bluuebunny/crossref_metadata_2025 huggingface dataset:
Mycobacterium tuberculosis
supports protein tyrosine phosphorylation
Authors: Kusebauch Ulrike , Ortega Corrie , Ollodart Anja , Rogers Richard S. , Sherman David R. , Moritz Robert L. , Grundner Christoph
Published: June 2014

Significance

Reversible protein phosphorylation is a major regulatory mechanism by which bacteria sense and respond to changes in their environment. In
Mycobacterium tuberculosis
(
Mtb
), however, protein phosphorylation on Tyr residues had not been described and was thought to be absent. We show that
Mtb
phosphorylates diverse proteins on Tyr, suggesting a broad functional role. We identify the Ser/Thr kinases as the kinases responsible for phosphorylation on Tyr and show that Tyr phosphorylation regulates Ser/Thr protein kinase activity. Together, our study provides the basis for understanding how this new
Mtb
posttranslational modification affects physiology and pathogenesis.
Targeted inversion and reversion of the blood coagulation factor 8 gene in human iPS cells using TALENs
Authors: Park Chul-Yong , Kim Jungeun , Kweon Jiyeon , Son Jeong Sang , Lee Jae Souk , Yoo Jeong-Eun , Cho Sung-Rae , Kim Jong-Hoon , Kim Jin-Soo , Kim Dong-Wook
Published: June 2014

Significance

Hemophilia A, a genetic bleeding disorder, is often caused by chromosomal inversions that involve a portion of the blood coagulation
factor VIII
(
F8
) gene that encodes one of the key enzymes in blood clotting. In this study, we developed enzymes known as transcription activator-like effector nucleases (TALENs) that cleave chromosomal DNA in a targeted manner to invert the 140-kbp chromosomal segment that spans the portion of the
F8
gene in human induced pluripotent stem cells (iPSCs) to create a hemophilia A model cell line. In addition, we reverted the inverted segment back to its normal orientation using the same enzymes. This strategy provides an iPSC-based novel therapeutic option for the treatment of hemophilia A.
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
Authors: Seaver Samuel M. D. , Gerdes Svetlana , Frelin Océane , Lerma-Ortiz Claudia , Bradbury Louis M. T. , Zallot Rémi , Hasnain Ghulam , Niehaus Thomas D. , El Yacoubi Basma , Pasternak Shiran , Olson Robert , Pusch Gordon , Overbeek Ross , Stevens Rick , de Crécy-Lagard Valérie , Ware Doreen , Hanson Andrew D. , Henry Christopher S.
Published: June 2014

Significance

Genes must be annotated with their correct functions if genome data are to support hypothesis building and metabolic engineering. PlantSEED was developed to streamline the process of annotating plant genome sequences, to construct metabolic models based on genome annotations automatically, and to use models to test the annotation of these sequences, allowing the detection of gaps and errors in gene annotations and the prediction of new functions. PlantSEED is designed to grow in an iterative manner by including new plant genome sequences, new annotations harvested from the literature, and improved biochemical data, all of which are integrated in a consistent manner into the PlantSEED genomes and metabolic models.
Badger responses to small-scale culling may compromise targeted control of bovine tuberculosis
Authors: Bielby Jon , Donnelly Christl A. , Pope Lisa C. , Burke Terry , Woodroffe Rosie
Published: June 2014

Significance

Bovine tuberculosis (TB) killed 1,500 people annually in 1930s Britain. TB control efforts still entail slaughtering many thousands of cattle annually, costing British farmers and taxpayers millions of dollars. Transmission from wild badgers impedes control of cattle TB, but nonselective badger culls confer limited benefits because culling changes badger behavior in ways that increase disease spread. A new plan to cull only test-positive badgers, and vaccinate test-negative badgers [termed test–vaccinate/remove (TVR)], is probably more publicly acceptable, and might be more effective if culling small numbers of badgers prompts no behavioral change. Unfortunately, this study shows that small-scale culling (such as TVR) changes badgers’ behavior in ways that risk increasing TB transmission among badgers and exacerbating cattle TB incidence rather than reducing it.
Targeting and in vivo imaging of non-small–cell lung cancer using nebulized multimodal contrast agents
Authors: Bianchi Andrea , Dufort Sandrine , Lux François , Fortin Pierre-Yves , Tassali Nawal , Tillement Olivier , Coll Jean-Luc , Crémillieux Yannick
Published: June 2014

Significance

One of the main reasons for the dismal prognosis of lung cancer is related to late diagnosis of this pathology. In this work we show that the synergic employment of a properly chosen free-breathing MRI protocol and gadolinium-based nanoparticles allow early-stage accurate and noninvasive detection of millimetric-size lung tumor and of its contours. In addition, this work shows for the first time, to our knowledge, the advantages that can come from the choice of an orotracheal administration route instead of a more conventional systemic administration when studying pathomorphological changes due to lung cancers. Potential applications of this result may range from effective lung pathology detection and follow-up to pulmonary therapeutic applications of selected drugs.
Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape
Authors: Ichihashi Yasunori , Aguilar-Martínez José Antonio , Farhi Moran , Chitwood Daniel H. , Kumar Ravi , Millon Lee V. , Peng Jie , Maloof Julin N. , Sinha Neelima R.
Published: June 2014

Significance

Ever since Darwin’s pioneering research, a major challenge in biology has been to understand the genetic basis of morphological evolution. Utilizing the natural variation in leaf morphology between tomato and two related wild species, we identified a gene network module that leads to a dynamic rewiring of interactions in the whole leaf developmental gene regulatory network. Our work experimentally validates the hypothesis that peripheral regions of network, rather than network hubs, are more likely to contribute to evolutionary innovations. Our data also suggest that, likely due to their bottleneck location in the network, the regulation in KNOX homeobox genes was repeatedly manipulated to generate natural variation in leaf shape.
Cofactor-dependent conformational heterogeneity of GAD65 and its role in autoimmunity and neurotransmitter homeostasis
Authors: Kass Itamar , Hoke David E. , Costa Mauricio G. S. , Reboul Cyril F. , Porebski Benjamin T. , Cowieson Nathan P. , Leh Hervé , Pennacchietti Eugenia , McCoey Julia , Kleifeld Oded , Borri Voltattorni Carla , Langley David , Roome Brendan , Mackay Ian R. , Christ Daniel , Perahia David , Buckle Malcolm , Paiardini Alessandro , De Biase Daniela , Buckle Ashley M.
Published: June 2014

Significance

Autoimmune type 1 diabetes is characterized by the formation of self-reactive antibodies. A prevalent human autoantigen is glutamate decarboxylase (GAD)65, a highly predictive marker that can precede the emergence of disease by up to several years. Intriguingly, the closely related isoform GAD67 is not immunogenic. What are the determinants of the unique self-reactivity of GAD65 vs. GAD67? We show that, unlike GAD67, GAD65 is highly flexible and exists in multiple structural forms. We show that self-antibodies bind differentially to these GAD65 forms. These properties may be an undesirable consequence of conformational flexibility necessary for enzyme function. Our findings, thus, provide insights into how structural flexibility governs protein immunogenicity in autoimmune diabetes and have implications for therapeutic antibody and vaccine design.
Packing density of rigid aggregates is independent of scale
Authors: Zangmeister Christopher D. , Radney James G. , Dockery Lance T. , Young Jessica T. , Ma Xiaofei , You Rian , Zachariah Michael R.
Published: June 2014

Significance

Particle aggregates are one of the most ubiquitous structural arrangements in the universe, making up large interstellar planetary seedlings and comets, microscale powdered pharmaceuticals, and nanoscale atmospheric particles. The packing of aggregates determines structure and, in many cases, chemical, physical, and mechanical properties. Here we show that packing in weakly compacted aggregated materials is scale invariant over many orders of magnitude. We demonstrate that the effective density of compacted soot aggregates and comets are equivalent, and conclude that the packing of aggregated materials appear to be remarkably independent of the aggregating forces, mechanisms, or initial conditions.
Economic scarcity alters the perception of race
Authors: Krosch Amy R. , Amodio David M.
Published: June 2014

Significance

Racial disparities on socioeconomic indices expand dramatically during economic recession. Although prior explanations for this phenomenon have focused on institutional causes, our research reveals that perceived scarcity influences people’s visual representations of race in a way that may promote discrimination. Across four studies, scarce conditions led perceivers to view Black people as “darker” and “more stereotypically Black” in appearance, relative to control conditions, and this shift in perception under scarcity was sufficient to elicit reduced resource allocations to African American recipients. These findings introduce a “motivated perception” account for the proliferation of racial and ethnic discrimination during times of economic duress.
Evidence for elevated and spatially variable geothermal flux beneath the West Antarctic Ice Sheet
Authors: Schroeder Dustin M. , Blankenship Donald D. , Young Duncan A. , Quartini Enrica
Published: June 2014

Significance

Thwaites Glacier is one of the West Antarctica's most prominent, rapidly evolving, and potentially unstable contributors to global sea level rise. Uncertainty in the amount and spatial pattern of geothermal flux and melting beneath this glacier is a major limitation in predicting its future behavior and sea level contribution. In this paper, a combination of radar sounding and subglacial water routing is used to show that large areas at the base of Thwaites Glacier are actively melting in response to geothermal flux consistent with rift-associated magma migration and volcanism. This supports the hypothesis that heterogeneous geothermal flux and local magmatic processes could be critical factors in determining the future behavior of the West Antarctic Ice Sheet.
An iron-regulated and glycosylation-dependent proteasomal degradation pathway for the plasma membrane metal transporter ZIP14
Authors: Zhao Ningning , Zhang An-Sheng , Worthen Christal , Knutson Mitchell D. , Enns Caroline A.
Published: June 2014

Significance

The canonical degradation pathway for plasma membrane proteins is through endocytosis and targeting to lysosomes. In some cases, plasma membrane proteins undergo retrograde trafficking to the endoplasmic reticulum (ER) for extraction through an endoplasmic reticulum-associated degradation pathway. We identified a novel proteasome-mediated pathway for the degradation of a plasma membrane iron transporter, ZIP14. Extraction and degradation of ZIP14 occurred after endocytosis, but did not occur by retrograde trafficking to the ER. Both ubiquitination and deglycosylation of ZIP14 were identified prior to degradation. To our knowledge, ZIP14 is the first identified multispanning plasma membrane protein to undergo such a pathway. In addition, we showed that membrane extraction is regulated by cellular iron content, providing insight into the disorders of iron metabolism.
Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes
Authors: Chakrabarti Shaon , Hinczewski Michael , Thirumalai D.
Published: June 2014

Significance

Selectins and integrins are receptor proteins on cell surfaces responsible for adhesion to extracellular biomolecules, a critical component of physiological processes like white blood cell localization at sites of inflammation. The bonds which the receptors form with their targets are regulated by mechanical forces (for example due to blood flow). The bond lifetimes before rupture increase with force before decreasing. Based on crystal structures of selectin and integrin, we created a general analytic theory which for the first time, to our knowledge, relates microscopic structural rearrangements at the receptor–ligand interface to macroscopic bond lifetimes. We quantitatively explain experimental data from diverse systems spanning four decades of lifetime scales, and also predict the outcome of mutations in specific residues.
Medically important differences in snake venom composition are dictated by distinct postgenomic mechanisms
Authors: Casewell Nicholas R. , Wagstaff Simon C. , Wüster Wolfgang , Cook Darren A. N. , Bolton Fiona M. S. , King Sarah I. , Pla Davinia , Sanz Libia , Calvete Juan J. , Harrison Robert A.
Published: June 2014

Significance

The toxic composition of snake venom varies between species. Such variation can have major medical implications for the treatment of human snakebite victims. Venom variation is largely attributed to differences in toxin-encoding genes present in the genome or venom gland of snakes. Here, we demonstrate that mechanisms affecting the transcription, translation, and posttranslational modification of toxins also significantly contribute to the diversity of venom protein composition. Venom variation observed between related snake species is therefore the result of a complex interaction between a variety of genetic and postgenomic factors acting on toxin genes. Ultimately, this variation results in significant differences in venom-induced pathology and lethality and can undermine the efficacy of antivenom therapies used to treat human snakebite victims.
Structural and mechanistic studies of polymerase η bypass of phenanthriplatin DNA damage
Authors: Gregory Mark T. , Park Ga Young , Johnstone Timothy C. , Lee Young-Sam , Yang Wei , Lippard Stephen J.
Published: June 2014

Significance

In this work we investigated the ability of phenanthriplatin, a novel, potent monofunctional platinum anticancer agent, to inhibit DNA replication. Biochemical assays using site-specifically platinated DNA probes revealed the ability of phenanthriplatin lesions to block DNA replication by all polymerases tested except for Pol η, which exhibited inefficient but high-fidelity lesion bypass. Crystallographic studies of Pol η stalled at different stages of translesion synthesis past phenanthriplatin-platinated DNA provided insight into the mechanism by which the lesion inhibits DNA polymerases to induce cellular toxicity. Cytotoxicity studies using cells derived from patients who do not express functional Pol η suggest that phenanthriplatin-based therapy will be useful to treat cancers resistant to cisplatin by upregulating Pol η expression.
Mechanism of staphylococcal multiresistance plasmid replication origin assembly by the RepA protein
Authors: Schumacher Maria A. , Tonthat Nam K. , Kwong Stephen M. , Chinnam Naga babu , Liu Michael A. , Skurray Ronald A. , Firth Neville
Published: June 2014

Significance

The large staphylococcal multiresistance plasmids harbored in Gram-positive pathogens contribute significantly to the spread of multidrug-resistant bacteria and are typified by the presence of a highly conserved replication initiator protein, RepA, which is required for plasmid retention. RepA proteins contain N-terminal (NTD) and C-terminal (CTD) domains, which are both required for replication. We show that the RepA NTD and CTD show striking homology to the host primosome protein DnaD yet perform distinct functions; the NTD binds origin DNA in a novel manner and the CTD recruits the replicative helicase. Moreover, NTD–DNA structures reveal the first mechanism of origin handcuffing. Combined, the data unveil the minimal mechanism by which multiresistance plasmids mediate origin assembly via the highly conserved RepA protein.
Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA–like structural element in the ribosomal decoding center
Authors: Koh Cha San , Brilot Axel F. , Grigorieff Nikolaus , Korostelev Andrei A.
Published: June 2014

Significance

Ribosomes decode genetic information encoded in mRNAs to synthesize cellular proteins. Initiation of translation is a key step, during which the ORF coding for a protein gets properly positioned on the ribosome with the AUG start codon and its cognate tRNA located in the ribosomal peptidyl site. Here, we report molecular structures of a eukaryotic ribosome complexed with viral mRNA, which uncover an unusual mechanism of initiation. The structures reveal that viral mRNAs carrying an intergenic RNA structure known as the internal ribosome entry site (IRES) initiate translation by binding a tRNA-mRNA–like element in the aminoacyl site of the ribosome. A structural mechanism of how viral mRNAs with intergenic IRESs hijack host ribosomes is proposed.
Recovery of consciousness is mediated by a network of discrete metastable activity states
Authors: Hudson Andrew E. , Calderon Diany Paola , Pfaff Donald W. , Proekt Alex
Published: June 2014

Significance

How does the brain recover consciousness after significant perturbations such as anesthesia? The simplest answer is that as the anesthetic washes out, the brain follows a steady and monotonic path toward consciousness. We show that this simple intuition is incorrect. We varied the anesthetic concentration to parametrically control the magnitude of perturbation to brain dynamics while analyzing the characteristics of neuronal activity during recovery of consciousness. We find that, en route to consciousness, the brain passes through several discrete activity states. Although transitions between certain of these activity states occur spontaneously, transitions between others are not observed. Thus, the network formed by these state transitions gives rise to an ordered sequence of states that mediates recovery of consciousness.
Distinct phases in the positive selection of CD8+T cells distinguished by intrathymic migration and T-cell receptor signaling patterns
Authors: Ross Jenny O. , Melichar Heather J. , Au-Yeung Byron B. , Herzmark Paul , Weiss Arthur , Robey Ellen A.
Published: June 2014

Significance

Developing T cells are positively selected in the thymus to ensure that their antigen receptors can interact with self-MHC. For CD8 T cells, this process takes days to complete, yet the steps involved are poorly understood. We followed a synchronized wave of cells undergoing positive selection within three-dimensional thymic tissue. Surprisingly, migration from the cortex to the medulla occurred before CD4 down-regulation and while thymocytes still required TCR signaling for efficient positive selection. There was a gradual change in the pattern of calcium signaling over time, with an upward shift in basal intracellular calcium correlating with increased speed and brief signaling events. Our data have interesting implications for how positive and negative selection shape the mature CD8 T-cell repertoire.
Linear integration of spine Ca
2+
signals in layer 4 cortical neurons in vivo
Authors: Jia Hongbo , Varga Zsuzsanna , Sakmann Bert , Konnerth Arthur
Published: June 2014

Significance

In the mammalian brain, sensory information reaches the cortex through thalamic axons, which provide a strong drive to layer 4 (L4). The thalamic inputs are characterized by their synchronous mode of activation and their high efficacy. Here, by using two-photon imaging in vivo, we analyze sensory-stimulation–evoked calcium transients on the level of individual excitatory synapses located on dendritic spines in L4 spiny stellate cells. We demonstrate that the rapid transfer of peripheral signals to the cortical network is associated with the activation of synapses that are widely dispersed throughout the entire dendritic tree. The dendritic integration of the synaptic responses is linear and does not involve cooperativity between individual synapses.
Correlating the motion of electrons and nuclei with two-dimensional electronic–vibrational spectroscopy
Authors: Oliver Thomas A. A. , Lewis Nicholas H. C. , Fleming Graham R.
Published: June 2014

Significance

To have a full understanding of the role of nuclear motions involved in nonradiative relaxation dynamics of complex molecular systems such as carotenoids, nanomaterials, and molecular photoswitches, the ability to correlate the electronic and nuclear degrees of freedom is imperative. We have developed 2D electronic–vibrational spectroscopy to observe this correlation, and this new spectroscopic technique will provide a direct probe of the coupling between electronic and nuclear dynamics at conical intersections, and thus the underlying mechanisms driving the ensuing photochemistry.
The Place of Classifiers in the History of Linguistics
Authors: Kilarski Marcin
Published: June 2014

This article examines the approaches to classifiers within the Western tradition, ranging from the earliest accounts of the languages of Mesoamerica and East Asia from the 16th-17th centuries to ongoing discussions regarding their semantic motivation and functionality. I show that in spite of the limited attention they attracted before the 1970s, classifiers have played an important role in discussions concerning such notions as the functions of grammatical categories, the distinction between grammar and lexicon as well as the cognitive and cultural correlates of linguistic structure. In addition, I attribute common assumptions about classifiers to projections of typical properties of grammatical gender and, more generally, semantic and morphosyntactic properties of non-classifier languages.
Can infants use robot gaze for object learning?
Authors: Okumura Yuko , Kanakogi Yasuhiro , Kanda Takayuki , Ishiguro Hiroshi , Itakura Shoji
Published: June 2014

Previous research has shown that although infants follow the gaze direction of robots, robot gaze does not facilitate infants’ learning for objects. The present study examined whether robot gaze affects infants’ object learning when the gaze behavior was accompanied by verbalizations. Twelve-month-old infants were shown videos in which a robot with accompanying verbalizations gazed at an object. The results showed that infants not only followed the robot’s gaze direction but also preferentially attended to the cued object when the ostensive verbal signal was present. Moreover, infants showed enhanced processing of the cued object when ostensive and referential verbal signals were increasingly present. These effects were not observed when mere nonverbal sound stimuli instead of verbalizations were added. Taken together, our findings indicate that robot gaze accompanying verbalizations facilitates infants’ object learning, suggesting that verbalizations are important in the design of robot agents from which infants can learn. Keywords: gaze following; humanoid robot; infant learning; verbalization; cognitive development
Verb concepts from affordances
Authors: Kalkan Sinan , Dag Nilgün , Yürüten Onur , Borghi Anna M. , Şahin Erol
Published: June 2014

In this paper, we investigate how the interactions of a robot with its environment can be used to create concepts that are typically represented by verbs in language. Towards this end, we utilize the notion of affordances to argue that verbs typically refer to the generation of a specific type of effect rather than a specific type of action. Then, we show how a robot can form these concepts through interactions with the environment and how humans can use these concepts to ease their communication with the robots. We demonstrate that iCub, a humanoid robot, can use the concepts, which it has developed, to to understand what a human performs, perform multi-step planning for reaching a goal state as well as to specify a goal to the robot using symbolic descriptions.
Infant-directed visual prosody
Authors: Smith Nicholas A. , Strader Heather L.
Published: June 2014

Acoustical changes in the prosody of mothers’ speech to infants are distinct and near universal. However, less is known about the visible properties of mothers’ infant-directed (ID) speech, and their relation to speech acoustics. Mothers’ head movements were tracked as they interacted with their infants using ID speech, and compared to movements accompanying their adult-directed (AD) speech. Movement measures along three dimensions of head translation, and three axes of head rotation were calculated. Overall, more head movement was found for ID than AD speech, suggesting that mothers exaggerate their visual prosody in a manner analogous to the acoustical exaggerations in their speech. Regression analyses examined the relation between changing head position and changing acoustical pitch (F0) over time. Head movements and voice pitch were more strongly related in ID speech than in AD speech. When these relations were examined across time windows of different durations, stronger relations were observed for shorter time windows (< 5 sec). However, the particular form of these more local relations did not extend or generalize to longer time windows. This suggests that the multimodal correspondences in speech prosody are variable in form, and occur within limited time spans.
Robot companions for children with down syndrome
Authors: Lehmann Hagen , Iacono Iolanda , Dautenhahn Kerstin , Marti Patrizia , Robins Ben
Published: June 2014

We describe an exploratory case study about the applicability of different robotic platforms in an educational context with a child with Down syndrome. The robotic platforms tested are the humanoid robot KASPAR and the mobile robotic platform IROMEC. During the study we observed the effects KASPAR and IROMEC had in helping the child with the development and improvement of her social skills while playing different interactive games with the robots. Conceptually similar play scenarios were performed with both robots and the behaviour of the child was monitored during her interactions with them.
Translation Studies in Europe—reasons for it, and problems to work on
Authors: Pym Anthony
Published: June 2014

As a social and political context for research on translation, the European Union offers pertinent commitments to multilingualism, inclusive territorial democracy, transparent governance and the welfare state, with enough public funding to pursue these aims seriously. All these features concern translation, not only to the extent that they create social demands for translations but more importantly in that they give our research an ethical and political dimension, in addition to the demands of various markets. However, when the consequences of these commitments are compared with actual European research and public policies concerning translation, several shortcomings become apparent. The comparison suggests that future tasks for Translation Studies in Europe should include: (1) serious attention to far more than the large territorial languages; (2) enhanced exchange with neighboring disciplines, especially with scholars working on language acquisition; (3) an acceptance that translated communication should concern involvement and interaction, in addition to public information; (4) a questioning of the Western translation form as the model best suited to interactive cross-lingual governance; and (5) experimentation with technologies that stimulate citizen involvement.
Zimbabwe's ‘new’ smallholders: who got land and where did they come from?
Authors: James Gareth David
Published: June 2014

In March 2000, land occupations in Zimbabwe intensified, forcing the government to implement the Fast Track Land Reform Programme, which significantly altered the agrarian structure of the country. Ever since, there have been widespread misconceptions about the nature and character of the land occupations and the identities of new land beneficiaries. Using survey data and in-depth interviews from 166 newly resettled households, this article shows the majority were ‘ordinary’ poor and near-landless people from communal and other rural areas. While there is some significant variation within and between new communities, they are far from what we might call ‘elites’.
Sphingosine-1-phosphate receptor 2 is critical for follicular helper T cell retention in germinal centers
Authors: Moriyama Saya , Takahashi Noriko , Green Jesse A. , Hori Shohei , Kubo Masato , Cyster Jason G. , Okada Takaharu
Published: June 2014

Follicular helper T (Tfh) cells access the B cell follicle to promote antibody responses and are particularly important for germinal center (GC) reactions. However, the molecular mechanisms of how Tfh cells are physically associated with GCs are incompletely understood. We report that the sphingosine-1-phosphate receptor 2 (S1PR2) gene is highly expressed in a subpopulation of Tfh cells that localizes in GCs. S1PR2-deficient Tfh cells exhibited reduced accumulation in GCs due to their impaired retention. T cells deficient in both S1PR2 and CXCR5 were ineffective in supporting GC responses compared with T cells deficient only in CXCR5. These results suggest that S1PR2 and CXCR5 cooperatively regulate localization of Tfh cells in GCs to support GC responses.
Neutrophils recruited by chemoattractants in vivo induce microvascular plasma protein leakage through secretion of TNF
Authors: Finsterbusch Michaela , Voisin Mathieu-Benoit , Beyrau Martina , Williams Timothy John , Nourshargh Sussan
Published: June 2014

Microvascular plasma protein leakage is an essential component of the inflammatory response and serves an important function in local host defense and tissue repair. Mediators such as histamine and bradykinin act directly on venules to increase the permeability of endothelial cell (EC) junctions. Neutrophil chemoattractants also induce leakage, a response that is dependent on neutrophil adhesion to ECs, but the underlying mechanism has proved elusive. Through application of confocal intravital microscopy to the mouse cremaster muscle, we show that neutrophils responding to chemoattractants release TNF when in close proximity of EC junctions. In vitro, neutrophils adherent to ICAM-1 or ICAM-2 rapidly released TNF in response to LTB4, C5a, and KC. Further, in TNFR−/− mice, neutrophils accumulated normally in response to chemoattractants administered to the cremaster muscle or dorsal skin, but neutrophil-dependent plasma protein leakage was abolished. Similar results were obtained in chimeric mice deficient in leukocyte TNF. A locally injected TNF blocking antibody was also able to inhibit neutrophil-dependent plasma leakage, but had no effect on the response induced by bradykinin. The results suggest that TNF mediates neutrophil-dependent microvascular leakage. This mechanism may contribute to the effects of TNF inhibitors in inflammatory diseases and indicates possible applications in life-threatening acute edema.
The Transition to Modern Agriculture: Contract Farming in Developing Economies
Authors: Wang H. Holly , Wang Yanbing , Delgado Michael S.
Published: June 2014

Recent years have seen considerable interest in the impact of contract farming on farmers in developing countries, motivated out of belief that contract farming spurs transition to modern agriculture. In this article, we provide a thorough review of the empirical literature on contract farming in both developed and developing countries, using China as a special case of the latter. We pay careful attention to broad implications of this research for economic development. We first find empirical studies consistently support the positive contribution of contract farming to production and supply chain efficiency. We also find that most empirical studies identify a positive and significant effect of contract farming on farmer welfare, yet are often unable to reach consistent conclusions as to significant correlates of contract participation.
An evaluation of fishing mortality reference points under varying levels of population productivity in three Atlantic cod (Gadus morhua) stocks
Authors: Morgan M. J. , Shelton P. A. , Rideout R. M.
Published: June 2014

Variation in productivity will affect the level of fishing mortality that a population can sustain without decline. We examined three Atlantic cod (Gadus morhua) stocks off Canada for evidence of changing productivity and determined the impact this variation would have on different fishing mortality reference points and their sustainability. Productivity was found to vary greatly over time within all three cod stocks. Under high productivity conditions, G0 (i.e. the potential growth in spawning-stock biomass at a fishing mortality of zero) for the three populations was 20–30%. But under low productivity conditions, G0 was much less. Two of the populations had G0 that was near zero or negative when productivity was low, indicating the possibility of population decline even in the absence of fishing. The degree to which the levels of common fishing mortality reference points (FMSY, FMAX, F0.1, and F40%SPR) changed across productivity periods was variable. All showed significant variation with changing productivity; however, the differences in reference points between productivity periods were generally very small except for FMAX and FMSY. All four reference points examined here were sustainable under conditions of high and average productivity. YPR and SPR reference points do not incorporate recruitment in their calculation. During periods of low productivity, recruitment was reduced and these reference points generally became unsustainable. FMAX was similar to FMSY only under high and average productivity but was not a good proxy for FMSY under lower levels of productivity. Reference points should incorporate recruitment because of its importance in determining the productivity of the stock and should be updated as productivity changes.
Geographic Distribution of Cryptic Species of Plasmopara viticola Causing Downy Mildew on Wild and Cultivated Grape in Eastern North America
Authors: Rouxel Mélanie , Mestre Pere , Baudoin Anton , Carisse Odile , Delière Laurent , Ellis Michael A. , Gadoury David , Lu Jiang , Nita Mizuho , Richard-Cervera Sylvie , Schilder Annemiek , Wise Alice , Delmotte François
Published: June 2014

The putative center of origin of Plasmopara viticola, the causal agent of grape downy mildew, is eastern North America, where it has been described on several members of the family Vitaceae (e.g., Vitis spp., Parthenocissus spp., and Ampelopsis spp.). We have completed the first large-scale sampling of P. viticola isolates across a range of wild and cultivated host species distributed throughout the above region. Sequencing results of four partial genes indicated the presence of a new P. viticola species on Vitis vulpina in Virginia, adding to the four cryptic species of P. viticola recently recorded. The phylogenetic analysis also indicated that the P. viticola species found on Parthenocissus quinquefolia in North America is identical to Plasmopara muralis in Europe. The geographic distribution and host range of five pathogen species was determined through analysis of the internal transcribed spacer polymorphism of 896 isolates of P. viticola. Among three P. viticola species found on cultivated grape, one was restricted to Vitis interspecific hybrids within the northern part of eastern North America. A second species was recovered from V. vinifera and V. labrusca, and was distributed across most of the sampled region. A third species, although less abundant, was distributed across a larger geographical range, including the southern part of eastern North America. P. viticola clade aestivalis predominated (83% of isolates) in vineyards of the European winegrape V. vinifera within the sampled area, indicating that a single pathogen species may represent the primary threat to the European host species within eastern North America.
Discrimination of Plant-Parasitic Nematodes from Complex Soil Communities Using Ecometagenetics
Authors: Porazinska Dorota L. , Morgan Matthew J. , Gaspar John M. , Court Leon N. , Hardy Christopher M. , Hodda Mike
Published: June 2014

Many plant pathogens are microscopic, cryptic, and difficult to diagnose. The new approach of ecometagenetics, involving ultrasequencing, bioinformatics, and biostatistics, has the potential to improve diagnoses of plant pathogens such as nematodes from the complex mixtures found in many agricultural and biosecurity situations. We tested this approach on a gradient of complexity ranging from a few individuals from a few species of known nematode pathogens in a relatively defined substrate to a complex and poorly known suite of nematode pathogens in a complex forest soil, including its associated biota of unknown protists, fungi, and other microscopic eukaryotes. We added three known but contrasting species (Pratylenchus neglectus, the closely related P. thornei, and Heterodera avenae) to half the set of substrates, leaving the other half without them. We then tested whether all nematode pathogens—known and unknown, indigenous, and experimentally added—were detected consistently present or absent. We always detected the Pratylenchus spp. correctly and with the number of sequence reads proportional to the numbers added. However, a single cyst of H. avenae was only identified approximately half the time it was present. Other plant-parasitic nematodes and nematodes from other trophic groups were detected well but other eukaryotes were detected less consistently. DNA sampling errors or informatic errors or both were involved in misidentification of H. avenae; however, the proportions of each varied in the different bioinformatic pipelines and with different parameters used. To a large extent, false-positive and false-negative errors were complementary: pipelines and parameters with the highest false-positive rates had the lowest false-negative rates and vice versa. Sources of error identified included assumptions in the bioinformatic pipelines, slight differences in primer regions, the number of sequence reads regarded as the minimum threshold for inclusion in analysis, and inaccessible DNA in resistant life stages. Identification of the sources of error allows us to suggest ways to improve identification using ecometagenetics.
Development of a Multiplex Assay for Genus- and Species-Specific Detection ofPhytophthoraBased on Differences in Mitochondrial Gene Order
Authors: Bilodeau Guillaume J. , Martin Frank N. , Coffey Michael D. , Blomquist Cheryl L.
Published: June 2014

A molecular diagnostic assay for Phytophthora spp. that is specific, sensitive, has both genus- and species-specific detection capabilities multiplexed, and can be used to systematically develop markers for detection of a wide range of species would facilitate research and regulatory efforts. To address this need, a marker system was developed based on the high copy sequences of the mitochondrial DNA utilizing gene orders that were highly conserved in the genus Phytophthora but different in the related genus Pythium and plants to reduce the importance of highly controlled annealing temperatures for specificity. An amplification primer pair designed from conserved regions of the atp9 and nad9 genes produced an amplicon of ≈340 bp specific for the Phytophthora spp. tested. The TaqMan probe for the genus-specific Phytophthora test was designed from a conserved portion of the atp9 gene whereas variable intergenic spacer sequences were used for designing the species-specific TaqMan probes. Specific probes were developed for 13 species and the P. citricola species complex. In silico analysis suggests that species-specific probes could be developed for at least 70 additional described and provisional species; the use of locked nucleic acids in TaqMan probes should expand this list. A second locus spanning three tRNAs (trnM-trnP-trnM) was also evaluated for genus-specific detection capabilities. At 206 bp, it was not as useful for systematic development of a broad range of species-specific probes as the larger 340-bp amplicon. All markers were validated against a test panel that included 87 Phytophthora spp., 14 provisional Phytophthora spp., 29 Pythium spp., 1 Phytopythium sp., and 39 plant species. Species-specific probes were validated further against a range of geographically diverse isolates to ensure uniformity of detection at an intraspecific level, as well as with other species having high levels of sequence similarity to ensure specificity. Both diagnostic assays were also validated against 130 environmental samples from a range of hosts. The only limitation observed was that primers for the 340 bp atp9-nad9 locus did not amplify Phytophthora bisheria or P. frigida. The identification of species present in a sample can be determined without the need for culturing by sequencing the genus-specific amplicon and comparing that with a reference sequence database of known Phytophthora spp.
Agroecological Factors Correlated to Soil DNA Concentrations of Rhizoctonia in Dryland Wheat Production Zones of Washington State, USA
Authors: Okubara Patricia A. , Schroeder Kurtis L. , Abatzoglou John T. , Paulitz Timothy C.
Published: June 2014

The necrotrophic soilborne fungal pathogens Rhizoctonia solani AG8 and R. oryzae are principal causal agents of Rhizoctonia root rot and bare patch of wheat in dryland cropping systems of the Pacific Northwest. A 3-year survey of 33 parcels at 11 growers' sites and 60 trial plots at 12 Washington State University cereal variety test locations was undertaken to understand the distribution of these pathogens. Pathogen DNA concentrations in soils, quantified using real-time polymerase chain reaction, were correlated with precipitation, temperature maxima and minima, and soil texture factors in a pathogen-specific manner. Specifically, R. solani AG8 DNA concentration was negatively correlated with precipitation and not correlated with temperature minima, whereas R. oryzae concentration was correlated with temperature minima but not with precipitation. However, both pathogens were more abundant in soils with higher sand and lower clay content. Principal component analysis also indicated that unique groups of meteorological and soil factors were associated with each pathogen. Furthermore, tillage did not affect R. oryzae but affected R. solani AG8 at P = 0.06. Lower soil concentrations of R. solani AG8 but not R. oryzae occurred when the previously planted crop was a broadleaf (P < 0.05). Our findings showed that R. solani AG8 concentrations were consistent with the general distribution of bare patch symptoms, based on field observations and surveys of other pathogens, but was present at many sites in which bare patch symptoms were not evident. Management of Rhizoctonia root rot and bare patch should account for the likelihood that each pathogen is affected by a unique group of agroecological variables.
Diffraction before destruction
Authors: Chapman Henry N. , Caleman Carl , Timneanu Nicusor
Published: June 2014

X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense femtosecond X-ray pulses with materials and discuss the implications for structure determination. We identify various dose regimes and conclude that the strongest achievable signals for a given sample are attained at the highest possible dose rates, from highest possible pulse intensities.
Femtosecond crystallography of membrane proteins in the lipidic cubic phase
Authors: Liu Wei , Wacker Daniel , Wang Chong , Abola Enrique , Cherezov Vadim
Published: June 2014

Despite recent technological advances in heterologous expression, stabilization and crystallization of membrane proteins (MPs), their structural studies remain difficult and require new transformative approaches. During the past two years, crystallization in lipidic cubic phase (LCP) has started gaining a widespread acceptance, owing to the spectacular success in high-resolution structure determination of G protein-coupled receptors (GPCRs) and to the introduction of commercial instrumentation, tools and protocols. The recent appearance of X-ray free-electron lasers (XFELs) has enabled structure determination from substantially smaller crystals than previously possible with minimal effects of radiation damage, offering new exciting opportunities in structural biology. The unique properties of LCP material have been exploited to develop special protocols and devices that have established a new method of serial femtosecond crystallography of MPs in LCP (LCP-SFX). In this method, microcrystals are generated in LCP and streamed continuously inside the same media across the intersection with a pulsed XFEL beam at a flow rate that can be adjusted to minimize sample consumption. Pioneering studies that yielded the first room temperature GPCR structures, using a few hundred micrograms of purified protein, validate the LCP-SFX approach and make it attractive for structure determination of difficult-to-crystallize MPs and their complexes with interacting partners. Together with the potential of femtosecond data acquisition to interrogate unstable intermediate functional states of MPs, LCP-SFX holds promise to advance our understanding of this biomedically important class of proteins.
Observation of correlated X-ray scattering at atomic resolution
Authors: Mendez Derek , Lane Thomas J. , Sung Jongmin , Sellberg Jonas , Levard Clément , Watkins Herschel , Cohen Aina E. , Soltis Michael , Sutton Shirley , Spudich James , Pande Vijay , Ratner Daniel , Doniach Sebastian
Published: June 2014

Tools to study disordered systems with local structural order, such as proteins in solution, remain limited. Such understanding is essential for e.g. rational drug design. Correlated X-ray scattering (CXS) has recently attracted new interest as a way to leverage next-generation light sources to study such disordered matter. The CXS experiment measures angular correlations of the intensity caused by the scattering of X-rays from an ensemble of identical particles, with disordered orientation and position. Averaging over 15 496 snapshot images obtained by exposing a sample of silver nanoparticles in solution to a micro-focused synchrotron radiation beam, we report on experimental efforts to obtain CXS signal from an ensemble in three dimensions. A correlation function was measured at wide angles corresponding to atomic resolution that matches theoretical predictions. These preliminary results suggest that other CXS experiments on disordered ensembles—such as proteins in solution—may be feasible in the future.