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Kelin Xia
In this paper, a multiscale virtual particle based elastic network model (MVP-ENM) is proposed for the normal mode analysis of large-sized biomolecules. The multiscale virtual particle (MVP) model is proposed for the discretization of biomolecular density data. With this model, large-sized biomolecular structures can be coarse-grained into virtual particles such that a balance between model accuracy and computational cost can be achieved. An elastic network is constructed by assuming "connections" between virtual particles...
December 11, 2017: Physical Chemistry Chemical Physics: PCCP
Feng Dong, Chih-Ming Hung, Xin-Lei Li, Jian-Yun Gao, Qiang Zhang, Fei Wu, Fu-Min Lei, Shou-Hsien Li, Xiao-Jun Yang
BACKGROUND: The glacial-interglacial cycles in the Pleistocene caused repeated range expansion and contraction of species in several regions in the world. However, it remains uncertain whether such climate oscillations had similar impact on East Asian biota, despite its widely recognized importance in global biodiversity. Here we use both molecular and ecological niche profiles on 11 East Asian avian species with various elevational ranges to reveal their response to the late Pleistocene climate changes...
December 6, 2017: BMC Evolutionary Biology
Irina Guseva Canu, Paul A Schulte, Michael Riediker, Liliya Fatkhutdinova, Enrico Bergamaschi
Engineered nanomaterials (ENMs) raise questions among the scientific community and public health authorities about their potential risks to human health. Studying a prospective cohort of workers exposed to ENMs would be considered the gold standard for identifying potential health effects of nanotechnology and confirming the 'no effect' levels derived from cellular and animal models. However, because only small, cross-sectional studies have been conducted in the past 5 years, questions remain about the health risks of ENMs...
December 4, 2017: Journal of Epidemiology and Community Health
Shinya Suzuki, Florian Part, Yasushi Matsufuji, Marion Huber-Humer
To date construction materials that contain engineered nanomaterials (ENMs) are available at the markets, but at the same time very little is known about their environmental fate. Therefore, this study aimed at modeling the potential fate of ENMs by using the example of the Japanese construction sector and by conducting a dynamic material flow analysis. Expert interviews and national reports revealed that about 3920-4660 tons of ENMs are annually used for construction materials in Japan. Nanoscale TiO2, SiO2, Al2O3 and carbon black have already been applied for decades to wall paints, road markings or concrete...
November 28, 2017: Waste Management
Arzu Uyar, Vardan Karamyan, Alex Dickson
Crystal structures of neurolysin, a zinc metallopeptidase, do not show a significant conformational change upon the binding of an allosteric inhibitor. Neurolysin has a deep channel where it hydrolyzes a short neuropeptide neurotensin to create inactive fragments and thus controls its level in the tissue. Neurolysin is of interest as a therapeutic target since changes in neurotensin level have been implicated in cardiovascular disorders, neurological disorders and cancer, and inhibitors of neurolysin have been developed...
November 27, 2017: Journal of Chemical Theory and Computation
Antonio Pietroiusti, Enrico Bergamaschi, Marcello Campagna, Luisa Campagnolo, Giuseppe De Palma, Sergio Iavicoli, Veruscka Leso, Andrea Magrini, Michele Miragoli, Paola Pedata, Leonardo Palombi, Ivo Iavicoli
BACKGROUND: There is a fundamental gap of knowledge on the health effects caused by the interaction of engineered nanomaterials (ENM) with the gastro-intestinal tract (GIT). This is partly due to the incomplete knowledge of the complex physical and chemical transformations that ENM undergo in the GIT, and partly to the widespread belief that GIT health effects of ENM are much less relevant than pulmonary effects. However, recent experimental findings, considering the role of new players in gut physiology (e...
November 25, 2017: Particle and Fibre Toxicology
Yoon Kyeung Lee, Ki Jun Yu, Enming Song, Amir Barati Farimani, Flavia Vitale, Zhaoqian Xie, Younghee Yoon, Yerim Kim, Andrew Richardson, Haiwen Luan, Yixin Wu, Xu Xie, Timothy H Lucas, Kaitlyn Crawford, Yongfeng Mei, Xue Feng, Yonggang Huang, Brian Litt, Narayana R Aluru, Lan Yin, John A Rogers
The chemistry that governs the dissolution of device-grade, monocrystalline silicon nanomembranes into benign end products by hydrolysis serves as the foundation for fully eco/biodegradable classes of high performance electronics. This paper examines these processes in aqueous solutions with chemical compositions relevant to ground water and biofluids. The results show that the presence of Si(OH)4 and proteins in these solutions can slow the rates of dissolution and that ion specific effects associated with Ca2+ can significantly increase these rates...
November 27, 2017: ACS Nano
Yoon Kyeung Lee, Ki Jun Yu, Yerim Kim, Younghee Yoon, Zhaoqian Xie, Enming Song, Haiwen Luan, Xue Feng, Yonggang Huang, John A Rogers
Flexible electronic systems for bio-implants with long-term (multi-decade) stability and safety in operation require thin, bio-compatible layers that can prevent bio-fluid penetration. Recent work shows that ultrathin films of silicon dioxide thermally grown (TG-SiO2) on device-grade silicon wafers and then released as transferrable barriers offer a remarkable set of attributes in this context. This paper examines the chemical stability of these materials in aqueous solutions with different combinations of chemistries that are present in biofluids...
November 27, 2017: ACS Applied Materials & Interfaces
Bruno B Kubiak, Eliécer E Gutiérrez, Daniel Galiano, Renan Maestri, Thales R O de Freitas
Species with similar ecological requirements coexisting in the same geographic region are prone to competitively exclude each other. Alternatively, they may coexist if character displacement acts to change the niche requirements of one or both species. We used two methodological approaches (ecological niche modeling [ENM] and geometric morphometrics) to test two hypotheses: given their behavioral, morphological, and ecological similarities, one species competitively excludes the other; and, character displacement enables their coexistence at two sites in which the species are known to occur in sympatry...
November 24, 2017: Scientific Reports
Donald H Atha, Amber Nagy, Andrea Steinbrück, Allison M Dennis, Jennifer A Hollingsworth, Varsha Dua, Rashi Iyer, Bryant C Nelson
BACKGROUND: When evaluating the toxicity of engineered nanomaterials (ENMS) it is important to use multiple bioassays based on different mechanisms of action. In this regard we evaluated the use of gene expression and common cytotoxicity measurements using as test materials, two selected nanoparticles with known differences in toxicity, 5 nm mercaptoundecanoic acid (MUA)-capped InP and CdSe quantum dots (QDs). We tested the effects of these QDs at concentrations ranging from 0.5 to 160 µg/mL on cultured normal human bronchial epithelial (NHBE) cells using four common cytotoxicity assays: the dichlorofluorescein assay for reactive oxygen species (ROS), the lactate dehydrogenase assay for membrane viability (LDH), the mitochondrial dehydrogenase assay for mitochondrial function, and the Comet assay for DNA strand breaks...
November 9, 2017: Journal of Nanobiotechnology
R Roshan Manesh, G Grassi, E Bergami, L F Marques-Santos, C Faleri, G Liberatori, I Corsi
Recent developments on environmental fate models indicate that as nano waste, engineered nanomaterials (ENMs) could reach terrestrial ecosystems thus potentially affecting environmental and human health. Plants can be therefore exposed to ENMs but controversial data in terms of fate and toxicity are currently available. Furthermore, there is a current lack of information on complex interactions/transformations to which ENMs undergo in the natural environment as for instance interacting with existing toxic compounds...
November 6, 2017: Ecotoxicology and Environmental Safety
Luis E Escobar, Scott Carver, Daniel Romero-Alvarez, Sue VandeWoude, Kevin R Crooks, Michael R Lappin, Meggan E Craft
Traditional epidemiological studies of disease in animal populations often focus on directly transmitted pathogens. One reason pathogens with complex lifecycles are understudied could be due to challenges associated with detection in vectors and the environment. Ecological niche modeling (ENM) is a methodological approach that overcomes some of the detection challenges often seen with vector or environmentally dependent pathogens. We test this approach using a unique dataset of two pathogens in wild felids across North America: Toxoplasma gondii and Bartonella spp...
2017: Frontiers in Veterinary Science
David Shevlin, Niall O'Brien, Enda Cummins
Growth in the nanotechnology sector is likely introducing unnatural formations of materials on the nanoscale (10(-9)m) to the environment. Disposal and degradation of products incorporating engineered nanomaterials (ENMs) are likely being released into natural aquatic systems un-intentionally primarily via waste water effluents. The fate and behaviour of metallic based nanoparticles (NPs) such as silver (Ag) in aquatic waters is complex with high levels of variability and uncertainty. In-situ physical, biological and chemical (natural attenuation) processes are likely to influence ENM fate and behaviour in freshwater systems...
October 24, 2017: Science of the Total Environment
Kelsey R Babik, Matthew M Dahm, Kevin H Dunn, Kevin L Dunn, Mary K Schubauer-Berigan
OBJECTIVE: Toxicology studies suggest that exposure to certain types of engineered nanomaterials (ENMs) may cause adverse health effects, but little is known about the workforce in the United States that produces or uses these materials. In addition, occupational exposure control strategies in this industry are not well characterized. This study identified US ENM manufacturers and users (other than carbon nanotubes and nanofibers, which have been characterized elsewhere), determined workforce size, characterized types and quantities of materials used, occupational exposure control strategies, and the feasibility of occupational ENM exposure studies...
October 20, 2017: Journal of Occupational and Environmental Hygiene
Zheng Dong, Hongyu Zhou, Peng Tao
OBJECTIVES: PAS domains are widespread in archaea, bacteria and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. METHODS: We collected protein sequences and crystal structures data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity and transferase activity)...
October 20, 2017: Protein Science: a Publication of the Protein Society
Messika Revel, Amélie Châtel, Catherine Mouneyrac
In recent years, the implication of genomics into ecotoxicological studies has been studied closely to allow a better understanding of organism's responses to environmental contaminants including engineering nanomaterials (ENMs). ENMs are increasingly produced for various applications including cosmetics, electronics, sports equipment, biomedicine and agriculture. Because of their small size, ENMs possess chemical or physical characteristics improved compared to the corresponding macro-sized material. As their application expend, the release of manufactured ENMs into the environment is likely to increase and concern over impacts for the aquatic ecosystem is growing...
October 12, 2017: Aquatic Toxicology
Santiago José Elías Velazco, Franklin Galvão, Fabricio Villalobos, Paulo De Marco Júnior
Ecological niche modeling (ENM) is a broadly used tool in different fields of plant ecology. Despite the importance of edaphic conditions in determining the niche of terrestrial plant species, edaphic data have rarely been included in ENMs of plant species perhaps because such data are not available for many regions. Recently, edaphic data has been made available at a global scale allowing its potential inclusion and evaluation on ENM performance for plant species. Here, we take advantage of such data and address the following main questions: What is the influence of distinct predictor variables (e...
2017: PloS One
Glen M DeLoid, Yanli Wang, Klara Kapronezai, Laura Rubio Lorente, Roujie Zhang, Georgios Pyrgiotakis, Nagarjun V Konduru, Maria Ericsson, Jason C White, Roberto De La Torre-Roche, Hang Xiao, David Julian McClements, Philip Demokritou
BACKGROUND: Engineered nanomaterials (ENMs) are increasingly added to foods to improve their quality, sensory appeal, safety and shelf-life. Human exposure to these ingested ENMs (iENMS) is inevitable, yet little is known of their hazards. To assess potential hazards, efficient in vitro methodologies are needed to evaluate particle biokinetics and toxicity. These methodologies must account for interactions and transformations of iENMs in foods (food matrix effect) and in the gastrointestinal tract (GIT) that are likely to determine nano-biointeractions...
October 13, 2017: Particle and Fibre Toxicology
Runsheng Song, Yuwei Qin, Sangwon Suh, Arturo A Keller
Most existing life-cycle release models for engineered nanomaterials (ENM) are static, ignoring the dynamics of stock and flows of ENMs. Our model, nanoRelease, estimates the annual releases of ENMs from manufacturing, use, and disposal of a product explicitly taking stock and flow dynamics into account. Given the variabilities in key parameters (e.g., service life of products and annual release rate during use) nanoRelease is designed as a stochastic model. We apply nanoRelease to three ENMs (TiO2, SiO2 and FeOx) used in paints and coatings through seven product applications, including construction and building, household and furniture, and automotive for the period from 2000 to 2020 using production volume and market projection information...
November 7, 2017: Environmental Science & Technology
Natasha M Sanabria, Mary Gulumian
BACKGROUND: RT-qPCR is routinely used in expression profiling of toxicity pathway genes. However, genetic and molecular level studies used to determine, understand and clarify potential risks of engineered nanomaterials (ENMs) are still incomplete. Concerns regarding possible interference caused by intracellular ENMs during analyses have been raised. The aim of this study was to verify a qPCR procedure for gene expression assays, which can be used in toxicity and exposure assessments...
October 10, 2017: Journal of Nanobiotechnology
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