bluuebunny/crossref_metadata_2025 huggingface dataset:
Computing protein dynamics from protein structure with elastic network models
Authors: Bastolla Ugo
Published: April 2014

Elastic network models ENMs allow to analytically predict the equilibrium dynamics of proteins without the need of lengthy simulations and force fields, and they depend on a small number of parameters and choices. Despite they are valid only for small fluctuations from the mean native structure, it was observed that large functional conformation changes are well described by a small number of low frequency normal modes. This observation has greatly stimulated the application of ENMs for studying the functional dynamics of proteins, and it is prompting the question whether this functional dynamics is a target of natural selection. From a physical point of view, the agreement between low frequency normal modes and large conformation changes is stimulating the study of anharmonicity in protein dynamics, probably one of the most interesting direction of development in ENMs. ENMs have many applications, of which we will review four general types: (1) the efficient sampling of native conformation space, with applications to molecular replacement in X‐ray spectroscopy, cryo electro‐miscroscopy, docking and homology modeling; (2) the prediction of paths of conformation change between two known end states; (3) the comparison of the dynamics of evolutionarily related proteins; (4) the prediction of dynamical couplings that allow the allosteric regulation of the active site from a distant control regions, with possible applications in the development of allosteric drugs. These goals have important biotechnological applications that are driving more and more attention on the analytical study of protein dynamics through ENMs. WIREs Comput Mol Sci 2014, 4:488–503.

This article is categorized under:

Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Two‐year cyclicity in recruitment of a fish population is driven by an inter‐stage effect
Authors: Marjomäki Timo J. , Urpanen Olli , Karjalainen Juha
Published: April 2014

A 25‐year time series for a vendace (Coregonus albula (L.)) population was analysed with mathematical models to reveal the factors that regulate its recruitment. The fitted recruitment model was an age‐structured model incorporating the compensatory effects of the spawning population and the abundance of the previous year class. Wind forcing index was also added as an example of an external source of recruitment variability. The auto‐correlation analysis revealed a tendency for 2‐year generation cyclicity in recruitment. The compensatory effects of both spawning biomass and previous year class abundance on recruitment had to be incorporated into the model to remove cyclicity from residuals. Wind forcing during the larval and early juvenile periods negatively affected recruitment. Re‐estimating the parameters of the Cushing recruitment function and the effect of previous year‐class from simulated data revealed that the time series structure and measurement errors induce strong biases in parameters exaggerating the density independent population growth rate parameter and the amount of compensation. The negative effect of previous year class was also exaggerated but less severely. Simulations with the artificially perturbed deterministic model skeleton revealed a tendency for cyclicity in recruitment. The model typically generated dampening oscillations, but the dynamics appeared as limit cycles when assuming high mortality, a low level of compensation by spawning biomass and a considerable negative effect of the previous year‐class. No single ultimate mechanism for inter‐stage effects causing cyclicity can be presently designated despite the rather extensive studies on vendace population dynamics. Several of the suggested mechanisms may be operating in concert.
Covariation between mean vole density and variability drives the numerical response of storks to vole prey
Authors: Barraquand Frédéric , Hušek Jan
Published: April 2014

Hušek et al. (Popul Ecol 55:363–375, 2013) showed that the numerical response of storks to vole prey was stronger in regions where variability in vole density was higher. This finding is, at first sight, in contradiction with the predictions of life‐history theory in stochastic environments. Since the stork productivity‐vole density relationship is concave, theory predicts a negative association between the temporal variability in vole density and stork productivity. Here, we illustrate this negative effect of vole variability on stork productivity with a simple mathematical model relating expected stork productivity to vole dynamics. When comparing model simulations to the observed mean density and variability of thirteen Czech and Polish vole populations, we find that the observed positive effect of vole variability on stork numerical response is most likely due to an unusual positive correlation between mean and variability of vole density.
Does darkness limit the use of tree cavities for nesting by birds?
Authors: Maziarz Marta , Wesołowski Tomasz
Published: April 2014

Tree cavities are usually superabundant, and offer the safest nest sites. However, not all bird species utilize them. One of the reasons could be insufficient illumination in such places. As no visual system can operate in complete darkness, some nest cavities may be too dark to be usable even by cavity nesters, and some species may not have sufficient visual sensitivity to make use of dark cavities. So, presumably, light conditions could constrain both the evolution of the cavity-nesting habit and the selection of the nest site by the cavity-nesting birds. However, due to a paucity of data on light conditions in cavities, these suggestions have not been investigated to date. To provide more information on illumination inside tree cavities, we took measurements inside the nest cavities of Collared FlycatchersFicedula albicollisbreeding in a primeval forest (Białowieża National Park, Poland). Illuminance inside cavities was recorded at daybreak, just after the parents commenced feeding nestlings. We found that only ca. 4 % of incoming light reached the nest level, and birds could adjust light conditions inside cavities by placing their nests closer to smaller entrances. Illuminance at nests (median = 0.05 lx) fell within the mesopic–scotopic range of vertebrate eyes. Measurements performed on a sunny, cloudless midday in a model cavity showed that illuminance strongly decreased with distance from the entrance. Our results indicate cavities are always dark places where colour vision is usually impaired or absent and the “lighting” requirements of cavity nesters can affect their use of tree cavities. We discuss the implications of the findings for understanding the adaptations of cavity nesting in birds.
Characterization of miRNomes in Acute and Chronic Myeloid Leukemia Cell Lines
Authors: Xiong Qian , Yang Yadong , Wang Hai , Li Jie , Wang Shaobin , Li Yanming , Yang Yaran , Cai Kan , Ruan Xiuyan , Yan Jiangwei , Hu Songnian , Fang Xiangdong
Published: April 2014

Myeloid leukemias are highly diverse diseases and have been shown to be associated with microRNA (miRNA) expression aberrations. The present study involved an in-depth miRNome analysis of two human acute myeloid leukemia (AML) cell lines, HL-60 and THP-1, and one human chronic myeloid leukemia (CML) cell line, K562, via massively parallel signature sequencing. mRNA expression profiles of these cell lines that were established previously in our lab facilitated an integrative analysis of miRNA and mRNA expression patterns. miRNA expression profiling followed by differential expression analysis and target prediction suggested numerous miRNA signatures in AML and CML cell lines. Some miRNAs may act as either tumor suppressors or oncomiRs in AML and CML by targeting key genes in AML and CML pathways. Expression patterns of cell type-specific miRNAs could partially reflect the characteristics of K562, HL-60 and THP-1 cell lines, such as actin filament-based processes, responsiveness to stimulus and phagocytic activity. miRNAs may also regulate myeloid differentiation, since they usually suppress differentiation regulators. Our study provides a resource to further investigate the employment of miRNAs in human leukemia subtyping, leukemogenesis and myeloid development. In addition, the distinctive miRNA signatures may be potential candidates for the clinical diagnosis, prognosis and treatment of myeloid leukemias.
Integrating Historic Site-Based Laboratories into Pre-Service Teacher Education
Authors: Baron Christine , Woyshner Christine , Haberkern Philip
Published: April 2014

In order to change the perception of history as collection facts, historians and history educators must countermand pre-service history teachers’ experience with and perception of historians as mere transmitters of knowledge. To do this, historians and history educators must provide pre-service history teachers’ opportunities to work alongside historians in the field as a regular feature of their preparation programs. This exposure not only changes the pre-service teachers’ perceptions of the work of history practitioners and provides deeper understanding of the construction of history, but also enables future teachers to expand their use of site-based learning in their classrooms. Rather than advocating the development of entirely new programs, the authors outline two models, based on the history education programs at Temple University and Boston University, for integrating historic site-based laboratory work into the existing structures of teacher education programs.
Expression patterns of bone morphogenetic protein antagonists in colorectal cancer desmoplastic invasion fronts
Authors: Karagiannis George S. , Treacy Ann , Messenger David , Grin Andrea , Kirsch Richard , Riddell Robert H. , Diamandis Eleftherios P.
Published: April 2014

Bone morphogenetic proteins (BMPs) are a group of growth factors with dual functions in cancer development and progression. Recently, certain tumor‐promoting roles have been identified for selected antagonists/inhibitors (BMPIs) of this developmental pathway. A recent focus on the implication of BMP in colorectal cancer progression has emerged, mainly due to the presence of inactivating mutations in several members of the canonical signaling cascade. However, the detailed expression profiles of BMPIs remain largely unknown. Based on our previous work, whereby three specific BMPIs, gremlin‐1 (GREM1), high‐temperature requirement A3 (HTRA3) and follistatin (FST) were collectively overexpressed in desmoplastic cocultures of colorectal cancer (CRC), here, we undertook an immunohistochemical approach to describe the patterns of their expression in CRC patients. Two major characteristics described the BMPI expression signature: First, the synchronous and coordinated stromal and epithelial overexpression of individual BMPIs in desmoplastic lesions, which demonstrated that all three of them contribute to increasing levels of BMP antagonism in such areas. Second, the presence of microenvironmental polarity in the BMPI pattern of expression, which was indicated through the preferential expression of HTRA3 in the stromal, and the parallel FST/GREM1 expression in the epithelial component of the investigated sections. In addition, expression of HTRA3 in the epithelial compartment of the tumors demonstrated a significant predictive power to discriminate between tumor‐budding‐bearing and tumor‐budding‐free desmoplastic microenvironments. Together, these findings contribute to the understanding of signaling dynamics of BMP antagonism in the colorectal cancer desmoplastic invasion front.
Interventions for Attention Problems After Pediatric Traumatic Brain Injury: What Is the Evidence?
Authors: Backeljauw Barynia , Kurowski Brad G.
Published: April 2014

Objective

To gain an understanding of the current state of the evidence for management of attention problems after traumatic brain injury (TBI) in children, determine gaps in the literature, and make recommendations for future research.

Type

Focused systematic review.

Literature Survey

PubMed/Medline and PsychINFO databases were searched for relevant articles published in English during the last 20 years. Keywords included “attention” “attention deficit and disruptive behavior disorders,” and “brain injuries.” Studies were limited to children.

Methodology

Titles were examined first and eliminated based on lack of relevancy to attention problems after brain injury in children. This was followed by an abstract and full text review. Article quality was determined based on the US Preventative Services Task Force recommendations for evidence grading.

Synthesis

Four pharmacologic and 10 cognitive therapy intervention studies were identified. These studies varied in level of evidence quality but were primarily nonrandomized or cohort studies.

Conclusions

There are studies that demonstrate benefits of varying pharmacologic and cognitive therapies for the management of attention problems after TBI. However, there is a paucity of evidence available to definitively guide management of attention problems after pediatric TBI. Larger randomized, controlled trials and multicenter studies are needed to elucidate optimal treatment strategies in this population.
Interesting Case: Displacement of Fractured Maxilla into Pharyngeal Space
Authors: Krishnan Balasubramanian , Parida PradiptaKumar , Gopalakrishnan Surianarayanan
Published: April 2014

Atypical fracture patterns of the facial region have been reported infrequently. An unusual displacement of fractured posterior maxillary segment into the lateral pharyngeal space is described.
A Biomechanical Comparison of Three 1.5-mm Plate and Screw Configurations and a Single 2.0-mm Plate for Internal Fixation of a Mandibular Condylar Fracture
Authors: Aquilina Peter , Parr William C.H. , Chamoli Uphar , Wroe Stephen , Clausen Philip
Published: April 2014

The most stable pattern of internal fixation for mandibular condyle fractures is an area of ongoing discussion. This study investigates the stability of three patterns of plate fixation using readily available, commercially pure titanium implants. Finite element models of a simulated mandibular condyle fracture were constructed. The completed models were heterogeneous in bone material properties, contained approximately 1.2 million elements and incorporated simulated jaw adducting musculature. Models were run assuming linear elasticity and isotropic material properties for bone. No human subjects were involved in this investigation. The stability of the simulated condylar fracture reduced with the different implant configurations, and the von Mises stresses of a 1.5-mm X-shaped plate, a 1.5-mm rectangular plate, and a 1.5-mm square plate (all Synthes (Synthes GmbH, Zuchwil, Switzerland) were compared. The 1.5-mm X plate was the most stable of the three 1.5-mm profile plate configurations examined and had comparable mechanical performance to a single 2.0-mm straight four-hole plate. This study does not support the use of rectangular or square plate patterns in the open reduction and internal fixation of mandibular condyle fractures. It does provide some support for the use of a 1.5-mm X plate to reduce condylar fractures in selected clinical cases.
Cortical control of adaptation and sensory relay mode in the thalamus
Authors: Mease Rebecca A. , Krieger Patrik , Groh Alexander
Published: April 2014

Significance

Given the mismatch between the nervous system's limited computational capability and the immense information content of the sensory environment, the brain must selectively focus attention on relevant stimulus aspects. “Sensory gating” describes the filtering of relevant sensory cues from irrelevant or redundant stimuli. One such filter may involve cortical control of sensory relay through the thalamus. Using optogenetics to turn on specific cortical input to the thalamus, we investigated how the brain actively controls and gates the information that reaches higher stages of processing in the cortex. We found that this pathway, conserved across most mammalian sensory systems, serves as an effective top-down controller of thalamic gating of dynamic patterns of sensory input.
Long-range repulsion of colloids driven by ion exchange and diffusiophoresis
Authors: Florea Daniel , Musa Sami , Huyghe Jacques M. R. , Wyss Hans M.
Published: April 2014

Significance

The ability to displace particles or solutes relative to a background liquid is of central importance to technologies such as filtration/separation, chromatography, and water purification. Such behavior is observed in so-called exclusion zone formation, an effect where particles are pushed away from a surface over long distances of up to hundreds of micrometers. However, it is still unclear which physical mechanisms are responsible. Our work provides a detailed understanding of this exclusion zone formation, enabling a precise control of the behavior. This could be exploited, for instance, for sorting in microfluidic devices, in advanced antifouling coatings, or for elucidating biological processes where it is likely to play an important, yet unexplored role.
Stoichiometry and specific assembly of Best ion channels
Authors: Bharill Shashank , Fu Zhu , Palty Raz , Isacoff Ehud Y.
Published: April 2014

Significance

Human Bestrophin (hBest) proteins represent a four-member family of calcium-activated chloride channels that regulate neuronal excitability, synaptic activity and retinal homeostasis. The number of subunits in a hBest channel and the ability to form heteromeric channels have been matters of debate. Using single molecule subunit analysis, we find that each of the hBest channels forms a homotetrameric channel. Despite considerable conservation among hBests, the members have little or no tendency to hetero-assemble. We identify the domain responsible for homo-assembly specificity.
CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference
Authors: Hochstrasser Megan L. , Taylor David W. , Bhat Prashant , Guegler Chantal K. , Sternberg Samuel H. , Nogales Eva , Doudna Jennifer A.
Published: April 2014

Significance

Bacteria use clustered regularly interspaced short palindromic repeats (CRISPRs) together with CRISPR-associated (Cas) proteins to defend themselves against viral infection. The CRISPR locus contains short segments acquired from viral genomes, and RNAs derived from these segments assemble with Cas proteins into programmable DNA-binding complexes that target DNA molecules complementary to the guide RNA for cleavage. In type I CRISPR-Cas systems, the CRISPR-associated complex for antiviral defense (Cascade) binds to target DNA sequences and then recruits the Cas3 enzyme to repeatedly cleave the bound DNA. In this study, we show how Cascade positions both the DNA and Cas3 to ensure DNA cleavage.
Critical Perspectives on Successful Aging: Does It “Appeal More Than It Illuminates”?
Authors: Katz Stephen , Calasanti Toni
Published: April 2014

“Successful aging” is one of gerontology’s most successful ideas. Applied as a model, a concept, an approach, an experience, and an outcome, it has inspired researchers to create affiliated terms such as “healthy,” “positive,” “active,” “productive,” and “effective” aging. Although embraced as an optimistic approach to measuring life satisfaction and as a challenge to ageist traditions based on decline, successful aging as defined by John Rowe and Robert Kahn has also invited considerable critical responses. This article takes a critical gerontological perspective to explore such responses to the Rowe–Kahn successful aging paradigm by summarizing its empirical and methodological limitations, theoretical assumptions around ideas of individual choice and lifestyle, and inattention to intersecting issues of social inequality, health disparities, and age relations. The latter point is elaborated with an examination of income, gender, racial, ethnic, and age differences in the United States. Conclusions raise questions of social exclusion and the future of successful aging research.
Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes
Authors: Melnikov Alexandre , Rogov Peter , Wang Li , Gnirke Andreas , Mikkelsen Tarjei S
Published: April 2014

Deep mutational scanning has emerged as a promising tool for mapping sequence-activity relationships in proteins, RNA and DNA. In this approach, diverse variants of a sequence of interest are first ranked according to their activities in a relevant pooled assay, and this ranking is then used to infer the shape of the fitness landscape around the wild-type sequence. Little is currently know, however, about the degree to which such fitness landscapes are dependent on the specific assay conditions from which they are inferred. To explore this issue, we performed deep mutational scanning of APH(3')II, a Tn5 transposon-derived kinase that confers resistance to aminoglycoside antibiotics, in E. coli under selection with each of six structurally diverse antibiotics at a range of inhibitory concentrations. We found that the resulting fitness landscapes showed significant dependence on both antibiotic structure and concentration. This shows that the notion of essential amino acid residues is context-dependent, but also that this dependence can be exploited to guide protein engineering. Specifically, we found that differential analysis of fitness landscapes allowed us to generate synthetic APH(3')II variants with orthogonal substrate specificities.
The ARC1 E3 Ligase Promotes Two Different Self-Pollen Avoidance Traits inArabidopsis
Authors: Indriolo Emily , Safavian Darya , Goring Daphne R.
Published: April 2014

Flowering plants have evolved various strategies for avoiding self-pollen to drive genetic diversity. These strategies include spatially separated sexual organs (herkogamy), timing differences between male pollen release and female pistil receptivity (dichogamy), and self-pollen rejection. Within the Brassicaceae, these outcrossing systems are the evolutionary default state, and many species display these traits, including Arabidopsis lyrata. In contrast to A. lyrata, closely related Arabidopsis thaliana has lost these self-pollen traits and thus represents an excellent system to test genes for reconstructing these evolutionary traits. We previously demonstrated that the ARC1 E3 ligase is required for self-incompatibility in two diverse Brassicaceae species, Brassica napus and A. lyrata, and is frequently deleted in self-compatible species, including A. thaliana. In this study, we examined ARC1's requirement for reconstituting self-incompatibility in A. thaliana and uncovered an important role for ARC1 in promoting a strong and stable pollen rejection response when expressed with two other A. lyrata self-incompatibility factors. Furthermore, we discovered that ARC1 promoted an approach herkogamous phenotype in A. thaliana flowers. Thus, ARC1's expression resulted in two different A. lyrata traits for self-pollen avoidance and highlights the key role that ARC1 plays in the evolution and retention of outcrossing systems.
The Enzyme-Like Domain of Arabidopsis Nuclear β-Amylases Is Critical for DNA Sequence Recognition and Transcriptional Activation
Authors: Soyk Sebastian , Šimková Klára , Zürcher Evelyne , Luginbühl Leonie , Brand Luise H. , Vaughan Cara K. , Wanke Dierk , Zeeman Samuel C.
Published: April 2014

Plant BZR1-BAM transcription factors contain a β-amylase (BAM)–like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains appear to be noncatalytic, but they determine the function of the two Arabidopsis thaliana BZR1-BAM isoforms (BAM7 and BAM8) during transcriptional initiation. Removal or swapping of the BAM domains demonstrates that the BAM7 BAM domain restricts DNA binding and transcriptional activation, while the BAM8 BAM domain allows both activities. Furthermore, we demonstrate that BAM7 and BAM8 interact on the protein level and cooperate during transcriptional regulation. Site-directed mutagenesis of residues in the BAM domain of BAM8 shows that its function as a transcriptional activator is independent of catalysis but requires an intact substrate binding site, suggesting it may bind a ligand. Microarray experiments with plants overexpressing truncated versions lacking the BAM domain indicate that the pseudo-enzymatic domain increases selectivity for the preferred cis-regulatory element BBRE (BZR1-BAM Responsive Element). Side specificity toward the G-box may allow crosstalk to other signaling networks. This work highlights the importance of the enzyme-derived domain of BZR1-BAMs, supporting their potential role as metabolic sensors.
The Cyanobacterial Photoactive Orange Carotenoid Protein Is an Excellent Singlet Oxygen Quencher
Authors: Sedoud Arezki , López-Igual Rocío , ur Rehman Ateeq , Wilson Adjélé , Perreau François , Boulay Clémence , Vass Imre , Krieger-Liszkay Anja , Kirilovsky Diana
Published: April 2014

Cyanobacteria have developed a photoprotective mechanism that decreases the energy arriving at the photosynthetic reaction centers under high-light conditions. The photoactive orange carotenoid protein (OCP) is essential in this mechanism as a light sensor and energy quencher. When OCP is photoactivated by strong blue-green light, it is able to dissipate excess energy as heat by interacting with phycobilisomes. As a consequence, charge separation and recombination leading to the formation of singlet oxygen diminishes. Here, we demonstrate that OCP has another essential role. We observed that OCP also protects Synechocystis cells from strong orange-red light, a condition in which OCP is not photoactivated. We first showed that this photoprotection is related to a decrease of singlet oxygen concentration due to OCP action. Then, we demonstrated that, in vitro, OCP is a very good singlet oxygen quencher. By contrast, another carotenoid protein having a high similarity with the N-terminal domain of OCP is not more efficient as a singlet oxygen quencher than a protein without carotenoid. Although OCP is a soluble protein, it is able to quench the singlet oxygen generated in the thylakoid membranes. Thus, OCP has dual and complementary photoprotective functions as an energy quencher and a singlet oxygen quencher.
Calcitriol inhibits keratinocyte proliferation by upregulating leukocyte elastase inhibitor (serpin B1)
Authors: Hui Li , Yongxia Zheng , Zhili Guo , Jun Gu
Published: April 2014

Calcitriol had been proved to be effective for treatment of psoriasis vulgaris. However, the molecular events leading to the normalization of keratinocyte differentiation had not been fully explored. The aim of the study was to evaluate the role of calcitriol and serpin B1 in human keratinocyte cell line (HaCaT) proliferation. Proteins extracted from calcitriol‐treated and untreated HaCaT were separated by 2‐D differential gel electrophoresis (2DE). Then, the 2DE profiles were analyzed to screen for differentially expressed proteins, which were identified by matrix‐assisted laser desorption/ionization time of flight mass spectrometry. The upregulation of serpin B1 was confirmed by quantitative reverse transcription polymerase chain reaction (qRT–PCR) and western blot analysis. The effect of serpin B1 on HaCaT proliferation was analyzed by RNA interference experiments, methylthiazoletetrazolium assay and flow cytometry. Reproducible 2‐DE profiles of HaCaT were established. The result that serpin B1 was upregulated in the calcitriol‐treated group was confirmed by qRT–PCR and western blot analysis. Calcitriol could inhibit proliferation of HaCaT at the concentration of 10−9–10−6 mol/L. HaCaT proliferation was promoted when serpin B1 was interfered. The inhibition effect of calcitriol was stopped after serpin B1 was interfered. Serpin B1 was overexpressed in calcitriol‐treated HaCaT cells and may play an important role in inhibiting HaCaT proliferation by calcitriol.
Entero‐Behçet's disease coexisting with long‐term epilepsy and schizophrenia‐like symptoms
Authors: Ohtsuka Tsutomu
Published: April 2014

Entero‐Behçet's disease coexisting with long‐term epilepsy and schizophrenia‐like symptoms is presented. A 43‐year‐old woman presented with repeatedly occurring aphthous stomatitis for several years. She had been treated for absence seizures, epilepsy and schizophrenia since she was 9 years old. She presented with multiple aphthous stomatitis on her gingiva, erythema nodosum‐like symptoms on the right lateral aspect of her leg and genital ulcers on her perianal area. She also showed polyarthritis. Laboratory examinations revealed elevated C‐reactive protein, elevated neutrophil counts, decreased serum Fe and elevated serum Cu. Histological examination showed perivascular neutrophil and mononuclear cell infiltrates and eosinophilic change of the vessel wall in the lobules of subcutaneous fat tissue. Six weeks after the oral prednisolone therapy, she showed resolution of aphthous stomatitis, folliculitis‐like eruption and genital ulcer. She experienced severe abdominal pain after the start of treatment of Behçet's disease. Plain computed tomography revealed edematous change in the appendix, and ascending and transverse colon. These results led to the diagnosis of entero‐Behçet's disease acute exaggeration. Treatment with infliximab (300 mg/once) was started. Eight weeks after the start of infliximab, her abdominal pain disappeared and C‐reactive protein decreased, followed by the successful change to adalimumab infusion therapy.
Mouse bone marrow‐derived dendritic cells can phagocytize the Sporothrix schenckii, and mature and activate the immune response by secreting interleukin‐12 and presenting antigens to T lymphocytes
Authors: Kusuhara Masahiro , Qian Hua , Li Xiaoguang , Tsuruta Daisuke , Tsuchisaka Atsunari , Ishii Norito , Ohata Chika , Furumura Minao , Hashimoto Takashi
Published: April 2014

In sporotrichosis, dermal dendritic cells were considered to participate in induction of the immune responses against Sporothrix schenckii infection. However, it is still unclear whether and how dermal dendritic cells were involved in the progress. To clarify the pathogenic role of dermal dendritic cells (DC) in sporotrichosis, we examined the phagocytosis, maturation stages, cytokine production and antigen‐presenting ability of mouse bone marrow‐derived DC after stimulation with S. schenckii. By analysis of flow cytometry, electron microscope and confocal microscope, mouse bone marrow‐derived DC were proved to be able to phagocytize the S. schenckii. The increased expression of CD40, CD80 and CD86 on the surface of S. schenckii‐pulsed mouse bone marrow‐derived DC was detected by flow cytometer, indicating that the S. schenckii‐pulsed mouse bone marrow‐derived DC underwent the maturation program. The secretory enhancement of interleukin (IL)‐12, but not IL‐4, was found in S. schenckii‐pulsed mouse bone marrow‐derived DC, suggesting the possible activation of T‐helper 1 prone immune responses. Furthermore, S. schenckii‐pulsed mouse bone marrow‐derived DC were demonstrated to be capable of inducing the proliferation of T lymphocytes from BALB/c mice that were pre‐sensitized with S. schenckii. Together, all the results implied that dermal DC may participate in the induction of immune responses against S. schenckii infection in sporotrichosis.
Temperature‐ and latitude‐specific individual growth rates shape the vulnerability of damselfly larvae to a widespread pesticide
Authors: Dinh Van Khuong , Janssens Lizanne , Debecker Sara , Stoks Robby
Published: April 2014

Freshwater ecosystems are especially vulnerable to climate change and pollution. One key challenge for aquatic toxicology is to determine and manage the combined effects of temperature increase and contaminants across species' ranges.

We tested how thermal adaptation and life‐history evolution along a natural temperature gradient influence the vulnerability of an aquatic insect to a pesticide under global warming. We applied a space‐for‐time substitution approach to study the effect of warming on the vulnerability of Ischnura elegans damselfly larvae to the pesticide chlorpyrifos in a common garden warming experiment (20 and 24 °C) with replicated populations from three latitudes spanning >1500 km in Europe.

Chlorpyrifos was more toxic to damselfly larvae at the higher temperature: mortality only occurred at 24 °C and the reductions in growth rate were stronger at 24 °C. This could partly be explained by parallel reductions in food intake but not by the activities of two widespread enzymatic biomarkers, glutathione S‐transferase (GST) and acetylcholinesterase (AChE).

There was some evidence that the increased toxicity of the high chlorpyrifos concentration at 24 °C was stronger in terms of growth reduction in the faster‐growing larvae from the low‐latitude populations. This is consistent with energy allocation trade‐offs between growth rate and pesticide tolerance, but suggests that local thermal adaptation does not play a role in coping with pesticide stress.

Synthesis and applications. Damselfly larvae from populations in lower latitudes were more vulnerable to a common pesticide at higher temperatures and pesticide concentrations, whereas evidence for the influence of local thermal adaptation on the vulnerability of larvae was weak. These results emphasize the need for spatially explicit bioassessment and conservation tools. Management practices aimed at mitigating pesticide run‐off into aquatic ecosystems are particularly important in agricultural areas at low latitudes.
Detection and monitoring of pink bollworm moths and invasive insects using pheromone traps and encounter rate models
Authors: Byers John A. , Naranjo Steven E.
Published: April 2014

The pink bollworm moth Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) is one of the most destructive pests in agriculture. An ongoing eradication program using a combination of sex pheromone monitoring and mating disruption, irradiated sterile moth releases, genetically modified Bt cotton and local insecticide applications have all but exterminated the pink bollworm from the south‐western USA and portions of northern Mexico. However, the continued threat of reinvasion from Mexico reinforces the need to improve pheromone‐based monitoring. Invasions from other parts of the world such as India, where resistance to single‐gene transgenic Bt cotton has evolved, further heightens the need for better monitoring strategies.

The mean flight height and standard deviation (SD) of the vertical flight distribution of pink bollworm males were estimated from catches on transparent sticky cylinder traps baited with synthetic pheromone at several heights above‐ground. An effective attraction radius (EAR) of a standard pheromone lure was estimated from male moth catches on the pheromone‐baited sticky traps and many similar blank traps. The circular EARc was estimated from the spherical EAR and SD.

The EAR of a pheromone lure for pink bollworm was 1·03 m, and the EARc was 2·61 m. The mean flight height of males was 0·82 m, and the vertical flight distribution SD was 0·26 m.

A computer program simulated male moth movement and capture on various numbers of traps of EARc distributed over areas of 1–100 km2. The simulated catch results were comparable to predictions using the EARc with modified encounter rate equations of Royama and Rogers. The encounter rate equations were solved for initial populations of male moths in the regions, and Poisson statistics were used to calculate population confidence limits.

Synthesis and applications. Encounter rate models and Poisson methods can be used to determine levels of pheromone trap densities that are likely to detect and estimate low population levels of resident or invasive pink bollworms and many other pest insect species.
Identifying pathways for managing multiple disturbances to limit plant invasions
Authors: Tanentzap Andrew J. , Lee William G. , Monks Adrian , Ladley Kate , Johnson Peter N. , Rogers Geoffrey M. , Comrie Joy M. , Clarke Dean A. , Hayman Ella
Published: April 2014

Plant invasions are predicted to accelerate in a world with increased anthropogenic disturbance. Non‐native species pre‐adapted to these disturbances may especially be poised to invade novel communities. Conservation managers therefore need predictions of how to alter disturbances to maximize the persistence of native biodiversity.

We tested a multivariate hypothesis about the causal mechanisms underlying plant invasions in an ephemeral wetland in South Island, New Zealand, to inform management of this biodiverse but globally imperilled habitat. Our approach details among the first applications in ecology of Bayesian structural equation modelling, demonstrating its potential to inform management by disentangling the relative importance of strongly intercorrelated processes.

We found that invasion by non‐native plants was lowest in sites where the physical disturbance caused by flooding was both intense and frequent. This effect was stronger than the positive response of non‐native species to high soil N supply, which was positively related to flooding.

Sites flooded over a 4‐year period had greater reductions in invasion than those associated with floods in the year prior to plot measurement because non‐native species lacked traits for long‐term persistence beneath water. Grazer exclusion had a small positive effect on invasion, as non‐native species were preferentially selected by the herbivores at our site.

Our results show that only species adapted to the dominant disturbance regimes at a site may become successful invaders. Species native to ephemeral wetlands have specially evolved traits that allow them to persist and dominate in these sites.

Synthesis and applications. Predictions of invasions in a world of multiple disturbances clearly need to consider whether the evolutionary history of non‐native species predisposes them to invade novel communities. Maintaining hydrological and nutrient regimes of ephemeral wetlands will limit the number of introduced species that are pre‐adapted to become invasive.
How much of the world is woody?
Authors: FitzJohn Richard G. , Pennell Matthew W. , Zanne Amy E. , Stevens Peter F. , Tank David C. , Cornwell William K.
Published: April 2014

The question posed by the title of this study is a basic one, and it is surprising that the answer is not known. Recently, assembled trait data sets provide an opportunity to address this, but scaling these data sets to the global scale is challenging because of sampling bias. Although we currently know the growth form of tens of thousands of species, these data are not a random sample of global diversity; some clades are exhaustively characterized, while others we know little to nothing about.

Starting with a data base of woodiness for 39 313 species of vascular plants (12% of taxonomically resolved species, 59% of which were woody), we estimated the status of the remaining taxonomically resolved species by randomization. To compare the results of our method to conventional wisdom, we informally surveyed a broad community of biologists. No consensus answer to the question existed, with estimates ranging from 1% to 90% (mean: 31.7%).

After accounting for sampling bias, we estimated the proportion of woodiness among the world's vascular plants to be between 45% and 48%. This was much lower than a simple mean of our data set and much higher than the conventional wisdom.

Synthesis. Alongside an understanding of global taxonomic diversity (i.e. number of species globally), building a functional understanding of global diversity is an important emerging research direction. This approach represents a novel way to account for sampling bias in functional trait data sets and to answer basic questions about functional diversity at a global scale.
Decoupled evolution of foliar freezing resistance, temperature niche and morphological leaf traits inChileanMyrceugenia
Authors: Pérez Fernanda , Hinojosa Luis F. , Ossa Carmen G. , Campano Francisca , Orrego Fabiola
Published: April 2014

Phylogenetic conservatism of tolerance to freezing temperatures has been cited to explain the tendency of plant lineages to grow in similar climates. However, there is little information about whether or not freezing resistance is conserved across phylogenies, and whether conservatism of physiological traits could explain conservatism of realized climatic niches. Here, we compared the phylogenetical lability of realized climatic niche, foliar freezing resistance and four morphological leaf traits that are generally considered to be adaptations to frost resistance in the Chilean species ofMyrceugenia, which grows in a wide range of habitats.

We estimated the predicted niche occupancy profiles with respect to minimum temperature (minT) of all species. We measured foliar freezing resistance (using chlorophyll fluorescence), leaf size, leaf mass per area (LMA), stomatal and trichome densities of 10 individuals per species. Finally, we estimated phylogenetic signal, and we performed independent contrast analyses among all variables.

We found that both foliar freezing resistance and minT were subject to a significant phylogenetic signal, but the former had a stronger signal. We also detected a significant, but weak correlation between them (r = 0.49,Pone tail = 0.04). Morphological traits evolved independent of any phylogenetic effect.

Synthesis. Our results show that freezing resistance evolved in association with temperature niche, but with some delay that could result from phylogenetic inertia. Our results also show that morphological leaf traits are more labile than realized climatic niche and frost tolerance and that the formers probably evolved in association with microhabitat preferences.
Both flowering time and distance to conspecific plants affect reproduction in Echinacea angustifolia, a common prairie perennial
Authors: Ison Jennifer L. , Wagenius Stuart
Published: April 2014

In small fragmented plant populations, reproductive failure due to pollen limitation is often attributed to spatial isolation of individuals. While flowering time has been shown to affect seed set, its role in pollen limited fragmented populations is less understood.

In this study, we quantified near‐neighbour distances, flowering phenology, and how they interact to affect seed set in individual plants. We followed the daily flowering phenology of over 2400 heads on over 500 Echinacea angustifolia individuals and quantified the resulting seed set during three consecutive flowering seasons. The study was conducted in an experimental plot where we randomized planting locations to eliminate spatial patterns of mate availability which are common in fragmented populations of Echinacea, a self‐incompatible plant.

We found that individual flowering time had a larger and more consistent effect on seed set than did spatial location. Seed set in the earliest flowering plants exceeded seed set in the latest by 46–70% in all three years. The role of spatial isolation, characterized both by individual distance to conspecific plants and by location in the plot, was less consistent and showed a weaker relationship with seed set than did flowering phenology. The most isolated plants set 20–27% less seed than the least isolated plants in 2005–2006 with no difference in 2007.

In one year, we quantified seed set by floret position within a flowering head. We found significant positional effects; however, effects due to flowering time were much greater. These results were more consistent with the pollen limitation hypothesis than the resources limitation hypothesis.

Synthesis. Our results illustrate that flowering time and distance to neighbouring conspecifics can cause reproductive failure in fragmented populations, even in the absence of mate limitation caused by mating incompatibility. These findings suggest that flowering time may be an underappreciated contributor to reproductive failure in small fragmented populations.
Interactions between anaerobic ammonium and sulfur‐oxidizing bacteria in a laboratory scale model system
Authors: Russ Lina , Speth Daan R. , Jetten Mike S. M. , Op den Camp Huub J. M. , Kartal Boran
Published: April 2014

Fixed nitrogen is released by anaerobic ammonium oxidation (anammox) and/or denitrification from (marine) ecosystems. Nitrite, the terminal electron acceptor of the anammox process, occurs in nature at very low concentrations and is produced via (micro)aerobic oxidation of ammonium or nitrate reduction. The coupling of sulfide‐dependent denitrification to anammox is particularly interesting because besides hydrogen, sulfide is the most important reductant at the chemocline of anoxic marine basins and is abundant within sediments. Although at μM concentrations, sulfide may be toxic and inhibiting anammox activity, a denitrifying microorganism could convert sulfide and nitrate at sufficiently high rates to allow anammox bacteria to stay active despite an influx of sulfide. To test this hypothesis, a laboratory scale model system containing a co‐culture of anammox bacteria and the autotrophic denitrifier Sulfurimonas denitrificans DSM1251 was started. Complementary techniques revealed that the gammaproteobacterial Sedimenticola sp. took over the intended role of Su. denitrificans. A stable coculture of anammox bacteria and Sedimenticola sp. consumed sulfide, nitrate, ammonium and CO2. Anammox bacteria contributed 65–75% to the nitrogen loss from the reactor. The cooperation between anammox and sulfide‐dependent denitrification may play a significant role in environments where sulfur cycling is active and where actual sulfide concentrations stay below μM range.
15N‐ and 2H proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity
Authors: Justice Nicholas B. , Li Zhou , Wang Yingfeng , Spaudling Susan E. , Mosier Annika C. , Hettich Robert L. , Pan Chongle , Banfield Jillian F.
Published: April 2014

Understanding how individual species contribute to nutrient transformations in a microbial community is critical to prediction of overall ecosystem function. We conducted microcosm experiments in which floating acid mine drainage (AMD) microbial biofilms were submerged – recapitulating the final stage in a natural biofilm life cycle. Biofilms were amended with either 15NH4+ or deuterium oxide (2H2O) and proteomic stable isotope probing (SIP) was used to track the extent to which different members of the community used these molecules in protein synthesis across anaerobic iron‐reducing, aerobic iron‐reducing and aerobic iron‐oxidizing environments. Sulfobacillus spp. synthesized 15N‐enriched protein almost exclusively under iron‐reducing conditions whereas the Leptospirillum spp. synthesized 15N‐enriched protein in all conditions. There were relatively few 15N‐enriched archaeal proteins, and all showed low atom% enrichment, consistent with Archaea synthesizing protein using the predominantly 14N biomass derived from recycled biomolecules. In parallel experiments using 2H2O, extensive archaeal protein synthesis was detected in all conditions. In contrast, the bacterial species showed little protein synthesis using 2H2O. The nearly exclusive ability of Archaea to synthesize proteins using 2H2O may be due to archaeal heterotrophy, whereby Archaea offset deleterious effects of 2H by accessing 1H generated by respiration of organic compounds.
Inequality in the ‘Conflict of Conflicts’? The Impact of Citizen Sophistication on Agenda-setting Effects
Authors: Stubager Rune
Published: April 2014

Influence upon the societal agenda is an important power resource in modern democracies. Consequently, inequalities in such influence across different segments of the public have important democratic implications. Using time-series methods on a unique Danish dataset, this article investigates the existence of inequalities in agenda power across groups with different levels of political sophistication and finds that the most sophisticated members of the public possess more such power vis-à-vis the media and politicians than the less sophisticated. The existence of inequalities in agenda power across different segments of the public, even in the homogenous Danish society, implies that countries characterised by higher levels of inequality should experience even larger disparities, thereby jeopardising the democratic principle that all citizens have equal access to placing issues on the agenda.