bluuebunny/crossref_metadata_2025 huggingface dataset:
Public Purpose as a Justification for Expropriation of Rural Land Rights in Ethiopia
Authors: Gebremichael Brightman
Published: February 2016

Expropriation of private land rights involves two contradictory interests: there is a public need for land; and landholders expect security of tenure and protection of their private property rights. A satisfactory expropriation policy must strike a balance between these interests. Legislation must therefore only authorize the government to expropriate land rights for a clear and limited public purpose under the supervision of an independent body. The author argues that Ethiopia's rural land laws have defined the public purpose for the expropriation of rural land rights in different ways depending on the nature of the landholders. For peasants and pastoralists the public purpose requirement is defined vaguely and broadly, whereas for investors the concept is limited to projects implemented by government. The author argues that the protection of private property rights and security of tenure are further undermined by a legislative failure to authorize affected people to appeal to an independent body on the basis that the public purpose requirement has not been satisfied.
The aetiology of post-traumatic stress following childbirth: a meta-analysis and theoretical framework
Authors: Ayers S. , Bond R. , Bertullies S. , Wijma K.
Published: February 2016

There is evidence that 3.17% of women report post-traumatic stress disorder (PTSD) after childbirth. This meta-analysis synthesizes research on vulnerability and risk factors for birth-related PTSD and refines a diathesis–stress model of its aetiology. Systematic searches were carried out on PsycINFO, PubMed, Scopus and Web of Science using PTSD terms crossed with childbirth terms. Studies were included if they reported primary research that examined factors associated with birth-related PTSD measured at least 1 month after birth. In all, 50 studies (n = 21 429) from 15 countries fulfilled inclusion criteria. Pre-birth vulnerability factors most strongly associated with PTSD were depression in pregnancy (r = 0.51), fear of childbirth (r = 0.41), poor health or complications in pregnancy (r = 0.38), and a history of PTSD (r = 0.39) and counselling for pregnancy or birth (r = 0.32). Risk factors in birth most strongly associated with PTSD were negative subjective birth experiences (r = 0.59), having an operative birth (assisted vaginal or caesarean, r = 0.48), lack of support (r = −0.38) and dissociation (r = 0.32). After birth, PTSD was associated with poor coping and stress (r = 0.30), and was highly co-morbid with depression (r = 0.60). Moderator analyses showed that the effect of poor health or complications in pregnancy was more apparent in high-risk samples. The results of this meta-analysis are used to update a diathesis–stress model of the aetiology of postpartum PTSD and can be used to inform screening, prevention and intervention in maternity care.
Development and Psychometric Testing of the Humanistic Nurse-Patient Scale
Authors: Boscart Veronique M. , Pringle Dorothy , Peter Elizabeth , Wynn Francine , McGilton Katherine S.
Published: February 2016

La qualité de vie et le bien-être des patients âgés dans les installations pour les soins chroniques dépendent souvent de leurs relations avec les infirmières. Les auteurs ont développé et testé une échelle pour évaluer les points de vue des patients sur ce qui compte le plus relative aux infirmières. Basé sur la théorie de soins infirmiers humanistes par Paterson et Zderad (1988), 69 articles ont été créés et testés avec un échantillon de 40 patients, résultant dans le raffinement d'une échelle avec 24 articles. Cette échelle a ensuite été soumise à une analyse factorielle sur les réponses de 249 patients résidant dans cinq installations en Ontario, Canada. L'Échelle de l'importance des relations humanistes a démontré une forte cohérence interne, la stabilité et la fiabilité avec une solution de cinq facteurs (α = 0,87). La validité de la construction a été soutenue par l'identification factuelle. Cette échelle est une mesure valide des points de vue des patients sur une relation infirmière-patient en soins chroniques, et peut être utilisée pour mesurer les relations des professionnels de la santé avec leur patients âgés et d'évaluer les interventions visant à améliorer la relation de soins.
Water and beverage consumption among children aged 4–13 years in France: analyses of INCA 2 (Étude Individuelle Nationale des Consommations Alimentaires 2006–2007) data
Authors: Vieux Florent , Maillot Matthieu , Constant Florence , Drewnowski Adam
Published: February 2016

Objective

To examine the consumption of plain water among children in France and compare total water intakes with guidelines issued by the European Food Safety Authority (EFSA).

Design

Nationally representative data were used to assess food, beverage and water consumption by sex, age group (4–8 years, 9–13 years), income-to-poverty ratio, eating occasion and location. Beverages were classified into nine groups: water (tap or bottled), milk, 100 % fruit juice, sodas, fruit drinks, hot beverages, sports drinks and flavoured waters. Total water volume in relation to energy intake (litres/kcal) was also examined.

Setting

INCA 2 study (Étude Individuelle Nationale des Consommations Alimentaires 2006–2007).

Subjects

French children (n 835) aged 4–13 years.

Results

Total water intakes were accounted for by plain water (34 %), beverages (26 %) and food moisture (40 %). Plain water could be tap (18 %) or bottled (16 %). Older children drank more plain water than did younger children and boys drank more plain water than did girls. No socio-economic gradient for plain water consumption was observed. About 90 % of children did not meet the EFSA water intake recommendations. The daily water shortfall ranged from 367 to 594 ml/d. Water-to-energy ratio was 0·75–0·77 litres/1000 kcal (4184 kJ). Children drank milk at breakfast and plain water during lunch and dinner. Caloric beverages provided 10 % of dietary energy; consumption patterns varied by eating location.

Conclusions

Total water intakes among young children in France were below EFSA-recommended levels. Analyses of beverage consumption patterns by eating occasion and location can help identify ways to increase water consumption among children.
Adolescents’ non-core food intake: a description of what, where and with whom adolescents consume non-core foods
Authors: Toumpakari Zoi , Haase Anne M , Johnson Laura
Published: February 2016

Objective

Little is known about adolescents’ non-core food intake in the UK and the eating context in which they consume non-core foods. The present study aimed to describe types of non-core foods consumed by British adolescents in total and across different eating contexts.

Design

A descriptive analysis, using cross-sectional data from food diaries. Non-core foods were classified based on cut-off points of fat and sugar from the Australian Guide to Healthy Eating. Eating context was defined as ‘where’ and ‘with whom’ adolescents consumed each food. Percentages of non-core energy were calculated for each food group in total and across eating contexts. A combined ranking was then created to account for each food’s contribution to non-core energy intake and its popularity of consumption (percentage of consumers).

Setting

The UK National Diet and Nutrition Survey 2008–2011.

Subjects

Adolescents across the UK aged 11–18 years (n 666).

Results

Non-core food comprised 39·5 % of total energy intake and was mostly ‘Regular soft drinks’, ‘Crisps & savoury snacks’, ‘Chips & potato products’, ‘Chocolate’ and ‘Biscuits’. Adolescents ate 57·0 % and 51·3 % of non-core food at ‘Eateries’ or with ‘Friends’, compared with 33·2 % and 32·1 % at ‘Home’ or with ‘Parents’. Persistent foods consumed across eating contexts were ‘Regular soft drinks’ and ‘Chips & potato products’.

Conclusions

Regular soft drinks contribute the most energy and are the most popular non-core food consumed by adolescents regardless of context, and represent a good target for interventions to reduce non-core food consumption.
Identifying small groups of foods that can predict achievement of key dietary recommendations: data mining of the UK National Diet and Nutrition Survey, 2008–12
Authors: Giabbanelli Philippe J , Adams Jean
Published: February 2016

Objective

Many dietary assessment methods attempt to estimate total food and nutrient intake. If the intention is simply to determine whether participants achieve dietary recommendations, this leads to much redundant data. We used data mining techniques to explore the number of foods that intake information was required on to accurately predict achievement, or not, of key dietary recommendations.

Design

We built decision trees for achievement of recommendations for fruit and vegetables, sodium, fat, saturated fat and free sugars using data from a national dietary surveillance data set. Decision trees describe complex relationships between potential predictor variables (age, sex and all foods listed in the database) and outcome variables (achievement of each of the recommendations).

Setting

UK National Diet and Nutrition Survey (NDNS, 2008–12).

Subjects

The analysis included 4156 individuals.

Results

Information on consumption of 113 out of 3911 (3 %) foods, plus age and sex was required to accurately categorize individuals according to all five recommendations. The best trade-off between decision tree accuracy and number of foods included occurred at between eleven (for fruit and vegetables) and thirty-two (for fat, plus age) foods, achieving an accuracy of 72 % (for fat) to 83 % (for fruit and vegetables), with similar values for sensitivity and specificity.

Conclusions

Using information on intake of 113 foods, it is possible to predict with 72–83 % accuracy whether individuals achieve key dietary recommendations. Substantial further research is required to make use of these findings for dietary assessment.
Quantitative Imaging of FRET-Based Biosensors for Cell- and Organelle-Specific Analyses in Plants
Authors: Banerjee Swayoma , Garcia Luis Rene , Versaw Wayne K.
Published: February 2016

Genetically encoded Förster resonance energy transfer (FRET)-based biosensors have been used to report relative concentrations of ions and small molecules, as well as changes in protein conformation, posttranslational modifications, and protein–protein interactions. Changes in FRET are typically quantified through ratiometric analysis of fluorescence intensities. Here we describe methods to evaluate ratiometric imaging data acquired through confocal microscopy of a FRET-based inorganic phosphate biosensor in different cells and subcellular compartments of Arabidopsis thaliana. Linear regression was applied to donor, acceptor, and FRET-derived acceptor fluorescence intensities obtained from images of multiple plants to estimate FRET ratios and associated location-specific spectral correction factors with high precision. FRET/donor ratios provided a combination of high dynamic range and precision for this biosensor when applied to the cytosol of both root and leaf cells, but lower precision when this ratiometric method was applied to chloroplasts. We attribute this effect to quenching of donor fluorescence because high precision was achieved with FRET/acceptor ratios and thus is the preferred ratiometric method for this organelle. A ligand-insensitive biosensor was also used to distinguish nonspecific changes in FRET ratios. These studies provide a useful guide for conducting quantitative ratiometric studies in live plants that is applicable to any FRET-based biosensor.
The development of the international initiative on the humanitarian impact of nuclear weapons and its effect on the nuclear weapons debate
Authors: Kmentt Alexander
Published: February 2016

This article describes the genesis of the humanitarian initiative and the political context in which it has developed in the course of the joint cross-regional statements and the three international conferences on this issue in Norway, Mexico and Austria. It examines the key substantive conclusions that have emerged as a result of this debate and assesses their relevance for the global nuclear disarmament and non-proliferation regime. It concludes that these facts and findings warrant an urgent reassessment of the so-called security value of nuclear weapons and a nuclear deterrence-based notion of stability and security.
Prenatal smoking and childhood behavior problems: is the association mediated by birth weight?
Authors: Parker S. E. , Collett B. R. , Speltz M. L. , Werler M. M.
Published: February 2016

Maternal smoking during pregnancy is associated with both reduced birth weight and adverse neurobehavioral outcomes. The aim of this study was to investigate longitudinal associations between maternal smoking during pregnancy and childhood behavioral outcomes, and to determine the role of birth weight in mediating such associations. The study included 489 mother–child pairs. Prenatal exposures were assessed via maternal interviews conducted on average 1 year after delivery and child behavior assessments were completed at 5–12 years of age using the Child Behavior Checklist (CBCL) and Teacher Report Form (TRF). Maternal smoking during pregnancy was associated with externalizing and total behavior problems according to both mother and teacher report. Maternal smoking was also associated with the following percentage increases in scores: 41% (CBCL) and 44% (TRF) for aggressive behavior and 65% (CBCL) and 47% (TRF) for attention problems. Associations with behavior problems were attenuated or no longer observed for mothers that quit smoking in early pregnancy. The proportion of the total effect of maternal smoking on behavioral outcomes explained by differences in birth weight was small and ranged from 6.6% for externalizing behavior on the CBCL to 20.1% for rule-breaking behavior on the CBCL. Our results suggest that birth weight differences explain only a small proportion of the magnitude of association between maternal smoking during pregnancy and selected behavioral outcomes.
The bacterial microbiome of Dermacentor andersoni ticks influences pathogen susceptibility
Authors: Gall Cory A , Reif Kathryn E , Scoles Glen A , Mason Kathleen L , Mousel Michelle , Noh Susan M , Brayton Kelly A
Published: February 2016

Ticks are of medical importance owing to their ability to transmit pathogens to humans and animals. The Rocky Mountain wood tick, Dermacentor andersoni, is a vector of a number of pathogens, including Anaplasma marginale, which is the most widespread tick-borne pathogen of livestock. Although ticks host pathogenic bacteria, they also harbor bacterial endosymbionts that have a role in tick physiology, survival, as well as pathogen acquisition and transmission. The goal of this study was to characterize the bacterial microbiome and examine the impact of microbiome disruption on pathogen susceptibility. The bacterial microbiome of two populations of D. andersoni with historically different susceptibilities to A. marginale was characterized. In this study, the microbiome was disrupted and then ticks were exposed to A. marginale or Francisella novicida to determine whether the microbiome correlated with pathogen susceptibility. Our study showed that an increase in proportion and quantity of Rickettsia bellii in the microbiome was negatively correlated to A. marginale levels in ticks. Furthermore, a decrease in Francisella endosymbionts was associated with lower F. novicida infection levels, demonstrating a positive pathogen–endosymbiont relationship. We demonstrate that endosymbionts and pathogens have varying interactions, and suggest that microbiome manipulation may provide a possible method for biocontrol by decreasing pathogen susceptibility of ticks.
Microbial community modeling using reliability theory
Authors: Zilles Julie L , Rodríguez Luis F , Bartolerio Nicholas A , Kent Angela D
Published: February 2016

Linking microbial community composition with the corresponding ecosystem functions remains challenging. Because microbial communities can differ in their functional responses, this knowledge gap limits ecosystem assessment, design and management. To develop models that explicitly incorporate microbial populations and guide efforts to characterize their functional differences, we propose a novel approach derived from reliability engineering. This reliability modeling approach is illustrated here using a microbial ecology dataset from denitrifying bioreactors. Reliability modeling is well-suited for analyzing the stability of complex networks composed of many microbial populations. It could also be applied to evaluate the redundancy within a particular biochemical pathway in a microbial community. Reliability modeling allows characterization of the system’s resilience and identification of failure-prone functional groups or biochemical steps, which can then be targeted for monitoring or enhancement. The reliability engineering approach provides a new perspective for unraveling the interactions between microbial community diversity, functional redundancy and ecosystem services, as well as practical tools for the design and management of engineered ecosystems.
Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota
Authors: Kozlowski Jessica A , Stieglmeier Michaela , Schleper Christa , Klotz Martin G , Stein Lisa Y
Published: February 2016

Chemolithotrophic ammonia-oxidizing bacteria and Thaumarchaeota are central players in the global nitrogen cycle. Obligate ammonia chemolithotrophy has been characterized for bacteria; however, large gaps remain in the Thaumarchaeotal pathway. Using batch growth experiments and instantaneous microrespirometry measurements of resting biomass, we show that the terrestrial Thaumarchaeon Nitrososphaera viennensis EN76T exhibits tight control over production and consumption of nitric oxide (NO) during ammonia catabolism, unlike the ammonia-oxidizing bacterium Nitrosospira multiformis ATCC 25196T. In particular, pulses of hydroxylamine into a microelectrode chamber as the sole substrate for N. viennensis resulted in iterative production and consumption of NO followed by conversion of hydroxylamine to nitrite. In support of these observations, oxidation of ammonia in growing cultures of N. viennensis, but not of N. multiformis, was inhibited by the NO-scavenger PTIO. When based on the marginal nitrous oxide (N2O) levels detected in cell-free media controls, the higher levels produced by N. multiformis were explained by enzyme activity, whereas N2O in N. viennensis cultures was attributed to abiotic reactions of released N-oxide intermediates with media components. Our results are conceptualized in a pathway for ammonia-dependent chemolithotrophy in Thaumarchaea, which identifies NO as an essential intermediate in the pathway and implements known biochemistry to be executed by a proposed but still elusive copper enzyme. Taken together, this work identifies differences in ammonia-dependent chemolithotrophy between bacteria and the Thaumarchaeota, advances a central catabolic role of NO only in the Thaumarchaeotal pathway and reveals stark differences in how the two microbial cohorts contribute to N2O emissions.
High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection
Authors: De Smet Jeroen , Zimmermann Michael , Kogadeeva Maria , Ceyssens Pieter-Jan , Vermaelen Wesley , Blasdel Bob , Bin Jang Ho , Sauer Uwe , Lavigne Rob
Published: February 2016

Phage-mediated metabolic changes in bacteria are hypothesized to markedly alter global nutrient and biogeochemical cycles. Despite their theoretic importance, experimental data on the net metabolic impact of phage infection on the bacterial metabolism remains scarce. In this study, we tracked the dynamics of intracellular metabolites using untargeted high coverage metabolomics in Pseudomonas aeruginosa cells infected with lytic bacteriophages from six distinct phage genera. Analysis of the metabolomics data indicates an active interference in the host metabolism. In general, phages elicit an increase in pyrimidine and nucleotide sugar metabolism. Furthermore, clear phage-specific and infection stage-specific responses are observed, ranging from extreme metabolite depletion (for example, phage YuA) to complete reorganization of the metabolism (for example, phage phiKZ). As expected, pathways targeted by the phage-encoded auxiliary metabolic genes (AMGs) were enriched among the metabolites changing during infection. The effect on pyrimidine metabolism of phages encoding AMGs capable of host genome degradation (for example, YuA and LUZ19) was distinct from those lacking nuclease-encoding genes (for example, phiKZ), which demonstrates the link between the encoded set of AMGs of a phage and its impact on host physiology. However, a large fraction of the profound effect on host metabolism could not be attributed to the phage-encoded AMGs. We suggest a potentially crucial role for small, ‘non-enzymatic’ peptides in metabolism take-over and hypothesize on potential biotechnical applications for such peptides. The highly phage-specific nature of the metabolic impact emphasizes the potential importance of the ‘phage diversity’ parameter when studying metabolic interactions in complex communities.
Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice
Authors: Hatam Ido , Lange Benjamin , Beckers Justin , Haas Christian , Lanoil Brian
Published: February 2016

Arctic sea ice can be classified into two types: seasonal ice (first-year ice, FYI) and multi-year ice (MYI). Despite striking differences in the physical and chemical characteristics of FYI and MYI, and the key role sea ice bacteria play in biogeochemical cycles of the Arctic Ocean, there are a limited number of studies comparing the bacterial communities from these two ice types. Here, we compare the membership and composition of bacterial communities from FYI and MYI sampled north of Ellesmere Island, Canada. Our results show that communities from both ice types were dominated by similar class-level phylogenetic groups. However, at the operational taxonomic unit (OTU) level, communities from MYI and FYI differed in both membership and composition. Communities from MYI sites had consistent structure, with similar membership (presence/absence) and composition (OTU abundance) independent of location and year of sample. By contrast, communities from FYI were more variable. Although FYI bacterial communities from different locations and different years shared similar membership, they varied significantly in composition. Should these findings apply to sea ice across the Arctic, we predict increased compositional variability in sea ice bacterial communities resulting from the ongoing transition from predominantly MYI to FYI, which may impact nutrient dynamics in the Arctic Ocean.
Neuronal differentiation is associated with a redox-regulated increase of copper flow to the secretory pathway
Authors: Hatori Yuta , Yan Ye , Schmidt Katharina , Furukawa Eri , Hasan Nesrin M. , Yang Nan , Liu Chin-Nung , Sockanathan Shanthini , Lutsenko Svetlana
Published: February 2016

Brain development requires a fine-tuned copper homoeostasis. Copper deficiency or excess results in severe neuro-pathologies. We demonstrate that upon neuronal differentiation, cellular demand for copper increases, especially within the secretory pathway. Copper flow to this compartment is facilitated through transcriptional and metabolic regulation. Quantitative real-time imaging revealed a gradual change in the oxidation state of cytosolic glutathione upon neuronal differentiation. Transition from a broad range of redox states to a uniformly reducing cytosol facilitates reduction of the copper chaperone Atox1, liberating its metal-binding site. Concomitantly, expression of Atox1 and its partner, a copper transporter ATP7A, is upregulated. These events produce a higher flux of copper through the secretory pathway that balances copper in the cytosol and increases supply of the cofactor to copper-dependent enzymes, expression of which is elevated in differentiated neurons. Direct link between glutathione oxidation and copper compartmentalization allows for rapid metabolic adjustments essential for normal neuronal function.
Integrating geological archives and climate models for the mid-Pliocene warm period
Authors: Haywood Alan M. , Dowsett Harry J. , Dolan Aisling M.
Published: February 2016

The mid-Pliocene Warm Period (mPWP) offers an opportunity to understand a warmer-than-present world and assess the predictive ability of numerical climate models. Environmental reconstruction and climate modelling are crucial for understanding the mPWP, and the synergy of these two, often disparate, fields has proven essential in confirming features of the past and in turn building confidence in projections of the future. The continual development of methodologies to better facilitate environmental synthesis and data/model comparison is essential, with recent work demonstrating that time-specific (time-slice) syntheses represent the next logical step in exploring climate change during the mPWP and realizing its potential as a test bed for understanding future climate change.
Tenomodulin promotes human adipocyte differentiation and beneficial visceral adipose tissue expansion
Authors: Senol-Cosar Ozlem , Flach Rachel J. Roth , DiStefano Marina , Chawla Anil , Nicoloro Sarah , Straubhaar Juerg , Hardy Olga T. , Noh Hye Lim , Kim Jason K. , Wabitsch Martin , Scherer Philipp E. , Czech Michael P.
Published: February 2016

Proper regulation of energy storage in adipose tissue is crucial for maintaining insulin sensitivity and molecules contributing to this process have not been fully revealed. Here we show that type II transmembrane protein tenomodulin (TNMD) is upregulated in adipose tissue of insulin-resistant versus insulin-sensitive individuals, who were matched for body mass index (BMI). TNMD expression increases in human preadipocytes during differentiation, whereas silencing TNMD blocks adipogenesis. Upon high-fat diet feeding, transgenic mice overexpressing Tnmd develop increased epididymal white adipose tissue (eWAT) mass, and preadipocytes derived from Tnmd transgenic mice display greater proliferation, consistent with elevated adipogenesis. In Tnmd transgenic mice, lipogenic genes are upregulated in eWAT, as is Ucp1 in brown fat, while liver triglyceride accumulation is attenuated. Despite expanded eWAT, transgenic animals display improved systemic insulin sensitivity, decreased collagen deposition and inflammation in eWAT, and increased insulin stimulation of Akt phosphorylation. Our data suggest that TNMD acts as a protective factor in visceral adipose tissue to alleviate insulin resistance in obesity.
An open access pilot freely sharing cancer genomic data from participants in Texas
Authors: Becnel Lauren B. , Pereira Stacey , Drummond Jennifer A. , Gingras Marie-Claude , Covington Kyle R. , Kovar Christie L. , Doddapaneni Harsha Vardhan , Hu Jianhong , Muzny Donna , McGuire Amy L. , Wheeler David A. , Gibbs Richard A.
Published: February 2016

Genomic data sharing in cancer has been restricted to aggregate or controlled-access initiatives to protect the privacy of research participants. By limiting access to these data, it has been argued that the autonomy of individuals who decide to participate in data sharing efforts has been superseded and the utility of the data as research and educational tools reduced. In a pilot Open Access (OA) project from the CPRIT-funded Texas Cancer Research Biobank, many Texas cancer patients were willing to openly share genomic data from tumor and normal matched pair specimens. For the first time, genetic data from 7 human cancer cases with matched normal are freely available without requirement for data use agreements nor any major restriction except that end users cannot attempt to re-identify the participants (http://txcrb.org/open.html).
First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids
Authors: Ropo Matti , Schneider Markus , Baldauf Carsten , Blum Volker
Published: February 2016

We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to a total of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building blocks of life, for the parametrization of protein force fields, and for the calculation of reference spectra for biophysical applications.
X-ray Irradiated Vaccine Confers protection against Pneumonia caused by Pseudomonas Aeruginosa
Authors: Li Yanyan , Wang Zhenling , Liu Xiaoxiao , Tang Jianying , Peng Bin , Wei Yuquan
Published: February 2016

Pseudomonas aeruginosa is a gram-negative bacterium and one of the leading causes of nosocomial infection worldwide, however, no effective vaccine is currently available in the market. Here, we demonstrate that inactivation of the bacteria by X-ray irradiation inhibits its replication capability but retained antigenic expression functionally thus allowing its use as a potential vaccine. Mice immunized by this vaccine were challenged by the parental strain, the O-antigen-homologous strain PAO-1 (O2/O5) and heterologous strain PAO-6 (O6) in an acute pneumonia model. We further measured the protective effect of the vaccine, as well as host innate and cellular immunity responses. We found immunized mice could protect against both strains. Notably, the antiserum only had significant protective role against similar bacteria, while adoptive transfer of lymphocytes significantly controlled the spread of the virulent heterologous serogroup PAO-6 infection and the protective role could be reversed by CD4 rather than CD8 antibody. We further revealed that vaccinated mice could rapidly recruit neutrophils to the airways early after intranasal challenge by PAO-6 and the irradiated vaccine was proved to be protective by the generated CD4+ IL-17+ Th17 cells. In conclusion, the generation of inactivated but metabolically active microbes is a promising strategy for safely vaccinating against Pseudomonas aeruginosa.
Deciphering the biological effects of acupuncture treatment modulating multiple metabolism pathways
Authors: Zhang Aihua , Yan Guangli , Sun Hui , Cheng Weiping , Meng Xiangcai , Liu Li , Xie Ning , Wang Xijun
Published: February 2016

Acupuncture is an alternative therapy that is widely used to treat various diseases. However, detailed biological interpretation of the acupuncture stimulations is limited. We here used metabolomics and proteomics technology, thereby identifying the serum small molecular metabolites into the effect and mechanism pathways of standardized acupuncture treatments at ‘Zusanli’ acupoint which was the most often used acupoint in previous reports. Comprehensive overview of serum metabolic profiles during acupuncture stimulation was investigated. Thirty-four differential metabolites were identified in serum metabolome and associated with ten metabolism pathways. Importantly, we have found that high impact glycerophospholipid metabolism, fatty acid metabolism, ether lipid metabolism were acutely perturbed by acupuncture stimulation. As such, these alterations may be useful to clarify the biological mechanism of acupuncture stimulation. A series of differentially expressed proteins were identified and such effects of acupuncture stimulation were found to play a role in transport, enzymatic activity, signaling pathway or receptor interaction. Pathway analysis further revealed that most of these proteins were found to play a pivotal role in the regulation of multiple metabolism pathways. It demonstrated that the metabolomics coupled with proteomics as a powerful approach for potential applications in understanding the biological effects of acupuncture stimulation.
Schizophrenia-Associated hERG channel Kv11.1-3.1 Exhibits a Unique Trafficking Deficit that is Rescued Through Proteasome Inhibition for High Throughput Screening
Authors: Calcaterra Nicholas E. , Hoeppner Daniel J. , Wei Huijun , Jaffe Andrew E. , Maher Brady J. , Barrow James C.
Published: February 2016

The primate-specific brain voltage-gated potassium channel isoform Kv11.1-3.1 has been identified as a novel therapeutic target for the treatment of schizophrenia. While this ether-a-go-go related K + channel has shown clinical relevance, drug discovery efforts have been hampered due to low and inconsistent activity in cell-based assays. This poor activity is hypothesized to result from poor trafficking via the lack of an intact channel-stabilizing Per-Ant-Sim (PAS) domain. Here we characterize Kv11.1-3.1 cellular localization and show decreased channel expression and cell surface trafficking relative to the PAS-domain containing major isoform, Kv11.1-1A. Using small molecule inhibition of proteasome degradation, cellular expression and plasma membrane trafficking are rescued. These findings implicate the importance of the unfolded-protein response and endoplasmic reticulum associated degradation pathways in the expression and regulation of this schizophrenia risk factor. Utilizing this identified phenomenon, an electrophysiological and high throughput in-vitro fluorescent assay platform has been developed for drug discovery in order to explore a potentially new class of cognitive therapeutics.
Cell contractility arising from topography and shear flow determines human mesenchymal stem cell fate
Authors: Sonam Surabhi , Sathe Sharvari R. , Yim Evelyn K.F. , Sheetz Michael P. , Lim Chwee Teck
Published: February 2016

Extracellular matrix (ECM) of the human Mesenchymal Stem Cells (MSCs) influences intracellular tension and is known to regulate stem cell fate. However, little is known about the physiological conditions in the bone marrow, where external forces such as fluid shear stress, apart from the physical characteristics of the ECM, influence stem cell response. Here, we hypothesize that substrate topography and fluid shear stress alter the cellular contractile forces, influence the genetic expression of the stem cells and hence alter their lineage. When fluid shear stress was applied, human MSCs with higher contractility (seeded on 1 μm wells) underwent osteogenesis, whereas those with lower contractility (seeded on 2 μm gratings) remained multipotent. Compared to human MSCs seeded on gratings, those seeded on wells exhibited altered alignment and an increase in the area and number of focal adhesions. When actomyosin contractility was inhibited, human MSCs did not exhibit differentiation, regardless of the topographical feature they were being cultured on. We conclude that the stresses generated by the applied fluid flow impinge on cell contractility to drive the stem cell differentiation via the contractility of the stem cells.
Thermally stable dielectric responses in uniaxially (001)-oriented CaBi4Ti4O15 nanofilms grown on a Ca2Nb3O10− nanosheet seed layer
Authors: Kimura Junichi , Takuwa Itaru , Matsushima Masaaki , Shimizu Takao , Uchida Hiroshi , Kiguchi Takanori , Shiraishi Takahisa , Konno Toyohiko J. , Shibata Tatsuo , Osada Minoru , Sasaki Takayoshi , Funakubo Hiroshi
Published: February 2016

To realize a high-temperature capacitor, uniaxially (001)-oriented CaBi4Ti4O15 films with various film thicknesses were prepared on (100)cSrRuO3/Ca2Nb3O10− nanosheet/glass substrates. As the film thickness decreases to 50 nm, the out-of-plane lattice parameters decrease while the in-plane lattice ones increase due to the in-plane tensile strain. However, the relative dielectric constant (εr) at room temperature exhibits a negligible degradation as the film thickness decreases to 50 nm, suggesting that εr of (001)-oriented CaBi4Ti4O15 is less sensitive to the residual strain. The capacitance density increases monotonously with decreasing film thickness, reaching a value of 4.5 μF/cm2 for a 50-nm-thick nanofilm and is stable against temperature changes from room temperature to 400 °C irrespective of film thickness. This behaviour differs from that of the widely investigated perovskite-structured dielectrics. These results show that (001)-oriented CaBi4Ti4O15 films derived using Ca2Nb3O10− nanosheets as seed layers can be made candidates for high-temperature capacitor applications by a small change in the dielectric properties against film thickness and temperature variations.
Production, Characterization, and Epitope Mapping of Monoclonal Antibodies Against Different Subtypes of Rabbit Hemorrhagic Disease Virus (RHDV)
Authors: Kong Desheng , Liu Jiasen , Jiang Qian , Yu Zuo , Hu Xiaoliang , Guo Dongchun , Huang Qianqian , Jiao Meihui , Qu Liandong
Published: February 2016

In 2010, a new rabbit hemorrhagic disease virus (RHDV) variant, designated RHDV2, was identified for the first time in Italy. Studies have shown that RHDV2 differs from RHDV1 (traditional RHDV) in terms of its antigenic profile and genetic characteristics. The VP60 protein of RHDV is a structural protein that plays important roles in viral replication, assembly, and immunogenicity. In this study, we immunized BALB/c mice with recombinant VP60 proteins from different RHDV subtypes. After three rounds of subcloning, type-specific positive hybridoma clones of RHDV1 and RHDV2 were further identified by an enzyme-linked immunosorbent assay, Western blotting, and an indirect immunofluorescence assay. Finally, three monoclonal antibodies (MAbs) (1D6, 1H2, and 3F2) that only recognize RHDV1, and four MAbs (1G2, 2C1, 3B7, and 5D6) that only recognize RHDV2 were identified. The epitopes recognized by these MAbs were mapped by Western blotting. Sequence analysis showed that the epitope sequences recognized by 1D6, 1H2, and 3F2 are highly conserved (98%) among RHDV1 strains, whereas the epitope sequences recognized by 1G2, 2C1, 3B7, and 5D6 are 100% conserved among RHDV2 strains. The high conservation of the epitope sequence showed that the screened MAbs were type-specific, and that they could distinguish different RHDV subtypes.
Identification of a Vibrio cholerae chemoreceptor that senses taurine and amino acids as attractants
Authors: Nishiyama So-ichiro , Takahashi Yohei , Yamamoto Kentaro , Suzuki Daisuke , Itoh Yasuaki , Sumita Kazumasa , Uchida Yumiko , Homma Michio , Imada Katsumi , Kawagishi Ikuro
Published: February 2016

Vibrio cholerae, the etiological agent of cholera, was found to be attracted by taurine (2-aminoethanesulfonic acid), a major constituent of human bile. Mlp37, the closest homolog of the previously identified amino acid chemoreceptor Mlp24, was found to mediate taxis to taurine as well as L-serine, L-alanine, L-arginine, and other amino acids. Methylation of Mlp37 was enhanced upon the addition of taurine and amino acids. Isothermal titration calorimetry demonstrated that a purified periplasmic fragment of Mlp37 binds directly to taurine, L-serine, L-alanine and L-arginine. Crystal structures of the periplamic domain of Mlp37 revealed that L-serine and taurine bind to the membrane-distal PAS domain in essentially in the same way. The structural information was supported by characterising the in vivo properties of alanine-substituted mutant forms of Mlp37. The fact that the ligand-binding domain of the L-serine complex had a small opening, which would accommodate a larger R group, accounts for the broad ligand specificity of Mlp37 and allowed us to visualise ligand binding to Mlp37 with fluorescently labelled L-serine. Taken together, we conclude that Mlp37 serves as the major chemoreceptor for taurine and various amino acids.
Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting
Authors: Bajar Bryce T. , Wang Emily S. , Lam Amy J. , Kim Bongjae B. , Jacobs Conor L. , Howe Elizabeth S. , Davidson Michael W. , Lin Michael Z. , Chu Jun
Published: February 2016

Many genetically encoded biosensors use Förster resonance energy transfer (FRET) to dynamically report biomolecular activities. While pairs of cyan and yellow fluorescent proteins (FPs) are most commonly used as FRET partner fluorophores, respectively, green and red FPs offer distinct advantages for FRET, such as greater spectral separation, less phototoxicity, and lower autofluorescence. We previously developed the green-red FRET pair Clover and mRuby2, which improves responsiveness in intramolecular FRET reporters with different designs. Here we report the engineering of brighter and more photostable variants, mClover3 and mRuby3. mClover3 improves photostability by 60% and mRuby3 by 200% over the previous generation of fluorophores. Notably, mRuby3 is also 35% brighter than mRuby2, making it both the brightest and most photostable monomeric red FP yet characterized. Furthermore, we developed a standardized methodology for assessing FP performance in mammalian cells as stand-alone markers and as FRET partners. We found that mClover3 or mRuby3 expression in mammalian cells provides the highest fluorescence signals of all jellyfish GFP or coral RFP derivatives, respectively. Finally, using mClover3 and mRuby3, we engineered an improved version of the CaMKIIα reporter Camuiα with a larger response amplitude.
99mTc-labelled anti-CD11b SPECT/CT imaging allows detection of plaque destabilization tightly linked to inflammation
Authors: Liu Guobing , Hu Yan , Xiao Jie , Li Xiao , Li Yanli , Tan Hui , Zhao Yanzhao , Cheng Dengfeng , Shi Hongcheng
Published: February 2016

It remains challenging to predict the risk of rupture for a specific atherosclerotic plaque timely, a thrombotic trigger tightly linked to inflammation. CD11b, is a biomarker abundant on inflammatory cells, not restricted to monocytes/macrophages. In this study, we fabricated a probe named as 99mTc-MAG3-anti-CD11b for detecting inflamed atherosclerotic plaques with single photon emission computed tomography/computed tomography (SPECT/CT). The ApoE-knockout (ApoE−/−) mice were selected to establish animal models, with C57BL/6J mice used for control. A higher CD11b+-cell recruitment with higher CD11b expression and more serious whole-body inflammatory status were identified in ApoE−/− mice. The probe showed high in vitro affinity and specificity to the Raw-264.7 macrophages, as well as inflammatory cells infiltrated in atherosclerotic plaques, either in ex vivo fluorescent imaging or in in vivo micro-SPECT/CT imaging, which were confirmed by ex vivo planar gamma imaging, Oil-Red-O staining and CD11b-immunohistochemistry staining. A significant positive relationship was identified between the radioactivity intensity on SPECT/CT images and the CD11b expression in plaques. In summary, this study demonstrates the feasibility of anti-CD11b antibody mediated noninvasive SPECT/CT imaging of inflammatory leukocytes in murine atherosclerotic plaques. This imaging strategy can identify inflammation-rich plaques at risk for rupture and evaluate the effectiveness of inflammation-targeted therapies in atheroma.
Theta synchronization between medial prefrontal cortex and cerebellum is associated with adaptive performance of associative learning behavior
Authors: Chen Hao , Wang Yi-jie , Yang Li , Sui Jian-feng , Hu Zhi-an , Hu Bo
Published: February 2016

Associative learning is thought to require coordinated activities among distributed brain regions. For example, to direct behavior appropriately, the medial prefrontal cortex (mPFC) must encode and maintain sensory information and then interact with the cerebellum during trace eyeblink conditioning (TEBC), a commonly-used associative learning model. However, the mechanisms by which these two distant areas interact remain elusive. By simultaneously recording local field potential (LFP) signals from the mPFC and the cerebellum in guinea pigs undergoing TEBC, we found that theta-frequency (5.0–12.0 Hz) oscillations in the mPFC and the cerebellum became strongly synchronized following presentation of auditory conditioned stimulus. Intriguingly, the conditioned eyeblink response (CR) with adaptive timing occurred preferentially in the trials where mPFC-cerebellum theta coherence was stronger. Moreover, both the mPFC-cerebellum theta coherence and the adaptive CR performance were impaired after the disruption of endogenous orexins in the cerebellum. Finally, association of the mPFC -cerebellum theta coherence with adaptive CR performance was time-limited occurring in the early stage of associative learning. These findings suggest that the mPFC and the cerebellum may act together to contribute to the adaptive performance of associative learning behavior by means of theta synchronization.
Comparative and phylogenetic analysis of the mitochondrial genomes in basal hymenopterans
Authors: Song Sheng-Nan , Tang Pu , Wei Shu-Jun , Chen Xue-Xin
Published: February 2016

The Symphyta is traditionally accepted as a paraphyletic group located in a basal position of the order Hymenoptera. Herein, we conducted a comparative analysis of the mitochondrial genomes in the Symphyta by describing two newly sequenced ones, from Trichiosoma anthracinum, representing the first mitochondrial genome in family Cimbicidae, and Asiemphytus rufocephalus, from family Tenthredinidae. The sequenced lengths of these two mitochondrial genomes were 15,392 and 14,864 bp, respectively. Within the sequenced region, trnC and trnY were rearranged to the upstream of trnI-nad2 in T. anthracinum, while in A. rufocephalus all sequenced genes were arranged in the putative insect ancestral gene arrangement. Rearrangement of the tRNA genes is common in the Symphyta. The rearranged genes are mainly from trnL1 and two tRNA clusters of trnI-trnQ-trnM and trnW-trnC-trnY. The mitochondrial genomes of Symphyta show a biased usage of A and T rather than G and C. Protein-coding genes in Symphyta species show a lower evolutionary rate than those of Apocrita. The Ka/Ks ratios were all less than 1, indicating purifying selection of Symphyta species. Phylogenetic analyses supported the paraphyly and basal position of Symphyta in Hymenoptera. The well-supported phylogenetic relationship in the study is Tenthredinoidea + (Cephoidea + (Orussoidea + Apocrita)).
Late Arc/Arg3.1 expression in the basolateral amygdala is essential for persistence of newly-acquired and reactivated contextual fear memories
Authors: Nakayama Daisuke , Hashikawa-Yamasaki Yoshiko , Ikegaya Yuji , Matsuki Norio , Nomura Hiroshi
Published: February 2016

A feature of fear memory is its persistence, which could be a factor for affective disorders. Memory retrieval destabilizes consolidated memories and then rapid molecular cascades contribute to early stabilization of reactivated memories. However, persistence of reactivated memories has been poorly understood. Here, we discover that late Arc (also known as Arg3.1) expression in the mouse basolateral amygdala (BLA) is involved in persistence of newly-acquired and reactivated fear memories. After both fear learning and retrieval, Arc levels increased at 2 h, returned to basal levels at 6 h but increased again at 12 h. Inhibiting late Arc expression impaired memory retention 7 d, but not 2 d, after fear learning and retrieval. Moreover, blockade of NR2B-containing N-methyl-D-aspartate receptors (NMDARs) prevented memory destabilization and inhibited late Arc expression. These findings indicate that NR2B-NMDAR and late Arc expression plays a critical role in the destabilization and persistence of reactivated memories.