bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient metabolic pathway engineering in transgenic tobacco and tomato plastids with synthetic multigene operons
Authors: Lu Yinghong , Rijzaani Habib , Karcher Daniel , Ruf Stephanie , Bock Ralph
Published: February 2013

The engineering of complex metabolic pathways requires the concerted expression of multiple genes. In plastids (chloroplasts) of plant cells, genes are organized in operons that are coexpressed as polycistronic transcripts and then often are processed further into monocistronic mRNAs. Here we have used the tocochromanol pathway (providing tocopherols and tocotrienols, collectively also referred to as “vitamin E”) as an example to establish principles of successful multigene engineering by stable transformation of the chloroplast genome, a technology not afflicted with epigenetic variation and/or instability of transgene expression. Testing a series of single-gene constructs (encoding homogentisate phytyltransferase, tocopherol cyclase, and γ-tocopherol methyltransferase) and rationally designed synthetic operons in tobacco and tomato plants, we (
i
) confirmed previous results suggesting homogentisate phytyltransferase as the limiting enzymatic step in the pathway, (
ii
) comparatively characterized the bottlenecks in tocopherol biosynthesis in transplastomic leaves and tomato fruits, and (
iii
) achieved an up to tenfold increase in total tocochromanol accumulation. In addition, our results uncovered an unexpected light-dependent regulatory link between tocochromanol metabolism and the pathways of photosynthetic pigment biosynthesis. The synthetic operon design developed here will facilitate future synthetic biology applications in plastids, especially the design of artificial operons that introduce novel biochemical pathways into plants.
Neisseria
infection of rhesus macaques as a model to study colonization, transmission, persistence, and horizontal gene transfer
Authors: Weyand Nathan J. , Wertheimer Anne M. , Hobbs Theodore R. , Sisko Jennifer L. , Taku Nyiawung A. , Gregston Lindsay D. , Clary Susan , Higashi Dustin L. , Biais Nicolas , Brown Lewis M. , Planer Shannon L. , Legasse Alfred W. , Axthelm Michael K. , Wong Scott W. , So Magdalene
Published: February 2013

The strict tropism of many pathogens for man hampers the development of animal models that recapitulate important microbe–host interactions. We developed a rhesus macaque model for studying
Neisseria
–host interactions using
Neisseria
species indigenous to the animal. We report that
Neisseria
are common inhabitants of the rhesus macaque.
Neisseria
isolated from the rhesus macaque recolonize animals after laboratory passage, persist in the animals for at least 72 d, and are transmitted between animals.
Neisseria
are naturally competent and acquire genetic markers from each other in vivo, in the absence of selection, within 44 d after colonization.
Neisseria macacae
encodes orthologs of known or presumed virulence factors of human-adapted
Neisseria
, as well as current or candidate vaccine antigens. We conclude that the rhesus macaque model will allow studies of the molecular mechanisms of
Neisseria
colonization, transmission, persistence, and horizontal gene transfer. The model can potentially be developed further for preclinical testing of vaccine candidates.
Defective immunoregulation in RSV vaccine-augmented viral lung disease restored by selective chemoattraction of regulatory T cells
Authors: Loebbermann Jens , Durant Lydia , Thornton Hannah , Johansson Cecilia , Openshaw Peter J.
Published: February 2013

Human trials of formaldehyde-inactivated respiratory syncytial virus (FI-RSV) vaccine in 1966–1967 caused disastrous worsening of disease and death in infants during subsequent natural respiratory syncytial virus (RSV) infection. The reasons behind vaccine-induced augmentation are only partially understood, and fear of augmentation continues to hold back vaccine development. We now show that mice vaccinated with FI-RSV show enhanced local recruitment of conventional CD4
+
T cells accompanied by a profound loss of regulatory T cells (Tregs) in the airways. This loss of Tregs was so complete that additional depletion of Tregs (in transgenic depletion of regulatory T-cell mice) produced no additional disease enhancement. Transfer of conventional CD4
+
T cells from FI-RSV–vaccinated mice into naive RSV-infected recipients also caused a reduction in airway Treg responses; boosting Tregs with IL-2 immune complexes failed to restore normal levels of Tregs or to ameliorate disease. However, delivery of chemokine ligands (CCL) 17/22 via the airway selectively recruited airway Tregs and attenuated vaccine-augmented disease, reducing weight loss and inhibiting local recruitment of pathogenic CD4
+
T cells. These findings reveal an unexpected mechanism of vaccine-induced disease augmentation and indicate that selective chemoattraction of Tregs into diseased sites may offer a novel approach to the modulation of tissue-specific inflammation.
Loss of electrostatic cell-surface repulsion mediates myelin membrane adhesion and compaction in the central nervous system
Authors: Bakhti Mostafa , Snaidero Nicolas , Schneider David , Aggarwal Shweta , Möbius Wiebke , Janshoff Andreas , Eckhardt Matthias , Nave Klaus-Armin , Simons Mikael
Published: February 2013

During the development of the central nervous system (CNS), oligodendrocytes wrap their plasma membrane around axons to form a multilayered stack of tightly attached membranes. Although intracellular myelin compaction and the role of myelin basic protein has been investigated, the forces that mediate the close interaction of myelin membranes at their external surfaces are poorly understood. Such extensive bilayer–bilayer interactions are usually prevented by repulsive forces generated by the glycocalyx, a dense and confluent layer of large and negatively charged oligosaccharides. Here we investigate the molecular mechanisms underlying myelin adhesion and compaction in the CNS. We revisit the role of the proteolipid protein and analyze the contribution of oligosaccharides using cellular assays, biophysical tools, and transgenic mice. We observe that differentiation of oligodendrocytes is accompanied by a striking down-regulation of components of their glycocalyx. Both in vitro and in vivo experiments indicate that the adhesive properties of the proteolipid protein, along with the reduction of sialic acid residues from the cell surface, orchestrate myelin membrane adhesion and compaction in the CNS. We suggest that loss of electrostatic cell-surface repulsion uncovers weak and unspecific attractive forces in the bilayer that bring the extracellular surfaces of a membrane into close contact over long distances.
Engineering a lysosomal enzyme with a derivative of receptor-binding domain of apoE enables delivery across the blood–brain barrier
Authors: Wang Daren , El-Amouri Salim S. , Dai Mei , Kuan Chia-Yi , Hui David Y. , Brady Roscoe O. , Pan Dao
Published: February 2013

To realize the potential of large molecular weight substances to treat neurological disorders, novel approaches are required to surmount the blood–brain barrier (BBB). We investigated whether fusion of a receptor-binding peptide from apolipoprotein E (apoE) with a potentially therapeutic protein can bind to LDL receptors on the BBB and be transcytosed into the CNS. A lysosomal enzyme, α-
L
-iduronidase (IDUA), was used for biological and therapeutic evaluation in a mouse model of mucopolysaccharidosis (MPS) type I, one of the most common lysosomal storage disorders with CNS deficits. We identified two fusion candidates, IDUAe1 and IDUAe2, by in vitro screening, that exhibited desirable receptor-mediated binding, endocytosis, and transendothelial transport as well as appropriate lysosomal enzyme trafficking and biological function. Robust peripheral IDUAe1 or IDUAe2 generated by transient hepatic expression led to elevated enzyme levels in capillary-depleted, enzyme-deficient brain tissues and protein delivery into nonendothelium perivascular cells, neurons, and astrocytes within 2 d of treatment. Moreover, 5 mo after long-term delivery of moderate levels of IDUAe1 derived from maturing red blood cells, 2% to 3% of normal brain IDUA activities were obtained in MPS I mice, and IDUAe1 protein was detected in neurons and astrocytes throughout the brain. The therapeutic potential was demonstrated by normalization of brain glycosaminoglycan and β-hexosaminidase in MPS I mice 5 mo after moderate yet sustained delivery of IDUAe1. These findings provide a noninvasive and BBB-targeted procedure for the delivery of large-molecule therapeutic agents to treat neurological lysosomal storage disorders and potentially other diseases that involve the brain.
Essential requirement for IRF8 and SLC15A4 implicates plasmacytoid dendritic cells in the pathogenesis of lupus
Authors: Baccala Roberto , Gonzalez-Quintial Rosana , Blasius Amanda L. , Rimann Ivo , Ozato Keiko , Kono Dwight H. , Beutler Bruce , Theofilopoulos Argyrios N.
Published: February 2013

In vitro evidence suggests that plasmacytoid dendritic cells (pDCs) are intimately involved in the pathogenesis of lupus. However, it remains to be determined whether these cells are required in vivo for disease development, and whether their contribution is restricted to hyperproduction of type I IFNs. To address these issues, we created lupus-predisposed mice lacking the IFN regulatory factor 8 (IRF8) or carrying a mutation that impairs the peptide/histidine transporter solute carrier family 15, member 4 (SLC15A4). IRF8-deficient NZB mice, lacking pDCs, showed almost complete absence of anti-nuclear, anti-chromatin, and anti-erythrocyte autoantibodies, along with reduced kidney disease. These effects were observed despite normal B-cell responses to Toll-like receptor (TLR) 7 and TLR9 stimuli and intact humoral responses to conventional T-dependent and -independent antigens. Moreover,
Slc15a4
mutant C57BL/6-
Fas

lpr

mice, in which pDCs are present but unable to produce type I IFNs in response to endosomal TLR ligands, also showed an absence of autoantibodies, reduced lymphadenopathy and splenomegaly, and extended survival. Taken together, our results demonstrate that pDCs and the production of type I IFNs by these cells are critical contributors to the pathogenesis of lupus-like autoimmunity in these models. Thus, IRF8 and SLC15A4 may provide important targets for therapeutic intervention in human lupus.
Random pinning glass model
Authors: Karmakar Smarajit , Parisi Giorgio
Published: February 2013

Glass transition, in which viscosity of liquids increases dramatically upon decrease of temperature without any major change in structural properties, remains one of the most challenging problems in condensed matter physics despite tremendous research efforts in past decades. On the other hand, disordered freezing of spins in magnetic materials with decreasing temperature, the so-called “spin glass transition,” is understood relatively better. A previously found similarity between some spin glass models and the structural glasses inspired development of theories of structural glasses based on the scenario of spin glass transition. This scenario, although it looks very appealing, is still far from being well established. One of the main differences between standard spin systems and molecular systems is the absence of quenched disorder and the presence of translational invariance: it often is assumed that this difference is not relevant, but this conjecture still needs to be established. The quantities, which are well-defined and characterized for spin models, are not easily calculable for molecular glasses because of the lack of quenched disorder that breaks the translational invariance in the system. Thus the characterization of the similarity between spin and the structural glass transition remains an elusive subject. In this study, we introduced a model structural glass with built-in quenched disorder that alleviates this main difference between the spin and molecular glasses, thereby helping us compare these two systems: the possibility of producing a good thermalization at rather low temperatures is one of the advantages of this model.
H–Y antigen-binding B cells develop in male recipients of female hematopoietic cells and associate with chronic graft vs. host disease
Authors: Sahaf Bita , Yang Yang , Arai Sally , Herzenberg Leonard A. , Herzenberg Leonore A. , Miklos David B.
Published: February 2013

B cells are known to play an important role in pathogenesis of human chronic graft vs. host disease (cGVHD). Our group has previously shown that IgG allo-antibodies recognize Y chromosome-encoded proteins (H–Y) and a dominant H–Y epitope, DEAD box protein (DBY-2) detectable 6–12 mo after transplant in male patients who receive grafts from female donors (F→M) hematopoietic cell transplantation (HCT). Here we present FACS studies of peripheral blood mononuclear cells collected 6 mo after transplant showing that 16 of 28 (57%) F→M HCT patients have circulating donor B cells that express B-cell receptor (mainly IgM and Igλ) specific for DBY-2. The detection of these DBY-2 B cells 6 mo after HCT are associated with cGVHD development (
P
= 0.004). Specifically, 15 of 16 F→M with DBY-2 B cells developed cGVHD. In contrast, cGVHD developed in only 5 of the 12 who did not have DBY-2 B cells detected. This demonstrates circulating human B cells binding an alloantigen (DBY-2) and that these DBY-2–specific B cells appear before development of cGVHD in roughly half of the F→M patients. Our study suggests that detection of anti–DBY-2 B cells may predict cGVHD and that this prediction may have clinical utility. Validation of this hypothesis will require larger prospective studies.
Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants
Authors: De Smet Riet , Adams Keith L. , Vandepoele Klaas , Van Montagu Marc C. E. , Maere Steven , Van de Peer Yves
Published: February 2013

The importance of gene gain through duplication has long been appreciated. In contrast, the importance of gene loss has only recently attracted attention. Indeed, studies in organisms ranging from plants to worms and humans suggest that duplication of some genes might be better tolerated than that of others. Here we have undertaken a large-scale study to investigate the existence of duplication-resistant genes in the sequenced genomes of 20 flowering plants. We demonstrate that there is a large set of genes that is convergently restored to single-copy status following multiple genome-wide and smaller scale duplication events. We rule out the possibility that such a pattern could be explained by random gene loss only and therefore propose that there is selection pressure to preserve such genes as singletons. This is further substantiated by the observation that angiosperm single-copy genes do not comprise a random fraction of the genome, but instead are often involved in essential housekeeping functions that are highly conserved across all eukaryotes. Furthermore, single-copy genes are generally expressed more highly and in more tissues than non–single-copy genes, and they exhibit higher sequence conservation. Finally, we propose different hypotheses to explain their resistance against duplication.
Human CD1d knock-in mouse model demonstrates potent antitumor potential of human CD1d-restricted invariant natural killer T cells
Authors: Wen Xiangshu , Rao Ping , Carreño Leandro J. , Kim Seil , Lawrenczyk Agnieszka , Porcelli Steven A. , Cresswell Peter , Yuan Weiming
Published: February 2013

Despite a high degree of conservation, subtle but important differences exist between the CD1d antigen presentation pathways of humans and mice. These differences may account for the minimal success of natural killer T (NKT) cell-based antitumor therapies in human clinical trials, which contrast strongly with the powerful antitumor effects in conventional mouse models. To develop an accurate model for in vivo human CD1d (hCD1d) antigen presentation, we have generated a hCD1d knock-in (hCD1d-KI) mouse. In these mice, hCD1d is expressed in a native tissue distribution pattern and supports NKT cell development. Reduced numbers of invariant NKT (iNKT) cells were observed, but at an abundance comparable to that in most normal humans. These iNKT cells predominantly expressed mouse Vβ8, the homolog of human Vβ11, and phenotypically resembled human iNKT cells in their reduced expression of CD4. Importantly, iNKT cells in hCD1d knock-in mice exert a potent antitumor function in a melanoma challenge model. Our results show that replacement of mCD1d by hCD1d can select a population of functional iNKT cells closely resembling human iNKT cells. These hCD1d knock-in mice will allow more accurate in vivo modeling of human iNKT cell responses and will facilitate the preclinical assessment of iNKT cell-targeted antitumor therapies.
In vivo quantitative proteomics of somatosensory cortical synapses shows which protein levels are modulated by sensory deprivation
Authors: Butko Margaret T. , Savas Jeffrey N. , Friedman Beth , Delahunty Claire , Ebner Ford , Yates John R. , Tsien Roger Y.
Published: February 2013

Significance

We applied quantitative mass spectrometry to define how sensory experience alters the synaptic proteome in primary sensory cortex. Our results demonstrate that sensory deprivation reduced proteins implicated in spine enlargement and synaptic strength and increased protein-degradation machinery at synapses. Importantly, we identified novel synaptic proteins whose levels were affected by sensory deprivation but whose synaptic roles have not yet been characterized in mammalian neurons. Thus, this study provides a crucial starting point for numerous investigations of the molecular basis for synaptic modulation and demonstrates the feasibility of using this method to define synaptic proteomes under different sensory rearing conditions.
A Positive Patterning Advantage with Complex but not Simple Patterning: A Cue Constellation Approach
Authors: Whitlow J. W.
Published: February 2013

Determinants of a positive patterning advantage (that is, an advantage for positive patterning over negative patterning) in human causal reasoning were examined in an experiment that compared simple patterning discriminations (A, B vs. AB) to complex patterning discriminations (AB, BC, AC vs. ABC). As predicted by a cue constellation analysis of complex discriminations, a positive patterning advantage was found with complex patterning but not with simple patterning discriminations. This result may explain why some recent studies have found a positive patterning advantage where earlier studies had failed to find one. The interaction of patterning complexity with the positive patterning advantage appears to pose problems for rule-based accounts of patterning. The results support the view that associative theories of human causal reasoning are more easily distinguished from rule-based approaches when applied to conditions that make simple rules difficult to identify or implement.
The Ataxia Telangiectasia mutated kinase controls Igκ allelic exclusion by inhibiting secondary Vκ-to-Jκ rearrangements
Authors: Steinel Natalie C. , Lee Baeck-Seung , Tubbs Anthony T. , Bednarski Jeffrey J. , Schulte Emily , Yang-Iott Katherine S. , Schatz David G. , Sleckman Barry P. , Bassing Craig H.
Published: February 2013

Allelic exclusion is enforced through the ability of antigen receptor chains expressed from one allele to signal feedback inhibition of V-to-(D)J recombination on the other allele. To achieve allelic exclusion by such means, only one allele can initiate V-to-(D)J recombination within the time required to signal feedback inhibition. DNA double-strand breaks (DSBs) induced by the RAG endonuclease during V(D)J recombination activate the Ataxia Telangiectasia mutated (ATM) and DNA-dependent protein kinase (DNA-PK) kinases. We demonstrate that ATM enforces Igκ allelic exclusion, and that RAG DSBs induced during Igκ recombination in primary pre–B cells signal through ATM, but not DNA-PK, to suppress initiation of additional Igκ rearrangements. ATM promotes high-density histone H2AX phosphorylation to create binding sites for MDC1, which functions with H2AX to amplify a subset of ATM-dependent signals. However, neither H2AX nor MDC1 is required for ATM to enforce Igκ allelic exclusion and suppress Igκ rearrangements. Upon activation in response to RAG Igκ cleavage, ATM signals down-regulation of Gadd45α with concomitant repression of the Gadd45α targets Rag1 and Rag2. Our data indicate that ATM kinases activated by RAG DSBs during Igκ recombination transduce transient H2AX/MDC1-independent signals that suppress initiation of further Igκ rearrangements to control Igκ allelic exclusion.
Macroautophagy substrates are loaded onto MHC class II of medullary thymic epithelial cells for central tolerance
Authors: Aichinger Martin , Wu Chunyan , Nedjic Jelena , Klein Ludger
Published: February 2013

Macroautophagy serves cellular housekeeping and metabolic functions through delivery of cytoplasmic constituents for lysosomal degradation. In addition, it may mediate the unconventional presentation of intracellular antigens to CD4+ T cells; however, the physiological relevance of this endogenous MHC class II loading pathway remains poorly defined. Here, we characterize the role of macroautophagy in thymic epithelial cells (TECs) for negative selection. Direct presentation for clonal deletion of MHC class II–restricted thymocytes required macroautophagy for a mitochondrial version of a neo-antigen, but was autophagy-independent for a membrane-bound form. A model antigen specifically expressed in Aire+ medullary TECs (mTECs) induced efficient deletion via direct presentation when targeted to autophagosomes, whereas interference with autophagosomal routing of this antigen through exchange of a single amino acid or ablation of an essential autophagy gene abolished direct presentation for negative selection. Furthermore, when this autophagy substrate was expressed by mTECs in high amounts, endogenous presentation and indirect presentation by DCs operated in a redundant manner, whereas macroautophagy-dependent endogenous loading was essential for clonal deletion at limiting antigen doses. Our findings suggest that macroautophagy supports central CD4+ T cell tolerance through facilitating the direct presentation of endogenous self-antigens by mTECs.
Phosphocholine-binding antibody activities are hierarchically encoded in the sequence of the heavy-chain variable region: dominance of self-association activity in the T15 idiotype
Authors: Srdiċ-Rajiċ Tatjana , Kekoviċ Goran , Davidoviċ Dragomir M. , Metlas Radmila
Published: February 2013

A methodology based on the representation of each amino acid of a protein sequence by the electron-ion interaction potential and subsequent analysis by signal processing was used to determine the characteristic or common frequency (in Hz) that reflects the biological activity shared among phosphocholine (PC)-binding antibodies. The common frequency for the variable portion of the heavy chain (VH) of the PC-specific antibodies is found to be at f = 0.37 Hz. The VH sequences of the PC-binding antibodies exhibit three subsites for the PC moiety where hypervariable region 2 (CDR2) plays a role in the interaction with the phosphate group. Mutations in this VH region have an impact on the ability of mutant variants to bind PC and its carrier molecule, as well as on the characteristic frequency shift toward f = 0.12 Hz for mutants failing to bind both hapten and carrier. The VH sequence of mutants that retain the ability to bind PC still shows f = 0.37 Hz, suggesting that this frequency determines PC binding. However, this statement was not confirmed as mutation in another PC subsite impairs PC binding but retains both the phosphate-group recognition and the frequency at f = 0.37 Hz. Herein, this finding is discussed to promote the idea that the VH sequence of the PC-binding antibodies encodes the subsite for phosphate-group binding as a dominant functional activity and that only CDR2 of the T15-idiotype antibodies together with FR3 region form an autonomous self-association function represented by the T15VH50–73 peptide with f = 0.37±0.05 Hz. Thus, these data confirmed that T15VH50-73 peptide might be used in superantibody technology.
Unusual displacement of H i due to tidal interaction in Arp 181
Authors: Sengupta Chandreyee , Dwarakanath K. S. , Saikia D. J. , Scott T. C.
Published: February 2013

We present results from Giant Metrewave Radio Telescope H i 21 cm line observations of the interacting galaxy pair Arp 181 (NGC 3212 and NGC 3215) at z = 0.032. We find almost all of the detected H i (90 per cent) is displaced well beyond the optical discs of the pair with the highest density H i located ∼70 kpc west of the pair. An H i bridge extending between the optical pair and the bulk of H i together with their H i deficiencies provide strong evidence that the interaction between the pair has removed most of their H i to the current projected position. H i to the west of the pair has two approximately equal intensity peaks. The H i intensity maximum furthest to the west coincides with a small spiral companion SDSS J102726.32+794911.9 which shows enhanced mid-infrared (Spitzer), ultraviolet (UV; GALEX) and Hα emission indicating intense star-forming activity. The H i intensity maximum close to the Arp 181 pair, coincides with a diffuse optical cloud detected in UV (GALEX) at the end of the stellar and H i tidal tails originating at NGC 3212 and, previously proposed to be a tidal dwarf galaxy in formation. Future sensitive H i surveys by telescopes like Australian Square Kilometre Array Pathfinder should prove to be powerful tools for identifying tidal dwarfs at moderate to large redshifts to explore in detail the evolution of dwarf galaxies in the Universe.
Seedling Stage Resistance of Iranian Bread Wheat Germplasm to Race Ug99 of Puccinia graminis f. sp. tritici
Authors: Mohammadi Mohsen , Torkamaneh Davoud , Patpour Mehran
Published: February 2013

Following emergence of Ug99, the new virulent race of Puccinia graminis f. sp. tritici in Africa, a global effort for identification and utilization of new sources of Ug99-resistant germplasm has been undertaken. In this study, we conducted replicated experiments to evaluate the resistance of Iranian wheat germplasm to the TTKSK lineage of the Ug99 race of P. graminis f. sp. tritici. We also evaluated for presence of stem rust resistance genes (i.e., Sr2, Sr24, Sr26, Sr38, Sr39, Sr31, and Sr1RSAmigo) in wheat cultivars and breeding lines widely cultivated in Iran. Our phenotyping data revealed high levels of susceptibility to Ug99 in Iranian bread wheat germplasm. Our genotyping data revealed that Iranian cultivars do not carry Sr24, Sr26, or Sr1RSAmigo. Only a few salt-tolerant cultivars and breeding lines tested positively for Sr2, Sr31, Sr38, or Sr39 markers. In conclusion, the genetic basis for resistance to Ug99 in Iranian wheat cultivars was found to be vulnerable. Acquiring knowledge about existing resistance genes and haplotypes in wheat cultivars and breeding lines will help breeders, cereal pathologists, and policy makers to select and pyramid effective stem rust resistance genes.
Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints
Authors: Faria Nuno Rodrigues , Suchard Marc A. , Rambaut Andrew , Streicker Daniel G. , Lemey Philippe
Published: February 2013

The factors that determine the origin and fate of cross-species transmission events remain unclear for the majority of human pathogens, despite being central for the development of predictive models and assessing the efficacy of prevention strategies. Here, we describe a flexible Bayesian statistical framework to reconstruct virus transmission between different host species based on viral gene sequences, while simultaneously testing and estimating the contribution of several potential predictors of cross-species transmission. Specifically, we use a generalized linear model extension of phylogenetic diffusion to perform Bayesian model averaging over candidate predictors. By further extending this model with branch partitioning, we allow for distinct host transition processes on external and internal branches, thus discriminating between recent cross-species transmissions, many of which are likely to result in dead-end infections, and host shifts that reflect successful onwards transmission in the new host species. Our approach corroborates genetic distance between hosts as a key determinant of both host shifts and cross-species transmissions of rabies virus in North American bats. Furthermore, our results indicate that geographical range overlap is a modest predictor for cross-species transmission, but not for host shifts. Although our evolutionary framework focused on the multi-host reservoir dynamics of bat rabies virus, it is applicable to other pathogens and to other discrete state transition processes.
Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission
Authors: Viboud Cécile , Nelson Martha I. , Tan Yi , Holmes Edward C.
Published: February 2013

In the past decade, rapid increases in the availability of high-resolution molecular and epidemiological data, combined with developments in statistical and computational methods to simulate and infer migration patterns, have provided key insights into the spatial dynamics of influenza A viruses in humans. In this review, we contrast findings from epidemiological and molecular studies of influenza virus transmission at different spatial scales. We show that findings are broadly consistent in large-scale studies of inter-regional or inter-hemispheric spread in temperate regions, revealing intense epidemics associated with multiple viral introductions, followed by deep troughs driven by seasonal bottlenecks. However, aspects of the global transmission dynamics of influenza viruses are still debated, especially with respect to the existence of tropical source populations experiencing high levels of genetic diversity and the extent of prolonged viral persistence between epidemics. At the scale of a country or community, epidemiological studies have revealed spatially structured diffusion patterns in seasonal and pandemic outbreaks, which were not identified in molecular studies. We discuss the role of sampling issues in generating these conflicting results, and suggest strategies for future research that may help to fully integrate the epidemiological and evolutionary dynamics of influenza virus over space and time.
Virulence attenuation during an influenza A/H5N1 pandemic
Authors: Boni Maciej F. , Nguyen Tran Dang , de Jong Menno D. , van Doorn H. Rogier
Published: February 2013

More than 15 years after the first human cases of influenza A/H5N1 in Hong Kong, the world remains at risk for an H5N1 pandemic. Preparedness activities have focused on antiviral stockpiling and distribution, development of a human H5N1 vaccine, operationalizing screening and social distancing policies, and other non-pharmaceutical interventions. The planning of these interventions has been done in an attempt to lessen the cumulative mortality resulting from a hypothetical H5N1 pandemic. In this theoretical study, we consider the natural limitations on an H5N1 pandemic's mortality imposed by the virus' epidemiological–evolutionary constraints. Evolutionary theory dictates that pathogens should evolve to be relatively benign, depending on the magnitude of the correlation between a pathogen's virulence and its transmissibility. Because the case fatality of H5N1 infections in humans is currently 60 per cent, it is doubtful that the current viruses are close to their evolutionary optimum for transmission among humans. To describe the dynamics of virulence evolution during an H5N1 pandemic, we build a mathematical model based on the patterns of clinical progression in past H5N1 cases. Using both a deterministic model and a stochastic individual-based simulation, we describe (i) the drivers of evolutionary dynamics during an H5N1 pandemic, (ii) the range of case fatalities for which H5N1 viruses can successfully cause outbreaks in humans, and (iii) the effects of different kinds of social distancing on virulence evolution. We discuss two main epidemiological–evolutionary features of this system (i) the delaying or slowing of an epidemic which results in a majority of hosts experiencing an attenuated virulence phenotype and (ii) the strong evolutionary pressure for lower virulence experienced by the virus during a period of intense social distancing.
Global mapping of infectious disease
Authors: Hay Simon I. , Battle Katherine E. , Pigott David M. , Smith David L. , Moyes Catherine L. , Bhatt Samir , Brownstein John S. , Collier Nigel , Myers Monica F. , George Dylan B. , Gething Peter W.
Published: February 2013

The primary aim of this review was to evaluate the state of knowledge of the geographical distribution of all infectious diseases of clinical significance to humans. A systematic review was conducted to enumerate cartographic progress, with respect to the data available for mapping and the methods currently applied. The results helped define the minimum information requirements for mapping infectious disease occurrence, and a quantitative framework for assessing the mapping opportunities for all infectious diseases. This revealed that of 355 infectious diseases identified, 174 (49%) have a strong rationale for mapping and of these only 7 (4%) had been comprehensively mapped. A variety of ambitions, such as the quantification of the global burden of infectious disease, international biosurveillance, assessing the likelihood of infectious disease outbreaks and exploring the propensity for infectious disease evolution and emergence, are limited by these omissions. An overview of the factors hindering progress in disease cartography is provided. It is argued that rapid improvement in the landscape of infectious diseases mapping can be made by embracing non-conventional data sources, automation of geo-positioning and mapping procedures enabled by machine learning and information technology, respectively, in addition to harnessing labour of the volunteer ‘cognitive surplus’ through crowdsourcing.
Coalescent inference for infectious disease: meta-analysis of hepatitis C
Authors: Dearlove Bethany , Wilson Daniel J.
Published: February 2013

Genetic analysis of pathogen genomes is a powerful approach to investigating the population dynamics and epidemic history of infectious diseases. However, the theoretical underpinnings of the most widely used, coalescent methods have been questioned, casting doubt on their interpretation. The aim of this study is to develop robust population genetic inference for compartmental models in epidemiology. Using a general approach based on the theory of metapopulations, we derive coalescent models under susceptible–infectious (SI), susceptible–infectious–susceptible (SIS) and susceptible–infectious–recovered (SIR) dynamics. We show that exponential and logistic growth models are equivalent to SI and SIS models, respectively, when co-infection is negligible. Implementing SI, SIS and SIR models in BEAST, we conduct a meta-analysis of hepatitis C epidemics, and show that we can directly estimate the basic reproductive number (R0) and prevalence under SIR dynamics. We find that differences in genetic diversity between epidemics can be explained by differences in underlying epidemiology (age of the epidemic and local population density) and viral subtype. Model comparison reveals SIR dynamics in three globally restricted epidemics, but most are better fit by the simpler SI dynamics. In summary, metapopulation models provide a general and practical framework for integrating epidemiology and population genetics for the purposes of joint inference.
Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin
Authors: Meyer Austin G. , Dawson Eric T. , Wilke Claus O.
Published: February 2013

We investigate the causes of site-specific evolutionary-rate variation in influenza haemagglutinin (HA) between human and avian influenza, for subtypes H1, H3, and H5. By calculating the evolutionary-rate ratio,ω= dN/dSas a function of a residue's solvent accessibility in the three-dimensional protein structure, we show that solvent accessibility has a significant but relatively modest effect on site-specific rate variation. By comparing rates within HA subtypes among host species, we derive an upper limit to the amount of variation that can be explained by structural constraints of any kind. Protein structure explains only 20–40% of the variation inω. Finally, by comparingωat sites near the sialic-acid-binding region toωat other sites, we show thatωnear the sialic-acid-binding region is significantly elevated in both human and avian influenza, with the exception of avian H5. We conclude that protein structure, HA subtype, and host biology all impose distinct selection pressures on sites in influenza HA.
Cadmium(II) iodide and thiocyanate complexes adopted by polycyclic 1,4-bis(pyridazin-4-yl)benzene: interplay of coordination and π–π stacking interactions
Authors: Degtyarenko Anna S. , Domasevitch Konstantin V.
Published: February 2013

New complexes containing the 1,4-bis(pyridazin-4-yl)benzene ligand, namely diaquatetrakis[1,4-bis(pyridazin-4-yl)benzene-κN2]cadmium(II) hexaiodidodicadmate(II), [Cd(C14H10N4)4(H2O)2][Cd2I6], (I), and poly[[μ-1,4-bis(pyridazin-4-yl)benzene-κ2N2:N2′]bis(μ-thiocyanato-κ2N:S)cadmium(II)], [Cd(NCS)2(C14H10N4)]n, (II), demonstrate the adaptability of the coordination geometries towards the demands of slipped π–π stacking interactions between the extended organic ligands. In (I), the discrete cationic [Cd—N = 2.408 (3) and 2.413 (3) Å] and anionic [Cd—I = 2.709 (2)–3.1201 (14) Å] entities are situated across centres of inversion. The cations associateviacomplementary O—H...N2′hydrogen bonding [O...N = 2.748 (4) and 2.765 (4) Å] and extensive triple π–π stacking interactions between pairs of pyridazine and phenylene rings [centroid–centroid distances (CCD) = 3.782 (4)–4.286 (3) Å] to yield two-dimensional square nets. The [Cd2I6]2−anions reside in channels generated by packing of successive nets. In (II), the CdIIcation lies on a centre of inversion and the ligand is situated across a centre of inversion. A two-dimensional coordination array is formed by crosslinking of linear [Cd(μ-NCS)2]nchains [Cd—N = 2.3004 (14) Å and Cd—S = 2.7804 (5) Å] withN2:N2′-bidentate organic bridges [Cd—N = 2.3893 (12) Å], which generate π–π stacks by double-slipped interactions between phenylene and pyridazine rings [CCD = 3.721 (2) Å].
In vivo evidence suggesting reciprocal renal hypoxia‐inducible factor‐1 upregulation and signal transducer and activator of transcription 3 activation in response to hypoxic and non‐hypoxic stimuli
Authors: Nechemia‐Arbely Yael , Khamaisi Mogher , Rosenberger Christian , Koesters Robert , Shina Ahuva , Geva Carmit , Shriki Anat , Klaus Stephen , Rosen Seymour , Rose‐John Stefan , Galun Eithan , Axelrod Jonathan H , Heyman Samuel N
Published: February 2013

In vitro studies suggest that combined activation of hypoxia‐inducible factor (HIF) and signal transducer and activator of transcription 3 (STAT3) promotes the hypoxia response. However, their interrelationship in vivo remains poorly defined. The present study investigated the possible relationship between HIF‐1 upregulation and STAT3 activation in the rodent kidney in vivo.

Activation of HIF‐1 and STAT3 was analysed by immunohistochemical staining and western blot analysis in: (i) models of hypoxia‐associated kidney injury induced by radiocontrast media or rhabdomyolysis; (ii) following activation of STAT3 by the interleukin (IL)‐6–soluble IL‐6 receptor complex; or (iii) following HIF‐1α stabilization using hypoxic and non‐hypoxic stimuli (mimosine, FG‐4497, CO, CoCl2) and in targeted von Hippel‐Lindau‐knockout mice.

Western blot analysis and immunostaining revealed marked induction of both transcription factors under all conditions tested, suggesting that in vivo STAT3 can trigger HIF and vice versa.

Colocalization of HIF‐1α and phosphorylated STAT3 was detected in some, but not all, renal cell types, suggesting that in some cells a paracrine mechanism may be responsible for the reciprocal activation of the two transcription factors. Nevertheless, in several cell types spatial concordance was observed under the majority of conditions tested, suggesting that HIF‐1 and STAT3 may act as cotranscription factors.

These in vivo studies suggest that, in response to renal hypoxic‐stress, upregulation of HIF‐1 and activation of STAT3 may be both reciprocal and cell type dependent.
Behavioural disturbance requiring medical referral: A case of anti‐N‐methyl‐D‐aspartate receptor encephalitis in the emergency department
Authors: Hegarty Cherie P , Mikli Jane E
Published: February 2013

A 17‐year‐old woman presented to the ED with behavioural disturbance and psychotic features. Brief dystonic jerks were noted so she was referred to the medical team. A diagnosis of anti‐N‐methyl‐D‐aspartate receptor encephalitis was made. Immunotherapy was instituted early and the clinical outcome was excellent. It is important to consider this condition in young women presenting with acute behavioural or psychotic symptoms.
Diabetes mellitus in South Asia: Scientific evaluation of the research output (南亚糖尿病：要科学地评估研究成果)
Authors: Ranasinghe Priyanga , Jayawardena Ranil , Katulanda Prasad
Published: February 2013

Background

Diabetes in South Asia represents a different disease entity in terms of its onset, progression, and complications. In the present study, we systematically analyzed the medical research output on diabetes in South Asia.

Methods

The online SciVerse Scopus database was searched using the search terms “diabetes” and “diabetes mellitus” in the article Title, Abstract or Keywords fields, in conjunction with the names of each regional country in the Author Affiliation field.

Results

In total, 8478 research articles were identified. Most were from India (85.1%) and Pakistan (9.6%) and the contribution to the global diabetes research output was 2.1%. Publications from South Asia increased markedly after 2007, with 58.7% of papers published between 2000 and 2010 being published after 2007. Most papers were Research Articles (75.9%) and Reviews (12.9%), with only 90 (1.1%) clinical trials. Publications predominantly appeared in local national journals. Indian authors and institutions had the most number of articles and the highest h‐index. There were 136 (1.6%) intraregional collaborative studies. Only 39 articles (0.46%) had >100 citations.

Conclusions

Regional research output on diabetes mellitus is unsatisfactory, with only a minimal contribution to global diabetes research. Publications are not highly cited and only a few randomized controlled trials have been performed. In the coming decades, scientists in the region must collaborate and focus on practical and culturally acceptable interventional studies on diabetes mellitus.
Laryngeal morbidity after tracheal intubation: the Endoflex® tube compared to conventional endotracheal intubation with stylet
Authors: SØRENSEN M. K. , RASMUSSEN N. , KRISTENSEN M. S. , BØTTGER M. , FREDENSBORG B. B. , HANSEN C. M. , RASMUSSEN L. S.
Published: February 2013

Background

Tracheal intubation may cause vocal fold damage. The trial was designed to assess laryngeal morbidity comparing the Endoflex® tube with a conventional endotracheal tube with stylet. We hypothesised that laryngeal morbidity within the first 24 h after extubation would be lower with the Endoflex tube than with the conventional endotracheal tube with stylet because of less rigidity.

Methods

This randomised trial included 130 elective surgical patients scheduled for general anaesthesia with endotracheal intubation. Pre‐ and post‐operative assessment of hoarseness, vocal fold pathology, and voice analysis using the Multidimensional Voice Program was performed. Induction of anaesthesia was standardised. After complete neuromuscular paralysis, intubation was done with an Endoflex tube or a conventional endotracheal tube with stylet.

Results

Post‐operative hoarseness was found in 45% with the Endoflex tube and 55% with the endotracheal tube with stylet at 24 h after extubation (P = 0.44). Post‐operative vocal fold injury was present in 23% in the Endoflex tube group and in 36% in the endotracheal tube with stylet group (P = 0.13). The increase in shimmer, the voice analysis variable reflecting vocal fold oedema, was 0.5% in the Endoflex tube group and 2.5% in the endotracheal tube with stylet group (P = 0.02).

Conclusion

No significant difference was found in the incidence of hoarseness or vocal fold injury using the Endoflex tube. However, the statistically significant lower increase in the shimmer values in that group implies that the Endoflex may be associated with less laryngeal morbidity.
Childhood Maltreatment Affects the Serotonergic System in Male Alcohol‐Dependent Individuals
Authors: Berglund Kristina J. , Balldin Jan , Berggren Ulf , Gerdner Arne , Fahlke Claudia
Published: February 2013

Background

Reduced central serotonergic neurotransmission has been demonstrated in individuals with excessive alcohol consumption and/or alcohol dependence. Childhood maltreatment has also been found to have a negative impact on central serotonergic neurotransmission. The aim of this study was to evaluate the impact of childhood maltreatment on central serotonergic dysfunction in alcohol‐dependent individuals.

Methods

Adult men with a diagnosis of alcohol dependence (n = 18) were recruited from outpatient treatment units for alcoholism. Central serotonergic neurotransmission was assessed by a neuroendocrine method, that is, the prolactin (PRL) response to the selective 5‐HTreuptake inhibitor citalopram. Childhood maltreatment was assessed retrospectively by theChildhoodTraumaQuestionnaire.

Results

Alcohol‐dependent individuals with childhood experience of emotional abuse had significantly lowerPRLresponse compared with those without such abuse (3 ± 5 and 64 ± 24 mU/l, respectively;t = 6.51,p < 0.001). Among those who reported childhood emotional abuse, 4 of 7 individuals had flatPRLresponses in comparison with none in those with no report of such abuse (p < 0.01).

Conclusions

This is the first study to show that self‐reported childhood maltreatment, in particular emotional abuse, in male alcohol‐dependent individuals is associated with a quite dramatic (more than 90%) reduction in central serotonergic neurotransmission. It should, however, be noted that the number of individuals is relatively small, and the results should therefore be considered as preliminary.
Adhesion of Streptococci to various orthodontic composite resins
Authors: Velazquez‐Enriquez U , Scougall‐Vilchis RJ , Contreras‐Bulnes R , Flores‐Estrada J , Uematsu S , Yamaguchi R
Published: February 2013

Background

This investigation aimed to determine quantitatively the adhesion of Streptococcus mutans and Streptococcus sobrinus to orthodontic composite resins that were tested simultaneously using radio‐markers.

Methods

Seven orthodontic composite resins were classified into seven groups: BeautyOrtho Bond (GI), Blugloo (GII), Enlight (GIII), Grengloo (GIV), Kurasper F (GV), Transbond CC (GVI) and Turbo Bond II (GVII). Thirty 4 x 4 x 1 mm blocks of each orthodontic composite resin were made (a total of 210 blocks). Both Streptococcus species were cultivated independently. For the quantitative analysis, radioactive markers were used to codify the bacteria (3H for Streptococcus mutans and 14C for Streptococcus sobrinus). The blocks were submerged in a solution with microorganisms previously radiolabelled for 2 hours at 37 °C in constant movement. The blocks were placed in a combustion system to quantify the Streptococcus adhering to the surface of the materials by capturing the residues and measuring the radiation.

Results

Significant differences in bacterial adhesion were found among the groups. The lowest significant scores for both microorganisms were observed in GIII.

Conclusions

The orthodontic composite resin evaluated in GIII exhibited the lowest adhesion of Streptococcus mutans and Streptococcus sobrinus, which may reduce enamel demineralization and the risk of white spot lesion formation.