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https://www.readbyqxmd.com/read/28209973/structural-basis-for-fragmenting-the-exopolysaccharide-of-acinetobacter-baumannii-by-bacteriophage-%C3%AE-ab6-tailspike-protein
#1
I-Ming Lee, I-Fan Tu, Feng-Ling Yang, Tzu-Ping Ko, Jiahn-Haur Liao, Nien-Tsung Lin, Chung-Yi Wu, Chien-Tai Ren, Andrew H-J Wang, Ching-Ming Chang, Kai-Fa Huang, Shih-Hsiung Wu
With an increase in antibiotic-resistant strains, the nosocomial pathogen Acinetobacter baumannii has become a serious threat to global health. Glycoconjugate vaccines containing fragments of bacterial exopolysaccharide (EPS) are an emerging therapeutic to combat bacterial infection. Herein, we characterize the bacteriophage ΦAB6 tailspike protein (TSP), which specifically hydrolyzed the EPS of A. baumannii strain 54149 (Ab-54149). Ab-54149 EPS exhibited the same chemical structure as two antibiotic-resistant A...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28208578/role-of-cortico-cancellous-heterologous-bone-in-human-periodontal-ligament-stem-cell-xeno-free-culture-studied-by-synchrotron-radiation-phase-contrast-microtomography
#2
Serena Mazzoni, Sara Mohammadi, Giuliana Tromba, Francesca Diomede, Adriano Piattelli, Oriana Trubiani, Alessandra Giuliani
This study was designed to quantitatively demonstrate via three-dimensional (3D) images, through the Synchrotron Radiation Phase-Contrast Microtomography (SR-PhC-MicroCT), the osteoinductive properties of a cortico-cancellous scaffold (Osteobiol Dual Block-DB) cultured with human Periodontal Ligament Stem Cells (hPDLSCs) in xeno-free media. In vitro cultures of hPDLSCs, obtained from alveolar crest and horizontal fibers of the periodontal ligament, were seeded onto DB scaffolds and cultured in xeno-free media for three weeks...
February 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28206708/physiological-metabolic-and-biotechnological-features-of-extremely-thermophilic-microorganisms
#3
REVIEW
James A Counts, Benjamin M Zeldes, Laura L Lee, Christopher T Straub, Michael W W Adams, Robert M Kelly
The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as 'extreme thermophiles' and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs-basically, anywhere there is hot water...
February 16, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28203643/establishing-elements-of-a-synthetic-biology-platform-for-vaccinia-virus-production-biobrick%C3%A2-design-serum-free-virus-production-and-microcarrier-based-cultivation-of-cv-1-cells
#4
Shuchang Liu, Ludmila Ruban, Yaohe Wang, Yuhong Zhou, Darren N Nesbeth
Vaccinia virus (VACV) is an established vector for vaccination and is beginning to prove effective as an oncolytic agent. Industrial production of VACV stands to benefit in future from advances made by synthetic biology in genome engineering and standardisation. The CV-1 cell line can be used for VACV propagation and has been used extensively with the CRISPR/Cas9 system for making precise edits of the VACV genome. Here we take first steps toward establishing a scalable synthetic biology platform for VACV production with CV-1 cells featuring standardised biological tools and serum free cell cultivation...
February 2017: Heliyon
https://www.readbyqxmd.com/read/28199986/a-tree-shrew-glioblastoma-model-recapitulates-features-of-human-glioblastoma
#5
Yaohui Tong, Junjun Hao, Qiu Tu, Hualin Yu, Lanzhen Yan, Yuan Li, Longbao Lv, Fei Wang, Antonio Iavarone, Xudong Zhao
Tupaia belangeri (tree shrew), an animal species whose genome has significantly higher similarity to primates than rodents, has been used in biomedical research. To generate animal models that reproduce the human tumors more faithfully than rodents, we present the first report of a cancer model mimicking human tumor genetics in tree shrew. By engineering a lentiviral system for the transduction of mutant H-Ras and a shRNA against tree shrew p53, we successfully generated malignant glioma in tree shrew. The tree shrew glioma exhibited aggressive behavior and a relatively short latency, and markedly reduced animal survival...
February 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28199119/engineering-a-catalytically-efficient-recombinant-protein-ligase
#6
Renliang Yang, Yee Hwa Wong, Giang K T Nguyen, James P Tam, Julien Lescar, Bin Wu
Breaking and forming peptidyl bonds are fundamental biochemical reactions in protein chemistry. Unlike proteases that are abundantly available, fast-acting ligases are rare. OaAEP1 is an enzyme isolated from the cyclotide-producing plant oldenlandia affinis that displayed weak peptide cyclase activity, despite having a similar structural fold with other asparaginyl endopeptidases (AEP). Here we report the first atomic structure of OaAEP1, at a resolution of 2.56 Å, in its pre-activation form. Our structure and biochemical analysis of this enzyme reveals its activation mechanism as well as structural features important for its ligation activity...
February 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28195494/electrical-and-thermal-transport-in-coplanar-polycrystalline-graphene-hbn-heterostructures
#7
José-Eduardo Barrios-Vargas, Bohayra Mortazavi, Aron W Cummings, Rafael Martinez-Gordillo, Miguel Pruneda, Luciano Colombo, Timon Rabczuk, Stephan Roche
We present a theoretical study of electronic and thermal transport in polycrystalline heterostructures combining graphene (G) and hexagonal boron nitride (hBN) grains of varying size and distribution. By increasing the hBN grain density from a few percent to 100%, the system evolves from a good conductor to an insulator, with the mobility dropping by orders of magnitude and the sheet resistance reaching the MΩ regime. The Seebeck coefficient is suppressed above 40% mixing, while the thermal conductivity of polycrystalline hBN is found to be on the order of 30-120 Wm(-1)K(-1)...
February 14, 2017: Nano Letters
https://www.readbyqxmd.com/read/28193853/spontaneous-mirror-symmetry-breaking-induces-inverse-energy-cascade-in-3d-active-fluids
#8
Jonasz Słomka, Jörn Dunkel
Classical turbulence theory assumes that energy transport in a 3D turbulent flow proceeds through a Richardson cascade whereby larger vortices successively decay into smaller ones. By contrast, an additional inverse cascade characterized by vortex growth exists in 2D fluids and gases, with profound implications for meteorological flows and fluid mixing. The possibility of a helicity-driven inverse cascade in 3D fluids had been rejected in the 1970s based on equilibrium-thermodynamic arguments. Recently, however, it was proposed that certain symmetry-breaking processes could potentially trigger a 3D inverse cascade, but no physical system exhibiting this phenomenon has been identified to date...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28192772/direct-3d-bioprinting-of-prevascularized-tissue-constructs-with-complex-microarchitecture
#9
Wei Zhu, Xin Qu, Jie Zhu, Xuanyi Ma, Sherrina Patel, Justin Liu, Pengrui Wang, Cheuk Sun Edwin Lai, Maling Gou, Yang Xu, Kang Zhang, Shaochen Chen
Living tissues rely heavily on vascular networks to transport nutrients, oxygen and metabolic waste. However, there still remains a need for a simple and efficient approach to engineer vascularized tissues. Here, we created prevascularized tissues with complex three-dimensional (3D) microarchitectures using a rapid bioprinting method - microscale continuous optical bioprinting (μCOB). Multiple cell types mimicking the native vascular cell composition were encapsulated directly into hydrogels with precisely controlled distribution without the need of sacrificial materials or perfusion...
February 2, 2017: Biomaterials
https://www.readbyqxmd.com/read/28188997/china-s-landscape-in-regenerative-medicine
#10
REVIEW
Xin Tang, Hua Qin, Xiaosong Gu, Xiaobing Fu
Regenerative medicine is a burgeoning interdisciplinary research field that can impact healthcare by offering new therapeutic strategies to replace or regenerate human cells, tissues, or organs with the ultimate goal of restoring or establishing normal human functions. The past decade has seen significant progress of regenerative medicine in China, the world's most populous developing country. With government backing, the progress in regenerative medicine is driven by increasing medical demands of people, accompanied by the economic growth, population aging, and lifestyle change in China...
February 3, 2017: Biomaterials
https://www.readbyqxmd.com/read/28187891/automated-classification-of-maxillofacial-cysts-in-cone-beam-ct-images-using-contourlet-transformation-and-spherical-harmonics
#11
Fatemeh Abdolali, Reza Aghaeizadeh Zoroofi, Yoshito Otake, Yoshinobu Sato
BACKGROUND AND OBJECTIVE: Accurate detection of maxillofacial cysts is an essential step for diagnosis, monitoring and planning therapeutic intervention. Cysts can be of various sizes and shapes and existing detection methods lead to poor results. Customizing automatic detection systems to gain sufficient accuracy in clinical practice is highly challenging. For this purpose, integrating the engineering knowledge in efficient feature extraction is essential. METHODS: This paper presents a novel framework for maxillofacial cysts detection...
February 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28187407/synthetic-biology-open-language-sbol-version-2-1-0
#12
Jacob Beal, Robert Sidney Cox, Raik Grünberg, James McLaughlin, Tramy Nguyen, Bryan Bartley, Michael Bissell, Kiri Choi, Kevin Clancy, Chris Macklin, Curtis Madsen, Goksel Misirli, Ernst Oberortner, Matthew Pocock, Nicholas Roehner, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John Gennari, Chris Myers, Herbert Sauro, Anil Wipat
Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28183187/effect-of-zinc-oxide-film-morphologies-on-the-formation-of-shewanella-putrefaciens-biofilm
#13
Yue Dai, Tong Sun, Zhibing Zhang, Zhenyu J Zhang, Jian-Rong Li
Zinc oxide (ZnO) films were prepared on aluminum substrate by a hydrothermal method to investigate the effect of their surface characteristics, including morphology and hydrophobicity, on the corresponding antibiofilm performance. The surface characteristics of the prepared ZnO films were examined by a comprehensive range of methodologies, suggesting that films of distinctive surface morphologies were successfully formed. Subsequently, their antibiofilm activities, using Shewanella putrefaciens as a model bacterium, were assessed...
February 9, 2017: Biointerphases
https://www.readbyqxmd.com/read/28181430/ellipsoidal-colloids-with-a-controlled-surface-roughness-via-bio-inspired-surface-engineering-building-blocks-for-liquid-marbles-and-superhydrophobic-surfaces
#14
Pengjiao Zhang, Lu Yang, Qiang Li, Songhai Wu, Shaoyi Jia, Zhanyong Li, Zhenkun Zhang, Linqi Shi
Understanding the important role of the surface roughness of nano-/colloidal particles and harnessing them for practical applications need novel strategies to control the particles' surface topology. Although there are many examples of spherical particles with a specific surface roughness, non-spherical ones with similar surface features are rare. The current work report a one-step, straightforward and bio-inspired surface engineering strategy to prepare ellipsoidal particles with a controlled surface roughness...
February 9, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28181412/aligned-nanofibrous-cell-derived-extracellular-matrix-for-anisotropic-vascular-graft-construction
#15
Qi Xing, Zichen Qian, Mitchell Tahtinen, Ai Hui Yap, Keegan Yates, Feng Zhao
There is a large demand for tissue engineered vascular grafts for the application of vascular reconstruction surgery or in vitro drug screening tissue model. The extracellular matrix (ECM) composition along with the structural and mechanical anisotropy of native blood vessels is critical to their functional performance. The objective of this study is to develop a biomimetic vascular graft recapitulating the anisotropic features of native blood vessels by employing nanofibrous aligned fibroblast-derived ECM and human mesenchymal stem cells (hMSCs)...
February 9, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28179425/structural-insights-into-the-broad-substrate-specificity-of-a-novel-endo-glycoceramidase-i-belonging-to-a-new-subfamily-of-gh5-glycosidase
#16
Yun-Bin Han, Liu-Qing Chen, Zhuo Li, Yu-Meng Tan, Yan Feng, Guang-Yu Yang
Endoglycoceramidases (EGCases) specifically hydrolyze the glycosidic linkage between the oligosaccharide and the ceramide moieties of various glycosphingolipids, and they have received substantial attention in the emerging field of glycosphingolipidology. However, the mechanism regulating the strict substrate specificity of these GH5 glycosidases has not been identified. In this study, we report a novel EGCase I from Rhodococcus equi 103S (103S_EGCase I) with remarkably broad substrate specificity. Based on phylogenetic analyses, the enzyme may represent a new subfamily of GH5 glycosidases...
February 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28177255/exploring-the-thermoelectric-performance-of-bagd2nio5-haldane-gap-materials
#17
Narendar Nasani, Carlos Miguel Oliveira Rocha, Andrei V Kovalevsky, Gonzalo Otero Irurueta, Sascha Populoh, Philipp Thiel, Anke Weidenkaff, Fernando Neto da Silva, Duncan P Fagg
One-dimensional Haldane gap materials, such as the rare earth barium chain nickelates, have received great interest due to their vibrant one-dimensional spin antiferromagnetic character and unique structure. Herein we report how these 1D structural features can also be highly beneficial for thermoelectric applications by analysis of the system CaxBaGd2-xNiO5 0 ≤ x ≤ 0.25. Attractive Seebeck coefficients of 140-280 μV K(-1) at 350-1300 K are retained even at high acceptor-substitution levels, provided by the interplay of low dimensionality and electronic correlations...
February 8, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28174251/a-process-engineering-approach-to-increase-organoid-yield
#18
Natasha Arora, Jasmin Imran Alsous, Jacob W Guggenheim, Michael Mak, Jorge Munera, James M Wells, Roger D Kamm, H Harry Asada, Stanislav Y Shvartsman, Linda G Griffith
Temporal manipulation of the in vitro environment and growth factors can direct differentiation of human pluripotent stem cells into organoids, aggregates with multiple tissue-specific cell types and three-dimensional structure mimicking native organs. A mechanistic understanding of early organoid formation is essential for improving the robustness of these methods, which is necessary prior to use in drug development and regenerative medicine. We investigated intestinal organoid emergence, focusing on measurable parameters of hindgut spheroids, the intermediate step between definitive endoderm and mature organoids...
February 7, 2017: Development
https://www.readbyqxmd.com/read/28174092/pancreatic-cancer-models-for-translational-research
#19
REVIEW
Diana Behrens, Wolfgang Walther, Iduna Fichtner
Pancreatic cancer is a cruel, progressive disease that is highly metastatic and barely treatable, a situation that is devastating for patients, family members, oncologists, clinicians and scientists. Open questions that need to be resolved by research into pancreatic cancer relate to its aggressiveness, the underlying molecular causes, the factors that promote tumor progression, the ways cancer cells interact with their environments, and whether more effective therapeutic options can be developed. Studies over the last 15 years have provided some partial answers, but in the absence of a real cure the main agenda remains: to identify new therapeutic targets, predictive markers and novel treatment strategies that would help the disease under control...
February 4, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28173698/a-visual-language-for-protein-design
#20
Robert Sidney Cox Iii, James Alastair McLaughlin, Raik Gruenberg, Jake Beal, Anil Wipat, Herbert Sauro
As protein engineering becomes more sophisticated, practitioners increasingly need to share diagrams for communicating protein designs. To this end, we present a draft visual language, Protein Language, that describes the high-level architecture of an engineered protein with a few easy-to-draw glyphs, intended to be compatible with other biological diagram languages such as SBOL and SBGN. Protein Language con- sists of glyphs for representing important features (e.g., globular domains, recognition and localization sequences, sites of covalent modification, cleavage and catalysis), rules for composing these glyphs to represent complex architectures, and rules constraining the scaling and styling of diagrams...
February 7, 2017: ACS Synthetic Biology
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