bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential transcriptomic responses of ancient and modern Daphnia genotypes to phosphorus supply
Authors: Roy Chowdhury Priyanka , Frisch Dagmar , Becker Dörthe , Lopez Jacqueline A. , Weider Lawrence J. , Colbourne John K. , Jeyasingh Punidan D. 
Published: November 2014

AbstractLittle is known about the role of transcriptomic changes in driving phenotypic evolution in natural populations, particularly in response to anthropogenic environmental change. Previous analyses of Daphnia genotypes separated by centuries of evolution in a lake using methods in resurrection ecology revealed striking genetic and phenotypic shifts that were highly correlated with anthropogenic environmental change, specifically phosphorus (P)‐driven nutrient enrichment (i.e. eutrophication). Here, we compared the transcriptomes of two ancient (~700‐year‐old) and two modern (~10‐year‐old) genotypes in historic (low P) and contemporary (high P) environmental conditions using microarrays. We found considerable transcriptomic variation between ‘ancient’ and ‘modern’ genotypes in both treatments, with stressful (low P) conditions eliciting differential expression (DE) of a larger number of genes. Further, more genes were DE between ‘ancient’ and ‘modern’ genotypes than within these groups. Expression patterns of individual genes differed greatly among genotypes, suggesting that different transcriptomic responses can result in similar phenotypes. While this confounded patterns between ‘ancient’ and ‘modern’ genotypes at the gene level, patterns were discernible at the functional level: annotation of DE genes revealed particular enrichment of genes involved in metabolic pathways in response to P‐treatments. Analyses of gene families suggested significant DE in pathways already known to be important in dealing with P‐limitation in Daphnia as well as in other organisms. Such observations on genotypes of a single natural population, separated by hundreds of years of evolution in contrasting environmental conditions before and during anthropogenic environmental changes, highlight the important role of transcriptional mechanisms in the evolutionary responses of populations.
Biomechanical consequences of branching in flexible wave‐swept macroalgae
Authors: Starko Samuel , Claman Barry Z. , Martone Patrick T. 
Published: November 2014

Summary

Wave‐swept macroalgae present an excellent system for studying the effects of chronic physical stress on the morphological evolution of plants. Wave‐induced water velocities impose great drag forces, leading to a morphological tradeoff between light interception and drag reduction/tolerance. What are the hydrodynamic consequences of morphological diversification, such as increased branching?

Drag was measured on artificial macroalgae of constant ‘photosynthetic’ area, but differing branching patterns, in a high‐speed flume at water velocities up to 3.5 m s−1. A meta‐analysis was used to compare dislodgement forces of branched and unbranched species of comparable sizes in the field to determine if drag‐prone morphologies had greater attachment strengths.

Branched fronds experienced greater drag than unbranched fronds of the same size. Greater drag in branched forms was not the result of increased projected area but probably resulted from greater pressure or friction drag. In the field, branched species resisted greater dislodgement forces than unbranched species of comparable size, suggesting that branched species compensate for increased drag with stronger attachment to the substratum.

Branching has clear biomechanical consequences, increasing drag and the need for increased attachment. This raises questions about physiological and ecological advantages that may have driven the repeated evolution of biomechanically costly, branched morphologies.
Internal and external factors affecting photosynthetic pigment composition in plants: a meta‐analytical approach
Authors: Esteban Raquel , Barrutia Oihana , Artetxe Unai , Fernández‐Marín Beatriz , Hernández Antonio , García‐Plazaola José Ignacio 
Published: November 2014

Summary

Photosynthetic pigment composition has been a major study target in plant ecophysiology during the last three decades. Although more than 2000 papers have been published, a comprehensive evaluation of the responses of photosynthetic pigment composition to environmental conditions is not yet available.

After an extensive survey, we compiled data from 525 papers including 809 species (subkingdom Viridiplantae) in which pigment composition was described. A meta‐analysis was then conducted to assess the ranges of photosynthetic pigment content.

Calculated frequency distributions of pigments were compared with those expected from the theoretical pigment composition. Responses to environmental factors were also analysed. The results revealed that lutein and xanthophyll cycle pigments (VAZ) were highly responsive to the environment, emphasizing the high phenotypic plasticity of VAZ, whereas neoxanthin was very stable.

The present meta‐analysis supports the existence of relatively narrow limits for pigment ratios and also supports the presence of a pool of free ‘unbound’ VAZ. Results from this study provide highly reliable ranges of photosynthetic pigment contents as a framework for future research on plant pigments.
Loss of periodicity in breeding success of waders links to changes in lemming cycles in Arctic ecosystems
Authors: Aharon‐Rotman Yaara , Soloviev Mikhail , Minton Clive , Tomkovich Pavel , Hassell Chris , Klaassen Marcel 
Published: November 2014

Lemming population cycles in the Arctic have an important impact on the Arctic food web, indirectly also affecting breeding success in Arctic‐nesting birds through shared predators. Over the last two decades lemming cycles have changed in amplitude and even disappeared in parts of the Arctic. To examine the large scale effect of these recent changes we re‐analysed published data from the East Atlantic Flyway (EAF), where a relationship between lemming cycles and wader breeding success was earlier found, and new data on breeding success of waders in the East Asian–Australasian Flyway (EAAF).We found that 1) any long‐term periodicities in wader breeding success existed only until the year 2000 in the EAAF and until the 1980s in the EAF; 2) studying these patterns at a smaller spatial scale, where the Siberian–Alaskan breeding grounds were divided into five geographical units largely based on landscape features, breeding success of waders from the EAAF was not correlated to an index of predation pressure, but positively correlated to Arctic summer temperatures in some species. We argue that fading out of lemming cycles in some parts of the Arctic is responsible for faltering periodicity in wader breeding success along both flyways. These changed conditions have not yet resulted in any marked changing trends in breeding success across years, and declining numbers of waders along the EAAF are therefore more likely a result of changing conditions at stop‐over and wintering sites.
Safety and Immunogenicity of Escalating Dosages of a Single Oral Administration of Peru-15 pCTB, a Candidate Live, Attenuated Vaccine against Enterotoxigenic Escherichia coli and Vibrio cholerae
Authors: Chen Wilbur H. , Garza Jose , Choquette Monique , Hawkins Jennifer , Hoeper Amy , Bernstein David I. , Cohen Mitchell B. 
Published: November 2014

ABSTRACTEnterotoxigenicEscherichia coli(ETEC) organisms are a leading cause of infectious diarrhea in developing countries. A live, attenuated cholera strain that expresses high levels of the nontoxic B subunit of cholera toxin, which might also serve as an ETEC protective antigen, was evaluated for safety, excretion, and immunogenicity in healthy volunteers. We enrolled four inpatient dose-escalation cohorts of 15 to 16 eligible subjects to randomly (3:1) receive a single oral dose of vaccine or placebo (buffer alone), evaluating 1 ×107, 1 ×108, 1 ×109, and 1 ×1010CFU of the vaccine. The vaccine was well tolerated, although some subjects experienced moderate diarrhea. The serum Inaba vibriocidal antibody response appeared to display a dose-response relationship with increasing dosages of vaccine, plateauing at the 109-CFU dosage. The serum antitoxin (cholera toxin and heat-labile enterotoxin) antibody seroconversion rate (4-fold increase over baseline) also appeared to display a dose-response relationship. The vaccine strain was excreted in stool cultures, displaying a dose-response relationship. A single oral dose of Peru-15 pCTB at dosages up to 1 ×1010CFU was safe and immunogenic in this first-in-human trial. These encouraging data support the ongoing clinical development of this candidate combined cholera and ETEC vaccine. (This study has been registered at ClinicalTrials.gov under registration no. NCT00654108.)
Successful Protection against Tularemia in C57BL/6 Mice Is Correlated with Expansion of Francisella tularensis-Specific Effector T Cells
Authors: Griffin Amanda J. , Crane Deborah D. , Wehrly Tara D. , Bosio Catharine M. 
Published: November 2014

ABSTRACTFrancisella tularensisis an intracellular, Gram-negative bacterium that causes the fatal disease tularemia. Currently, there are no licensed vaccines for tularemia and the requirements for protection against infection are poorly defined. To identify correlates of vaccine-induced immunity against tularemia, we compared different strains of the live vaccine strain (LVS) for their relative levels of virulence and ability to protect C57BL/6 mice against challenge with virulentF. tularensisstrain SchuS4. Successful vaccination, as defined by survival of C57BL/6 mice, was correlated with significantly greater numbers of effector T cells in the spleen and lung. Further, lung cells and splenocytes from fully protected animals were more effective than lung cells and splenocytes from vaccinated but nonimmune animals in limiting intracellular replication of SchuS4in vitro. Together, our data provide a unique model to compare efficacious vaccines to nonefficacious vaccines, which will enable comprehensive identification of host and bacterial components required for immunization against tularemia.
First Case Report of Fatal Sepsis Due to Campylobacter upsaliensis
Authors: Nakamura Itaru , Omori Nami , Umeda Ayaka , Ohkusu Kiyofumi , Matsumoto Tetsuya 
Published: November 2014

ABSTRACT

We encountered a rare case of severe fatal infection in a 70-year-old woman due to
Campylobacter upsaliensis
, identified by PCR amplification and sequencing analysis of the 16S rRNA gene using DNA extracted from the isolates. To our knowledge, fatal sepsis due to this organism has never been described to date.
Campylobacter concisus Pseudo-Outbreak Caused by Improved Culture Conditions
Authors: Casanova Carlo , Schweiger Alexander , von Steiger Niklaus , Droz Sara , Marschall Jonas 
Published: November 2014

ABSTRACTAn unusual increase in the number ofCampylobacter concisusisolates found in stool cultures provoked an outbreak investigation at Bern University Hospital. No epidemiological links were found between the cases, and theCampylobacterisolates were clonally unrelated. A change in culture conditions to a hydrogen-rich atmosphere enhancing growth ofC. concisuswas deemed responsible for this pseudo-outbreak.
Microsatellite (STR
Af
) Genotyping Cannot Differentiate between Invasive and Colonizing Aspergillus fumigatus Isolates
Authors: Escribano Pilar , Peláez Teresa , Bouza Emilio , Guinea Jesús 
Published: November 2014

ABSTRACT

We studied whether short tandem repeats of
Aspergillus fumigatus
(STR
Af
) can differentiate between invasive and colonizing genotypes of
A. fumigatus
. Of the 395 genotypes detected (
n
= 1,373 isolates), 50 were clusters and 24 (6% of all genotypes) involved the patients with invasive aspergillosis and those colonized with
A. fumigatus
, indicating that genotyping cannot discriminate between invasive and colonizing isolates.
Identification of RISC-Associated Adenoviral MicroRNAs, a Subset of Their Direct Targets, and Global Changes in the Targetome upon Lytic Adenovirus 5 Infection
Authors: Bellutti Florian , Kauer Maximilian , Kneidinger Doris , Lion Thomas , Klein Reinhard 
Published: November 2014

ABSTRACT
Adenoviruses encode a set of highly abundant microRNAs (mivaRNAs), which are generated by Dicer-mediated cleavage of the larger noncoding virus-associated RNAs (VA RNAs) I and II. We performed deep RNA sequencing to thoroughly investigate the relative abundance of individual single strands of mivaRNA isoforms in human A549 cells lytically infected with human adenovirus 5 (Ad5) at physiologically relevant multiplicities of infection (MOIs). In addition, we investigated their relative abundance in the endogenous RNA-induced silencing complexes (RISCs). The occupation of endogenous RISCs by mivaRNAs turned out to be pronounced but not as dominant as previously inferred from experiments with AGO2-overexpressing cells infected at high MOIs. In parallel, levels of RISC-incorporated mRNAs were investigated as well. Analysis of mRNAs enriched in RISCs in Ad5-infected cells revealed that only mRNAs with complementarity to the seed sequences of mivaRNAs derived from VA RNAI but not VA RNAII were overrepresented among them, indicating that only mivaRNAs derived from VA RNAI are likely to contribute substantially to the posttranscriptional downregulation of host gene expression. Furthermore, to generate a comprehensive picture of the entire transcriptome/targetome in lytically infected cells, we determined changes in cellular miRNA levels in both total RNA and RISC RNA as well, and bioinformatical analysis of mRNAs of total RNA/RISC fractions revealed a general, genome-wide trend toward detargeting of cellular mRNAs upon infection. Lastly, we identified the direct targets of both single strands of a VA RNAI-derived mivaRNA that constituted one of the two most abundant isoforms in RISCs of lytically infected A549 cells.

IMPORTANCE
Viral and cellular miRNAs have been recognized as important players in virus-host interactions. This work provides the currently most comprehensive picture of the entire mRNA/miRNA transcriptome and of the complete RISC targetome during lytic adenovirus infection and thus represents the basis for a deeper understanding of the interplay between the virus and the cellular RNA interference machinery. Our data suggest that, at least in the model system that was employed, lytic infection by Ad5 is accompanied by a measurable global net detargeting effect on cellular mRNAs, and analysis of RISC-associated viral small RNAs revealed that the VA RNAs are the only source of virus-encoded miRNAs. Moreover, this work allows to assess the power of individual viral miRNAs to regulate cellular gene expression and provides a list of proven and putative direct targets of these miRNAs, which is of importance, given the fact that information about validated targets of adenovirus-encoded miRNAs is scarce.
A Live Attenuated Equine H3N8 Influenza Vaccine Is Highly Immunogenic and Efficacious in Mice and Ferrets
Authors: Baz Mariana , Paskel Myeisha , Matsuoka Yumiko , Zengel James , Cheng Xing , Treanor John J. , Jin Hong , Subbarao Kanta 
Published: November 2014

ABSTRACTEquine influenza viruses (EIV) are responsible for rapidly spreading outbreaks of respiratory disease in horses. Although natural infections of humans with EIV have not been reported, experimental inoculation of humans with these viruses can lead to a productive infection and elicit a neutralizing antibody response. Moreover, EIV have crossed the species barrier to infect dogs, pigs, and camels and therefore may also pose a threat to humans. Based on serologic cross-reactivity of H3N8 EIV from different lineages and sublineages, A/equine/Georgia/1/1981 (eq/GA/81) was selected to produce a live attenuated candidate vaccine by reverse genetics with the hemagglutinin and neuraminidase genes of the eq/GA/81 wild-type (wt) virus and the six internal protein genes of the cold-adapted (ca) A/Ann Arbor/6/60 (H2N2) vaccine donor virus, which is the backbone of the licensed seasonal live attenuated influenza vaccine. In both mice and ferrets, intranasal administration of a single dose of the eq/GA/81cavaccine virus induced neutralizing antibodies and conferred complete protection from homologous wt virus challenge in the upper respiratory tract. One dose of the eq/GA/81cavaccine also induced neutralizing antibodies and conferred complete protection in mice and nearly complete protection in ferrets upon heterologous challenge with the H3N8 (eq/Newmarket/03) wt virus. These data support further evaluation of the eq/GA/81cavaccine in humans for use in the event of transmission of an equine H3N8 influenza virus to humans.IMPORTANCEEquine influenza viruses have crossed the species barrier to infect other mammals such as dogs, pigs, and camels and therefore may also pose a threat to humans. We believe that it is important to develop vaccines against equine influenza viruses in the event that an EIV evolves, adapts, and spreads in humans, causing disease. We generated a live attenuated H3N8 vaccine candidate and demonstrated that the vaccine was immunogenic and protected mice and ferrets against homologous and heterologous EIV.
Syntaxin 5-Dependent Retrograde Transport to the
trans
-Golgi Network Is Required for Adeno-Associated Virus Transduction
Authors: Nonnenmacher Mathieu E. , Cintrat Jean-Christophe , Gillet Daniel , Weber Thomas 
Published: November 2014

ABSTRACT

Intracellular transport of recombinant adeno-associated virus (AAV) is still incompletely understood. In particular, the trafficking steps preceding the release of incoming AAV particles from the endosomal system into the cytoplasm, allowing subsequent nuclear import and the initiation of gene expression, remain to be elucidated fully. Others and we previously showed that a significant proportion of viral particles are transported to the Golgi apparatus and that Golgi apparatus disruption caused by the drug brefeldin A efficiently blocks AAV serotype 2 (AAV2) transduction. However, because brefeldin A is known to exert pleiotropic effects on the entire endosomal system, the functional relevance of transport to the Golgi apparatus for AAV transduction remains to be established definitively. Here, we show that AAV2 trafficking toward the
trans
-Golgi network (TGN) and the Golgi apparatus correlates with transduction efficiency and relies on a nonclassical retrograde transport pathway that is independent of the retromer complex, late endosomes, and recycling endosomes. AAV2 transduction is unaffected by the knockdown of syntaxins 6 and 16, which are two major effectors in the retrograde transport of both exogenous and endogenous cargo. On the other hand, inhibition of syntaxin 5 function by small interfering RNA silencing or treatment with cyclized Retro-2 strongly decreases AAV2 transduction and transport to the Golgi apparatus. This inhibition of transduction is observed with several AAV serotypes and a number of primary and immortalized cells. Together, our data strongly suggest that syntaxin 5-mediated retrograde transport to the Golgi apparatus is a broadly conserved feature of AAV trafficking that appears to be independent of the identity of the receptors used for viral attachment.

IMPORTANCE
Gene therapy constitutes a promising approach for the treatment of life-threatening conditions refractory to any other form of remedy. Adeno-associated virus (AAV) vectors are currently being evaluated for the treatment of diseases such as Duchenne muscular dystrophy, hemophilia, heart failure, Parkinson's disease, and others. Despite their promise as gene delivery vehicles, a better understanding of the biology of AAV-based vectors is necessary to improve further their efficacy. AAV vectors must reach the nucleus in order to deliver their genome, and their intracellular transport is not fully understood. Here, we dissect an important step of the intracellular journey of AAV by showing that retrograde transport of capsids to the
trans
-Golgi network is necessary for gene delivery. We show that the AAV trafficking route differs from that of known Golgi apparatus-targeted cargos, and we raise the possibility that this nonclassical pathway is shared by most AAV variants, regardless of their attachment receptors.
Identification of the Physiological Gene Targets of the Essential Lytic Replicative Kaposi's Sarcoma-Associated Herpesvirus ORF57 Protein
Authors: Verma Dinesh , Li Da-Jiang , Krueger Brian , Renne Rolf , Swaminathan Sankar 
Published: November 2014

ABSTRACT
The Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 gene product is essential for lytic KSHV replication and virion production. Recombinant ORF57-null mutants fail to accumulate several lytic cycle mRNAs at wild-type levels, leading to decreased production of lytic proteins necessary for efficient replication. Several mechanisms by which ORF57 may enhance expression of lytic KSHV mRNAs have been proposed, including mRNA stabilization, mRNA nuclear export, increased polyadenylation, and transcriptional activation. ORF57 activity is also gene specific, with some genes being highly dependent on ORF57, whereas others are relatively independent. Most experiments have utilized transfection models for ORF57 and have not systematically examined the gene specificity and potential mechanisms of action of ORF57 in the context of KSHV-infected cells. In this study, the KSHV genes that are most highly upregulated by ORF57 during KSHV lytic replication were identified by a combination of high-throughput deep RNA sequencing, quantitative PCR, Northern blotting, and rapid amplification of cDNA ends methods. Comparison of gene expression from a ΔORF57 KSHV recombinant, a rescued ΔORF57 KSHV recombinant, and wild-type KSHV revealed that two clusters of lytic genes are most highly dependent on ORF57 for efficient expression. Despite contiguous location in the genome and shared polyadenylation of several of the ORF57-dependent genes, ORF57 regulation was promoter and polyadenylation signal independent, suggesting that the mRNAs are stabilized by ORF57. The eight genes identified to critically require ORF57 belong to both early and late lytic temporal classes, and seven are involved in DNA replication, virion assembly, or viral infectivity, explaining the essential role of ORF57 in infectious KSHV production.

IMPORTANCE
Kaposi's sarcoma-associated herpesvirus (KSHV) is a human herpesvirus involved in the causation of several human cancers. The KSHV ORF57 protein is required for KSHV to replicate and produce infectious virus. We have identified several KSHV genes whose expression is highly dependent on ORF57 and shown that ORF57 increases expression of these genes specifically. These genes code for proteins that are required for the virus to replicate its DNA and to infect other cells. Identifying the targets and mechanism of action of ORF57 provides further approaches to discover antiviral therapy.