bluuebunny/crossref_metadata_2025 huggingface dataset:
A unique wheat disease resistance-like gene governs effector-triggered susceptibility to necrotrophic pathogens
Authors: Faris Justin D. , Zhang Zengcui , Lu Huangjun , Lu Shunwen , Reddy Leela , Cloutier Sylvie , Fellers John P. , Meinhardt Steven W. , Rasmussen Jack B. , Xu Steven S. , Oliver Richard P. , Simons Kristin J. , Friesen Timothy L.
Published: July 2010

Plant disease resistance is often conferred by genes with nucleotide binding site (NBS) and leucine-rich repeat (LRR) or serine/threonine protein kinase (S/TPK) domains. Much less is known about mechanisms of susceptibility, particularly to necrotrophic fungal pathogens. The pathogens that cause the diseases tan spot and Stagonospora nodorum blotch on wheat produce effectors (host-selective toxins) that induce susceptibility in wheat lines harboring corresponding toxin sensitivity genes. The effector ToxA is produced by both pathogens, and sensitivity to ToxA is governed by the
Tsn1
gene on wheat chromosome arm 5BL. Here, we report the cloning of
Tsn1
, which was found to have disease resistance gene-like features, including S/TPK and NBS-LRR domains. Mutagenesis revealed that all three domains are required for ToxA sensitivity, and hence disease susceptibility.
Tsn1
is unique to ToxA-sensitive genotypes, and insensitive genotypes are null. Sequencing and phylogenetic analysis indicated that
Tsn1
arose in the B-genome diploid progenitor of polyploid wheat through a gene-fusion event that gave rise to its unique structure. Although
Tsn1
is necessary to mediate ToxA recognition, yeast two-hybrid experiments suggested that the Tsn1 protein does not interact directly with ToxA.
Tsn1
transcription is tightly regulated by the circadian clock and light, providing further evidence that
Tsn1
-ToxA interactions are associated with photosynthesis pathways. This work suggests that these necrotrophic pathogens may thrive by subverting the resistance mechanisms acquired by plants to combat other pathogens.
Essential genes from Arctic bacteria used to construct stable, temperature-sensitive bacterial vaccines
Authors: Duplantis Barry N. , Osusky Milan , Schmerk Crystal L. , Ross Darrell R. , Bosio Catharine M. , Nano Francis E.
Published: July 2010

All bacteria share a set of evolutionarily conserved essential genes that encode products that are required for viability. The great diversity of environments that bacteria inhabit, including environments at extreme temperatures, place adaptive pressure on essential genes. We sought to use this evolutionary diversity of essential genes to engineer bacterial pathogens to be stably temperature-sensitive, and thus useful as live vaccines. We isolated essential genes from bacteria found in the Arctic and substituted them for their counterparts into pathogens of mammals. We found that substitution of nine different essential genes from psychrophilic (cold-loving) bacteria into mammalian pathogenic bacteria resulted in strains that died below their normal-temperature growth limits. Substitution of three different psychrophilic gene orthologs of
ligA
, which encode NAD-dependent DNA ligase, resulted in bacterial strains that died at 33, 35, and 37 °C. One
ligA
gene was shown to render
Francisella tularensis
,
Salmonella enterica
, and
Mycobacterium smegmati
s temperature-sensitive, demonstrating that this gene functions in both Gram-negative and Gram-positive lineage bacteria. Three temperature-sensitive
F. tularensis
strains were shown to induce protective immunity after vaccination at a cool body site. About half of the genes that could be tested were unable to mutate to temperature-resistant forms at detectable levels. These results show that psychrophilic essential genes can be used to create a unique class of bacterial temperature-sensitive vaccines for important human pathogens, such as
S. enterica
and
Mycobacterium tuberculosis
.
Ordering dynamics of blue phases entails kinetic stabilization of amorphous networks
Authors: Henrich Oliver , Stratford Kevin , Marenduzzo Davide , Cates Michael E.
Published: July 2010

The cubic blue phases of liquid crystals are fascinating and technologically promising examples of hierarchically structured soft materials, comprising ordered networks of defect lines (disclinations) within a liquid crystalline matrix. We present large-scale simulations of their domain growth, starting from a blue phase nucleus within a supercooled isotropic or cholesteric background. The nucleated phase is thermodynamically stable; one expects its slow orderly growth, creating a bulk cubic phase. Instead, we find that the strong propensity to form disclinations drives the rapid disorderly growth of a metastable amorphous defect network. During this process, the original nucleus is destroyed; reemergence of the stable phase may therefore require a second nucleation step. Our findings suggest that blue phases exhibit hierarchical behavior in their ordering dynamics, to match the hierarchy in their structure.
Cryptochrome 2 and phototropin 2 regulate resistance protein-mediated viral defense by negatively regulating an E3 ubiquitin ligase
Authors: Jeong Rae-Dong , Chandra-Shekara A. C. , Barman Subhankar Roy , Navarre Duroy , Klessig Daniel F. , Kachroo Aardra , Kachroo Pradeep
Published: July 2010

Light harvested by plants is essential for the survival of most life forms. This light perception ability requires the activities of proteins termed photoreceptors. We report a function for photoreceptors in mediating resistance (R) protein-derived plant defense. The blue-light photoreceptors, cryptochrome (CRY) 2 and phototropin (PHOT) 2, are required for the stability of the R protein HRT, and thereby resistance to Turnip Crinkle virus (TCV). Exposure to darkness or blue-light induces degradation of CRY2, and in turn HRT, resulting in susceptibility. Overexpression of HRT can compensate for the absence of PHOT2 but not CRY2. HRT does not directly associate with either CRY2 or PHOT2 but does bind the CRY2-/PHOT2-interacting E3 ubiquitin ligase, COP1. Application of the proteasome inhibitor, MG132, prevents blue-light-dependent degradation of HRT, consequently these plants show resistance to TCV under blue-light. We propose that CRY2/PHOT2 negatively regulate the proteasome-mediated degradation of HRT, likely via COP1, and blue-light relieves this repression resulting in HRT degradation.
Structural basis for agonism and antagonism of hepatocyte growth factor
Authors: Tolbert W. David , Daugherty-Holtrop Jennifer , Gherardi Ermanno , Vande Woude George , Xu H. Eric
Published: July 2010

Hepatocyte growth factor (HGF) is an activating ligand of the Met receptor tyrosine kinase, whose activity is essential for normal tissue development and organ regeneration but abnormal activation of Met has been implicated in growth, invasion, and metastasis of many types of solid tumors. HGF has two natural splice variants, NK1 and NK2, which contain the N-terminal domain (N) and the first kringle (K1) or the first two kringle domains of HGF. NK1, which is a Met agonist, forms a head-to-tail dimer complex in crystal structures and mutations in the NK1 dimer interface convert NK1 to a Met antagonist. In contrast, NK2 is a Met antagonist, capable of inhibiting HGF’s activity in cell proliferation without clear mechanism. Here we report the crystal structure of NK2, which forms a “closed” monomeric conformation through interdomain interactions between the N- domain and the second kringle domain (K2). Mutations that were designed to open up the NK2 closed conformation by disrupting the N/K2 interface convert NK2 from a Met antagonist to an agonist. Remarkably, this mutated NK2 agonist can be converted back to an antagonist by a mutation that disrupts the NK1/NK1 dimer interface. These results reveal the molecular determinants that regulate the agonist/antagonist properties of HGF NK2 and provide critical insights into the dimerization mechanism that regulates the Met receptor activation by HGF.
Metacaspase Yca1 is required for clearance of insoluble protein aggregates
Authors: Lee Robin E. C. , Brunette Steve , Puente Lawrence G. , Megeney Lynn A.
Published: July 2010

In complex organisms, caspase proteases mediate a variety of cell behaviors, including proliferation, differentiation, and programmed cell death/apoptosis. Structural homologs to the caspase family (termed metacaspases) engage apoptosis in single-cell eukaryotes, yet the molecular mechanisms that contribute to nondeath roles are currently undefined. Here, we report an unexpected role for the
Saccharomyces cerevisiae
metacaspase Yca1 in protein quality control. Quantitative proteomic analysis of Δ
yca1
cells identified significant alterations to vacuolar catabolism and stress-response proteins in the absence of induced stress. Yca1 protein complexes are enriched for aggregate-remodeling chaperones that colocalize with Yca1-GFP fusions. Finally, deletion and inactivation mutants of Yca1 accrue protein aggregates and autophagic bodies during log-phase growth. Together, our results show that Yca1 contributes to the fitness and adaptability of growing yeast through an aggregate remodeling activity.
Arsenic antagonizes the Hedgehog pathway by preventing ciliary accumulation and reducing stability of the Gli2 transcriptional effector
Authors: Kim Jynho , Lee John J. , Kim James , Gardner Dale , Beachy Philip A.
Published: July 2010

Aberrant Hedgehog (Hh) pathway activation has been implicated in cancers of diverse tissues and organs, and the tumor growth-inhibiting effects of pathway antagonists in animal models have stimulated efforts to develop pathway antagonists for human therapeutic purposes. These efforts have focused largely on cyclopamine derivatives or other compounds that mimic cyclopamine action in binding to and antagonizing Smoothened, a membrane transductory component. We report here that arsenicals, in contrast, antagonize the Hh pathway by targeting Gli transcriptional effectors; in the short term, arsenic blocks Hh-induced ciliary accumulation of Gli2, the primary activator of Hh-dependent transcription, and with prolonged incubation arsenic reduces steady-state levels of Gli2. Arsenicals active in Hh pathway antagonism include arsenic trioxide (ATO), a curative agent in clinical use for acute promyelocytic leukemia (APL); in our studies, ATO inhibited growth of Hh pathway-driven medulloblastoma allografts derived from

Ptch
+/−
p53
−/−

mice within a range of serum levels comparable to those achieved in treatment of human APL. Arsenic thus could be tested rapidly as a therapeutic agent in malignant diseases associated with Hh pathway activation and could be particularly useful in such diseases that are inherently resistant or have acquired resistance to cyclopamine mimics.
Programmed death-1 (PD-1)–deficient mice are extraordinarily sensitive to tuberculosis
Authors: Lázár-Molnár Eszter , Chen Bing , Sweeney Kari A. , Wang Emilie J. , Liu Weijun , Lin Juan , Porcelli Steven A. , Almo Steven C. , Nathenson Stanley G. , Jacobs William R.
Published: July 2010

The programmed death-1 (PD-1) costimulatory receptor inhibits T and B cell responses and plays a crucial role in peripheral tolerance. PD-1 has recently been shown to inhibit T cell responses during chronic viral infections such as HIV. In this study, we examined the role of PD-1 in infection with
Mycobacterium tuberculosis
, a common co-infection with HIV. PD-1–deficient mice showed dramatically reduced survival compared with wild-type mice. The lungs of the PD-1
−/−
mice showed uncontrolled bacterial proliferation and focal necrotic areas with predominantly neutrophilic infiltrates, but a lower number of infiltrating T and B cells. Proinflammatory cytokines, such as TNF-α, IL-1, and especially IL-6 and IL-17 were significantly increased in the lung and sera of infected PD-1
−/−
mice, consistent with an aberrant inflammation. Microarray analysis of the lungs infected with
M. tuberculosis
showed dramatic differences between PD-1
−/−
and control mice. Using high-stringency analysis criteria (changes of twofold or greater), 367 transcripts of genes were differentially expressed between infected PD-1
−/−
and wild-type mice, resulting in profoundly altered inflammatory responses with implications for both innate and adaptive immunity. Overall, our studies show that the PD-1 pathway is required to control excessive inflammatory responses after
M. tuberculosis
infection in the lungs.
Kinetic phases of distribution and tumor targeting by T cell receptor engineered lymphocytes inducing robust antitumor responses
Authors: Koya Richard C. , Mok Stephen , Comin-Anduix Begoña , Chodon Thinle , Radu Caius G. , Nishimura Michael I. , Witte Owen N. , Ribas Antoni
Published: July 2010

A key issue in advancing the use of adoptive cell transfer (ACT) of T cell receptor (TCR) engineered lymphocytes for cancer therapy is demonstrating how TCR transgenic cells repopulate lymphopenic hosts and target tumors in an antigen-specific fashion. ACT of splenocytes from fully immunocompetent HLA-A2.1/K
b
mice transduced with a chimeric murine/human TCR specific for tyrosinase, together with lymphodepletion conditioning, dendritic cell (DC)-based vaccination, and high-dose interleukin-2 (IL-2), had profound antitumor activity against large established MHC- and antigen-matched tumors. Genetic labeling with bioluminescence imaging (BLI) and positron emitting tomography (PET) reporter genes allowed visualization of the distribution and antigen-specific tumor homing of TCR transgenic T cells, with trafficking correlated with antitumor efficacy. After an initial brief stage of systemic distribution, TCR-redirected and genetically labeled T cells demonstrated an early pattern of specific distribution to antigen-matched tumors and locoregional lymph nodes, followed by a more promiscuous distribution 1 wk later with additional accumulation in antigen-mismatched tumors. This approach of TCR engineering and molecular imaging reporter gene labeling is directly translatable to humans and provides useful information on how to clinically develop this mode of therapy.
Mammalian life-span determinant p66
shcA
mediates obesity-induced insulin resistance
Authors: Ranieri Sofia Chiatamone , Fusco Salvatore , Panieri Emiliano , Labate Valentina , Mele Marina , Tesori Valentina , Ferrara Anna Maria , Maulucci Giuseppe , De Spirito Marco , Martorana Giuseppe Ettore , Galeotti Tommaso , Pani Giovambattista
Published: July 2010

Obesity and metabolic syndrome result from excess calorie intake and genetic predisposition and are mechanistically linked to type II diabetes and accelerated body aging; abnormal nutrient and insulin signaling participate in this pathologic process, yet the underlying molecular mechanisms are incompletely understood. Mice lacking the p66 kDa isoform of the Shc adaptor molecule live longer and are leaner than wild-type animals, suggesting that this molecule may have a role in metabolic derangement and premature senescence by overnutrition. We found that p66 deficiency exerts a modest but significant protective effect on fat accumulation and premature death in lep
Ob/Ob
mice, an established genetic model of obesity and insulin resistance; strikingly, however, p66 inactivation improved glucose tolerance in these animals, without affecting (hyper)insulinaemia and independent of body weight. Protection from insulin resistance was cell autonomous, because isolated p66KO preadipocytes were relatively resistant to insulin desensitization by free fatty acids in vitro. Biochemical studies revealed that p66shc promotes the signal-inhibitory phosphorylation of the major insulin transducer IRS-1, by bridging IRS-1 and the mTOR effector p70S6 kinase, a molecule previously linked to obesity-induced insulin resistance. Importantly, IRS-1 was strongly up-regulated in the adipose tissue of p66KO lep
Ob/Ob
mice, confirming that effects of p66 on tissue responsiveness to insulin are largely mediated by this molecule. Taken together, these findings identify p66shc as a major mediator of insulin resistance by excess nutrients, and by extension, as a potential molecular target against the spreading epidemic of obesity and type II diabetes.
Rhetorical unit analysis and Bakhtin’s chronotype
Authors: Cloran Carmel
Published: July 2010

Bakhtin introduced the concept of chronotope (chronos = time; topos = space) to facilitate his exploration of the ways in which space-time intersections occur in literary texts. However, he also suggests that chronotopes characterise non-literary texts — indeed, that “every entry into the sphere of meaning is accomplished only through the gates of the chronotope” (1981: 258) — this historical, biographical and social time-space configuration. This formulation immediately suggests that these categories should be accessible via the categories of language and indeed, in English, they are most generally expressed via the Mood categories Subject and Finite. These same Mood categories of English are crucially involved in the identification of a unit of discourse — the rhetorical unit (Cloran 1994). Thus, this discourse unit provides a useful means of concretising, from a linguistic perspective, Bakhtin’s concept of chronotope and investigating the presence of such chronotopes in the everyday mundane discourse of mother-child interaction. Selections from such interaction are illustrations of authentic cultural chronotopes, and provide exempla of a (sub)cultural chronotopic motif within the broader culture, i.e. social positioning at a particular historical point in time (the late 20th century Australian culture).
Textbook language, ideology and citizenship
Authors: Moss Gillian
Published: July 2010

This paper presents aspects of the results of a long-term research project on the relations between language and ideology in text-teacher-student interaction in Social Science and Natural Science classrooms in northern Colombia and their implications for citizenship education. The results presented here concern a grammatical conspiracy (Martin 1988) of historical determinism found in the transitivity and grammatical metaphors of a history textbook. I present examples of each of the grammatical features in question, arguing for the inclusion in the category of grammatical metaphor of historical present, inanimate Sayers and Behavers and some non-ergative processes. I then consider how the various grammatical features conspire to present a deterministic view of history which precludes the possibility of change as a result of human intervention. Finally, I suggest that Colombia, in striving towards a more harmonious society, has need of a different view of historical processes as susceptible to human agency.
De la négation à la focalisation
Authors: Corteel Céline
Published: July 2010

This paper deals with adnominal autre in correlative structures (e.g. Pierre a suivi un autre chemin que Paul). In the first section, it is shown that this construction can be analysed as a case of relativisation. The subsequent sections propose a semantic-referential description of autre. The data suggest that the adjective functions as a negative operator, whose base meaning can be interpreted as a means of refuting an expectation. It is also concluded that this particular meaning, when combined with negation, enables the speaker to focalise the referent of the entity denoted by the complement, as “pas d’autre N que…” suggests a series of alternatives which are rejected in the same utterance (Cf. Pierre n’a pas d’autre solution que la fuite). Such a use could be interpreted as an emphatic version of adjectival seul
Collective nouns, aggregate nouns, and superordinates
Authors: Joosten Frank
Published: July 2010

‘Part of’ and ‘kind of’ relations in the lexicon have been matter of some linguistic research, but strangely enough, they have only rarely been investigated together. Strangely, since ‘part of’ and ‘kind of’ appear to be similar in a number of respects, and since nouns such as furniture or bétail combine both ‘part of’ and ‘kind of’ readings. As a consequence, linguistic terminology in this specific domain has been lacking in uniformity and transparency. This article aims to bring terminological clarity: it offers a rough survey of the entire ‘part of/kind of’ spectrum and pleads for an unambiguous linguistic metalanguage that distinguishes between collective nouns (e.g. team), aggregate nouns (e.g. furniture), and superordinates (e.g. vehicle). Arguments for the terminological distinctions proposed can be found in a thorough investigation of lexical form-meaning relationships.
Free conditionals in discourse
Authors: Lombardi Vallauri Edoardo
Published: July 2010

Conditional clauses in spoken Italian and other languages are often uttered with no main clause. It will be argued that in this case they constitute a construction in a technical sense, namely in the sense proposed by Simone (2006a), which is mainly reliant on the presence of specific pragmatic functions. The functions free conditionals actually cover are identified as the following: (1) posing a generic question of the type: what will happen? (2) making a statement to the effect that there is no point taking any action in the situation: there’s nothing we can/must do (3) acting as exclamatory rebuttal of what has just been stated: you are wrong! (4) making a request or offering to do something, (5) expressing desire.
The syntactic and semantic features that make conditional clauses particularly suited to endorsing such functions are examined. The analysis conducted on a corpus of spoken Italian and extensive samples from other languages, both current and dead, contributes to the understanding of the steps whereby free conditionals move from high frequency in discourse to ultimately becoming an established construction.
Analyse du figement et de ses possibles variations dans les constructions verbales espagnoles
Authors: Mogorrón Huerta Pedro
Published: July 2010

It has been traditionally believed that the main characteristic of set phrases is precisely their fixed nature. This paper gathers the results of a thorough study of verbal set phrases in Spanish, which was developed to observe this feature and for which a database of 15,300 expressions was used. It is worth noticing that, even if these phrases are fixed to different degrees, a considerable amount of them allow modifications in some of their components which do not alter the global meaning.
Exophony and literary translation
Authors: Wright Chantal
Published: July 2010

When writers of literary prose adopt a new language—a phenomenon known as exophony—this often leads them to mould the new language until it becomes suitable for their purposes, in a manner analogous to the strategies of appropriation observed in post-colonial literatures (Ashcroft, Griffiths and Tiffin 1989). This process often results in a defamiliarisation of the new language through stylistic innovation, which, in turn, has implications for the translation of these texts. This article, influenced byBerman’s ‘analytique négative’ (1985), proposes a series of guidelines for the translation of exophonic texts and illustrates these with examples taken from German exophonic prose texts by Franco Biondi, Emine Sevgi Özdamar and Yoko Tawada.
Schemata, scripts and the gay issue in contemporary dubbed sitcoms
Authors: Valdeón Roberto A.
Published: July 2010

This article examines the translational choices in the Spanish dubbed version of the American sitcomWill & Gracefor the terms ‘gay’, ‘homosexual’, ‘queer’ and ‘fag’. Firstly, I introduce the main features of the programme before moving on to present research on gay-related issues within Translation Studies. Drawing on Fairclough’s approach to discourse, the next section discusses the concepts of ‘schemata’ and ‘scripts’, as used here, and relates them to the concept of identity. The evolution of the lexical items ‘gay’, ‘homosexual’, ‘queer’ and ‘fag’ is examined (Hughes 1991; Allan & Burridge 2006) before presenting data on the preferred choices in the original programme as well as in the Spanish version. Baker’s strategies for word equivalence (1992) will be used to establish whether the use of negative terms such as ‘marica’ and ‘maricón’ aptly replace the source language term, ‘gay’. The article concludes with a discussion of whether the dysphemic nature of the terms prevails and whether traditional schemata are maintained.
An abstract framework for argumentation with structured arguments
Authors: Prakken Henry
Published: July 2010

An abstract framework for structured arguments is presented, which instantiates Dung's (‘On the Acceptability of Arguments and its Fundamental Role in Nonmonotonic Reasoning, Logic Programming, and n-Person Games’, Artificial Intelligence, 77, 321–357) abstract argumentation frameworks. Arguments are defined as inference trees formed by applying two kinds of inference rules: strict and defeasible rules. This naturally leads to three ways of attacking an argument: attacking a premise, attacking a conclusion and attacking an inference. To resolve such attacks, preferences may be used, which leads to three corresponding kinds of defeat: undermining, rebutting and undercutting defeats. The nature of the inference rules, the structure of the logical language on which they operate and the origin of the preferences are, apart from some basic assumptions, left unspecified. The resulting framework integrates work of Pollock, Vreeswijk and others on the structure of arguments and the nature of defeat and extends it in several respects. Various rationality postulates are proved to be satisfied by the framework, and several existing approaches are proved to be a special case of the framework, including assumption-based argumentation and DefLog.
Gαq-containing G proteins regulate B cell selection and survival and are required to prevent B cell–dependent autoimmunity
Authors: Misra Ravi S. , Shi Guixiu , Moreno-Garcia Miguel E. , Thankappan Anil , Tighe Michael , Mousseau Betty , Kusser Kim , Becker-Herman Shirly , Hudkins Kelly L. , Dunn Robert , Kehry Marilyn R. , Migone Thi-Sau , Marshak-Rothstein Ann , Simon Melvin , Randall Troy D. , Alpers Charles E. , Liggitt Denny , Rawlings David J. , Lund Frances E.
Published: July 2010

Survival of mature B cells is regulated by B cell receptor and BAFFR-dependent signals. We show that B cells from mice lacking the Gαq subunit of trimeric G proteins (Gnaq−/− mice) have an intrinsic survival advantage over normal B cells, even in the absence of BAFF. Gnaq−/− B cells develop normally in the bone marrow but inappropriately survive peripheral tolerance checkpoints, leading to the accumulation of transitional, marginal zone, and follicular B cells, many of which are autoreactive. Gnaq−/− chimeric mice rapidly develop arthritis as well as other manifestations of systemic autoimmune disease. Importantly, we demonstrate that the development of the autoreactive B cell compartment is the result of an intrinsic defect in Gnaq−/− B cells, resulting in the aberrant activation of the prosurvival factor Akt. Together, these data show for the first time that signaling through trimeric G proteins is critically important for maintaining control of peripheral B cell tolerance induction and repressing autoimmunity.
Novel mechanism for the generation of human xeno-autoantibodies against the nonhuman sialic acid N-glycolylneuraminic acid
Authors: Taylor Rachel E. , Gregg Christopher J. , Padler-Karavani Vered , Ghaderi Darius , Yu Hai , Huang Shengshu , Sorensen Ricardo U. , Chen Xi , Inostroza Jaime , Nizet Victor , Varki Ajit
Published: July 2010

The nonhuman sialic acid N-glycolylneuraminic acid (Neu5Gc) is metabolically incorporated into human tissues from certain mammalian-derived foods, and this occurs in the face of an anti-Neu5Gc “xeno-autoantibody” response. Given evidence that this process contributes to chronic inflammation in some diseases, it is important to understand when and how these antibodies are generated in humans. We show here that human anti-Neu5Gc antibodies appear during infancy and correlate with weaning and exposure to dietary Neu5Gc. However, dietary Neu5Gc alone cannot elicit anti-Neu5Gc antibodies in mice with a humanlike Neu5Gc deficiency. Other postnatally appearing anti-carbohydrate antibodies are likely induced by bacteria expressing these epitopes; however, no microbe is known to synthesize Neu5Gc. Here, we show that trace exogenous Neu5Gc can be incorporated into cell surface lipooligosaccharides (LOS) of nontypeable Haemophilus influenzae (NTHi), a human-specific commensal/pathogen. Indeed, infant anti-Neu5Gc antibodies appear coincident with antibodies against NTHi. Furthermore, NTHi that express Neu5Gc-containing LOS induce anti-Neu5Gc antibodies in Neu5Gc-deficient mice, without added adjuvant. Finally, Neu5Gc from baby food is taken up and expressed by NTHi. As the flora residing in the nasopharynx of infants can be in contact with ingested food, we propose a novel model for how NTHi and dietary Neu5Gc cooperate to generate anti-Neu5Gc antibodies in humans.
The RCK1 domain of the human BKCa channel transduces Ca2+ binding into structural rearrangements
Authors: Yusifov Taleh , Javaherian Anoosh D. , Pantazis Antonios , Gandhi Chris S. , Olcese Riccardo
Published: July 2010

Large-conductance voltage- and Ca2+-activated K+ (BKCa) channels play a fundamental role in cellular function by integrating information from their voltage and Ca2+ sensors to control membrane potential and Ca2+ homeostasis. The molecular mechanism of Ca2+-dependent regulation of BKCa channels is unknown, but likely relies on the operation of two cytosolic domains, regulator of K+ conductance (RCK)1 and RCK2. Using solution-based investigations, we demonstrate that the purified BKCa RCK1 domain adopts an α/β fold, binds Ca2+, and assembles into an octameric superstructure similar to prokaryotic RCK domains. Results from steady-state and time-resolved spectroscopy reveal Ca2+-induced conformational changes in physiologically relevant [Ca2+]. The neutralization of residues known to be involved in high-affinity Ca2+ sensing (D362 and D367) prevented Ca2+-induced structural transitions in RCK1 but did not abolish Ca2+ binding. We provide evidence that the RCK1 domain is a high-affinity Ca2+ sensor that transduces Ca2+ binding into structural rearrangements, likely representing elementary steps in the Ca2+-dependent activation of human BKCa channels.
Extracellular protons titrate voltage gating of a ligand-gated ion channel
Authors: Martínez-François Juan Ramón , Xu Yanping , Lu Zhe
Published: July 2010

Cyclic nucleotide–gated channels mediate transduction of light into electric signals in vertebrate photoreceptors. These channels are primarily controlled by the binding of intracellular cyclic GMP (cGMP). Glutamate residue 363 near the extracellular end of the ion selectivity filter interacts with the pore helix and helps anchor the filter to the helix. Disruption of this interaction by mutations renders the channels essentially fully voltage gated in the presence of saturating concentrations of cGMP. Here, we find that lowering extracellular pH makes the channels conduct in an extremely outwardly rectifying manner, as does a neutral glutamine substitution at E363. A pair of cysteine mutations, E363C and L356C (the latter located midway the pore helix), largely eliminates current rectification at low pH. Therefore, this low pH-induced rectification primarily reflects voltage-dependent gating involving the ion selectivity filter rather than altered electrostatics around the external opening of the ion pore and thus ion conduction. It then follows that protonation of E363, like the E363Q mutation, disrupts the attachment of the selectivity filter to the pore helix. Loosening the selectivity filter from its surrounding structure shifts the gating equilibrium toward closed states. At low extracellular pH, significant channel opening occurs only when positive voltages drive the pore from a low probability open conformation to a second open conformation. Consequently, at low extracellular pH the channels become practically fully voltage gated, even in the presence of a saturating concentration of cGMP.
An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes
Authors: Arunachalam Manonmani , Jayasurya Karthik , Tomancak Pavel , Ohler Uwe
Published: July 2010

Motivation: Evolutionarily conserved non-coding genomic sequences represent a potentially rich source for the discovery of gene regulatory region such as transcriptional enhancers. However, detecting orthologous enhancers using alignment-based methods in higher eukaryotic genomes is particularly challenging, as regulatory regions can undergo considerable sequence changes while maintaining their functionality.

Results: We have developed an alignment-free method which identifies conserved enhancers in multiple diverged species. Our method is based on similarity metrics between two sequences based on the co-occurrence of sequence patterns regardless of their order and orientation, thus tolerating sequence changes observed in non-coding evolution. We show that our method is highly successful in detecting orthologous enhancers in distantly related species without requiring additional information such as knowledge about transcription factors involved, or predicted binding sites. By estimating the significance of similarity scores, we are able to discriminate experimentally validated functional enhancers from seemingly equally conserved candidates without function. We demonstrate the effectiveness of this approach on a wide range of enhancers in Drosophila, and also present encouraging results to detect conserved functional regions across large evolutionary distances. Our work provides encouraging steps on the way to ab initio unbiased enhancer prediction to complement ongoing experimental efforts.

Availability: The software, data and the results used in this article are available at http://www.genome.duke.edu/labs/ohler/research/transcription/fly_enhancer/

Contact:  tomancak@mpi-cbg.de; uwe.ohler@duke.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
C-It: a knowledge database for tissue-enriched genes
Authors: Gellert Pascal , Jenniches Katharina , Braun Thomas , Uchida Shizuka
Published: July 2010

Motivation: Due to the development of high-throughput technologies such as microarrays, it has become possible to determine genome-wide expression changes in a single experiment. Although much attention has been paid to identify differentially expressed genes, the functions of tens of thousands of genes in different species still remain unknown.

Results: C-It is a knowledge database that has its focus on ‘uncharacterized genes’. C-It contains expression profiles of various tissues from human, mouse, rat, chicken and zebrafish. By applying our previously introduced algorithm DGSA (Database-Dependent Gene Selection and Analysis), it is possible to screen for uncharacterized, tissue-enriched genes in the species mentioned above. C-It is designed to include further expression studies, which might provide more comprehensive coverage of gene expression patterns and tissue-enriched splicing isoforms. We propose that C-It will be an excellent starting point to study uncharacterized genes.

Availability: C-It is freely available online without registration at http://C-It.mpi-bn.mpg.de

Contact:  thomas.braun@mpi-bn.mpg.de; shizuka.uchida@mpi-bn.mpg.de
Spatial Distribution of Raffaelea quercivora in Xylem of Naturally Infested and Inoculated Oak Trees
Authors: Takahashi Yukiko , Matsushita Norihisa , Hogetsu Taizo
Published: July 2010

Mass mortality of Japanese oak caused by Raffaelea quercivora due to Japanese oak wilt (JOW) has been tremendous since the late 1980s in Japan. We investigated detailed distribution of R. quercivora hyphae in a naturally infected Quercus serrata tree using fluorescein-conjugated wheat germ agglutinin and also examined spatial relationships between hyphal distribution, water conduction loss, and host reactions in xylem in inoculated Q. crispula saplings. Hyphae of R. quercivora elongated longitudinally in vessels and transversely in ray tissues in both naturally infected and inoculated Quercus trees. Hyphae were confined within a relatively small area near the inoculation site. Vessel dysfunction was also confined and overlapped with hyphal distribution. The reaction zone consisting of two types of fluorescent substance was formed surrounding the outside of the hyphal area in xylem and was always found in non-water-conductive zone. These results suggest that wilting of Quercus trees caused by JOW may not be induced by dysfunction of a small number of vessels, but by that of many vessels, and it requires that R. quercivora hyphae spread from many galleries bored by beetles during mass attacks.
Colonization of Dodder, Cuscuta indecora, by ‘Candidatus Liberibacter asiaticus’ and ‘Ca. L. americanus’
Authors: Hartung John S. , Paul Cristina , Achor Diann , Brlansky R. H.
Published: July 2010

Huanglongbing, or citrus greening, threatens the global citrus industry. The presumptive pathogens, ‘Candidatus Liberibacter asiaticus’ and ‘Ca. L. americanus’ can be transferred from citrus to more easily studied experimental hosts by using holoparasitic dodder plants. However, the interaction between ‘Candidatus Liberibacter’ spp. and the dodder has not been studied. We combined quantitative polymerase chain reaction with electron microscopy to show that only 65% of tendrils of Cuscuta indecora grown on ‘Ca. Liberibacter’ spp.-infected host plants had detectable levels of the pathogen. Among tendrils that were colonized by Liberibacter in at least one 2 cm segment, most were not colonized in all segments. Furthermore, the estimated population levels of the pathogen present in serial 2 cm segments of dodder tendrils varied widely and without any consistent pattern. Thus, there was generally not a concentration gradient of the pathogen from the source plant towards the recipient and populations of the pathogen were sometimes found in the distal segments of the dodder plant but not in the proximal or middle segments. Populations of the pathogens ranged from 2 × 102 to 3.0 × 108 cells per 2 cm segment. On a fresh weight basis, populations as high as 1.4 × 1010 cells per g of tissue were observed demonstrating that ‘Ca. Liberibacter’ spp. multiplies well in Cuscuta indecora. However, 55% of individual stem segments did not contain detectable levels of the pathogen, consistent with a pattern of nonuniform colonization similar to that observed in the much more anatomically complex citrus tree. Colonization of dodder by the pathogen is also nonuniform at the ultrastructural level, with adjacent phloem vessel elements being completely full of the pathogen or free of the pathogen. We also observed bacteria in the phloem vessels that belonged to two distinct size classes based on the diameters of cross sections of cells. In other sections from the same tendrils we observed single bacterial cells that were apparently in the process of differentiating between the large and round forms to the long and thin forms (or vice versa). The process controlling this morphological differentiation of the pathogen is not known. The highly reduced and simplified anatomy of the dodder plant as well as its rapid growth rate compared with citrus, and the ability of the plant to support multiplication of the pathogen to high levels, makes it an interesting host plant for further studies of host–pathogen interactions.
Biocontrol Activity and Induction of Systemic Resistance in Pepper by Compost Water Extracts Against Phytophthora capsici
Authors: Sang Mee Kyung , Kim Jeong-Gyu , Kim Ki Deok
Published: July 2010

We investigated the effects of water extracts of composts (CWE) from commercial compost facilities for controlling root and foliar infection of pepper plants by Phytophthora capsici. Among 47 CWE tested, CWE from composts Iljuk-3, Iljuk-7, Shinong-8, and Shinong-9 significantly (P < 0.05) inhibited zoospore germination, germ tube elongation, mycelial growth, and population of P. capsici. All selected CWE significantly (P < 0.05) reduced the disease incidence and severity in the seedling and plant assays compared with the controls. However, there were no significant differences in zoospore germination, disease incidence, and disease severity between treatments of untreated, autoclaved, and filtered CWE. In addition, CWE significantly (P < 0.05) suppressed leaf infection of P. capsici through induced systemic resistance (ISR) in plants root-drenched with CWE. The tested CWE enhanced the expression of the pathogenesis-related genes, CABPR1, CABGLU, CAChi2, CaPR-4, CAPO1, or CaPR-10 as well as β-1,3-glucanase, chitinase, and peroxidase activities, which resulted in enhanced plant defense against P. capsici in pepper plants. Moreover, the CWE enhanced the chemical and structural defenses of the plants, including H2O2 generation in the leaves and lignin accumulation in the stems. The CWE could also suppress other fungal pathogens (Colletotrichum coccodes in pepper leaves and C. orbiculare in cucumber leaves) through ISR; however, it failed to inhibit other bacterial pathogens (Xanthomonas campestris pv. vesicatoria in pepper leaves and Pseudomonas syringae pv. lachrymans in cucumber leaves). These results suggest that a heat-stable chemical(s) in the CWE can suppress root and foliar infection by P. capsici in pepper plants. In addition, these suppressions might result from direct inhibition of development and population of P. capsici for root infection, as well as indirect inhibition of foliar infection through ISR with broad-spectrum protection.
Pelargonium zonate spot virus Is Transmitted Vertically via Seed and Pollen in Tomato
Authors: Lapidot M. , Guenoune-Gelbart D. , Leibman D. , Holdengreber V. , Davidovitz M. , Machbash Z. , Klieman-Shoval S. , Cohen S. , Gal-On A.
Published: July 2010

In autumn 2007, a new disease with unknown etiology was observed in open-field tomato (Solanum lycopersicum) in the Lachish region of Israel. The symptoms included mild mosaic, leaf malformation, and severe stunting of the plants. The causal agent was readily transmitted mechanically from the sap of infected plants to indicator plants. Viral particles were purified from infected plants and cDNA was synthesized from RNA isolated from the particles. Cloning and sequencing of the cDNA showed 95% identity to RNA 3 of Pelargonium zonate spot virus (PZSV). Using reverse-transcription polymerase chain reaction, PZSV was detected in both seed and pollen grains of infected tomato plants. Attempts to disinfect seed by using hydrochloric acid and trisodium phosphate failed to eliminate this PZSV detection. Seed from infected tomato plants gave rise to infected seedlings with a seed-transmission rate of PZSV of 11 to 29%. Pollen grains collected from flowers of infected plants were used to hand pollinate healthy mother tomato plants. Although none of the pollinated mother plants became infected with PZSV, 29% of the seedlings produced from seed harvested from these plants were found to be infected. This is the first demonstration that PZSV is transmitted vertically via both pollen and seed in tomato plants.
Effects of Pseudomonas putida S1Pf1Rif Against Chrysanthemum Yellows Phytoplasma Infection
Authors: Gamalero Elisa , D'Amelio Romina , Musso Chiara , Cantamessa Simone , Pivato Barbara , D'Agostino Giovanni , Duan Jin , Bosco Domenico , Marzachì Cristina , Berta Graziella
Published: July 2010

Phytoplasmas cause damage on a number of plant species leading to relevant economical loss. Up to now, strategies to limit their spread led to only partial success. In this context, the use of plant-beneficial bacteria to control phytoplasmas has never been explored. The aim of this work was to assess the effect of Pseudomonas putida S1Pf1Rif against chrysanthemum yellows phytoplasma (CYP) infection of daisy. Plant biomass, root architecture, symptom severity, phytoplasma titer, and viability were evaluated in inoculated and control plants. CYP reduced plant growth and root development. Although the phytoplasma titer in young apical leaves was not affected by inoculation with S1Pf1Rif, the pseudomonad improved plant growth of CYP-infected plants. Whereas CYP titer increased over time in uninoculated plants, its viability decreased, regardless of the presence of P. putida S1Pf1Rif. Finally, phytoplasma cells in fully developed leaves of CYP-infected plants inoculated with S1Pf1Rif often appeared degenerated. Overall, our results indicate that P. putida S1Pf1Rif is able to alleviate the disease, although it does not affect the presence of viable phytoplasmas in young, developing leaves of the infected plants.
A Fertilization-Independent Developmental Program Triggers Partial Fruit Development and Senescence Processes in Pistils of Arabidopsis
Authors: Carbonell-Bejerano Pablo , Urbez Cristina , Carbonell Juan , Granell Antonio , Perez-Amador Miguel A.
Published: July 2010

The pistil is the specialized plant organ that enables appropriate pollination and ovule fertilization, after which it undergoes growth and differentiation to become a fruit. However, in most species, if ovules are not fertilized around anthesis the pistil irreversibly loses its growth capacity. We used physiological, molecular, and transcriptomic tools to characterize the post-anthesis development of the unfertilized Arabidopsis (Arabidopsis thaliana) pistil. Surprisingly, developmental processes that have been previously described in developing Arabidopsis fruits, such as the collapse of the adaxial epidermis, differentiation of a sclerenchyma layer in the adaxial subepidermis and the dehiscence zone, and valve dehiscence, were also observed in the unfertilized pistil. We determined that senescence is first established in the transmitting tract, stigma, and ovules immediately after anthesis, and that the timing of senescence in the stigma and ovules correlates with the loss of fruit-set responsiveness of the pistil to pollen and the hormone gibberellin (GA), respectively. Moreover, we showed that mutants with altered ovule development have impaired fruit-set response to the GA gibberellic acid, which further indicates that the presence of viable ovules is required for fruit-set responsiveness to GAs in the unfertilized pistil. Our data suggest that a fertilization-independent developmental program controls many of the processes during post-anthesis development, both in unfertilized pistils and seeded fruits, and point to a key role of the ovule in the capacity of pistils to undergo fruit set in response to GA.