bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs
Authors: Streicher Jeffrey W. , Devitt Thomas J. , Goldberg Caren S. , Malone John H. , Blackmon Heath , Fujita Matthew K.
Published: May 2014

Young species complexes that are widespread across ecologically disparate regions offer important insights into the process of speciation because of their relevance to how local adaptation and gene flow influence diversification. We used mitochondrial DNA and up to 28 152 genomewide single nucleotide polymorphisms from polytypic barking frogs (Craugastor augusti complex) to infer phylogenetic relationships and test for the signature of introgressive hybridization among diverging lineages. Our phylogenetic reconstructions suggest (i) a rapid Pliocene–Pleistocene radiation that produced at least nine distinct lineages and (ii) that geographic features of the arid Central Mexican Plateau contributed to two independent northward expansions. Despite clear lineage differentiation (many private alleles and high between‐lineage FST scores), D‐statistic tests, which differentiate introgression from ancestral polymorphism, allowed us to identify two putative instances of reticulate gene flow. Partitioned D‐statistics provided evidence that these events occurred in the same direction between clades but at different points in time. After correcting for geographic distance, we found that lineages involved in hybrid gene flow interactions had higher levels of genetic variation than independently evolving lineages. These findings suggest that the nature of hybrid compatibility can be conserved overlong periods of evolutionary time and that hybridization between diverging lineages may contribute to standing levels of genetic variation.
Adaptive admixture in the West African bovine hybrid zone: insight from the Borgou population
Authors: Flori Laurence , Thevenon Sophie , Dayo Guiguigbaza‐Kossigan , Senou Marcel , Sylla Souleymane , Berthier David , Moazami‐Goudarzi Katayoun , Gautier Mathieu
Published: May 2014

Understanding the adaptive response to environmental fluctuations represents a central issue in evolutionary biology. Population admixture between divergent ancestries has often been considered as an efficient short‐term adaptation strategy. Cattle populations from the West African Bos taurus × Bos indicus hybrid zone represent a valuable resource to characterize the effect of such adaptive admixture at the genome level. We here provide a detailed assessment of the global and local genome ancestries of the Borgou breed, one of the most representative cattle of this hybrid zone. We analysed a large data set consisting of 38 100 SNPs genotyped on 203 Borgou and 591 individuals representative of all the different cattle ancestries. At the global genomic level, we show that Borgou is a stabilized admixed breed whose origin (c. 130 years ago) traces back to the great African rinderpest pandemic, several centuries after the last admixture events, the West African zebus originate from (c. 500 years ago). To identify footprints of adaptive admixture, we combined the identification of signatures of selection and the functional annotation of the underlying genes using systems biology tools. The detection of the SILV coat coloration gene likely under artificial selection may be viewed as a validation of our approach. Overall, our results suggest that the long‐term presence of pathogens and the intermediate environmental conditions are the main acting selective pressures. Our analytical framework can be extended to other model or nonmodel species to understand the process that shapes the patterns of genetic variability in hybrid zones.
Rolf Bernander (1956–2014): pioneer of the archaeal cell cycle
Authors: Ettema Thijs J. G. , Lindås Ann‐Christin , Hjort Karin , Poplawski Andrzej B. , Kaessmann Henrik , Grogan Dennis W. , Kelman Zvi , Andersson Anders F. , Pelve Erik A. , Lundgren Magnus , Svärd Staffan G.
Published: May 2014

On 19 January 2014 Rolf (‘Roffe’) Bernander passed away unexpectedly. Rolf was a dedicated scientist; his research aimed at unravelling the cell biology of the archaeal domain of life, especially cell cycle‐related questions, but he also made important contributions in other areas of microbiology. Rolf had a professor position in the Molecular Evolution programme at Uppsala University, Sweden for about 8 years, and in January 2013 he became chair professor at the Department of Molecular Biosciences, The Wenner‐Gren Institute at Stockholm University in Sweden. Rolf was an exceptional colleague and will be deeply missed by his family and friends, and the colleagues and co‐workers that he leaves behind in the scientific community. He will be remembered for his endless enthusiasm for science, his analytical mind, and his quirky sense of humour.
The structure, function and properties of sirohaem decarboxylase – an enzyme with structural homology to a transcription factor family that is part of the alternative haem biosynthesis pathway
Authors: Palmer David J. , Schroeder Susanne , Lawrence Andrew D. , Deery Evelyne , Lobo Susana A. , Saraiva Ligia M. , McLean Kirsty J. , Munro Andrew W. , Ferguson Stuart J. , Pickersgill Richard W. , Brown David G. , Warren Martin J.
Published: May 2014

Some bacteria and archaea synthesize haem by an alternative pathway, which involves the sequestration of sirohaem as a metabolic intermediate rather than as a prosthetic group. Along this pathway the two acetic acid side‐chains attached to C12 and C18 are decarboxylated by sirohaem decarboxylase, a heterodimeric enzyme composed of AhbA and AhbB, to give didecarboxysirohaem. Further modifications catalysed by two related radical SAM enzymes, AhbC and AhbD, transform didecarboxysirohaem into Fe‐coproporphyrin III and haem respectively. The characterization of sirohaem decarboxylase is reported in molecular detail. Recombinant versions of Desulfovibrio desulfuricans, Desulfovibrio vulgaris and Methanosarcina barkeri AhbA/B have been produced and their physical properties compared. The D. vulgaris and M. barkeri enzyme complexes both copurify with haem, whose redox state influences the activity of the latter. The kinetic parameters of the D. desulfuricans enzyme have been determined, the enzyme crystallized and its structure has been elucidated. The topology of the enzyme reveals that it shares a structural similarity to the AsnC/Lrp family of transcription factors. The active site is formed in the cavity between the two subunits and a AhbA/B‐product complex with didecarboxysirohaem has been obtained. A mechanism for the decarboxylation of the kinetically stable carboxyl groups is proposed.
Development of a bipartite ecdysone‐responsive gene switch for the oomycete Phytophthora infestans and its use to manipulate transcription during axenic culture and plant infection
Authors: Gamboa‐Meléndez Heber , Judelson Howard S.
Published: May 2014

Conditional expression systems have been proven to be useful tools for the elucidation of gene function in many taxa. Here, we report the development of the first useful inducible promoter system for an oomycete, based on an ecdysone receptor (EcR) and the ecdysone analogue methoxyfenozide. In Phytophthora infestans, the potato late blight pathogen, a monopartite transactivator containing the VP16 activation domain from herpes simplex virus, the GAL4 DNA‐binding domain from yeast and the EcR receptor domain from the spruce budworm enabled high levels of expression of a β‐glucuronidase (GUS) reporter gene, but unacceptable basal activity in the absence of the methoxyfenozide inducer. Greatly improved performance was obtained using a bipartite system in which transcription is activated by a heterodimer between a chimera of VP16 and the migratory locust retinoid X receptor, and a separate EcR‐DNA‐binding domain chimera. Transformants were obtained that exhibited >100‐fold activation of the reporter by methoxyfenozide, with low basal levels of expression and induced activity approaching that of the strong ham34 promoter. Performance varied between transformants, probably as a result of position effects. The addition of methoxyfenozide enabled strong induction during hyphal growth, zoosporogenesis and colonization of tomato. No significant effects of the inducer or transactivators on growth, development or pathogenicity were observed. The technology should therefore be a useful addition to the arsenal of methods for the study of oomycete plant pathogens.
Regional data analysis of Candida non‐albicans strains collected in United States medical sites over a 6‐year period, 2006–2011
Authors: Pfaller Michael A. , Jones Ronald N. , Castanheira Mariana
Published: May 2014

Limited data are available on temporal and geographic variation of occurrence and antifungal resistance of non‐C. albicans Candida species (non‐CA‐CSP) from the USA. The objective of this study was to evaluate the occurrence and antifungal resistance of 1694 isolates of non‐CA‐CSP collected during the period 2006–2011. Isolates were recovered in 33 hospitals located in four regions: Northcentral, North‐east, South‐east and West and tested using CLSI reference broth microdilution methods. Non‐CA‐CSP represented 55.6% of all Candida. C. glabrata was most predominant (39–42% of non‐CA‐CSP). Infections due to C. glabrata, C. krusei and C. dubliniensis increased over the 6 years. Anidulafungin (3.6%) and caspofungin (5.7%) resistance were prominent among C. glabrata from the North‐east and West regions respectively. Resistance to micafungin was detected in 2.0% and 2.9% of C. glabrata from the West and North‐east regions respectively. Echinocandin resistance was low, except for C. dubliniensis. Azole resistance was most prominent among C. glabrata from the South‐east (13.6% fluconazole R) and the West (18.0%). Cross‐resistance among three tested azoles was observed in C. glabrata from all regions. Whereas differences in species distribution and antifungal R varied across geographic regions, there was little evidence of temporal increase in resistance to azoles or echinocandins in the monitored non‐CA‐CSP.
Synonymy of Philippine Ixora (Ixoreae, Rubiaceace) and Ixora silagoensis sp. nov
Authors: Banag Cecilia I. , Manalastas Nicole Marie B. , Alejandro Grecebio Jonathan D.
Published: May 2014

Two endemic Philippine species of Ixora collected in southern Leyte were studied, and investigation of type and other herbarium specimens revealed that one of the species is I. longissima Merr., and that the other does not match any of the known Philippine Ixora species. The recollection of I. longissima after almost a century was essential to investigate whether or not it is conspecific with I. salicifolia DC. This study supports the synonymy of I. longissima and I. salicifolia and provides a full description and illustration of the new species, Ixora silagoensis Manalastas, Banag & Alejandro. The conservation status of I. silagoensis is assessed as ‘Critically Endangered’ (CR) based on the criteria of IUCN.
Altered structural covariance of the striatum in functional dyspepsia patients
Authors: Liu P. , Zeng F. , Yang F. , Wang J. , Liu X. , Wang Q. , Zhou G. , Zhang D. , Zhu M. , Zhao R. , Wang A. , Gong Q. , Liang F.
Published: May 2014

Background

Functional dyspepsia (FD) is thought to be involved in dysregulation within the brain–gut axis. Recently, altered striatum activation has been reported in patients with FD. However, the gray matter (GM) volumes in the striatum and structural covariance patterns of this area are rarely explored. The purpose of this study was to examine the GM volumes and structural covariance patterns of the striatum between FD patients and healthy controls (HCs).

Methods

T1‐weighted magnetic resonance images were obtained from 44 FD patients and 39 HCs. Voxel‐based morphometry (VBM) analysis was adopted to examine the GM volumes in the two groups. The caudate‐ or putamen‐related regions identified from VBM analysis were then used as seeds to map the whole brain voxel‐wise structural covariance patterns. Finally, a correlation analysis was used to investigate the effects of FD symptoms on the striatum.

Key Results

The results showed increased GM volumes in the bilateral putamen and right caudate. Compared with the structural covariance patterns of the HCs, the FD‐related differences were mainly located in the amygdala, hippocampus/parahippocampus (HIPP/paraHIPP), thalamus, lingual gyrus, and cerebellum. And significant positive correlations were found between the volumes in the striatum and the FD duration in the patients.

Conclusions & Inferences

These findings provided preliminary evidence for GM changes in the striatum and different structural covariance patterns in patients with FD. The current results might expand our understanding of the pathophysiology of FD.
The link between negative affect, vagal tone, and visceral sensitivity in quiescent Crohn's disease
Authors: Rubio A. , Pellissier S. , Picot A. , Dantzer C. , Bonaz B.
Published: May 2014

Autonomic dysfunction and mood disorders are frequently described in Crohn's disease (CD) and are known to influence visceral sensitivity. We addressed the link between vagal tone, negative affect, and visceral sensitivity in CD patients without concomitant features of irritable bowel syndrome (IBS). Rectal distensions to a discomfort threshold of 70% and onset of pain were performed in nine CD patients in remission and eight healthy controls. Autonomic parameters were evaluated with heart rate variability and electrodermal reactivity. We showed that CD patients had (i) higher scores of depressive symptomatology (12 ± 3 in patients vs 4 ± 1 in controls on the Center for Epidemiologic Studies‐Depression Scale; p = 0.038), (ii) reduced vagal tone (HF 257 ± 84 ms2 vs 1607 ± 1032 ms2, p = 0.043; LF 455 ± 153 ms2 vs 1629 ± 585 ms2, p = 0.047), (iii) decreased sympathetic reactivity during an aversive stimulus, and (iv) higher tolerance to rectal distension pressures (43 ± 3 mmHg vs 30 ± 2 mmHg, p = 0.002) and low sensitivity index scores. In conclusion, our results provide preliminary evidence that patients with quiescent CD, in the absence of IBS, are hyposensate to experimental rectal distension. These data provide further evidence that anxiety and depressive symptomatology in addition to autonomic dysfunction modulate visceral pain perception in quiescent CD patients in the absence of IBS.
Case studies continue to illuminate the cognitive neuroscience of memory
Authors: Rosenbaum R. Shayna , Gilboa Asaf , Moscovitch Morris
Published: May 2014

The current ubiquity of functional neuroimaging studies, and the importance they have had in elucidating brain function, obscures the fact that much of what we know about brain–behavior relationships derives largely from the study of single‐ and multiple‐patient cases. A major goal of the present review is to describe how single cases continue to uniquely and critically contribute to cognitive neuroscience theory. With several recent examples from the literature, we demonstrate that single cases can both challenge accepted dogma and generate hypotheses and theories that steer the field in new directions. We discuss recent findings from case studies that specify critical functions of the hippocampus in episodic memory and recollection, and clarify its role in nonmnemonic abilities. Although we focus on the hippocampus, we discuss other regions and the occurrence of new associative learning, as well as the involvement of the ventromedial prefrontal and parietal cortices in memory encoding and retrieval. We also describe ways of dealing with the shortcomings of case studies, and emphasize the partnership of patient and neuroimaging methods in constraining neurocognitive models of memory.
PUBLIC MANAGEMENT IN POLITICAL INSTITUTIONS: EXPLAINING PERCEPTIONS OF WHITE HOUSE CHIEF OF STAFF INFLUENCE
Authors: VILLALOBOS JOSÉ D. , VAUGHN JUSTIN S. , COHEN DAVID B.
Published: May 2014

The notion that public managers influence organizational performance is common in public administration research. However, less is known about why some managers are better at influencing organizational performance than others. Furthermore, relatively few studies have systematically examined managerial influence and scholars have yet to investigate either quantitatively or systematically managerial influence in the White House. Utilizing original survey data collected from former White House officials who served in the Reagan, George H.W. Bush, and Clinton administrations, this study applies empirical public management theory to examine for the first time the key determinants that shape perceptions of chief of staff managerial influence. The findings demonstrate how several core concepts in public management theory help explain the dynamics that drive perceptions of managerial influence, thereby providing a new contribution to the literature on public management.
Giardia lamblia binding immunoglobulin protein triggers maturation of dendritic cells via activation of TLR4‐MyD88‐p38 and ERK1/2 MAPKs
Authors: Lee H.‐Y. , Kim J. , Noh H. J. , Kim H.‐P. , Park S.‐J.
Published: May 2014

Much remains unknown about the mammalian immune response to Giardia lamblia, a protozoan pathogen that causes diarrhoeal outbreaks. We fractionated protein extracts of G. lamblia trophozoites by Viva‐spin centrifugation, DEAE ion exchange and gel filtration chromatography. Resultant fractions were screened for antigenic molecules by western blots analysis using anti‐G. lamblia antibodies (Abs), resulting in identification of G. lamblia binding immunoglobulin protein (GlBiP). Maturation of mouse dendritic cells (DCs) in response to recombinant GlBiP (rGlBiP) was detected by increased expression of surface molecules such as CD80, CD86 and MHC class II; these mature DCs, produced pro‐inflammatory cytokines (TNF‐α, IL‐12 and IL‐6). Especially, the truncated rGlBiP containing the heat‐shock protein 70 domain‐induced cytokine production from mouse DCs. rGlBiP‐induced DC activation was initiated by TLR4 in a MyD88‐dependent way and occurred through activation of p38 and ERK1/2 MAPKs as well as increased activity of NF‐κB and AP‐1. Moreover, CD4+ T cells stimulated with rGlBiP‐treated DCs produced high levels of IL‐2 and IFN‐γ. Together, our results suggest that GlBiP contributes to maturation of DCs via activation of TLR4‐MyD88‐p38, ERK1/2 MAPK, NF‐κB and AP‐1.
Spatial and temporal dynamics of primary and secondary metabolism in Phaseolus vulgaris challenged by Pseudomonas syringae
Authors: Pérez‐Bueno María Luisa , Pineda Mónica , Díaz‐Casado Elena , Barón Matilde
Published: May 2014

Many defense mechanisms contribute to the plant immune system against pathogens, involving the regulation of different processes of the primary and secondary metabolism. At the same time, pathogens have evolved mechanisms to hijack the plant defense in order to establish the infection and proliferate. Localization and timing of the host response are essential to understand defense mechanisms and resistance to pathogens (Rico et al. 2011). Imaging techniques, such as fluorescence imaging and thermography, are a very valuable tool providing spatial and temporal information about a series of plant processes. In this study, bean plants challenged with two pathovars of Pseudomonas syringae have been investigated. Pseudomonas syringae pv. phaseolicola 1448A and P. syringae pv. tomato DC3000 elicit a compatible and incompatible interaction in bean, respectively. Both types of host–pathogen interaction triggered different changes in the activity of photosynthesis and the secondary metabolism. We conclude that the combined analysis of leaf temperature, chlorophyll fluorescence and green fluorescence emitted by phenolics allows to discriminate compatible from incompatible P. syringae–Phaseolus vulgaris interactions in very early times of the infection, prior to the development of symptoms. These can constitute disease signatures that would allow an early identification of emerging plagues in crops.
Transbronchial cryobiopsy in the diagnosis of interstitial lung disease: A cool new approach
Authors: Mikolasch Theresia A. , Porter Joanna C.
Published: May 2014

See article, page 683
How do nurses in palliative care perceive the concept of self‐image?
Authors: Jeppsson Margareth , Thomé Bibbi
Published: May 2014

Background

Nursing research indicates that serious illness and impending death influence the individual's self‐image. Few studies define what self‐image means. Thus it seems to be urgent to explore how nurses in palliative care perceive the concept of self‐image, to get a deeper insight into the concept′s applicability in palliative care.

Aim

To explore how nurses in palliative care perceive the concept of self‐image.

Design

Qualitative descriptive design.

Method

In‐depth interviews with 17 nurses in palliative care were analysed using phenomenography. The study gained ethical approval.

Results

The concept of self‐image was perceived as both a familiar and an unfamiliar concept. Four categories of description with a gradually increasing complexity were distinguished: Identity, Self‐assessment, Social function and Self‐knowledge. They represent the collective understanding of the concept and are illustrated in a ‘self‐image map’. The identity‐category emerged as the most comprehensive one and includes the understanding of ‘Who I am’ in a multidimensional way.

Conclusion

The collective understanding of the concept of self‐image include multi‐dimensional aspects which not always were evident for the individual nurse. Thus, the concept of self‐image needs to be more verbalised and reflected on if nurses are to be comfortable with it and adopt it in their caring context. The ‘self‐image map’ can be used in this reflection to expand the understanding of the concept. If the multi‐dimensional aspects of the concept self‐image could be explored there are improved possibilities to make identity‐promoting strategies visible and support person‐centred care.
The GUN4 protein plays a regulatory role in tetrapyrrole biosynthesis and chloroplast‐to‐nucleus signalling in Chlamydomonas reinhardtii
Authors: Brzezowski Pawel , Schlicke Hagen , Richter Andreas , Dent Rachel M. , Niyogi Krishna K. , Grimm Bernhard
Published: May 2014

The GENOMES UNCOUPLED 4 (GUN4) protein is found only in aerobic photosynthetic organisms. We investigated the role of GUN4 in metabolic activities of the Mg branch of the tetrapyrrole biosynthesis pathway and the plastid signal‐mediated changes of nuclear gene expression in Chlamydomonas reinhardtii. In light, gun4 accumulates only 40% of the wild‐type chlorophyll level. Light‐ or dark‐grown gun4 mutant accumulates high levels of protoporphyrin IX (Proto), and displays increased sensitivity to moderate light intensities. Despite the photooxidative stress, gun4 fails to downregulate mRNA levels of the tetrapyrrole biosynthesis and the photosynthesis‐associated nuclear genes (PhANGs). In contrast, upon illumination, the Proto‐accumulating and light‐sensitive chlD–1 mutant displays the expected downregulation of the same nuclear genes. Although chlD–1 and the wild type have similar GUN4 transcript levels, the GUN4 protein in chlD–1 is hardly detectable. Overexpression of GUN4 in chlD–1 modifies the downregulation of nuclear gene expression, but also increases light tolerance. Therefore, GUN4 is proposed to function in ‘shielding’ Proto, and most likely MgProto, by reducing reactivity with O2. Furthermore, GUN4 seems to be involved in sensing elevated levels of these photoreactive tetrapyrrole intermediates, and contributing to 1O2‐mediated retrograde signalling, originating from chlorophyll biosynthesis.
The evolutionary appearance of non‐cyanogenic hydroxynitrile glucosides in the Lotus genus is accompanied by the substrate specialization of paralogous β–glucosidases resulting from a crucial amino acid substitution
Authors: Lai Daniela , Abou Hachem Maher , Robson Fran , Olsen Carl Erik , Wang Trevor L. , Møller Birger L. , Takos Adam M. , Rook Fred
Published: May 2014

Lotus japonicus, like several other legumes, biosynthesizes the cyanogenic α–hydroxynitrile glucosides lotaustralin and linamarin. Upon tissue disruption these compounds are hydrolysed by a specific β–glucosidase, resulting in the release of hydrogen cyanide. Lotus japonicus also produces the non‐cyanogenic γ‐ and β–hydroxynitrile glucosides rhodiocyanoside A and D using a biosynthetic pathway that branches off from lotaustralin biosynthesis. We previously established that BGD2 is the only β–glucosidase responsible for cyanogenesis in leaves. Here we show that the paralogous BGD4 has the dominant physiological role in rhodiocyanoside degradation. Structural modelling, site‐directed mutagenesis and activity assays establish that a glycine residue (G211) in the aglycone binding site of BGD2 is essential for its ability to hydrolyse the endogenous cyanogenic glucosides. The corresponding valine (V211) in BGD4 narrows the active site pocket, resulting in the exclusion of non‐flat substrates such as lotaustralin and linamarin, but not of the more planar rhodiocyanosides. Rhodiocyanosides and the BGD4 gene only occur in L. japonicus and a few closely related species associated with the Lotus corniculatus clade within the Lotus genus. This suggests the evolutionary scenario that substrate specialization for rhodiocyanosides evolved from a promiscuous activity of a progenitor cyanogenic β–glucosidase, resembling BGD2, and required no more than a single amino acid substitution.
Phosphorylation of photosystem II core proteins prevents undesirable cleavage of D1 and contributes to the fine‐tuned repair of photosystem II
Authors: Kato Yusuke , Sakamoto Wataru
Published: May 2014

Photosystem II (PSII) is a primary target for light‐induced damage in photosynthetic protein complexes. To avoid photoinhibition, chloroplasts have evolved a repair cycle with efficient degradation of the PSII reaction center protein, D1, by the proteases FtsH and Deg. Earlier reports have described that phosphorylated D1 is a poor substrate for proteolysis, suggesting a mechanistic role for protein phosphorylation in PSII quality control, but its precise role remains elusive. STN8, a protein kinase, plays a central role in this phosphorylation process. To elucidate the relationship between phosphorylation of D1 and the protease function we assessed in this study the involvement of STN8, using Arabidopsis thaliana mutants lacking FtsH2 [yellow variegated2 (var2)] and Deg5/Deg8 (deg5 deg8). In support of our presumption we found that phosphorylation of D1 increased more in var2. Furthermore, the coexistence of var2 and stn8 was shown to recover the delay in degradation of D1, resulting in mitigation of the high vulnerability to photoinhibition of var2. Partial D1 cleavage fragments that depended on Deg proteases tended to increase, with concomitant accumulation of reactive oxygen species in the mutants lacking STN8. We inferred that the accelerated degradation of D1 in var2 stn8 presents a tradeoff in that it improved the repair of PSII but simultaneously enhanced oxidative stress. Together, these results suggest that PSII core phosphorylation prevents undesirable cleavage of D1 by Deg proteases, which causes cytotoxicity, thereby balancing efficient linear electron flow and photo‐oxidative damage. We propose that PSII core phosphorylation contributes to fine‐tuned degradation of D1.
Fatty acid synthesis and lipid metabolism in the obligate biotrophic fungus Rhizophagus irregularis during mycorrhization of Lotus japonicus
Authors: Wewer Vera , Brands Mathias , Dörmann Peter
Published: May 2014

Arbuscular mycorrhiza formation with fungi of the Glomeromycota represents a widespread symbiotic interaction of vascular plants. Different signaling events and metabolic adaptations are required for the close interaction between the two partners. Membrane lipid synthesis is a prerequisite for symbiosis, and membrane properties depend on lipid composition. Lipid profiling was performed by liquid chromatography mass spectrometry to study the role of triacylglycerol, diacylglycerol, phospholipids, galactolipids, sterols and sphingolipids during the colonization of Lotus japonicus roots with Rhizophagus irregularis (syn. Glomus intraradices). Mycorrhization leads to an increased phosphate supply and suppresses the increase in galactolipids commonly observed in phosphate‐deprived plants. In addition to free sterols and sterol esters, R. irregularis contains sterol glucosides and acylated sterol glucosides. Glycosylated sphingolipids (glucosylceramide, dihexosylceramide) and inositolphosphorylceramide were detected in the fungus. Lyso‐phosphatidylcholine, a lipid previously implicated in mycorrhiza signaling, is present in low amounts in mock‐infected and mycorrhized roots. The composition of fungal phospholipids changes after mycorrhization because molecular species with palmitvaccenic (di‐16:1) or tetracosenoic (24:1) acyl groups decrease in intraradical mycelium. This adaptation of lipid metabolism during intraradical growth is likely a prerequisite for symbiosis, achieving functional compatibility between the fungal and the periarbuscular membrane. Data mining in genomic and transcript databases revealed the presence of genes encoding enzymes of lipid biosynthesis in R. irregularis. However, no gene encoding multidomain fatty acid de novo synthase was detected in the genome sequence of this obligate biotrophic fungus.
Post‐transcriptional control of GRF transcription factors by microRNA miR396 and GIF co‐activator affects leaf size and longevity
Authors: Debernardi Juan M. , Mecchia Martin A. , Vercruyssen Liesbeth , Smaczniak Cezary , Kaufmann Kerstin , Inze Dirk , Rodriguez Ramiro E. , Palatnik Javier F.
Published: May 2014

The growth‐regulating factors (GRFs) are plant‐specific transcription factors. They form complexes with GRF‐interacting factors (GIFs), a small family of transcriptional co‐activators. In Arabidopsis thaliana, seven out of the nine GRFs are controlled by microRNA miR396. Analysis of Arabidopsis plants carrying a GRF3 allele insensitive to miR396 revealed a strong boost in the number of cells in leaves, which was further enhanced synergistically by an additional increase of GIF1 levels. Genetic experiments revealed that GRF3 can still increase cell number in gif1 mutants, albeit to a much lesser extent. Genome‐wide transcript profiling indicated that the simultaneous increase of GRF3 and GIF1 levels causes additional effects in gene expression compared to either of the transgenes alone. We observed that GIF1 interacts in vivo with GRF3, as well as with chromatin‐remodeling complexes, providing a mechanistic explanation for the synergistic activities of a GRF3–GIF1 complex. Interestingly, we found that, in addition to the leaf size, the GRF system also affects the organ longevity. Genetic and molecular analysis revealed that the functions of GRFs in leaf growth and senescence can be uncoupled, demonstrating that the miR396‐GRF‐GIF network impinges on different stages of leaf development. Our results integrate the post‐transcriptional control of the GRF transcription factors with the progression of leaf development.
Investigational screening for Babesia microti in a large repository of blood donor samples from nonendemic and endemic areas of the United States
Authors: Moritz Erin D. , Winton Colleen S. , Johnson Stephanie T. , Krysztof David E. , Townsend Rebecca L. , Foster Gregory A. , Devine Patricia , Molloy Philip , Brissette Edward , Berardi Victor P. , Stramer Susan L.
Published: May 2014

Background

Babesia microti, a transfusion‐transmissible intraerythrocytic parasite, is increasing in frequency in the United States with no available FDA‐licensed donor screening assay. We utilized investigational arrayed fluorescence immunoassay (AFIA) and polymerase chain reaction (PCR) to detect B. microti antibodies and DNA in blood donors.

Study Design and Methods

AFIA and real‐time PCR were performed on frozen paired EDTA plasma (AFIA) and EDTA whole blood (PCR) samples collected from May to September 2010 to 2011 in nonendemic (Arizona [AZ] and Oklahoma [OK]), moderately endemic (Minnesota [MN] and Wisconsin [WI]), and highly endemic (Connecticut [CT] and Massachusetts [MA]) areas of the United States. AFIA utilized B. microti piroplasm as an antigen substrate; PCR primers and probes targeted the B. microti 18S ribosomal RNA gene. Data from AZ and OK were used to calculate specificity. All AFIA‐ or PCR‐positive or ‐inconclusive donors were deferred, notified, and invited to participate in a follow‐up study involving repeat testing and a demographic and risk‐factor questionnaire. Recipient tracing was performed for any cellular component transfused at index, at subsequent donation, or within the prior 12 months.

Results

Testing of 13,269 paired samples included 4022 from AZ and OK, 4167 from MN and WI, and 5080 from CT and MA. B. microti antibody and/or DNA prevalences were 0.025% (95% confidence interval [CI], 0.00%‐0.14%), 0.12% (95% CI, 0.04%‐0.28%), and 0.75% (95% CI, 0.53%‐1.03%) in the nonendemic, mid‐endemic, and high‐endemic regions, respectively. Specificities were 99.95% (95% CI, 99.82%‐99.99%) at a 1‐in‐64 AFIA cutoff and 99.98% (95% CI, 99.86%‐100.00%) at a 1‐in‐128 cutoff.

Conclusions

B. microti prevalence followed expected geographical patterns. Screening was feasible with a performance comparable or superior to other infectious disease blood donor screening assays.
Writing in Water, or, Evanescence, Enchantment and Ethnography in aChinese Urban Park
Authors: Zito Angela
Published: May 2014

This article reflects upon my experience of filmmaking in a public park inBeijing whereIlearned to writeChinese calligraphy in water. The essay is committed to the idea that people simultaneously produce persons and worlds in practices that result in the material mediations within which those selves are entangled, and also powerfully engage the environment. Thus, the film features aesthetics that formthroughthe embodiment of a certain kind of politics. It emerged in performance but now exists as an artifact, an example of what philosopherJaneBennett calls “enchanted materialism.” By combining moments of liveness and objectification, it mimics, in a small way, the production of the social itself. Ethnography,Iargue here, should account for as much of this dialectical process as it can.
New approach to ‘top‐and‐bottom’ whole blood separation using the multiunit TACSI WB system: quality of blood components
Authors: Lotens A. , Najdovski T. , Cellier N. , Ernotte B. , Lambermont M. , Rapaille A.
Published: May 2014

Background and Objectives

TACSI whole blood system is designed to combine primary and secondary processing of six whole blood bags into plasma units, buffy coat and red blood cell concentrates. The aim of this study was to investigate the specifications and in vitro storage parameters of blood components compared with standard centrifugation and separation processing.

Materials and Methods

Whole blood bags, collected in CRC kits, were treated on a TACSI whole blood system. They were compared with whole blood bags collected in Composelect kits. In addition to routine quality control analyses, conservation studies were performed on red blood cell concentrates for 42 days and on plasma for 6 months. Platelets pools with five buffy coats were also created, and cellular contamination was evaluated.

Results

Red blood cell concentrates produced from TACSI whole blood met European quality requirements. For white blood cell count, one individual result exceeded 1 × 106 cells/unit. All plasma units fell within specifications for residual cellular contamination and storage parameters. The performances of the TACSI whole blood system allow for the preparation of low volume buffy coats with a recovery of 90% of whole blood platelets. Haemoglobin losses in TACSI BC are smaller, but this did not result in higher haemoglobin content of red cells. These BC are suitable for the production of platelet concentrates.

Conclusion

From these in vitro data, red blood cell concentrates produced using TACSI whole blood are suitable for clinical use with a quality at least equivalent to the control group.
Flexural Fatigue of Unbalanced Glass-Carbon Hybrid Composites
Authors: Cox Kevin B. , Vedvik Nils-Petter , Echtermeyer Andreas T.
Published: May 2014

Unbalanced composite layups with bend-twist coupling show potential for aeroelastic tailoring in wind turbine blades. Before these materials can be implemented, their responses to long term cyclic loading must be considered. This paper studies the fatigue characteristics of an unbalanced glass-carbon hybrid laminate with a [45glass/−45glass/24carbon/24carbon]s layup. Flexural fatigue was performed at 7 different load magnitudes up to 1 × 106 cycles to characterize the failure modes and fatigue life of the composite. Stiffness degradation occurred on the tension side due to matrix cracking and small regions of delamination on the glass plies, whereas the failure mechanism of the laminate was by delamination between the glass and carbon. S-N curves were generated from experimental results and static finite element analyses (FEA) based on interlaminar shear stresses and were compared with laminates from previous literature. It was determined that the interlaminar stresses were influenced more so by the lower stiffness of the unbalanced layup than by the induced torsional deflections: leading to the conclusion that bend-twist coupling had little influence on flexural fatigue of glass-carbon hybrid composites.
Selective Laser Sintered Versus Carbon Fiber Passive-Dynamic Ankle-Foot Orthoses: A Comparison of Patient Walking Performance
Authors: Harper Nicole G. , Russell Elizabeth M. , Wilken Jason M. , Neptune Richard R.
Published: May 2014

Selective laser sintering (SLS) is a well-suited additive manufacturing technique for generating subject-specific passive-dynamic ankle-foot orthoses (PD-AFOs). However, the mechanical properties of SLS PD-AFOs may differ from those of commonly prescribed carbon fiber (CF) PD-AFOs. Therefore, the goal of this study was to determine if biomechanical measures during gait differ between CF and stiffness-matched SLS PD-AFOs. Subject-specific SLS PD-AFOs were manufactured for ten subjects with unilateral lower-limb impairments. Minimal differences in gait performance occurred when subjects used the SLS versus CF PD-AFOs. These results support the use of SLS PD-AFOs to study the effects of altering design characteristics on gait performance.
Coherence extrapolation for underwater ambient noise
Authors: Quijano Jorge E. , Dosso Stan E. , Siderius Martin , Muzi Lanfranco
Published: May 2014

This paper considers extrapolation of the vertical coherence of surface-generated oceanic ambient noise to simulate measurements made on a longer sensor array. The extrapolation method consists of projecting the noise coherence measured with a limited aperture array into the domain spanned by prolate spheroidal wave functions, which are an orthogonal basis defined by array parameters and the noise frequency. Using simulated data corresponding to selected multi-layered seabeds as ground truth, the performance of the extrapolation method is explored. Application of the technique is also demonstrated on experimental data.
UPC2A
Is Required for High-Level Azole Antifungal Resistance in Candida glabrata
Authors: Whaley Sarah G. , Caudle Kelly E. , Vermitsky John-Paul , Chadwick Sean G. , Toner Geoffrey , Barker Katherine S. , Gygax Scott E. , Rogers P. David
Published: May 2014

Candida glabrata
, the second most common cause of
Candida
infections, is associated with high rates of mortality and often exhibits resistance to the azole class of antifungal agents. Upc2 and Ecm22 in
Saccharomyces cerevisiae
and Upc2 in
Candida albicans
are the transcriptional regulators of
ERG11
, the gene encoding the target of azoles in the ergosterol biosynthesis pathway. Recently two homologs for these transcription factors,
UPC2A
and
UPC2B
, were identified in
C. glabrata
. One of these,
UPC2A
, was shown to influence azole susceptibility. We hypothesized that due to the global role for Upc2 in sterol biosynthesis in
S. cerevisiae
and
C. albicans
, disruption of
UPC2A
would enhance the activity of fluconazole in both azole-susceptible dose-dependent (SDD) and -resistant
C. glabrata
clinical isolates. To test this hypothesis, we constructed mutants with disruptions in
UPC2A
and
UPC2B
alone and in combination in a matched pair of clinical azole-SDD and -resistant isolates. Disruption of
UPC2A
in both the SDD and resistant isolates resulted in increased susceptibility to sterol biosynthesis inhibitors, including a reduction in fluconazole MIC and minimum fungicidal concentration, enhanced azole activity by time-kill analysis, a decrease in ergosterol content, and downregulation of baseline and inducible expression of several sterol biosynthesis genes. Our results indicate that Upc2A is a key regulator of ergosterol biosynthesis and is essential for resistance to sterol biosynthesis inhibitors in
C. glabrata
. Therefore, the
UPC2A
pathway may represent a potential cotherapeutic target for enhancing azole activity against this organism.
In Vitro
and
In Vivo
Evaluation of 28DAP010, a Novel Diamidine for Treatment of Second-Stage African Sleeping Sickness
Authors: Wenzler Tanja , Yang Sihyung , Patrick Donald A. , Braissant Olivier , Ismail Mohamed A. , Tidwell Richard R. , Boykin David W. , Wang Michael Zhuo , Brun Reto
Published: May 2014

African sleeping sickness is a neglected tropical disease transmitted by tsetse flies. New and better drugs are still needed especially for its second stage, which is fatal if untreated. 28DAP010, a dipyridylbenzene analogue of DB829, is the second simple diamidine found to cure mice with central nervous system infections by a parenteral route of administration. 28DAP010 showed efficacy similar to that of DB829 in dose-response studies in mouse models of first- and second-stage African sleeping sickness. The
in vitro
time to kill, determined by microcalorimetry, and the parasite clearance time in mice were shorter for 28DAP010 than for DB829. No cross-resistance was observed between 28DAP010 and pentamidine on the tested
Trypanosoma brucei gambiense
isolates from melarsoprol-refractory patients. 28DAP010 is the second promising preclinical candidate among the diamidines for the treatment of second-stage African sleeping sickness.
Association between
pncA
Gene Mutations, Pyrazinamidase Activity, and Pyrazinamide Susceptibility Testing in Mycobacterium tuberculosis
Authors: Aono Akio , Chikamatsu Kinuyo , Yamada Hiroyuki , Kato Tomoko , Mitarai Satoshi
Published: May 2014

We determined MICs for, confirmed the presence of
pncA
mutations in, and performed pyrazinamidase testing on colonies (subclones) obtained from seven isolates that exhibited differential pyrazinamide (PZA) susceptibility. Six of the seven strains were found to exhibit characteristics resulting from the mixture of strains possessing different properties. In addition, our analysis revealed large
pncA
-spanning deletions (1,565 bp, 4,475 bp, and 6,258 bp) in three strains that showed high PZA resistance.
Antagonism between Bacteriostatic and Bactericidal Antibiotics Is Prevalent
Authors: Ocampo Paolo S. , Lázár Viktória , Papp Balázs , Arnoldini Markus , Abel zur Wiesch Pia , Busa-Fekete Róbert , Fekete Gergely , Pál Csaba , Ackermann Martin , Bonhoeffer Sebastian
Published: May 2014

Combination therapy is rarely used to counter the evolution of resistance in bacterial infections. Expansion of the use of combination therapy requires knowledge of how drugs interact at inhibitory concentrations. More than 50 years ago, it was noted that, if bactericidal drugs are most potent with actively dividing cells, then the inhibition of growth induced by a bacteriostatic drug should result in an overall reduction of efficacy when the drug is used in combination with a bactericidal drug. Our goal here was to investigate this hypothesis systematically. We first constructed time-kill curves using five different antibiotics at clinically relevant concentrations, and we observed antagonism between bactericidal and bacteriostatic drugs. We extended our investigation by performing a screen of pairwise combinations of 21 different antibiotics at subinhibitory concentrations, and we found that strong antagonistic interactions were enriched significantly among combinations of bacteriostatic and bactericidal drugs. Finally, since our hypothesis relies on phenotypic effects produced by different drug classes, we recreated these experiments in a microfluidic device and performed time-lapse microscopy to directly observe and quantify the growth and division of individual cells with controlled antibiotic concentrations. While our single-cell observations supported the antagonism between bacteriostatic and bactericidal drugs, they revealed an unexpected variety of cellular responses to antagonistic drug combinations, suggesting that multiple mechanisms underlie the interactions.
Gastrointestinal Colonization with a Cephalosporinase-Producing Bacteroides Species Preserves Colonization Resistance against Vancomycin-Resistant Enterococcus and Clostridium difficile in Cephalosporin-Treated Mice
Authors: Stiefel Usha , Nerandzic Michelle M. , Pultz Michael J. , Donskey Curtis J.
Published: May 2014

Antibiotics that are excreted into the intestinal tract may disrupt the indigenous intestinal microbiota and promote colonization by health care-associated pathogens. β-Lactam, or penicillin-type, antibiotics are among the most widely utilized antibiotics worldwide and may also adversely affect the microbiota. Many bacteria are capable, however, of producing β-lactamase enzymes that inactivate β-lactam antibiotics. We hypothesized that prior establishment of intestinal colonization with a β-lactamase-producing anaerobe might prevent these adverse effects of β-lactam antibiotics, by inactivating the portion of antibiotic that is excreted into the intestinal tract. Here, mice with a previously abolished microbiota received either oral normal saline or an oral cephalosporinase-producing strain of
Bacteroides thetaiotaomicron
for 3 days. Mice then received 3 days of subcutaneous ceftriaxone, followed by either oral administration of vancomycin-resistant
Enterococcus
(VRE) or sacrifice and assessment of
in vitro
growth of epidemic and nonepidemic strains of
Clostridium difficile
in murine cecal contents. Stool concentrations of VRE and ceftriaxone were measured, cecal levels of
C. difficile
24 h after incubation were quantified, and denaturing gradient gel electrophoresis (DGGE) of microbial 16S rRNA genes was performed to evaluate the antibiotic effect on the microbiota. The results demonstrated that establishment of prior colonization with a β-lactamase-producing intestinal anaerobe inactivated intraintestinal ceftriaxone during treatment with this antibiotic, allowed recovery of the normal microbiota despite systemic ceftriaxone, and prevented overgrowth with VRE and epidemic and nonepidemic strains of
C. difficile
in mice. These findings describe a novel probiotic strategy to potentially prevent pathogen colonization in hospitalized patients.