bluuebunny/crossref_metadata_2025 huggingface dataset:
2D Dendritic Gold Nanostructures Formed on Silica Nanosheets: Transferability, Clean Surface, and Their Biomedical Application
Authors: Wang Xiaoxiao , Yang Dandan , Chen Lizhu , Liu Bin , Teng Zhaogang , He Nongyue , Wang Zhifei
Published: August 2018

The fabrication of 2D dendritic gold nanostructures (2D Au DNSs) has aroused extensive research interest because of their complicated structural characteristic and the unique optical and catalytic properties. However, to obtain transferable 2D Au DNS with clean surface is still extremely difficult, which severely limits their applications. In this work, transferable 2D Au DNSs are designed and constructed by the combination of diffusion‐limited aggregation strategy and utilizing silica nanosheet as the substrate for gold deposition. The results show that the resulting 2D Au DNS has a 13.8% of photothermal conversion efficiency under the irradiation of a 980 nm laser and can be used for in vivo cancer therapy. Moreover, after the functionality of 4‐mercaptobenzoic acid and anti‐Her 2 antibody, 2D Au DNSs can also be used as a surface Raman enhancement label to specifically detect MCF‐7 cells.
A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis
Authors: Alanee Shaheen , El‐Zawahry Ahmed , Dynda Danuta , Dabaja Ali , McVary Kevin , Karr Mallory , Braundmeier‐Fleming Andrea
Published: August 2018

Introduction

There is accumulating evidence that variations in the human microbiota may promote disease states including cancer. Our goal was to examine the association between urinary and fecal microbial profiles and the diagnosis of prostate cancer (PC) in patients undergoing transrectal biopsy of the prostate.

Materials and Methods

We extracted total DNA from urine and fecal samples collected before a prostate biopsy performed for elevated prostatic specific antigen in patients suspected of having PC. We then amplified the extracted DNA and sequenced it using bacterial 16S rRNA gene high‐throughput next‐generation sequencing platform, and analyzed microbial profiles for taxonomy comparing those patients diagnosed with PC with those who did not receive that diagnosis.

Results

We included 30 patients in our analysis (60 samples, one urine and one fecal per patient). The majority of patients with PC (10/14) had similar bacterial communities within their urinary sample profile and clustered separately than patients without cancer (n = 16). Differential analysis of the operational taxonomical units (OTUs) in urine samples revealed decreased abundance of several bacterial species in patients with prostate cancer. Analysis of the bacterial taxonomies of the fecal samples did not reveal any clustering in concordance with benign or malignant prostate biopsies. Patients who had a Gleason score (GS) of 6 (n = 11) were present in both urine bacterial community clusters, but patients with GS 7 or higher (n = 3) did not cluster tightly with non‐cancer subjects.

Conclusions

The urinary microbiota of patients with PC tends to cluster separately from those without this disease. Further research is needed to investigate the urinary microbiome potential of serving as a biomarker that could be used to improve the accuracy of pre‐biopsy models predicting the presence of PC in post‐biopsy tissue examination.
Assessing inference of the basic reproduction number in an SIR model incorporating a growth‐scaling parameter
Authors: Ganyani Tapiwa , Faes Christel , Chowell Gerardo , Hens Niel
Published: August 2018

The standard mass action, which assumes that infectious disease transmission occurs in well‐mixed populations, is popular for formulating compartmental epidemic models. Compartmental epidemic models often follow standard mass action for simplicity and to gain insight into transmission dynamics as it often performs well at reproducing disease dynamics in large populations. In this work, we formulate discrete time stochastic susceptible‐infected‐removed models with linear (standard) and nonlinear mass action structures to mimic varying mixing levels. Using simulations and real epidemic data, we demonstrate the sensitivity of the basic reproduction number to these mathematical structures of the force of infection. Our results suggest the need to consider nonlinear mass action in order to generate more accurate estimates of the basic reproduction number although its uncertainty increases due to the addition of one growth scaling parameter.
Incorporation of Sensitive Ester and Chloropurine Groups into Oligodeoxynucleotides through Solid‐Phase Synthesis
Authors: Halami Bhaskar , Shahsavari Shahien , Nelson Zack , Prehoda Lucas , Eriyagama Dhananjani Nisansala Adikar Mudiyanselage , Fang Shiyue
Published: August 2018

Nucleosides containing ester groups that are sensitive to nucleophiles were incorporated into oligodeoxynucleotides (ODNs) through solid phase chemical synthesis. The sensitive esters are located on a purine nucleobase. They are the esters of ethyl, 2‐methoxyethyl, 4‐methoxyphenyl and phenyl groups, and a thioester. These esters cannot survive the deprotection and cleavage conditions used in known ODN synthesis technologies, which involve strong nucleophiles such as ammonium hydroxide and potassium methoxide (potassium carbonate in anhydrous methanol). To incorporate these sensitive groups into ODNs, the Dmoc (i. e. dimethyl‐1,3‐dithian‐2‐ylmethoxycarbonyl) phosphoramidites and linker were used for solid phase synthesis, which allowed ODN deprotection and cleavage to be carried out under non‐nucleophilic oxidative conditions. Sixteen ODN sequences containing these groups were synthesized and characterized with MALDI MS. In addition, the synthesis and characterization of three ODNs containing a nucleophile sensitive 6‐chloropurine using the same strategy are described.
Simple and Highly Efficient Synthesis of Thioamide Derivatives Using β‐Cyclodextrin as Supramolecular Catalyst in Water
Authors: Tayade Yogesh A. , Jangale Asha D. , Dalal Dipak S.
Published: August 2018

A simple, straightforward and highly efficient approach for the synthesis of thioamide derivatives in water at 100 oC has been developed. Total 22 compounds were prepared via a one‐pot multicomponent reaction between substituted aldehydes, sulfur powder and secondary amines by using recyclable catalyst β‐cyclodextrin indicating the broad substrate scope of this method. The salient features of the present protocol are water as a green solvent, non‐toxic catalyst, good to excellent yields of products, operational simplicity, eco‐friendliness and easy isolation of products. The used catalyst was recovered and reused several times without significant loss of catalytic activity, which is an essential parameter of green synthesis.
[FeFe]‐Hydrogenase Models Containing Long Diselenolato Linkers
Authors: Harb Mohammad K. , Alshurafa Hadil , El‐khateeb Mohammad , Al‐Zuheiri Aya , Görls Helmar , Abul‐Futouh Hassan , Weigand Wolfgang
Published: August 2018

Reactions of Fe3(CO)12 with cyclic diselenides or diselenocyanatoalkanes produced two different products, namely the dinuclear [Fe2(CO)6{μ‐(SeCH2)2(CH2)n}] (n= 5 (1 a), 6 (1 b), 7 (1 c), 8 (1 d)) and the tetranuclear models [Fe2(CO)6{μ‐(SeCH2)2(CH2)n}]2 (n=5 (2 a), 6 (2 b), 7 (2 c), 8 (2 d)). The resulting complexes were fully characterized by a variety of analytical techniques (NMR spectroscopy, elemental analysis, mass spectrometry) and by X‐ray structure determination of complexes 1 c, 1 d, 2 c and 2 d. Furthermore, we investigated the redox properties and the catalytic behaviour of complexes 1 a‐d in the presence of acetic acid (AcOH) as a source of protons.
Ultrathin Molybdenum Dioxide Nanosheets as Uniform and Reusable Surface‐Enhanced Raman Spectroscopy Substrates with High Sensitivity
Authors: Wu Hongrong , Zhou Xiaocheng , Li Jidong , Li Xuemei , Li Baowen , Fei Wenwen , Zhou Jianxin , Yin Jun , Guo Wanlin
Published: August 2018

Metal oxides have advantages over the traditional noble metals to be used as substrate materials for surface‐enhanced Raman spectroscopy (SERS) with low cost, versatility, and biocompatibility, but their enhancement factors are generally quite low with a poor limit of detection. Here, ultrathin molybdenum dioxide (MoO2) nanosheets synthesized by chemical vapor deposition demonstrated in large area are used as SERS substrates with superior signal uniformity in the whole area with a limit of detectable concentration down to 4 × 10−8m and enhancement factor up to 2.1 × 105, exceeding that of 2D materials and comparable to that of noble metal films. More practically important, the planar MoO2 substrate is more robust than noble metals and shows excellent reusability and uniformity, which is usually prohibited for nanostructured or nanoparticle‐based metal oxide substrates. The enhancement is mainly attributed to the surface plasmon resonance effect as evidenced by the first principle calculations and UV–vis absorption spectroscopy characterization, which can be further increased by decreasing the thickness of the MoO2 nanosheets. The overall superior performance makes the MoO2 nanosheets an ideal substrate for practical SERS applications.
Evaluation of the BET Theory for the Characterization of Meso and Microporous MOFs
Authors: Ambroz Filip , Macdonald Thomas J. , Martis Vladimir , Parkin Ivan P.
Published: August 2018

Surface area determination with the Brunauer–Emmett–Teller (BET) method is a widely used characterization technique for metal–organic frameworks (MOFs). Since these materials are highly porous, the use of the BET theory can be problematic. Several researchers have evaluated the BET method to gain insights into the usefulness of the obtained results and interestingly, their findings are not always consistent. In this review, the suitability of the BET method is discussed for MOFs that have a diverse range of pore widths below the diameters of N2 or Ar and above 20 Å. In addition, the surface area of MOFs that are obtained by implementing different approaches, such as grand canonical Monte Carlo simulations, calculations from the crystal structures or based on experimental N2, Ar, or CO2 adsorption isotherms, are compared and evaluated. Inconsistencies in the state‐of‐the‐art are also noted. Based on the current literature, an overview is provided of how the BET method can give useful estimations of the surface areas for the majority of MOFs, but there are some crucial and specific exceptions which are highlighted in this review.
Atomic Scale Materials for Emerging Robust Catalysis
Authors: Sun Xian , Chen Yunxu , Liu Keli , Ding Yu , Zeng Mengqi , Fu Lei
Published: August 2018

Atomic scale materials (ASMs) have drawn great interest from researchers in the field of catalysis, due to their novel structures and attractive properties. As a kind of high‐efficiency catalyst, ASMs exhibit massive active sites, fast charge diffusion rates, and maximum atomic utilization, which endow them with a superior catalytic performance. Herein, the current progress in the development of ASMs for core catalytic systems is summarized, which focuses on the distinct structural characteristics and great catalytic advantages of ASMs, as well as their underlying catalytic mechanism for various reactions. Significantly, it is indicated that ASMs are promising catalysts for robust catalysis, which possess high catalytic activity, good selectivity, long‐term stability, excellent poisoning tolerance, and strong conditional adaptability in catalytic applications, and are gradually applied in the field of industrialization. Finally, the opportunities and challenges of ASMs in the field of catalysis are discussed. This review provides a new impetus for the fundamental design and further exploration of catalysts.
An Experimental Technique for Investigating the Skulling Behavior in the Blast Furnace Hearth
Authors: Shao Lei , Taskinen Pekka , Jokilaakso Ari , Saxen Henrik , Qu Yingxia , Zou Zongshu
Published: August 2018

The skulling behavior in the blast furnace (BF) hearth has yet to be investigated as few (if any) industrial/experimental studies with particular focus on hot metal are reported in the open literature. As a necessary first step toward a better understanding of the sophisticated behavior, an experimental technique is introduced in the present paper. The experimental apparatus, which mainly consists of a vertical tube furnace, a rotating and moveable pedestal, and a moveable water‐cooled probe covered with a multi‐layer structured refractory sleeve can utilize industrial coke, pig iron, and BF hearth carbon brick as raw materials. The technique is shown to be capable of producing chemical, thermal, and mechanical conditions similar to those in the real process. The feasibility and potential of the technique are demonstrated by a set of experimental runs. The results indicate that the air gap between the cooling device and the refractory lining plays a decisive role in both skull formation and lining erosion. Furthermore, the microstructure of graphite precipitated during solidification is influenced by the cooling rate, which in practice is affected by the BF hearth operating parameters. It is hoped that the current contribution will stimulate the growing research interest in this subject.
Cu‐Based Nanoparticles as Emerging Environmental Catalysts
Authors: Deka Pangkita , Borah Biraj Jyoti , Saikia Himadri , Bharali Pankaj
Published: August 2018

This account provides an overview of current research activities on nanoparticles containing the earth‐abundant and inexpensive element copper (Cu) and Cu‐based nanoparticles, especially in the field of environmental catalysis. The different synthetic strategies with possible modification of the chemical/ physical properties of these nanoparticles using such strategies and/or conditions to improve catalytic activity are presented. The design and development of support and/or bimetallic systems (e. g., alloys, intermetallic, etc.) are also included. Herein, we report synthetic approaches of Cu and Cu‐based nanoparticles (monometallic copper, bimetallic copper and copper (II) oxide nanoparticles/nanostructures) and impregnation of such nanoparticles onto support material (e. g., Co3O4 nanostructure), along with their applications as environmental catalyst for various oxidation and reduction reactions. Finally, this account provides necessary advances and perspectives of Cu‐based nanoparticles in the environmental catalysis.
Lithium versus Mono/Polyvalent Ion Intercalation: Hybrid Metal Ion Systems for Energy Storage
Authors: Stoyanova Radostina , Koleva Violeta , Stoyanova Antonia
Published: August 2018

The energy storage by redox intercalation reactions is, nowadays, the most effective rechargeable ion battery. When lithium is used as intercalating agents, the high energy density is achieved at an expense of non‐sustainability. The replacement of Li+ with cheaper monovalent ions enables to make greener battery alternatives. The utilization of polyvalent ions instead of Li+ permits to multiplying the battery capacity. Contrary to Li+, the realization of quick and reversible intercalation of bigger monovalent and of polyvalent ions is a scientific challenge due to kinetic constraints, polarizing ion effects and Coulomb interactions. Herein we provide a vision how to make the intercalation of these ions feasible. The idea is to perform dual intercalation of ions having different charges, radii, preferred coordination and diffusion pathway topology. All these features are demonstrated by the recent knowledge on selective and non‐selective intercalation properties of oxides and polyanion compounds with layered and tunnel structures. Based on dual intercalation properties, the fabrication of hybrid metal ion batteries is presented and discussed.
Intratumoral recombinant human interferon alpha‐2a and vincristine combination therapy in canine transmissible venereal tumour
Authors: Kanca Halit , Tez Gizem , Bal Kazim , Ozen Dogukan , Alcigir Eray , Atalay Vural Sevil
Published: August 2018

Canine transmissible venereal tumour (CTVT) is a naturally occurring contagious neoplasm of dogs located mainly on the external genitalia of both sexes. The course of vincristine chemotherapy, the most effective and practical therapy, is affected by the immune status of the host. The aim was to investigate recombinant human interferon alpha‐2a (rhIFNα‐2a) and vincristine for treatment of CTVT. A total of 21 female dogs were included. In group I (n = 9), vincristine (0.025 mg/kg, IV) was administered weekly. In group II (n = 6), dogs were injected intratumorally weekly with 1.5 million IU rhIFNα‐2a. In group III (n = 6), rhIFNα‐2a and vincristine were combined. No tumour regression was observed after three injections of rhIFNα‐2a in group II and weekly vincristine was administered. The number of tumour infiltrating lymphocytes (TILs), mitotic figures and apoptotic cells were counted in subsequent incisional tumour biopsies. The Kaplan–Meier Method was used to analyse survival using complete tumour regression as the outcome and Breslow Test was used for comparison of survival curves. Differences in TILs, cell proliferation and apoptosis between groups were assessed by analysis of covariance. Complete regression was observed in all animals included. Mean duration of vincristine treatment for complete regression was shorter in group II (3.50 weeks, 95% CI, 3.06–3.94, P < 0.05) and group III (3.17 weeks, 95% CI, 2.84–3.49, P < 0.01) compared to group I (5.11 weeks, 95% CI, 4.42–5.80). Vincristine and rhIFNα‐2a combination increased TILs in CTVT biopsies compared to vincristine treatment (P = 0.017) and vincristine treatment after rhIFNα‐2a (P = 0.049). Vincristine treatment after rhIFNα‐2a (Group II; P < 0.001) and rhIFNα‐2a and vincristine combination (Group III; P < 0.001) decreased apoptosis. The results indicate that intratumoral rhIFNα‐2a treatment alone is not effective in CTVT. However, combination of rhIFNα‐2a and vincristine shortens the duration of treatment compared to vincristine therapy.
Ex post evaluation of energy efficiency programs: Case study of Czech Green Investment Scheme
Authors: Valentová Michaela , Karásek Jiří , Knápek Jaroslav
Published: August 2018

A significant amount of financing has been available for improvements in energy efficiency in buildings in recent years. However, careful evaluation of the real impacts of the programs is still inadequate. The paper provides an insight into the relationship between the expected outcomes and the actual results of an energy efficiency program. It does so on a case example of one of the most significant energy efficiency and renewable energy sources programs in Central Europe, the Green Savings Programme. In total, 206 measures were inspected in 124 projects of the program. The analysis of the inspections showed that there is a significant difference between the expected, verified CO2 emission reduction and ex post, real attained reduction (25% on average). The reasons are partly methodical, but most can be attributed to the behavioral factors of occupants in the respective buildings. The results therefore clearly show the need to tackle the relationship between the calculated (expected) energy savings (and related CO2 emission reduction) and the real savings which are highly influenced by building users. Ex post evaluations should be done, among other things, to provide a more accurate picture regarding the member states’ energy efficiency improvement obligations. Furthermore, such evaluation also provides an essential input for further optimisation of the future energy efficiency support programs.

This article is categorized under:

Energy Efficiency > Economics and Policy
Cover Image, Volume 9, Issue 5
Authors: Swarts Daan C. , Jinek Martin
Published: August 2018

The cover image, by Daan C. Swarts and Martin Jinek, is based on the Advanced Review Cas9 versus Cas12a/Cpf1: Structure–function comparisons and implications for genome editing, DOI: 10.1002/wrna.1481. Design Credit: Daan C. Swarts.

image
Determination of trace elements in normal and malignant breast tissues of different age group using total reflection X‐ray fluorescence spectrometer
Authors: Mirji Santosh , Badiger Nagappa M. , Sanyal Kaushik , Kulkarni Suyamindra.S. , Misra Nand Lal , Gai Pramod B.
Published: August 2018

The trace elements in normal and malignant breast tissues of different age groups have been determined using total reflection X‐ray fluorescence (TXRF) spectrometry. The low Z elements are detected using a vacuum chamber of low Z–high Z (WOBISTRAX) TXRF spectrometer and medium and high Z elements using Ital structures TX‐2000 TXRF spectrometers. The trace elements such as Al, P, S, Cl, K, Ca, Ti, Fe, Cu, Zn, Br, Sr, and Y have been detected in normal and malignant breast tissues in the age group 31–40, 41–50, 51–60, and 61–70 years. It is found that the concentration of trace elements such as Al and Ti, Cu and Zn, Ti and Br, and Al and Y are higher in normal breast tissues than in the malignant breast tissues in the samples of age group 31–40, 41–50, 51–60, and 61–70 years, respectively. It is very important to note that the trace element Pb is not observed in the samples of age group 31–40, 41–50, and 51–60, but it has been observed in the samples of age group 61–70 years.

Trace elements in normal and malignant tissues measured using TXRF spectrometers.

Tissues of different age group have been selected to ascertain the role of trace elements.

Trace elements P, S, Cl, K, Ca, Fe, and Sr are found to be higher in malignant tissues.

Trace element Pb is found to be higher in malignant tissues in the age group 61–70.
Factors Affecting Wine Price Mark-up in Restaurants
Authors: Livat Florine , Remaud Hervé
Published: August 2018

The purpose of this study is to examine how restaurants determine the percentage of wine mark-up. Wine sales are a substantial contributor to restaurants’ profitability, therefore a better understanding of the factors affecting mark-up is critical for the industry. Here, the mark-up is expressed as a percentage over the cost and refers to a cost-plus pricing strategy. Sommeliers from around the world, the majority of whom were members of the International Sommelier Association, were approached to complete our Internet-based questionnaire administered between February 2014 and May 2014. Of the 800 who began the survey, 267 fully completed the questionnaire, generating 1,869 observations. We regressed the declared percentage mark-up against restaurant and wine list characteristics, including managerial practices and wine steward characteristics, and showed that if the restaurants apply a simple rule of thumb to set wine prices, focusing on every price segment, it appears that sommeliers do not have much impact on the percentage mark-up. (JEL Classifications: C23, D21)
Perceived quality of life and living arrangements among older rural South Africans: do all households fare the same?
Authors: Ralston Margaret , Schatz Enid , Madhavan Sangeetha , Gómez-Olivé F. Xavier , Collinson Mark A.
Published: August 2018

This study explores how living arrangements influence perceived quality of life in an elderly population in rural South Africa. We use data from the longitudinal World Health Organization Study of Global Ageing and Adult Health Survey (WHO-SAGE) and from the Agincourt Health and Socio-Demographic Surveillance System (HDSS). On average, older men and women who reside in single-generation and complex-linked multigenerational households report worse quality of life than those in two-generation and linear-linked multigenerational households. However, after controlling for prior wellbeing status, we find living arrangements to have a significant impact on women's perceived quality of life only, and that it is moderated by age. We conclude that not all multigenerational arrangements are protective of older adults’ wellbeing and highlight the gendered impact of living arrangements on quality of life. These results suggest the necessity to understand how living arrangements influence the social roles of older adults and change with age.
Cell-penetrating artificial mitochondria-targeting peptide-conjugated metallothionein 1A alleviates mitochondrial damage in Parkinson’s disease models
Authors: Kang Young Cheol , Son Minuk , Kang Sora , Im Suyeol , Piao Ying , Lim Kwang Suk , Song Min-Young , Park Kang-Sik , Kim Yong-Hee , Pak Youngmi Kim
Published: August 2018

An excess of reactive oxygen species (ROS) relative to the antioxidant capacity causes oxidative stress, which plays a role in the development of Parkinson’s disease (PD). Because mitochondria are both sites of ROS generation and targets of ROS damage, the delivery of antioxidants to mitochondria might prevent or alleviate PD. To transduce the antioxidant protein human metallothionein 1A (hMT1A) into mitochondria, we computationally designed a cell-penetrating artificial mitochondria-targeting peptide (CAMP). The recombinant CAMP-conjugated hMT1A fusion protein (CAMP-hMT1A) successfully localized to the mitochondria. Treating a cell culture model of PD with CAMP-hMT1A restored tyrosine hydroxylase expression and mitochondrial activity and reduced ROS production. Furthermore, injection of CAMP-hMT1A into the brain of a mouse model of PD rescued movement impairment and dopaminergic neuronal degeneration. CAMP-hMT1A delivery into mitochondria might be therapeutic against PD by alleviating mitochondrial damage, and we predict that CAMP could be used to deliver other cargo proteins to the mitochondria.
Lysine benzoylation is a histone mark regulated by SIRT2
Authors: Huang He , Zhang Di , Wang Yi , Perez-Neut Mathew , Han Zhen , Zheng Y. George , Hao Quan , Zhao Yingming
Published: August 2018

Metabolic regulation of histone marks is associated with diverse biological processes through dynamically modulating chromatin structure and functions. Here we report the identification and characterization of a histone mark, lysine benzoylation (Kbz). Our study identifies 22 Kbzsites on histones from HepG2 and RAW cells. This type of histone mark can be stimulated by sodium benzoate (SB), an FDA-approved drug and a widely used chemical food preservative, via generation of benzoyl CoA. By ChIP-seq and RNA-seq analysis, we demonstrate that histone Kbzmarks are associated with gene expression and have physiological relevance distinct from histone acetylation. In addition, we demonstrate that SIRT2, a NAD+-dependent protein deacetylase, removes histone Kbzboth in vitro and in vivo. This study therefore reveals a new type of histone marks with potential physiological relevance and identifies possible non-canonical functions of a widely used chemical food preservative.
Author Correction: Reflection from a free carrier front via an intraband indirect photonic transition
Authors: Gaafar Mahmoud A. , Jalas Dirk , O’Faolain Liam , Li Juntao , Krauss Thomas F. , Petrov Alexander Yu. , Eich Manfred
Published: August 2018

The original version of this article contained an error in first sentence of the Acknowledgements, which incorrectly read ‘M.A.G, D.J., A.Y.P. and M.E. acknowledge the support of the German Research Foundation under grant no. EI 391/13-2, and appreciate the support of CST, Darmstadt, Germany, with their Microwave Studio Software.’ The correct version states ‘261759120’ in place of ‘EI 391/13-2’. This has been corrected in both the PDF and HTML versions of the article.
ESCRT-III mediates budding across the inner nuclear membrane and regulates its integrity
Authors: Arii Jun , Watanabe Mizuki , Maeda Fumio , Tokai-Nishizumi Noriko , Chihara Takahiro , Miura Masayuki , Maruzuru Yuhei , Koyanagi Naoto , Kato Akihisa , Kawaguchi Yasushi
Published: August 2018

Vesicle-mediated nucleocytoplasmic transport is a nuclear pore-independent mechanism for the nuclear export of macromolecular complexes, but the molecular basis for this transport remains largely unknown. Here we show that endosomal sorting complex required for transport-III (ESCRT-III) is recruited to the inner nuclear membrane (INM) during the nuclear export of herpes simplex virus 1 (HSV-1). Scission during HSV-1 budding through the INM is prevented by depletion of ESCRT-III proteins. Interestingly, in uninfected human cells, the depletion of ESCRT-III proteins induces aberrant INM proliferation. Our results show that HSV-1 expropriates the ESCRT-III machinery in infected cells for scission of the INM to produce vesicles containing progeny virus nucleocapsids. In uninfected cells, ESCRT-III regulates INM integrity by downregulating excess INM.
Root exudate metabolomes change under drought and show limited capacity for recovery
Authors: Gargallo-Garriga Albert , Preece Catherine , Sardans Jordi , Oravec Michal , Urban Otmar , Peñuelas Josep
Published: August 2018

Root exudates comprise a large variety of compounds released by plants into the rhizosphere, including low-molecular-weight primary metabolites (particularly saccharides, amino acids and organic acids) and secondary metabolites (phenolics, flavonoids and terpenoids). Changes in exudate composition could have impacts on the plant itself, on other plants, on soil properties (e.g. amount of soil organic matter), and on soil organisms. The effects of drought on the composition of root exudates, however, have been rarely studied. We used an ecometabolomics approach to identify the compounds in the exudates of Quercus ilex (holm oak) under an experimental drought gradient and subsequent recovery. Increasing drought stress strongly affected the composition of the exudate metabolome. Plant exudates under drought consisted mainly of secondary metabolites (71% of total metabolites) associated with plant responses to drought stress, whereas the metabolite composition under recovery shifted towards a dominance of primary metabolites (81% of total metabolites). These results strongly suggested that roots exude the most abundant root metabolites. The exudates were changed irreversibly by the lack of water under extreme drought conditions, and the plants could not recover.
H2S events in the Peruvian oxygen minimum zone facilitate enhanced dissolved Fe concentrations
Authors: Schlosser Christian , Streu Peter , Frank Martin , Lavik Gaute , Croot Peter L. , Dengler Marcus , Achterberg Eric P.
Published: August 2018

Dissolved iron (DFe) concentrations in oxygen minimum zones (OMZs) of Eastern Boundary Upwelling Systems are enhanced as a result of high supply rates from anoxic sediments. However, pronounced variations in DFe concentrations in anoxic coastal waters of the Peruvian OMZ indicate that there are factors in addition to dissolved oxygen concentrations (O2) that control Fe cycling. Our study demonstrates that sediment-derived reduced Fe (Fe(II)) forms the main DFe fraction in the anoxic/euxinic water column off Peru, which is responsible for DFe accumulations of up to 200 nmol L−1. Lowest DFe values were observed in anoxic shelf waters in the presence of nitrate and nitrite. This reflects oxidation of sediment-sourced Fe(II) associated with nitrate/nitrite reduction and subsequent removal as particulate Fe(III) oxyhydroxides. Unexpectedly, the highest DFe levels were observed in waters with elevated concentrations of hydrogen sulfide (up to 4 µmol L−1) and correspondingly depleted nitrate/nitrite concentrations (<0.18 µmol L−1). Under these conditions, Fe removal was reduced through stabilization of Fe(II) as aqueous iron sulfide (FeSaqu) which comprises complexes (e.g., FeSH+) and clusters (e.g., Fe2S2|4H2O). Sulfidic events on the Peruvian shelf consequently enhance Fe availability, and may increase in frequency in future due to projected expansion and intensification of OMZs.
Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort
Authors: Gurry Thomas ,   HST Microbiome Consortium*, Dannenberg Paul H. , Finlayson Samuel G. , Hughes Travis K. , Macias-Trevino Claudio , Owusu-Boaitey Kwadwo , Shomorony Andre , Tuang Suan Lian , Valenstein Max L. , Wang Kathy K. , Wu Michael Pei-hong , Zack Travis I. , Gibbons Sean M. , Nguyen Le Thanh Tu , Kearney Sean M. , Ananthakrishnan Ashwin , Jiang Xiaofang , Duvallet Claire , Kassam Zain , Alm Eric J.
Published: August 2018

Dietary interventions to manipulate the human gut microbiome for improved health have received increasing attention. However, their design has been limited by a lack of understanding of the quantitative impact of diet on a host’s microbiota. We present a highly controlled diet perturbation experiment in a healthy, human cohort in which individual micronutrients are spiked in against a standardized background. We identify strong and predictable responses of specific microbes across participants consuming prebiotic spike-ins, at the level of both strains and functional genes, suggesting fine-scale resource partitioning in the human gut. No predictable responses to non-prebiotic micronutrients were found. Surprisingly, we did not observe decreases in day-to-day variability of the microbiota compared to a complex, varying diet, and instead found evidence of diet-induced stress and an associated loss of biodiversity. Our data offer insights into the effect of a low complexity diet on the gut microbiome, and suggest that effective personalized dietary interventions will rely on functional, strain-level characterization of a patient’s microbiota.
Towards Functional Droplet Architectures: a Belousov-Zhabotinsky Medium for Networks
Authors: Chang Kai Ming , de Planque Maurits R. R. , Zauner Klaus-Peter
Published: August 2018

The confluence of droplet-compartmentalised chemical systems and architectures composed of interacting droplets points towards a novel technology mimicking core features of the cellular architecture that dominates biology. A key challenge to achieve such a droplet technology is long-term stability in conjunction with interdroplet communication. Here, we probed the parameter space of the Belousov-Zhabotinsky (BZ) medium, an extensively studied model for non-equilibrium chemical reactions, pipetted as 2.5 mm droplets in hexadecane oil. The presence of asolectin lipids enabled the formation of arrays of contacted BZ droplets, of which the wave patterns were characterised over time. We utilised laser-cut acrylic templates with over 40 linear oil-filled slots in which arrays are formed by pipetting droplets of the desired BZ composition, enabling parallel experiments and automated image analysis. Using variations of conventional malonic acid BZ medium, wave propagation over droplet-droplet interfaces was not observed. However, a BZ medium containing both malonic acid and 1,4-cyclohexanedione was found to enable inter-droplet wave propagation. We anticipate that the chemical excitation properties of this mixed-substrate BZ medium, in combination with the droplet stability of the networks demonstrated here for nearly 400 droplets in a template-defined topology, will facilitate the development of scalable functional droplet networks.
Spectra, intermittency, and extremes of weather, macroweather and climate
Authors: Lovejoy S.
Published: August 2018

It was recently found that the accepted picture of atmospheric variability was in error by a large factor. Rather than being dominated by a series of narrow scale-range quasi-oscillatory processes with an unimportant white noise “background”, it turned out that the variance was instead dominated by a few wide range scaling processes albeit occasionally interspersed with superposed quasi-oscillations. Although the classical model implied that successive million year global temperature averages would differ by mere micro Kelvins, the implausibility had not been noticed. In contrast, the new picture inverts the roles of background and foreground and involves four (possibly five) wide range scaling processes. As with any new paradigm, there are consequences; in this paper we focus on the implications for the spectra, intermittency and the extremes. Intermittency is an expression of the spatio-temporal sparseness of strong events whereas the extremes refer to the tails of their probability distributions and both affect the spectra. Although we give some results for the macro and mega climate regimes, we focus on weather, macroweather and climate: from dissipation to Milankovitch scales.
Topological motifs populate complex networks through grouped attachment
Authors: Choi Jaejoon , Lee Doheon
Published: August 2018

Network motifs are topological subgraph patterns that recur with statistical significance in a network. Network motifs have been widely utilized to represent important topological features for analyzing the functional properties of complex networks. While recent studies have shown the importance of network motifs, existing network models are not capable of reproducing real-world topological properties of network motifs, such as the frequency of network motifs and relative graphlet frequency distances. Here, we propose a new network measure and a new network model to reconstruct real-world network topologies, by incorporating our Grouped Attachment algorithm to generate networks in which closely related nodes have similar edge connections. We applied the proposed model to real-world complex networks, and the resulting constructed networks more closely reflected real-world network motif properties than did the existing models that we tested: the Erdös–Rényi, small-world, scale-free, popularity-similarity-optimization, and nonuniform popularity-similarity-optimization models. Furthermore, we adapted the preferential attachment algorithm to our model to gain scale-free properties while preserving motif properties. Our findings show that grouped attachment is one possible mechanism to reproduce network motif recurrence in real-world complex networks.
Magneto-Optical properties of noble-metal nanostructures: functional nanomaterials for bio sensing
Authors: Manera Maria Grazia , Colombelli Adriano , Taurino Antonietta , Martin Antonio Garcia , Rella Roberto
Published: August 2018

Metallic nanostructures supporting Localized Surface Plasmon Resonances (LSPR) are characterized by their unique ability to control and manipulate light at the nanoscale. Noble metal nanostructures, such as gold nanostructures, are demonstrating to exhibit magneto-optic activity in the presence of modulated magnetic field of low intensity in transversal configuration (T-MOKE). Validation of experimental findings was achieved by numerical simulations based on Finite Element Method (FEM) techniques. The developed numerical models allowed studying the combination of the T-MOKE effect with the localized surface plasmon resonance of metal nanoparticles. Numerical optical and magneto-optical spectra provided a deep insight on the physical aspects behind the magneto-optical activity of metal nanostructures strictly related to direction of oscillations electrical dipoles generated in resonance conditions. Additionally the MO signal was characterized as a transducing signal for refractive index sensing in liquid conditions. The outcome is an increase in the limit of detection of magneto optical transducer with respect to traditional plasmonic sensors. A new strategy for magneto-plasmonic sensing based on the use of glass supported -Au nanostructures based on their MO properties has put forward.
Toll-like Receptor 4 Pathway Polymorphisms Interact with Pollution to Influence Asthma Diagnosis and Severity
Authors: Schurman Shepherd H. , Bravo Mercedes A. , Innes Cynthia L. , Jackson W. Braxton , McGrath John A. , Miranda Marie Lynn , Garantziotis Stavros
Published: August 2018

Asthma is a common chronic lung disease, the incidence and severity of which may be influenced by gene-environment interactions. Our objective was to examine associations between single nucleotide polymorphisms (SNPs) and combinations of SNPs in the toll-like receptor 4 (TLR4) pathway, residential distance to roadway as a proxy for traffic-related air pollution exposure, and asthma diagnosis and exacerbations. We obtained individual-level data on genotype, residential address, and asthma diagnosis and exacerbations from the Environmental Polymorphisms Registry. Subjects (n = 2,704) were divided into three groups (hyper-responders, hypo-responders, and neither) based on SNP combinations in genes along the TLR4 pathway. We geocoded subjects and calculated distance, classified as <250 m or ≥250 m, between residence and nearest major road. Relationships between genotype, distance to road, and odds of asthma diagnosis and exacerbations were examined using logistic regression. Odds of an asthma diagnosis among hyper-responders <250 m from a major road was 2.37(0.97, 6.01) compared to the reference group (p < 0.10). Hypo-responders ≥250 m from the nearest road had lower odds of activity limitations (0.46 [0.21, 0.95]) and sleeplessness (0.36 [0.12, 0.91]) compared to neither-responders (p < 0.05). Specific genotype combinations when combined with an individual’s proximity to roadways, possibly due to traffic-related air pollution exposure, may affect the likelihood of asthma diagnosis and exacerbations.
The effect of Ganoderma lucidum extract on immunological function and identify its anti-tumor immunostimulatory activity based on the biological network
Authors: Zhao Ruolin , Chen Qilong , He Yu-min
Published: August 2018

Ganoderma lucidum extract (GLE) has shown positive effects for tumor treatment. However, the molecular mechanism of GLE treatment is unknown. In this study, a Hepa1-6-bearing C57 BL/6 mouse model was established to explore the anti-tumor and immunostimulatory activity of GLE treatment. The results showed that GLE effectively inhibited tumor growth without hepatic/renal toxicity and bone marrow suppression, and might enhancing immunological function. Based on the mRNA profiles of GLE treated and untreated mice, 302 differentially expressed (DE) mRNAs were identified and 6 kernel mRNAs were identified from the established protein-protein interaction (PPI) network. Quantitative RT-PCR and western-blot analysis indicated that 6 mRNAs have had statistically significant differences between the GLE treated and untreated mice. Furthermore, four kernel pathways were isolated from the KEGG-Target network, including the Jak-STAT signaling pathway, T cell receptor signaling pathway, PI3K-Akt signaling pathway, and cytokine-cytokine receptor interaction. Western-blot and cytokine detection results demonstrated that GLE suppressed growth and proliferation of tumors by the Jak-STAT signaling pathway, T cell receptor signaling pathway and PI3K-Akt signaling pathway, but also regulated the expression levels of serum immune cytokines and improved the anti-tumor immunostimulatory activity.
Expression of TCN1 in Blood is Negatively Associated with Verbal Declarative Memory Performance
Authors: Akkouh Ibrahim A. , Ueland Torill , Andreassen Ole A. , Brattbakk Hans-Richard , Steen Vidar M. , Hughes Timothy , Djurovic Srdjan
Published: August 2018

Memory is indispensable for normal cognitive functioning, and the ability to store and retrieve information is central to mental health and disease. The molecular mechanisms underlying complex memory functions are largely unknown, but multiple genome-wide association studies suggest that gene regulation may play a role in memory dysfunction. We performed a global gene expression analysis using a large and balanced case-control sample (n = 754) consisting of healthy controls and schizophrenia and bipolar disorder patients. Our aim was to discover genes that are differentially expressed in relation to memory performance. Gene expression in blood was measured using Illumina HumanHT-12 v4 Expression BeadChip and memory performance was assessed with the updated California Verbal Learning Test (CVLT-II). We found that elevated expression of the vitamin B12-related gene TCN1 (haptocorrin) was significantly associated with poorer memory performance after correcting for multiple testing (β = −1.50, p = 3.75e-08). This finding was validated by quantitative real-time PCR and followed up with additional analyses adjusting for confounding variables. We also attempted to replicate the finding in an independent case-control sample (n = 578). The relationship between TCN1 expression and memory impairment was comparable to that of important determinants of memory function such as age and sex, suggesting that TCN1 could be a clinically relevant marker of memory performance. Thus, we identify TCN1 as a novel genetic finding associated with poor memory function. This finding may have important implications for the diagnosis and treatment of vitamin B12-related conditions.
Optimal reference genes for normalization of qPCR gene expression data from proton and photon irradiated dermal fibroblasts
Authors: Nielsen Steffen , Bassler Niels , Grzanka Leszek , Swakon Jan , Olko Pawel , Andreassen Christian Nicolaj , Alsner Jan , Sørensen Brita Singers
Published: August 2018

The transcriptional response of cells exposed to proton radiation is not equivalent to the response induced by traditional photon beams. Changes in cellular signalling is most commonly studied using the method Quantitative polymerase chain reaction (qPCR). Stable reference genes must be used to accurately quantify target transcript expression. The study aim was to identify suitable reference genes for normalisation of gene expression levels in normal dermal fibroblasts irradiated with either proton or photon beams. The online tool RefFinder was used to analyse and identify the most stably expressed genes from a panel of 22 gene candidates. To assess the reliability of the identified reference genes, a selection of the most and least stable reference genes was used to normalise target transcripts of interest. Fold change levels varied considerably depending on the used reference gene. The top ranked genes IPO8, PUM1, MRPL19 and PSMC4 produced highly similar target gene expression, while expression using the worst ranked genes, TFRC and HPRT1, was clearly modified due to reference gene instability.
Tuning the upconversion photoluminescence lifetimes of NaYF4:Yb3+, Er3+ through lanthanide Gd3+ doping
Authors: Qin Heng , Wu Danyang , Sathian Juna , Xie Xiangyu , Ryan Mary , Xie Fang
Published: August 2018

The multiplexing capacity of conventional fluorescence materials are significantly limited by spectral overlap and background interference, mainly due to their short-lived fluorescence lifetimes. Here, we adopt a novel Gd3+ doping strategy in NaYF4 host materials, realized tuning of upconversion photoluminescence (UCPL) lifetimes at selective emissions. Time-correlated single-photon counting (TCSPC), was applied to measure the photoluminescence lifetimes accurately. We demonstrated the large dynamic range of lifetimes of upconversion nanoparticles with good upconversion quantum yields, mainly owing to the dominance of high efficient energy transfer upconversion mechanism. The exceptional tunable properties of upconversion materials allow great potential for them to be utilized in biotechnology and life sciences.