bluuebunny/crossref_metadata_2025 huggingface dataset:
A parametric study of coupled‐mode flutter for MW‐size wind turbine blades
Authors: Pourazarm Pariya , Modarres‐Sadeghi Yahya , Lackner Matthew
Published: May 2015

With the increasing size of offshore wind turbine rotors, the design criteria used for the blades may also evolve. Current offshore technology utilizes three relatively stiff blades in an upwind configuration. With the goal of minimizing the mass, there is an interest in the lightweight rotors that instead utilize two flexible blades oriented downwind. These longer blades are more flexible and thus susceptible to experience flow‐induced instability. Coupled‐mode flutter is one of the destructive aeroelastic instabilities that can occur in flexible structures subjected to aerodynamic loading. Because of variation in one of the system parameters, e.g., flow velocity, structural modes coalesce at a critical flow velocity, and coupled‐flutter occurs. In the present work, a parametric study is conducted in order to study the influence of the natural frequencies in the torsional and flapwise directions on the critical flutter speed for wind turbine blades. Three MW‐size wind turbine blades are studied using a three‐dimensional blade model, which includes coupled flapwise and torsional displacements. The results show that the three blades have very similar behavior as the system parameters vary. It is shown that the first torsional natural frequency and the ratio of the first torsional natural frequency to the first flapwise natural frequency are the most critical parameters affecting the onset of instability. Critical flutter speeds even lower than the blade rated speed can be observed for blades with low torsional natural frequencies. Copyright © 2015 John Wiley & Sons, Ltd.
Shaping the future of nanomedicine: anisotropy in polymeric nanoparticle design
Authors: Meyer Randall A. , Green Jordan J.
Published: May 2015

Nanofabrication and biomedical applications of polymeric nanoparticles have become important areas of research. Biocompatible polymeric nanoparticles have been investigated for their use as delivery vehicles for therapeutic and diagnostic agents. Although polymeric nanoconstructs have traditionally been fabricated as isotropic spheres, anisotropic, nonspherical nanoparticles have gained interest in the biomaterials community owing to their unique interactions with biological systems. Polymeric nanoparticles with different forms of anisotropy have been manufactured using a variety of novel methods in recent years. In addition, they have enhanced physical, chemical, and biological properties compared with spherical nanoparticles, including increased targeting avidity and decreased nonspecific in vivo clearance. With these desirable properties, anisotropic nanoparticles have been successfully utilized in many biomedical settings and have performed superiorly to analogous spherical nanoparticles. We summarize the current state‐of‐the‐art fabrication methods for anisotropic polymeric nanoparticles including top‐down, bottom‐up, and microfluidic design approaches. We also summarize the current and potential future applications of these nanoparticles, including drug delivery, biological targeting, immunoengineering, and tissue engineering. Ongoing research into the properties and utility of anisotropic polymeric nanoparticles will prove critical to realizing their potential in nanomedicine. WIREs Nanomed Nanobiotechnol 2016, 8:191–207. doi: 10.1002/wnan.1348

This article is categorized under:

Therapeutic Approaches and Drug Discovery > Emerging Technologies

Nanotechnology Approaches to Biology > Nanoscale Systems in Biology
A Rational Approach to IrPTe – DFT and CalPhaD Studies on Phase Stability, Formation, and Structure of IrPTe
Authors: Pielnhofer Florian , Schöneich Michael , Lorenz Tobias , Yan Wenjie , Nilges Tom , Weihrich Richard , Schmidt Peer
Published: May 2015

Phase formation, stability, crystal and electronic structures of IrPTe are investigated from experiment and quantum chemical calculations. The phase formation is studied from thermodynamic data and CalPhaD modeling. Applying a high‐temperature gas‐balance a formation pathway for IrPTe is studied from the elements and the binary parent compounds IrTe2 and IrP2. The obtained paracostibite (CoSbS) type structure contains rarely occurring heteroatomic P–Te dumbbells. The stability of IrPTe and the found structure is studied from DFT calculations with respect to the elements, IrTe2 and IrP2, and possible polymorphs. Probable metastable modifications with XY dumbbells (as known for isoelectronic compounds like CoAsS) are obtained from systematic DFT modelling. Phase transitions are predicted form the equation of states (EOS). According to its electronic band structure IrPTe is predicted as small gap (ΔEg = 0.5 eV) semiconductor.
Species diversity and vegetation distribution in nebkhas of Nitraria tangutorum in the Desert Steppes of China
Authors: Zhou Hai , Zhao Wen‐Zhi , Luo Wei‐Cheng , Liu Bing
Published: May 2015

Nebkhas (phytogenic miniature dunes) are mounds composed of wind‐borne sediment within or around shrub canopies and often develop under plants, creating microenvironments that affect the distribution of vegetation. In our study we investigated the vegetation of 397 nebkhas populated with the shrub Nitraria tangutorum in Yanchi County, in the northwest of China. We measured nebkha size (height, width and length) and soil moisture (from 0 to 100 cm). Distinct microsites of each nebkha (crest, mid‐slope, bottom, edge and internebkha space) were identified and plant species diversity was also measured. Four vegetation groups (N. tangutorum–Chloris virgata + Eragrostis pilosa, N. tangutorum–Artemisia scoparia, N. tangutorum–Salsola collina + Bassia dasyphylla, N. tangutorum–Agriophyllum squarrosum) were described by two way indicator species analysis (TWINSPAN) on the basis of classification and, concomitantly, the relationships between species composition and environmental gradients were explained by canonical correspondence analysis (CCA). Regression analysis indicated that as height and area of the nebkhas increased, species richness increased linearly, while the other species diversity indices (Simpson index, Pielou index and Shannon–Wiener evenness index) increased logarithmically. The response of species richness to heterogeneity of the microenvironment resulted from the four aspects (east, south, north and west) of the nebkhas, and varied among the different microsites of the nebkhas. Species composition was correlated with spatial variability in soil moisture along the gradient from the nebkha crest to the internebkha space. It appeared that the microheterogeneity of the nebkhas promoted the abundance of plant species.
Long-term changes and distribution of mercury concentrations in surface sediments of the Gdansk Basin (Southern Baltic Sea)
Authors: Jędruch Agnieszka , Bełdowski Jacek , Bełdowska Magdalena
Published: May 2015

Purpose

In the Baltic Sea, the reduction of mercury load is estimated to be 44 % compared to the end of the previous century. Confirmation of mercury load decrease is frequently based on sedimentary mercury profiles. This study aims to assess the inter-annual changes of mercury concentration and the net input in surface sediments, in order to assess the effect of decreased emissions and other processes.

Materials and methods

Surface sediments were collected in 2011–2013 from areas where existing data series were available. Sediments were freeze dried, and total mercury concentrations, loss on ignition and fine fraction content were analysed. We compared recent concentrations of mercury in the coastal zone of the Baltic Sea to values previously reported in the same area since 1993. Net mercury deposition in the analysed sediments and previously reported data were calculated. The observed variability was correlated to climate-related processes and input changes.

Results and discussion

Three studied areas—major river mouth, shallow bay and offshore area—were significantly different in terms of sediment type and mercury concentration. Total mercury concentrations in the study area in 2011–2013 ranged between 2 and 260 ng g−1 dry weight (dw) (mean 61 ng g−1 dw; median 36 ng g−1 dw). Nearly 75 % of the obtained results did not exceed 50 ng g−1 dw, while concentrations >200 ng g−1 dw accounted for a little over 5 % of all the obtained results. Mercury input calculated for the area was much smaller than that recorded for the 1990s, but was characterised with large inter-annual variability, attributed to climate-related processes.

Conclusions

Although a decreasing trend could be observed, it is modified by inter-annual variability. It follows from observations that in the present situation, where mercury emission has been successfully inhibited, that concentrations of this metal in sediments reflect natural metal migration processes rather than the direct influence of anthropogenic sources.
Putting Civic Participation in Context: Examining the Effects of Congregational Structure and Culture
Authors: Polson Edward C.
Published: May 2015

Research indicates that participation in organized religion is related to higher levels of civic engagement. It is often theorized that social connections developed in congregations facilitate this increased involvement in civic life. Yet, despite interest in the link between religion and civic engagement, few studies have explored the effects that varying congregational contexts have on attenders’ civic behavior. In an era when both religious culture and demographics are changing rapidly, understanding how organizational contexts affect attenders’ community involvement may be valuable for predicting future patterns of religion and civic engagement. I utilize multilevel data drawn from the 2001 US Congregational Life Survey to investigate the relationship between congregational context and three measures of civic engagement. Findings reveal that important structural and cultural characteristics of congregations are related to civic behavior and that these characteristics influence different types of engagement differently. Implications for the relationship between religion and civic participation are discussed.
Regulation of neuronal communication by G protein‐coupled receptors
Authors: Huang Yunhong , Thathiah Amantha
Published: May 2015

Neuronal communication plays an essential role in the propagation of information in the brain and requires a precisely orchestrated connectivity between neurons. Synaptic transmission is the mechanism through which neurons communicate with each other. It is a strictly regulated process which involves membrane depolarization, the cellular exocytosis machinery, neurotransmitter release from synaptic vesicles into the synaptic cleft, and the interaction between ion channels, G protein‐coupled receptors (GPCRs), and downstream effector molecules. The focus of this review is to explore the role of GPCRs and G protein‐signaling in neurotransmission, to highlight the function of GPCRs, which are localized in both presynaptic and postsynaptic membrane terminals, in regulation of intrasynaptic and intersynaptic communication, and to discuss the involvement of astrocytic GPCRs in the regulation of neuronal communication.
Cloning of a copper resistance gene cluster from the cyanobacterium Synechocystis sp. PCC 6803 by recombineering recovery
Authors: Gittins John R.
Published: May 2015

A copper resistance gene cluster (6 genes, ∼8.2 kb) was isolated from the cyanobacterium Synechocystis sp. PCC 6803 by recombineering recovery (RR). Following integration of a narrow‐host‐range plasmid vector adjacent to the target region in the Synechocystis genome (pSYSX), DNA was isolated from transformed cells and the plasmid plus flanking sequence circularized by recombineering to precisely clone the gene cluster. Complementation of a copper‐sensitive Escherichia coli mutant demonstrated the functionality of the pcopM gene encoding a copper‐binding protein. RR provides a novel alternative method for cloning large DNA fragments from species that can be transformed by homologous recombination.
A brief review of nucleosome structure
Authors: Cutter Amber R. , Hayes Jeffrey J.
Published: May 2015

The nucleosomal subunit organization of chromatin provides a multitude of functions. Nucleosomes elicit an initial ∼7‐fold linear compaction of genomic DNA. They provide a critical mechanism for stable repression of genes and other DNA‐dependent activities by restricting binding of trans‐acting factors to cognate DNA sequences. Conversely they are engineered to be nearly meta‐stable and disassembled (and reassembled) in a facile manner to allow rapid access to the underlying DNA during processes such as transcription, replication and DNA repair. Nucleosomes protect the genome from DNA damaging agents and provide a lattice onto which a myriad of epigenetic signals are deposited. Moreover, vast strings of nucleosomes provide a framework for assembly of the chromatin fiber and higher‐order chromatin structures. Thus, in order to provide a foundation for understanding these functions, we present a review of the basic elements of nucleosome structure and stability, including the association of linker histones.
An active second dihydrofolate reductase enzyme is not a feature of rat and mouse, but they do have activity in their mitochondria
Authors: Hughes Linda , Carton Robert , Minguzzi Stefano , McEntee Gráinne , Deinum Eva E. , O'Connell Mary J. , Parle-McDermott Anne
Published: May 2015

The identification of a second functional dihydrofolate reductase enzyme in humans, DHFRL1, led us to consider whether this is also a feature of rodents. We demonstrate that dihydrofolate reductase activity is also a feature of the mitochondria in both rat and mouse but this is not due to a second enzyme. While our phylogenetic analysis revealed that RNA‐mediated DHFR duplication events did occur across the mammal tree, the duplicates in brown rat and mouse are likely to be processed pseudogenes. Humans have evolved the need for two separate enzymes while laboratory rats and mice have just one.
Early‐life stress increases the survival of midbrain neurons during postnatal development and enhances reward‐related and anxiolytic‐like behaviors in a sex‐dependent fashion
Authors: Chocyk Agnieszka , Majcher‐Maślanka Iwona , Przyborowska Aleksandra , Maćkowiak Marzena , Wędzony Krzysztof
Published: May 2015

Clinical studies have suggested that early‐life stress (ELS) increases the risk of psychopathologies that are strongly associated with dysfunction of dopaminergic neurotransmission. Thus, ELS may interfere with the development and maturation of the dopaminergic system; however, the mechanisms involved in such interference are poorly understood. In the present study, we investigated the effect of ELS on the survival of specific populations of neurons in the substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) during postnatal development. First, we injected bromodeoxyuridine (BrdU) into pregnant rat dams on embryonic days 12, 13 and 14 to permanently label midbrain neurons. Then, after birth, the dams and litters were subjected to a maternal separation (MS) procedure to model ELS conditions. The number of BrdU+ neurons and the total number of neurons (cresyl violet+, CV+) were estimated in both male and female juvenile, adolescent, and adult rats. Moreover, sucrose preference and anxiety‐like behaviors were studied during adulthood. We found that MS permanently increased the number of BrdU+ and CV+ neurons in the VTA of males. In the SNc, a temporary increase in the number of BrdU+ neurons was observed in juvenile MS males; however, only adult MS males displayed an increase in the number of CV+ neurons. Immunofluorescence analysis implied that MS affected the fate of non‐dopaminergic neurons. MS males displayed anxiolytic‐like behavior and an increase in sucrose preference. These results suggest that ELS induces distinct dysregulation in the midbrain circuitry of males, which may lead to sex‐specific psychopathology of the reward system.
A meta‐analysis of risk of pregnancy loss and caffeine and coffee consumption during pregnancy
Authors: Li Ji , Zhao Hong , Song Ju‐Min , Zhang Jing , Tang Yin‐Lan , Xin Chang‐Mao
Published: May 2015

Background

Previous reports of the relationship between pregnancy loss and caffeine/coffee consumption have been inconsistent.

Objectives

To evaluate the association between pregnancy loss and caffeine and coffee consumption.

Search strategy

PubMed was searched for reports published before September 2014, with the keywords “caffeine,” “coffee,” “beverage,” “miscarriage,” “spontaneous abortion,” and “fetal loss.”

Selection criteria

Case‐control and cohort studies were included when they had been reported in English, the exposure of interest was caffeine/coffee consumption during pregnancy, the outcome of interest was spontaneous abortion or fetal death, and multivariate‐adjusted odds ratios (ORs) or risk ratios were provided or could be calculated.

Data collection and analysis

Data were extracted and combined ORs calculated.

Main results

Overall, 26 studies were included (20 of caffeine and eight of coffee). After adjustment for heterogeneity, caffeine consumption was associated with an increased risk of pregnancy loss (OR 1.32, 95% confidence interval [CI] 1.24–1.40), as was coffee consumption (OR 1.11, 95% CI 1.02–1.21). A dose–response analysis suggested that risk of pregnancy loss rose by 19% for every increase in caffeine intake of 150 mg/day and by 8% for every increase in coffee intake of two cups per day.

Conclusions

Consumption of caffeine and coffee during pregnancy seems to increase the risk of pregnancy loss.
High level PHGDH expression in breast is predominantly associated with keratin 5‐positive cell lineage independently of malignancy
Authors: Gromova Irina , Gromov Pavel , Honma Naoko , Kumar Sudha , Rimm David , Talman Maj-Lis Møller , Wielenga Vera Timmermans , Moreira José M.A.
Published: May 2015

We have previously reported the 2D PAGE‐based proteomic profiling of a prospective cohort of 78 triple negative breast cancer (TNBC) patients, and the establishment of a cumulative TNBC protein database. Analysis of this database identified a number of proteins as being specifically overexpressed in TNBC samples. One such protein was D‐3‐phosphoglycerate dehydrogenase (Phgdh), a candidate oncogene. We analysed expression of Phgdh in normal and TNBC mammary tissue samples by 2D gel‐based proteomics and immunohistochemistry (IHC), and show here that high‐level expression of Phgdh in mammary epithelial cells is primarily associated with cell lineage, as we found that Phgdh expression was predominant in CK5‐positive cells, normal as well as malignant, thus identifying an association of this protein with the basal phenotype. Quantitative IHC analysis of Phgdh expression in normal breast tissue showed high‐level expression of Phgdh in normal CK5‐positive mammary epithelial cells, indicating that expression of this protein was not associated with malignancy, but rather with cell lineage. However, proteomic profiling of Phgdh showed it to be expressed in two major protein forms, and that the ratio of expression between these variants was associated with malignancy. Overexpression of Phgdh in CK5‐positive cell lineages, and differential protein isoform expression, was additionally found in other tissues and cancer types, suggesting that overexpression of Phgdh is generally associated with CK5 cells, and that oncogenic function may be determined by isoform expression.
Corruption in sport: From the playing field to the field of policy
Authors: Masters Adam
Published: May 2015

How is corruption in sport evolving into a global public policy issue? In the past century, four trends have affected sport according to Paoli and Donati (2013) — de-amateurisation at the turn of the twentieth century, medicalisation since the 1960s, politicisation and commercialisation to the point where sport is now a business worth more than US$141 billion annually. Each of these trends had a corrupting effect on what is generally perceived as a past ‘golden age’ of sport. In the twenty-first century more public funding is being directed into sport in the developed and developing world. As a result this paper will argue organised sport has entered a fifth evolutionary trend — criminalisation. In this latest phase, public policy needs to grapple with what constitutes corruption in what has historically been a private market.
HEAVY AND LIGHT BODY PARTS: THE WEIGHING METAPHOR IN EARLY CHINESE DIALOGUES
Authors: Defoort Carine
Published: May 2015

The article analyses the metaphorical use of weighing body parts such as fingers, arms, or a head. Our understanding of the weighing metaphor has been much influenced by A. C. Graham's characterization of its rhetorical mechanism, followed by Griet Vankeerberghen in her description of one type of weighing (quanB). The basis of this understanding are two corrupt textual fragments in the dialectical chapters of theMozi. SeveralLü shi chunqiuchapters, however, contain a set of argumentative stories in which body parts are weighed in terms of light and heavy. These stories always argue in favor of life and health, they have a relatively consistent structure, and they may have constituted the core of a larger set of related arguments. Insight into their working can therefore enlighten our reading of other texts.
Interindividual Contacts and Carriage of Methicillin-ResistantStaphylococcus aureus: A Nested Case-Control Study
Authors: Obadia Thomas , Opatowski Lulla , Temime Laura , Herrmann Jean-Louis , Fleury Éric , Boëlle Pierre-Yves , Guillemot Didier
Published: May 2015

BACKGROUND

Reducing the spread of multidrug-resistant bacteria in hospitals remains a challenge. Current methods are screening of patients, isolation, and adherence to hygiene measures among healthcare workers (HCWs). More specific measures could rely on a better characterization of the contacts at risk of dissemination.

OBJECTIVE

To quantify how close-proximity interactions (CPIs) affectedStaphylococcus aureusdissemination.

DESIGN

Nested case-control study.

SETTING

French long-term care facility in 2009.

PARTICIPANTS

Patients (n=329) and HCWs (n=261).

METHODS

We recorded CPIs using electronic devices together withS. aureusnasal carriage during 4 months in all participants. Cases consisted of patients showing incidentS. aureuscolonization and were paired to 8 control patients who did not exhibit incident colonization at the same date. Conditional logistic regression was used to quantify associations between incidence and exposure to demographic, network, and carriage covariables.

RESULTS

The local structure of contacts informed on methicillin-resistantS. aureus(MRSA) carriage acquisition: CPIs with more HCWs were associated with incident MRSA colonization in patients (odds ratio [OR], 1.10 [95% CI, 1.04–1.17] for 1 more HCW), as well as longer CPI durations (1.03 [1.01–1.06] for a 1-hour increase). Joint analysis of carriage and contacts showed increased carriage acquisition in case of CPI with another colonized individual (OR, 1.55 [1.14–2.11] for 1 more HCW). Global network measurements did not capture associations between contacts and carriage.

CONCLUSIONS

Electronically recorded CPIs inform on the risk of MRSA carriage, warranting more study of in-hospital contact networks to design targeted intervention strategies.

Infect. Control Hosp. Epidemiol.2015;36(8):922–929
A completion-invariant extension of the concept of meet continuous lattices
Authors: ZHANG WENFENG , XU XIAOQUAN
Published: May 2015

In this paper, the concept of meet F-continuous posets is introduced. The main results are: (1) A poset P is meet F-continuous iff its normal completion is a meet continuous lattice iff a certain system γ(P) which is, in the case of complete lattices, the lattice of all Scott closed sets is a complete Heyting algebra; (2) A poset P is precontinuous iff P is meet F-continuous and quasiprecontinuous; (3) The category of meet continuous lattices with complete homomorphisms is a full reflective subcategory of the category of meet F-continuous posets with cut-stable maps.
Researchers Track Moving Ice Shelves to Estimate Antarctic Ice Loss
Authors: Rosen Julia
Published: May 2015

A new method will help scientists monitor the basal melt of ice sheets in Antarctica.
Rational combination treatment with histone deacetylase inhibitors and immunomodulatory drugs in multiple myeloma
Authors: Hideshima T , Cottini F , Ohguchi H , Jakubikova J , Gorgun G , Mimura N , Tai Y-T , Munshi N C , Richardson P G , Anderson K C
Published: May 2015

Immunomodulatory drugs (IMiDs) thalidomide, lenalidomide (Len) and pomalidomide trigger anti-tumor activities in multiple myeloma (MM) by targetting cereblon and thereby impacting IZF1/3, c-Myc and IRF4. Histone deacetylase inhibitors (HDACi) also downregulate c-Myc. We therefore determined whether IMiDs with HDACi trigger significant MM cell growth inhibition by inhibiting or downregulating c-Myc. Combination treatment of Len with non-selective HDACi suberoylanilide hydroxamic acid or class-I HDAC-selective inhibitor MS275 induces synergic cytotoxicity, associated with downregulation of c-Myc. Unexpectedly, we observed that decreased levels of cereblon (CRBN), a primary target protein of IMiDs, was triggered by these agents. Indeed, sequential treatment of MM cells with MS275 followed by Len shows less efficacy than simultaneous treatment with this combination. Importantly ACY1215, an HDAC6 inhibitor with minimal effects on class-I HDACs, together with Len induces synergistic MM cytotoxicity without alteration of CRBN expression. Our results showed that only modest class-I HDAC inhibition is able to induce synergistic MM cytotoxicity in combination with Len. These studies may provide the framework for utilizing HDACi in combination with Len to both avoid CRBN downregulation and enhance anti-MM activities.
BCR repertoire sequencing: different patterns of B‐cell activation after two Meningococcal vaccines
Authors: Galson Jacob D , Clutterbuck Elizabeth A , Trück Johannes , Ramasamy Maheshi N , Münz Márton , Fowler Anna , Cerundolo Vincenzo , Pollard Andrew J , Lunter Gerton , Kelly Dominic F
Published: May 2015

Next‐generation sequencing was used to investigate the B‐cell receptor heavy chain transcript repertoire of different B‐cell subsets (naive, marginal zone (MZ), immunoglobulin M (IgM) memory and IgG memory) at baseline, and of plasma cells (PCs) 7 days following administration of serogroup ACWY meningococcal polysaccharide and protein–polysaccharide conjugate vaccines. Baseline B‐cell subsets could be distinguished from each other using a small number of repertoire properties (clonality, mutation from germline and complementarity‐determining region 3 (CDR3) length) that were conserved between individuals. However, analyzing the CDR3 amino‐acid sequence (which is particularly important for antigen binding) of the baseline subsets showed few sequences shared between individuals. In contrast, day 7 PCs demonstrated nearly 10‐fold greater sequence sharing between individuals than the baseline subsets, consistent with the PCs being induced by the vaccine antigen and sharing specificity for a more limited range of epitopes. By annotating PC sequences based on IgG subclass usage and mutation, and also comparing them with the sequences of the baseline cell subsets, we were able to identify different signatures after the polysaccharide and conjugate vaccines. PCs produced after conjugate vaccination were predominantly IgG1, and most related to IgG memory cells. In contrast, after polysaccharide vaccination, the PCs were predominantly IgG2, less mutated and were equally likely to be related to MZ, IgM memory or IgG memory cells. High‐throughput B‐cell repertoire sequencing thus provides a unique insight into patterns of B‐cell activation not possible from more conventional measures of immunogenicity.
High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures
Authors: Sosa Oscar A , Gifford Scott M , Repeta Daniel J , DeLong Edward F
Published: May 2015

The role of bacterioplankton in the cycling of marine dissolved organic matter (DOM) is central to the carbon and energy balance in the ocean, yet there are few model organisms available to investigate the genes, metabolic pathways, and biochemical mechanisms involved in the degradation of this globally important carbon pool. To obtain microbial isolates capable of degrading semi-labile DOM for growth, we conducted dilution to extinction cultivation experiments using seawater enriched with high molecular weight (HMW) DOM. In total, 93 isolates were obtained. Amendments using HMW DOM to increase the dissolved organic carbon concentration 4x (280 μm) or 10x (700 μm) the ocean surface water concentrations yielded positive growth in 4–6% of replicate dilutions, whereas <1% scored positive for growth in non-DOM-amended controls. The majority (71%) of isolates displayed a distinct increase in cell yields when grown in increasing concentrations of HMW DOM. Whole-genome sequencing was used to screen the culture collection for purity and to determine the phylogenetic identity of the isolates. Eleven percent of the isolates belonged to the gammaproteobacteria including Alteromonadales (the SAR92 clade) and Vibrio. Surprisingly, 85% of isolates belonged to the methylotrophic OM43 clade of betaproteobacteria, bacteria thought to metabolically specialize in degrading C1 compounds. Growth of these isolates on methanol confirmed their methylotrophic phenotype. Our results indicate that dilution to extinction cultivation enriched with natural sources of organic substrates has a potential to reveal the previously unsuspected relationships between naturally occurring organic nutrients and the microorganisms that consume them.
Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon
Authors: Sorokin Dimitry Y , Kublanov Ilya V , Gavrilov Sergei N , Rojo David , Roman Pawel , Golyshin Peter N , Slepak Vladlen Z , Smedile Francesco , Ferrer Manuel , Messina Enzo , La Cono Violetta , Yakimov Michail M
Published: May 2015

Archaea domain is comprised of many versatile taxa that often colonize extreme habitats. Here, we report the discovery of strictly anaerobic extremely halophilic euryarchaeon, capable of obtaining energy by dissimilatory reduction of elemental sulfur using acetate as the only electron donor and forming sulfide and CO2 as the only products. This type of respiration has never been observed in hypersaline anoxic habitats and is the first example of such metabolic capability in the entire Archaea domain. We isolated and cultivated these unusual organisms, selecting one representative strain, HSR2, for detailed characterization. Our studies including physiological tests, genome sequencing, gene expression, metabolomics and [14C]-bicarbonate assimilation assays revealed that HSR2 oxidized acetate completely via the tricarboxylic acid cycle. Anabolic assimilation of acetate occurred via activated glyoxylate bypass and anaplerotic carboxylation. HSR2 possessed sulfurtransferase and an array of membrane-bound polysulfide reductase genes, all of which were expressed during the growth. Our findings suggest the biogeochemical contribution of haloarchaea in hypersaline anoxic environments must be reconsidered.
RNA structure determination by solid-state NMR spectroscopy
Authors: Marchanka Alexander , Simon Bernd , Althoff-Ospelt Gerhard , Carlomagno Teresa
Published: May 2015

Knowledge of the RNA three-dimensional structure, either in isolation or as part of RNP complexes, is fundamental to understand the mechanism of numerous cellular processes. Because of its flexibility, RNA represents a challenge for crystallization, while the large size of cellular complexes brings solution-state NMR to its limits. Here, we demonstrate an alternative approach on the basis of solid-state NMR spectroscopy. We develop a suite of experiments and RNA labeling schemes and demonstrate for the first time that ssNMR can yield a RNA structure at high-resolution. This methodology allows structural analysis of segmentally labelled RNA stretches in high-molecular weight cellular machines—independent of their ability to crystallize— and opens the way to mechanistic studies of currently difficult-to-access RNA-protein assemblies.
Wave energy budget analysis in the Earth’s radiation belts uncovers a missing energy
Authors: Artemyev A.V. , Agapitov O.V. , Mourenas D. , Krasnoselskikh V.V. , Mozer F.S.
Published: May 2015

Whistler-mode emissions are important electromagnetic waves pervasive in the Earth’s magnetosphere, where they continuously remove or energize electrons trapped by the geomagnetic field, controlling radiation hazards to satellites and astronauts and the upper-atmosphere ionization or chemical composition. Here, we report an analysis of 10-year Cluster data, statistically evaluating the full wave energy budget in the Earth’s magnetosphere, revealing that a significant fraction of the energy corresponds to hitherto generally neglected very oblique waves. Such waves, with 10 times smaller magnetic power than parallel waves, typically have similar total energy. Moreover, they carry up to 80% of the wave energy involved in wave–particle resonant interactions. It implies that electron heating and precipitation into the atmosphere may have been significantly under/over-valued in past studies considering only conventional quasi-parallel waves. Very oblique waves may turn out to be a crucial agent of energy redistribution in the Earth’s radiation belts, controlled by solar activity.
Atomistic design of microbial opsin-based blue-shifted optogenetics tools
Authors: Kato Hideaki E. , Kamiya Motoshi , Sugo Seiya , Ito Jumpei , Taniguchi Reiya , Orito Ayaka , Hirata Kunio , Inutsuka Ayumu , Yamanaka Akihiro , Maturana Andrés D. , Ishitani Ryuichiro , Sudo Yuki , Hayashi Shigehiko , Nureki Osamu
Published: May 2015

Microbial opsins with a bound chromophore function as photosensitive ion transporters and have been employed in optogenetics for the optical control of neuronal activity. Molecular engineering has been utilized to create colour variants for the functional augmentation of optogenetics tools, but was limited by the complexity of the protein–chromophore interactions. Here we report the development of blue-shifted colour variants by rational design at atomic resolution, achieved through accurate hybrid molecular simulations, electrophysiology and X-ray crystallography. The molecular simulation models and the crystal structure reveal the precisely designed conformational changes of the chromophore induced by combinatory mutations that shrink its π-conjugated system which, together with electrostatic tuning, produce large blue shifts of the absorption spectra by maximally 100 nm, while maintaining photosensitive ion transport activities. The design principle we elaborate is applicable to other microbial opsins, and clarifies the underlying molecular mechanism of the blue-shifted action spectra of microbial opsins recently isolated from natural sources.
Notes on stochastic (bio)-logic gates: computing with allosteric cooperativity
Authors: Agliari Elena , Altavilla Matteo , Barra Adriano , Dello Schiavo Lorenzo , Katz Evgeny
Published: May 2015

Recent experimental breakthroughs have finally allowed to implement in-vitro reaction kinetics (the so calledenzyme based logic) which code for two-inputs logic gates and mimic the stochastic AND (and NAND) as well as the stochastic OR (and NOR). This accomplishment, together with the already-known single-input gates (performing as YES and NOT), provides a logic base and paves the way to the development of powerful biotechnological devices. However, as biochemical systems are always affected by the presence of noise (e.g. thermal), standard logic is not the correct theoretical reference framework, rather we show that statistical mechanics can work for this scope: here we formulate a complete statistical mechanical description of the Monod-Wyman-Changeaux allosteric model for both single and double ligand systems, with the purpose of exploring their practical capabilities to express noisy logical operators and/or perform stochastic logical operations. Mixing statistical mechanics with logics and testing quantitatively the resulting findings on the available biochemical data, we successfully revise the concept of cooperativity (and anti-cooperativity) for allosteric systems, with particular emphasis on its computational capabilities, the related ranges and scaling of the involved parameters and its differences with classical cooperativity (and anti-cooperativity).
Genome-wide transcriptome profiling provides insights into floral bud development of summer-flowering Camellia azalea
Authors: Fan Zhengqi , Li Jiyuan , Li Xinlei , Wu Bin , Wang Jiangying , Liu Zhongchi , Yin Hengfu
Published: May 2015

The transition from vegetative to reproductive growth in woody perennials involves pathways controlling flowering timing, bud dormancy and outgrowth in responses to seasonal cues. However little is known about the mechanism governing the adaptation of signaling pathways to environmental conditions in trees. Camellia azalea is a rare species in this genus flowering during summer, which provides a unique resource for floral timing breeding. Here we reported a comprehensive transcriptomics study to capture the global gene profiles during floral bud development in C. azalea. We examined the genome-wide gene expression between three developmental stages including floral bud initiation, floral organ differentiation and bud outgrowth and identified nine co-expression clusters with distinctive patterns. Further, we identified the differential expressed genes (DEGs) during development and characterized the functional properties of DEGs by Gene Ontology analysis. We showed that transition from floral bud initiation to floral organ differentiation required changes of genes in flowering timing regulation, while transition to floral bud outgrowth was regulated by various pathways such as cold and light signaling, phytohormone pathways and plant metabolisms. Further analyses of dormancy associated MADS-box genes revealed that SVP- and AGL24- like genes displayed distinct expression patterns suggesting divergent roles during floral bud development.
Interfacing low-energy SAW nebulization with Liquid Chromatography-Mass Spectrometry for the analysis of biological samples
Authors: Tveen-Jensen Karina , Gesellchen Frank , Wilson Rab , Spickett Corinne M. , Cooper Jonathan M. , Pitt Andrew R.
Published: May 2015

Soft ionization methods for the introduction of labile biomolecules into a mass spectrometer are of fundamental importance to biomolecular analysis. Previously, electrospray ionization (ESI) and matrix assisted laser desorption-ionization (MALDI) have been the main ionization methods used. Surface acoustic wave nebulization (SAWN) is a new technique that has been demonstrated to deposit less energy into ions upon ion formation and transfer for detection than other methods for sample introduction into a mass spectrometer (MS). Here we report the optimization and use of SAWN as a nebulization technique for the introduction of samples from a low flow of liquid and the interfacing of SAWN with liquid chromatographic separation (LC) for the analysis of a protein digest. This demonstrates that SAWN can be a viable, low-energy alternative to ESI for the LC-MS analysis of proteomic samples.
Realization of a micrometre-scale spin-wave interferometer
Authors: Rousseau O. , Rana B. , Anami R. , Yamada M. , Miura K. , Ogawa S. , Otani Y.
Published: May 2015

The recent development of spin dynamics opens perspectives for various applications based on spin waves, including logic devices. The first important step in the realization of spin-wave-based logics is the manipulation of spin-wave interference. Here, we present the experimental realization of a micrometre-scale spin-wave interferometer consisting of two parallel spin-wave waveguides. The spin waves propagate through the waveguides and the superposition or interference of the electrical signals corresponding to the spin waves is measured. A direct current flowing through a metal wire underneath one of the spin-wave waveguides affects the propagation properties of the corresponding spin wave. The signal of constructive or destructive interference depends on the magnitude and direction of the applied direct current. Thus, the present work demonstrates a unique manipulation of spin-wave interference.
Prediction of Prostate Cancer Recurrence Using Quantitative Phase Imaging
Authors: Sridharan Shamira , Macias Virgilia , Tangella Krishnarao , Kajdacsy-Balla André , Popescu Gabriel
Published: May 2015

The risk of biochemical recurrence of prostate cancer among individuals who undergo radical prostatectomy for treatment is around 25%. Current clinical methods often fail at successfully predicting recurrence among patients at intermediate risk for recurrence. We used a label-free method, spatial light interference microscopy, to perform localized measurements of light scattering in prostatectomy tissue microarrays. We show, for the first time to our knowledge, that anisotropy of light scattering in the stroma immediately adjoining cancerous glands can be used to identify patients at higher risk for recurrence. The data show that lower value of anisotropy corresponds to a higher risk for recurrence, meaning that the stroma adjoining the glands of recurrent patients is more fractionated than in non-recurrent patients. Our method outperformed the widely accepted clinical tool CAPRA-S in the cases we interrogated irrespective of Gleason grade, prostate-specific antigen (PSA) levels and pathological tumor-node-metastasis (pTNM) stage. These results suggest that QPI shows promise in assisting pathologists to improve prediction of prostate cancer recurrence.
Adult-Onset Leukoencephalopathy with Axonal Spheroids and Pigmented Glia Caused by a Novel R782G Mutation in CSF1R
Authors: Foulds Nicola , Pengelly Reuben J. , Hammans Simon R. , Nicoll James A. R. , Ellison David W. , Ditchfield Adam , Beck Sarah , Ennis Sarah
Published: May 2015

We report a new family with autosomal dominant inheritance of a late onset rapidly progressive leukodystrophy in which exome sequencing has revealed a novel mutation p.R782G in the Colony-Stimulating Factor 1 Receptor gene (CSF1R). Neuropathology of two affected family members showed cerebral white matter degeneration with axonal swellings and pigmented macrophages. The few recently reported families with CSF1R mutations had been previously labelled “hereditary diffuse leukencephalopathy with axonal spheroids” (HDLS) and “pigmentary orthochromatic leukodystrophy” (POLD), disorders which now appear to form a disease continuum. The term “adult-onset leukoencephalopathy with axonal spheroids and pigmented glia” (ALSP) has been proposed to encompass this spectrum. As CSF1R regulates microglia this mutation implies that dysregulation of microglia is the primary cause of the disease.
Retinoic acid homeostasis through aldh1a2 and cyp26a1 mediates meiotic entry in Nile tilapia (Oreochromis niloticus)
Authors: Feng Ruijuan , Fang Lingling , Cheng Yunying , He Xue , Jiang Wentao , Dong Ranran , Shi Hongjuan , Jiang Dongneng , Sun Lina , Wang Deshou
Published: May 2015

Meiosis is a process unique to the differentiation of germ cells. Retinoic acid (RA) is the key factor controlling the sex-specific timing of meiotic initiation in tetrapods; however, the role of RA in meiotic initiation in teleosts has remained unclear. In this study, the genes encoding RA synthase aldh1a2 and catabolic enzyme cyp26a1 were isolated from Nile tilapia (Oreochromis niloticus), a species without stra8. The expression of aldh1a2 was up-regulated and expression of cyp26a1 was down-regulated before the meiotic initiation in ovaries and in testes. Treatment with RA synthase inhibitor or disruption of Aldh1a2 by CRISPR/Cas9 resulted in delayed meiotic initiation, with simultaneous down-regulation of cyp26a1 and up-regulation of sycp3. By contrast, treatment with an inhibitor of RA catabolic enzyme and disruption of cyp26a1 resulted in earlier meiotic initiation, with increased expression of aldh1a2 and sycp3. Additionally, treatment of XY fish with estrogen (E2) and XX fish with fadrozole led to sex reversal and reversion of meiotic initiation. These results indicate that RA is indispensable for meiotic initiation in teleosts via a stra8 independent signaling pathway where both aldh1a2 and cyp26a1 are critical. In contrast to mammals, E2 is a major regulator of sex determination and meiotic initiation in teleosts.
Quantitative investigation of the poly-adenine DNA dissociation from the surface of gold nanoparticles
Authors: Lu Weiwen , Wang Lihua , Li Jiang , Zhao Yun , Zhou Ziang , Shi Jiye , Zuo Xiaolei , Pan Dun
Published: May 2015

In recent years, poly adenine (polyA) DNA functionalized gold nanoparticles (AuNPs) free of modifications was fabricated with high density of DNA attachment and high hybridization ability similar to those of its thiolated counterpart. This nanoconjugate utilized poly adenine as an anchoring block for binding with the AuNPs surface thereby facilitated the appended recognition block a better upright conformation for hybridization, demonstrating its great potential to be a tunable plasmonic biosensor. It’s one of the key points for any of the practical applications to maintaining stable conjugation between DNA oligonucleotides and gold nanoparticles under various experimental treatments. Thus, in this research, we designed a simple but sensitive fluorescence turn-on strategy to systematically investigate and quantified the dissociation of polyA DNA on gold nanoparticles in diverse experimental conditions. DNA desorbed spontaneously as a function of elevated temperature, ion strength, buffer pH, organic solvents and keeping time. What’s more, evaluating this conjugate stability as affected by the length of its polyA anchor was another crucial aspect in our study. With the improved understanding from these results, we were able to control some of our experimental conditions to maintain a good stability of this kind of polyA DNA−AuNPs nanoconjugates.
Fast and fully-scalable synthesis of reduced graphene oxide
Authors: Abdolhosseinzadeh Sina , Asgharzadeh Hamed , Seop Kim Hyoung
Published: May 2015

Exfoliation of graphite is a promising approach for large-scale production of graphene. Oxidation of graphite effectively facilitates the exfoliation process, yet necessitates several lengthy washing and reduction processes to convert the exfoliated graphite oxide (graphene oxide, GO) to reduced graphene oxide (RGO). Although filtration, centrifugation and dialysis have been frequently used in the washing stage, none of them is favorable for large-scale production. Here, we report the synthesis of RGO by sonication-assisted oxidation of graphite in a solution of potassium permanganate and concentrated sulfuric acid followed by reduction with ascorbic acid prior to any washing processes. GO loses its hydrophilicity during the reduction stage which facilitates the washing step and reduces the time required for production of RGO. Furthermore, simultaneous oxidation and exfoliation significantly enhance the yield of few-layer GO. We hope this one-pot and fully-scalable protocol paves the road toward out of lab applications of graphene.