue of flexible respiratory chains, many of which are notable for the ability to reduce extracellular substrates including the Fe(III) and Mn(IV) contained in oxide and phyllosilicate minerals. Shewanella oneidensis MR-1 serves as a model organism to consider the biochemical basis of this flexibility. In the present paper, we summarize the various systems that serve to branch the respiratory chain of S. oneidensis MR-1 in order that electrons from quinol oxidation can be delivered the various terminal electron acceptors able to support aerobic and anaerobic growth. This serves to highlight several unanswered questions relating to the regulation of respiratory electron transport in Shewanella and the central role(s) of the tetrahaem-containing quinol dehydrogenase CymA in that process.
Small GTPases and Brucella entry into the endoplasmic reticulum
Authors: de Bolle Xavier , Letesson Jean-Jacques , Gorvel Jean-Pierre
Published: November 2012

A key determinant for intracellular pathogenic bacteria to ensure their virulence within host cells is their ability to bypass the endocytic pathway and to reach a safe niche of replication. In the case of Brucella, the bacterium targets the ER (endoplasmic reticulum) to create a replicating niche called the BCV (Brucella-containing vacuole). The ER is a suitable strategic place for pathogenic Brucella. Indeed, bacteria can be hidden from host cell defences to persist within the host, and they can take advantage of the membrane reservoir delivered by the ER to replicate. Interaction with the ER leads to the presence on the BCV of the GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and the small GTPase Rab2 known to be located on secretory vesicles that traffic between the ER and the Golgi apparatus. GAPDH and the small GTPase Rab2 controls Brucella replication at late times post-infection. A specific interaction between the human small GTPase Rab2 and a Brucella spp. protein named RicA was identified. Altered kinetics of intracellular trafficking and faster proliferation of the Brucella abortus ΔricA mutant was observed compared with the wild-type strain. RicA is the first reported effector with a proposed function for B. abortus.
Rab GTPase localization and Rab cascades in Golgi transport
Authors: Pfeffer Suzanne R.
Published: November 2012

Rab GTPases are master regulators of membrane traffic. By binding to distinct sets of effector proteins, Rabs catalyse the formation of function-specifying membrane microdomains. They are delivered to membranes by a protein named GDI (guanine-nucleotide-dissociation inhibitor) and are stabilized there after nucleotide exchange by effector binding. In the present mini-review, I discuss what we know about how Rab GTPases are delivered to the correct membrane-bound compartments and how Rab GTPase cascades order Rabs within the secretory and endocytic pathways. Finally, I describe how Rab cascades may establish the distinct compartments of the Golgi complex to permit ordered processing, sorting and secretion of secretory cargoes.
Roles for myosin Va in RNA transport and turnover
Authors: McCaffrey Mary W. , Lindsay Andrew J.
Published: November 2012

Mammals express three class V myosins. Myosin Va is widely expressed, but enriched in the brain, testes and melanocytes, myosin Vb is expressed ubiquitously, and myosin Vc is believed to be epithelium-specific. Myosin Va is the best characterized of the three and plays a key role in the transport of cargo to the plasma membrane. Its cargo includes cell-surface receptors, pigment and organelles such as the endoplasmic reticulum. It is also emerging that RNA and RNA-BPs (RNA-binding proteins) make up another class of myosin Va cargo. It has long been established that the yeast class V myosin, Myo4p, transports mRNAs along actin cables into the growing bud, and now several groups have reported a similar role for class V myosins in higher eukaryotes. Myosin Va has also been implicated in the assembly and maintenance of P-bodies (processing bodies), cytoplasmic foci that are involved in mRNA storage and degradation. The present review examines the evidence that myosin Va plays a role in the transport and turnover of mRNA.
The role of bacterial membrane proteins in the internalization of microcin MccJ25 and MccB17
Authors: Mathavan Indran , Beis Konstantinos
Published: November 2012

Microcins are gene-encoded antibacterial peptides of low molecular mass (<10 kDa), produced by Enterobactericeae. They are produced and secreted under conditions of limited essential nutrients and are active against related species. Bacterial strains under starvation conditions can produce and release microcins that can kill microcin-sensitive cells and therefore have more nutrients for survival. The outer-membrane protein OmpF and FhuA TonB-dependent pathways facilitate the internalization of the MccB17 and MccJ25 microcins into the target cell respectively. The inner-membrane protein SbmA transports the microcins through the inner membrane to the cytoplasmic face. Inside the cell, MccB17 targets DNA gyrase, whereas MccJ25 inhibits the bacterial RNA polymerase.
Energetics of colicin import revealed by genetic cross-complementation between the Tol and Ton systems
Authors: Lloubès Roland , Goemaere Emilie , Zhang Xiang , Cascales Eric , Duché Denis
Published: November 2012

Colicins are bacterial toxins that parasitize OM (outer membrane) receptors to bind to the target cells, use an import system to translocate through the cell envelope and then kill sensitive cells. Colicins classified as group A (colicins A, E1–E9, K and N) use the Tol system (TolA, TolB, TolQ and TolR), whereas group B colicins (colicins B, D, Ia, M and 5) use the ExbB–ExbD–TonB system. Genetic evidence has suggested that TolQ and ExbB, as well as TolR and ExbD, are interchangeable, whereas this is not possible with TolA and TonB. Early reports indicated that group B colicin uptake requires energy input, whereas no energy was necessary for the uptake of the pore-forming colicin A. Furthermore, energy is required to dissociate the complex formed with colicin E9 and its cognate immunity protein during the import process. In the present paper, we detail the functional phenotypes and colicin-sensitivity results obtained in tolQ and exbB mutants and cross-complementation data of amino acid substitutions that lie within ExbB or TolQ TMHs (transmembrane helices). We also discuss on a specific phenotype that corresponds to group A colicin-sensitivity associated with a non-functional Tol system.
Structure and uptake mechanism of bacteriocins targeting peptidoglycan renewal
Authors: Zeth Kornelius
Published: November 2012

Bacteriocins are narrow-spectrum protein antibiotics released to kill related bacteria of the same niche. Uptake of bacteriocins depends critically on the presence of an uptake receptor in the outer membrane, a translocation pore and an energy-dependent activating system of the inner membrane. Most bacteriocins act on the inner membrane as pore-forming toxins or they target cytoplasmic DNA/RNA and ribosomal synthesis respectively. Only two bacteriocins are known to become activated in the periplasmic space and to inhibit the renewal process of the peptidoglycan structure. In Escherichia coli, the Cma (colicin M) phosphatase is activated in the periplasmic space by the FkpA chaperone and subsequently degrades the C55-PP precursor unit of the peptidoglycan. Pst (pesticin) from Yersinia pestis carries a lysozyme homology domain to degrade peptidoglycan. Import of Pst is only achieved if the N-terminal translocation domain can span the outer membrane and if extensive unfolding of the protein during membrane passage is permitted. There is considerable plasticity in the import pathway since a chimaera comprising the activity domain replaced by T4 lysozyme is also translocated and active in killing those bacteria carrying the FyuA receptor.
Intrinsically disordered proteins: lessons from colicins
Authors: Hecht Oliver , Macdonald Colin , Moore Geoffrey R.
Published: November 2012

Defining structural features of IDPs (intrinsically disordered proteins) and relating these to biological function requires characterization of their dynamical properties. In the present paper, we review what is known about the IDPs of colicins, protein antibiotics that use their IDPs to enter bacterial cells. The structurally characterized colicin IDPs we consider contain linear binding epitopes for proteins within their target cells that the colicin hijacks during entry. We show that these binding epitopes take part in intramolecular interactions in the absence of protein partners, i.e. self-recognition, and consider the structural origins of this and its functional implications. We suggest that self-recognition is common in other IDPs that contain similar types of binding epitopes.
Microbial iron-redox cycling in subsurface environments
Authors: Roden Eric E.
Published: November 2012

In addition to its central role in mediating electron-transfer reactions within all living cells, iron undergoes extracellular redox transformations linked to microbial energy generation through utilization of Fe(II) as a source of chemical energy or Fe(III) as an electron acceptor for anaerobic respiration. These processes permit microbial populations and communities to engage in cyclic coupled iron oxidation and reduction within redox transition zones in subsurface environments. In the present paper, I review and synthesize a few case studies of iron-redox cycling in subsurface environments, highlighting key biochemical aspects of the extracellular iron-redox metabolisms involved. Of specific interest are the coupling of iron oxidation and reduction in field and experimental systems that model redox gradients and fluctuations in the subsurface, and novel pathways and organisms involved in the redox cycling of insoluble iron-bearing minerals. These findings set the stage for rapid expansion in our knowledge of the range of extracellular electron-transfer mechanisms utilized by subsurface micro-organisms. The observation that closely coupled oxidation and reduction of iron can take place under conditions common to the subsurface motivates this expansion in pursuit of molecular tools for studying iron-redox cycling communities in situ.
Bacteriocins active against plant pathogenic bacteria
Authors: Grinter Rhys , Milner Joel , Walker Daniel
Published: November 2012

Gram-negative phytopathogens cause significant losses in a diverse range of economically important crop plants. The effectiveness of traditional countermeasures, such as the breeding and introduction of resistant cultivars, is often limited by the dearth of available sources of genetic resistance. An alternative strategy to reduce loss to specific bacterial phytopathogens is to use narrow-spectrum protein antibiotics such as colicin-like bacteriocins as biocontrol agents. A number of colicin-like bacteriocins active against phytopathogenic bacteria have been described previously as have strategies for their application to biocontrol. In the present paper, we discuss these strategies and our own recent work on the identification and characterization of candidate bacteriocins and how these potent and selective antimicrobial agents can be effectively applied to the control of economically important plant disease.
Using a bacteriocin structure to engineer a phage lysin that targets Yersinia pestis
Authors: Lukacik Petra , Barnard Travis J. , Buchanan Susan K.
Published: November 2012

Purified phage lysins present an alternative to traditional antibiotics and work by hydrolysing peptidoglycan. Phage lysins have been developed against Gram-positive pathogens such as Bacillus anthracis and Streptococcus pneumoniae, where the peptidoglycan layer is exposed on the cell surface. Addition of the lysin to a bacterial culture results in rapid death of the organism. Gram-negative bacteria are resistant to phage lysins because they contain an outer membrane that protects the peptidoglycan from degradation. We solved crystal structures of a Yersinia pestis outer-membrane protein and the bacteriocin that targets it, which informed engineering of a bacterial–phage hybrid lysin that can be transported across the outer membrane to kill specific Gram-negative bacteria. This work provides a template for engineering phage lysins against a wide variety of bacterial pathogens.
Specific localization of Rabs at intracellular membranes
Authors: Blümer Julia , Wu Yao-Wen , Goody Roger S. , Itzen Aymelt
Published: November 2012

Despite over two decades of research, the mechanism of Rab targeting to specific intracellular membranes is still not completely understood. Present evidence suggests that the original hypothesis that the message for targeting resides solely in the hypervariable C-terminus is incorrect, and a second mechanism involving a GDF [GDI (guanine-nucleotide-dissociation inhibitor) displacement factor] to disrupt stable Rab–GDI complexes has only been shown to apply in one case, despite the need for targeting over 60 human Rab proteins. Evidence for the involvement of Rab–effector interactions has only been presented for a few cases or in a very specific context. There is mounting evidence that GEFs (guanine-nucleotide-exchange factors) are essential for membrane targeting, although contributions from additional factors are likely to be of importance, at least in specific cases.
The molecular biogeochemistry of manganese(II) oxidation
Authors: Geszvain Kati , Butterfield Cristina , Davis Richard E. , Madison Andrew S. , Lee Sung-Woo , Parker Dorothy L. , Soldatova Alexandra , Spiro Thomas G. , Luther George W. , Tebo Bradley M.
Published: November 2012

Micro-organisms capable of oxidizing the redox-active transition metal manganese play an important role in the biogeochemical cycle of manganese. In the present mini-review, we focus specifically on Mn(II)-oxidizing bacteria. The mechanisms by which bacteria oxidize Mn(II) include a two-electron oxidation reaction catalysed by a novel multicopper oxidase that produces Mn(IV) oxides as the primary product. Bacteria also produce organic ligands, such as siderophores, that bind to and stabilize Mn(III). The realization that this stabilized Mn(III) is present in many environments and can affect the redox cycles of other elements such as sulfur has made it clear that manganese and the bacteria that oxidize it profoundly affect the Earth's biogeochemistry.
Electron Transport at the Microbe–Mineral Interface: a synthesis of current research challenges
Authors: Richardson David J. , Fredrickson James K. , Zachara John M.
Published: November 2012

Many bacterial and archaeal species can couple growth to the respiratory reduction or oxidation of insoluble mineral oxides of transition metals. These solid substrates are abundant electron sinks and sources for life on Earth, but, since they are insoluble in water, they cannot enter the bacterial cells. So, to exploit these electron sinks and sources, specific respiratory electron-transfer mechanisms must overcome the physical limitations associated with electron transfer between a microbe and extracellular metal oxides. Recent microbiological, geochemical, biochemical, spectroscopic and structural work is beginning to shed light on the molecular mechanism and impacts of electron transfer at the microbe–mineral interface from a nanometre to kilometre scale. The research field is attracting attention in applied quarters from those with interests in nanowires, microbial fuel cells, bioremediation and microbial cell factories.
Relative humidity has dramatic impacts on leaf morphology but little effect on stomatal index or density in Nothofagus cunninghamii (Nothofagaceae)
Authors: Hovenden Mark J. , Vander Schoor Jacqueline K. , Osanai Yui
Published: November 2012

Reconstructing past environmental conditions using proxies based on fossil and subfossil leaves is difficult because leaf form is influenced by many interacting environmental factors such as temperature, CO2 concentration, light, soil water availability and, potentially, atmospheric relative humidity (RH). We used a species important for palaeo-environmental reconstruction, the southern beech, Nothofagus cunninghamii, to test for the effects of a 50% difference in RH on leaf morphology and epidermal anatomy in a glasshouse experiment. Leaf size, shape and thickness were all strongly affected by RH with leaves from high humidity being larger, narrower and thicker than those from low humidity regardless of plant accession. RH impacts on epidermal characters were generally slight and dependent upon accession. In particular, epidermal cell size was remarkably consistent across accessions and RH levels. Thus, gross leaf morphology of N. cunninghamii was sensitive to changes in RH but, on average, epidermal characters were not. Thus, palaeoenvironmental signals from the epidermis of this species are unlikely to be affected by variation in RH, provided sufficient numbers of leaves are investigated. Gross leaf morphology, however, was strongly related to RH and should not be used for palaeo-climatic reconstruction if changes in RH are likely.
Pest and disease abundance and dynamics in wheat and oilseed rape as affected by elevated atmospheric CO2 concentrations
Authors: Oehme Viktoriya , Högy Petra , Franzaring Jürgen , Zebitz Claus P. W. , Fangmeier Andreas
Published: November 2012

Future atmospheric CO2 concentrations are predicted to increase, and directly affect host plant phenology, which, in turn, is assumed to mediate the performance of herbivorous insects indirectly as well as the abundance and epidemiology of plant diseases. In a 4-year field experiment, spring wheat (Triticum aestivum L. cv. Triso) and spring oilseed rape (Brassica napus L. cv. Campino) were grown using a mini- free-air CO2 enrichment (FACE) system, which consisted of a control (CON), an ambient treatment (AMB) and FACE treatments. The CON and AMB treatments did not receive additional CO2, whereas the FACE plots were moderately elevated by 150 μL L–1 CO2. The impact of elevated CO2 was examined with regard to plant phenology, biomass, leaf nitrogen and carbon, abundance of insect pest species and their relative population growth by either direct counts or yellow sticky traps. Occurrence and damage of plants by pathogens on spring wheat and oilseed rape were directly assessed. Disease infestations on plants were not significantly different between ambient and elevated CO2 in any of the years. Plant phenology, aboveground biomass, foliar nitrogen and carbon concentrations were also not significantly affected by CO2 enrichment. In contrast, the abundance of some species of insects was significantly influenced by elevated CO2, showing either an increase or a decrease in infestation intensity.
Seed reserve dependency of Leucaena leucocephala seedling growth for nitrogen and phosphorus
Authors: Slot Martijn , Palow Danielle T. , Kitajima Kaoru
Published: November 2012

Mineral elements stored in seed reserves meet the nutrient demands of seedlings during their initial development and growth. We experimentally examined when seed reserves become insufficient to meet demands for nitrogen (N) and phosphorus (P) of seedlings of Leucaena leucocephala (Lam.) de Wit, a tropical woody legume. Seedlings were grown from seeds with four nutrient treatments: receiving all nutrients; all nutrients except N, all nutrients except P or deionised water. Growth curves were compared to quantify the time course of the onset of N and P deficiency during 8 weeks. N deficiency became significant for leaf area and biomass growth after 11 and 16 days, respectively, whereas P deficiency became significant after 31 days for both leaf area and biomass growth. Thus, seed reserves alone could support the P demands of seedlings for more than twice as long as N demands. As nutrient deficiency developed, seedlings adjusted increased relative biomass allocation to roots, diluted organ N and P concentrations but conserved 100% of the initial nutrient pool derived from the seed.
Soil water repellency persistence after recurrent forest fires on Mount Carmel, Israel
Authors: Tessler Naama , Wittenberg Lea , Greenbaum Noam
Published: November 2012

Variations in forest fires regime affect: (1) the natural patterns of community structure and vegetation; (2) the physico-chemical properties of soils and consequently (3) runoff, erosion and sediment yield. In recent decades the Mediterranean ecosystem of Mount Carmel, north-western Israel, is subjected to an increasing number of forest fires, thus, the objectives of the study were to evaluate the long-term effects of single and recurrent fires on soil water repellency (WR) and organic matter (OM) content. Water repellency was studied by applying water drop penetration time (WDPT) tests at sites burnt by single-fire, two fires, three fires and unburnt control sites. Water repellency in the burnt sites was significantly lower than in the unburnt control sites, and the soil maintained its wettability for more than 2 decades, whereas after recurrent fires, the rehabilitation was more complicated and protracted. The OM content was significantly lower after recurrent than after a single fire, causing a clear proportional decrease in WR. The rehabilitation of WR to natural values is highly dependent on restoration of organic matter and revegetation. Recurrent fires may cause a delay in recovery and reduced productivity of the soil for a long period.
Using distance correlation and SS-ANOVA to assess associations of familial relationships, lifestyle factors, diseases, and mortality
Authors: Kong Jing , Klein Barbara E. K. , Klein Ronald , Lee Kristine E. , Wahba Grace
Published: November 2012

We present a method for examining mortality as it is seen to run in families, and lifestyle factors that are also seen to run in families, in a subpopulation of the Beaver Dam Eye Study. We observe that pairwise distance between death age in related persons is on average less than pairwise distance in death age between random pairs of unrelated persons. Our goal is to examine the hypothesis that pairwise differences in lifestyle factors correlate with the observed pairwise differences in death age that run in families. Szekely and Rizzo [Szekely GJ, Rizzo ML (2009)
Ann Appl Stat
3(4): 1236–1265] have recently developed a method called distance correlation, which is suitable for this task with some enhancements. We build a Smoothing Spline ANOVA (SS-ANOVA) model for predicting death age based on four major lifestyle factors generally known to be related to mortality and four major diseases contributing to mortality, to develop a lifestyle mortality risk vector and a disease mortality risk vector. We then examine to what extent pairwise differences in these scores correlate with pairwise differences in mortality as they occur between family members and between unrelated persons. We find significant distance correlations between death ages, lifestyle factors, and family relationships. Considering only sib pairs compared with unrelated persons, distance correlation between siblings and mortality is, not surprisingly, stronger than that between more distantly related family members and mortality. The methodological approach here adapts to exploring relationships between multiple clusters of variables with observable (real-valued) attributes, and other factors for which only possibly nonmetric pairwise dissimilarities are observed.
Self-produced exopolysaccharide is a signal that stimulates biofilm formation inPseudomonas aeruginosa
Authors: Irie Yasuhiko , Borlee Bradley R. , O’Connor Jennifer R. , Hill Preston J. , Harwood Caroline S. , Wozniak Daniel J. , Parsek Matthew R.
Published: November 2012

Bacteria have a tendency to attach to surfaces and grow as structured communities called biofilms. Chronic biofilm infections are a problem because they tend to resist antibiotic treatment and are difficult to eradicate. Bacterial biofilms have an extracellular matrix that is usually composed of a mixture of polysaccharides, proteins, and nucleic acids. This matrix has long been assumed to play a passive structural and protective role for resident biofilm cells. Here we show that this view is an oversimplification and that the biofilm matrix can play an active role in stimulating its own synthesis. Working with the model biofilm bacteriumPseudomonas aeruginosa, we found that Psl, a major biofilm matrix polysaccharide for this species, acts as a signal to stimulate two diguanylate cyclases, SiaD and SadC, to produce the intracellular secondary messenger molecule c-di-GMP. Elevated intracellular concentrations of c-di-GMP then lead to the increased production of Psl and other components of the biofilm. This mechanism represents a unique positive feedback regulatory circuit, where the expression of an extracellular polysaccharide promotes biofilm growth in a manner analogous to autocrine signaling in eukaryotes.
Conservation of NLR-triggered immunity across plant lineages
Authors: Maekawa Takaki , Kracher Barbara , Vernaldi Saskia , Ver Loren van Themaat Emiel , Schulze-Lefert Paul
Published: November 2012

The nucleotide-binding domain and leucine-rich repeat (NLR) family of plant receptors detects pathogen-derived molecules, designated effectors, inside host cells and mediates innate immune responses to pathogenic invaders. Genetic evidence revealed species-specific coevolution of many NLRs with effectors from host-adapted pathogens, suggesting that the specificity of these NLRs is restricted to the host or closely related plant species. However, we report that an NLR immune receptor (MLA1) from monocotyledonous barley is fully functional in partially immunocompromised dicotyledonous
Arabidopsis thaliana
against the barley powdery mildew fungus,
Blumeria graminis
f. sp.
hordei
. This implies ∼200 million years of evolutionary conservation of the underlying immune mechanism. A time-course RNA-seq analysis in transgenic
Arabidopsis
lines detected sustained expression of a large MLA1-dependent gene cluster. This cluster is greatly enriched in genes known to respond to the fungal cell wall-derived microbe-associated molecular pattern chitin. The MLA1-dependent sustained transcript accumulation could define a conserved function of the nuclear pool of MLA1 detected in barley and
Arabidopsis
. We also found that MLA1-triggered immunity was fully retained in mutant plants that are simultaneously depleted of ethylene, jasmonic acid, and salicylic acid signaling. This points to the existence of an evolutionarily conserved and phytohormone-independent MLA1-mediated resistance mechanism. This also suggests a conserved mechanism for internalization of
B. graminis
f. sp.
hordei
effectors into host cells of flowering plants. Furthermore, the deduced connectivity of the NLR to multiple branches of immune signaling pathways likely confers increased robustness against pathogen effector-mediated interception of host immune signaling and could have contributed to the evolutionary preservation of the immune mechanism.
The conserved interaction of C7orf30 with MRPL14 promotes biogenesis of the mitochondrial large ribosomal subunit and mitochondrial translation
Authors: Fung Stephen , Nishimura Tamiko , Sasarman Florin , Shoubridge Eric A.
Published: November 2012

Mammalian mitochondria harbor a dedicated translation apparatus that is required for the synthesis of 13 mitochondrial DNA (mtDNA)-encoded polypeptides, all of which are essential components of the oxidative phosphorylation (OXPHOS) complexes. Little is known about the mechanism of assembly of the mitoribosomes that catalyze this process. Here we show that C7orf30, a member of the large family of DUF143 proteins, associates with the mitochondrial large ribosomal subunit (mt-LSU). Knockdown of C7orf30 by short hairpin RNA (shRNA) does not alter the sedimentation profile of the mt-LSU, but results in the depletion of several mt-LSU proteins and decreased monosome formation. This leads to a mitochondrial translation defect, involving the majority of mitochondrial polypeptides, and a severe OXPHOS assembly defect. Immunoprecipitation and mass spectrometry analyses identified mitochondrial ribosomal protein (MRP)L14 as the specific interacting protein partner of C7orf30 in the mt-LSU. Reciprocal experiments in which MRPL14 was depleted by small interfering RNA (siRNA) phenocopied the C7orf30 knockdown. Members of the DUF143 family have been suggested to be universally conserved ribosomal silencing factors, acting by sterically inhibiting the association of the small and large ribosomal subunits. Our results demonstrate that, although the interaction between C7orf30 and MRPL14 has been evolutionarily conserved, human C7orf30 is, on the contrary, essential for mitochondrial ribosome biogenesis and mitochondrial translation.
DOOSS: a tool for visual analysis of data overlaid on secondary structures
Authors: Golden Michael , Martin Darren
Published: November 2012

Motivation: DOOSS (Data Overlaid On Secondary Structures) is a tool for visualizing annotated secondary structures of large single-stranded nucleotide sequences (such as full-length virus genomes). The purpose of this tool is to assist investigators in evaluating the biological relevance of secondary structures within particular sequences.

Availability and implementation: DOOSS is written in Java and is available from: http://dooss.computingforbiology.org

Contact:  michaelgolden0@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.
Intron-centric estimation of alternative splicing from RNA-seq data
Authors: Pervouchine Dmitri D. , Knowles David G. , Guigó Roderic
Published: November 2012

Motivation: Novel technologies brought in unprecedented amounts of high-throughput sequencing data along with great challenges in their analysis and interpretation. The percent-spliced-in (PSI, ) metric estimates the incidence of single-exon–skipping events and can be computed directly by counting reads that align to known or predicted splice junctions. However, the majority of human splicing events are more complex than single-exon skipping.

Results: In this short report, we present a framework that generalizes the metric to arbitrary classes of splicing events. We change the view from exon centric to intron centric and split the value of into two indices, and , measuring the rate of splicing at the 5′ and 3′ end of the intron, respectively. The advantage of having two separate indices is that they deconvolute two distinct elementary acts of the splicing reaction. The completeness of splicing index is decomposed in a similar way. This framework is implemented as bam2ssj, a BAM-file–processing pipeline for strand-specific counting of reads that align to splice junctions or overlap with splice sites. It can be used as a consistent protocol for quantifying splice junctions from RNA-seq data because no such standard procedure currently exists.

Availability: The C code of bam2ssj is open source and is available at https://github.com/pervouchine/bam2ssj

Contact:  dp@crg.eu
Asking About Numbers: Why and How
Authors: Ansolabehere Stephen , Meredith Marc , Snowberg Erik
Published: November 2012

Survey questions about quantities offer a number of advantages over more common qualitative questions. However, concerns about survey respondents' abilities to accurately report numbers have limited the use of quantitative questions. This article shows quantitative questions are feasible and useful for the study of economic voting. First, survey respondents are capable of accurately assessing familiar economic quantities, such as the price of gas. Second, careful question design—in particular providing respondents with benchmark quantities—can reduce measurement error due to respondents not understanding the scale on which more complex quantities, such as the unemployment rate, are measured. Third, combining quantitative and qualitative questions sheds light on where partisan bias enters economic assessments: in perceiving, judging, or reporting economic quantities.
GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility
Authors: Theodorou Vasiliki , Stark Rory , Menon Suraj , Carroll Jason S.
Published: November 2012

Estrogen receptor (ESR1) drives growth in the majority of human breast cancers by binding to regulatory elements and inducing transcription events that promote tumor growth. Differences in enhancer occupancy by ESR1 contribute to the diverse expression profiles and clinical outcome observed in breast cancer patients. GATA3 is an ESR1-cooperating transcription factor mutated in breast tumors; however, its genomic properties are not fully defined. In order to investigate the composition of enhancers involved in estrogen-induced transcription and the potential role of GATA3, we performed extensive ChIP-sequencing in unstimulated breast cancer cells and following estrogen treatment. We find that GATA3 is pivotal in mediating enhancer accessibility at regulatory regions involved in ESR1-mediated transcription. GATA3 silencing resulted in a global redistribution of cofactors and active histone marks prior to estrogen stimulation. These global genomic changes altered the ESR1-binding profile that subsequently occurred following estrogen, with events exhibiting both loss and gain in binding affinity, implying a GATA3-mediated redistribution of ESR1 binding. The GATA3-mediated redistributed ESR1 profile correlated with changes in gene expression, suggestive of its functionality. Chromatin loops at the TFF locus involving ESR1-bound enhancers occurred independently of ESR1 when GATA3 was silenced, indicating that GATA3, when present on the chromatin, may serve as a licensing factor for estrogen–ESR1-mediated interactions between cis-regulatory elements. Together, these experiments suggest that GATA3 directly impacts ESR1 enhancer accessibility, and may potentially explain the contribution of mutant-GATA3 in the heterogeneity of ESR1+ breast cancer.
Structure of Cellulose Microfibrils in Primary Cell Walls from Collenchyma
Authors: Thomas Lynne H. , Forsyth V. Trevor , Šturcová Adriana , Kennedy Craig J. , May Roland P. , Altaner Clemens M. , Apperley David C. , Wess Timothy J. , Jarvis Michael C.
Published: November 2012

In the primary walls of growing plant cells, the glucose polymer cellulose is assembled into long microfibrils a few nanometers in diameter. The rigidity and orientation of these microfibrils control cell expansion; therefore, cellulose synthesis is a key factor in the growth and morphogenesis of plants. Celery (Apium graveolens) collenchyma is a useful model system for the study of primary wall microfibril structure because its microfibrils are oriented with unusual uniformity, facilitating spectroscopic and diffraction experiments. Using a combination of x-ray and neutron scattering methods with vibrational and nuclear magnetic resonance spectroscopy, we show that celery collenchyma microfibrils were 2.9 to 3.0 nm in mean diameter, with a most probable structure containing 24 chains in cross section, arranged in eight hydrogen-bonded sheets of three chains, with extensive disorder in lateral packing, conformation, and hydrogen bonding. A similar 18-chain structure, and 24-chain structures of different shape, fitted the data less well. Conformational disorder was largely restricted to the surface chains, but disorder in chain packing was not. That is, in position and orientation, the surface chains conformed to the disordered lattice constituting the core of each microfibril. There was evidence that adjacent microfibrils were noncovalently aggregated together over part of their length, suggesting that the need to disrupt these aggregates might be a constraining factor in growth and in the hydrolysis of cellulose for biofuel production.
Training for front‐line homeless workers: practicalities and ethics of teaching cognitive behavioural and dialectical behavioural psychological therapeutic techniques
Authors: Maguire Nick
Published: November 2012

Purpose

This paper seeks to discuss the need and scope for application of psychological therapeutic techniques in work with problems of chaotic or dysfunctional behaviour, as found among users of homelessness resettlement services.

Design/methodology/approach

The paper summarises recent research and UK policy guidance on the mental health needs encountered by frontline homelessness service resettlement staff on a daily basis. It goes on to discuss the impact of these experiences, and the value of training to help staff manage such encounters with greater awareness and skills. In particular, the paper considers the ethical dimension for staff, in responding to users' histories of emotional distress.

Findings

There is a relative dearth of studies providing evidence on stress and burn‐out amongst resettlement staff, compared to healthcare staff; nevertheless they face the same or similar pressures in their day‐to‐day work with clients. When asked to consider psychological techniques, some staff may initially fear being expected to be a psychotherapist; but research from clinical practice and recent training workshop experience suggest that training, especially where complemented by supervision or reflective practice, leaves staff feeling more confident.

Originality/value

The application of formal psychological thinking in homelessness resettlement is a relatively new field. This is the first paper to explore issues arising from the perspective of the ethical dilemmas faced by frontline staff in the work of relating to clients' distressed or distressing experiences.