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https://www.readbyqxmd.com/read/28335417/dna-sequencing-sensors-an-overview
#1
REVIEW
Jose Antonio Garrido-Cardenas, Federico Garcia-Maroto, Jose Antonio Alvarez-Bermejo, Francisco Manzano-Agugliaro
The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger...
March 14, 2017: Sensors
https://www.readbyqxmd.com/read/28335375/assessing-the-spectral-properties-of-sunlit-and-shaded-components-in-rice-canopies-with-near-ground-imaging-spectroscopy-data
#2
Kai Zhou, Xinqiang Deng, Xia Yao, Yongchao Tian, Weixing Cao, Yan Zhu, Susan L Ustin, Tao Cheng
Monitoring the components of crop canopies with remote sensing can help us understand the within-canopy variation in spectral properties and resolve the sources of uncertainties in the spectroscopic estimation of crop foliar chemistry. To date, the spectral properties of leaves and panicles in crop canopies and the shadow effects on their spectral variation remain poorly understood due to the insufficient spatial resolution of traditional spectroscopy data. To address this issue, we used a near-ground imaging spectroscopy system with high spatial and spectral resolutions to examine the spectral properties of rice leaves and panicles in sunlit and shaded portions of canopies and evaluate the effect of shadows on the relationships between spectral indices of leaves and foliar chlorophyll content...
March 13, 2017: Sensors
https://www.readbyqxmd.com/read/28335354/titanium-dioxide-nanoparticle-biomolecule-interactions-influence-oral-absorption
#3
Mi-Rae Jo, Jin Yu, Hyoung-Jun Kim, Jae Ho Song, Kyoung-Min Kim, Jae-Min Oh, Soo-Jin Choi
Titanium dioxide (TiO₂) nanoparticles (NPs) have been widely applied in various industrial fields, such as electronics, packaging, food, and cosmetics. Accordingly, concerns about the potential toxicity of TiO₂ NPs have increased. In order to comprehend their in vivo behavior and potential toxicity, we must evaluate the interactions between TiO₂ NPs and biomolecules, which can alter the physicochemical properties and the fate of NPs under physiological conditions. In the present study, in vivo solubility, oral absorption, tissue distribution, and excretion kinetics of food grade TiO₂ (f-TiO₂) NPs were evaluated following a single-dose oral administration to rats and were compared to those of general grade TiO₂ (g-TiO₂) NPs...
November 29, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334084/molecular-dynamics-recipes-for-genome-research
#4
Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer...
February 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28333580/air-quality-measurements-from-rubber-bands-to-tapping-the-rainbow
#5
George M Hidy, Peter K Mueller, Samuel L Altshuler, Judith C Chow, John G Watson
It is axiomatic that good measurements are integral to good public policy for environmental protection. The generalized term for "measurements" includes sampling and quantitation, data integrity, documentation, network design, sponsorship and operations, and archiving and accessing for applications. Each of these components has evolved and advanced over the last 200 years as knowledge of atmospheric chemistry and physics has matured. Air quality was first detected by what people could see smoke and smell contaminated air...
March 23, 2017: Journal of the Air & Waste Management Association
https://www.readbyqxmd.com/read/28332260/biological-characterization-of-novel-nitroimidazole-peptide-conjugates-in-vitro-and-in-vivo
#6
Ralf Bergmann, Katrin Splith, Jens Pietzsch, Michael Bachmann, Ines Neundorf
Recently, we reported on the design of a multimodal peptide conjugate useful as delivery platform for targeting hypoxic cells. A nitroimidazole (2-(2-nitroimidazol-1-yl)acetic acid, NIA) moiety, which is selectively entrapped in hypoxic cells, was coupled to a cell-penetrating peptide serving as the transporter. Furthermore, attachment of a bifunctional linker allowed the introduction of a diagnostic or therapeutic radiometal. However, although selective tumor accumulation could be detected in vivo, a fast renal clearance of the compound was observed...
March 23, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28329028/non-equilibrium-assembly-of-microtubules-from-molecules-to-autonomous-chemical-robots
#7
REVIEW
H Hess, Jennifer L Ross
Biological systems have evolved to harness non-equilibrium processes from the molecular to the macro scale. It is currently a grand challenge of chemistry, materials science, and engineering to understand and mimic biological systems that have the ability to autonomously sense stimuli, process these inputs, and respond by performing mechanical work. New chemical systems are responding to the challenge and form the basis for future responsive, adaptive, and active materials. In this article, we describe a particular biochemical-biomechanical network based on the microtubule cytoskeletal filament - itself a non-equilibrium chemical system...
March 22, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28326088/temperature-effects-on-biomass-and-regeneration-of-vegetation-in-a-geothermal-area
#8
Abdul Nishar, Martin K-F Bader, Eoin J O'Gorman, Jieyu Deng, Barbara Breen, Sebastian Leuzinger
Understanding the effects of increasing temperature is central in explaining the effects of climate change on vegetation. Here, we investigate how warming affects vegetation regeneration and root biomass and if there is an interactive effect of warming with other environmental variables. We also examine if geothermal warming effects on vegetation regeneration and root biomass can be used in climate change experiments. Monitoring plots were arranged in a grid across the study area to cover a range of soil temperatures...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28323105/automated-workflows-for-modelling-chemical-fate-kinetics-and-toxicity
#9
José Vicente Sala Benito, Alicia Paini, Andrea-Nicole Richarz, Thorsten Meinl, Michael R Berthold, Mark T D Cronin, Andrew P Worth
Automation is universal in today's society, from operating equipment such as machinery, in factory processes, to self-parking automobile systems. While these examples show the efficiency and effectiveness of automated mechanical processes, automated procedures that support the chemical risk assessment process are still in their infancy. Future human safety assessments will rely increasingly on the use of automated models, such as physiologically based kinetic (PBK) and dynamic models and the virtual cell based assay (VCBA)...
March 17, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28323071/the-central-role-of-trna-in-genetic-code-expansion
#10
REVIEW
Noah M Reynolds, Oscar Vargas-Rodriguez, Dieter Söll, Ana Crnković
BACKGROUND: The development of orthogonal translation systems (OTSs) for genetic code expansion (GCE) has allowed for the incorporation of a diverse array of non-canonical amino acids (ncAA) into proteins. Transfer RNA, the central molecule in the translation of the genetic message into proteins, plays a significant role in the efficiency of ncAA incorporation. SCOPE OF REVIEW: Here we review the biochemical basis of OTSs for genetic code expansion. We focus on the role of tRNA and discuss strategies used to engineer tRNA for the improvement of ncAA incorporation into proteins...
March 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28322560/subphthalocyanines-axially-substituted-with-a-tetracyanobuta-1-3-diene-aniline-moiety-synthesis-structure-and-physicochemical-properties
#11
Kim A Winterfeld, Giulia Lavarda, Julia Guilleme, Michael Sekita, Dirk M Guldi, Tomas Torres, Giovanni Bottari
A 1,1,4,4-tetracyanobuta-1,3-diene (TCBD)-aniline moiety has been introduced, for the first time, at the axial position of two subphthalocyanines (SubPcs) peripherally substituted with hydrogen (H12SubPc) or fluorine atoms (F12SubPc). Single-crystal X-ray analysis of both SubPc-TCBD-aniline systems showed that each conjugate is a racemic mixture of two atropisomers resulting from the almost orthogonal geometry adopted by the axial TCBD unit, which were separated by chiral HPLC. Remarkably, the single-crystal X-ray structure of one atropisomer of each SubPc-TCBD-aniline conjugate has been solved allowing to unambiguously assign the atropisomers' absolute configuration, something, to the best of our knowledge, unprecedented in TCBD-based conjugates...
March 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28322388/understanding-surface-site-structures-and-properties-by-first-principles-calculations-an-experimental-point-of-view
#12
Aleix Comas-Vives, Kim Larmier, Christophe Copéret
The characterization of the active sites in heterogeneous catalysts is highly challenging and hinders the rational development and design of better catalysts. One approach to achieve this goal is Surface Organometallic Chemistry (SOMC), which allows generation of well-defined active sites characterized at the molecular level using spectroscopic methods. Due to many advances in the field and the increase of computational power, Computational Chemistry (CompChem) plays a key role in providing an atomistic understanding of these systems and the nature of the active sites...
March 21, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28321445/planar-b38-and-b37-clusters-with-a-double-hexagonal-vacancy-molecular-motifs-for-borophenes
#13
Qiang Chen, Wen-Juan Tian, Lin-Yan Feng, Hai-Gang Lu, Yue-Wen Mu, Hua-Jin Zhai, Si-Dian Li, Lai-Sheng Wang
Boron clusters have been found to exhibit a variety of interesting electronic, structural, and bonding properties. Of particular interest are the recent discoveries of the 2D hexagonal B36(-/0) which led to the concept of borophenes and the 3D fullerene-like B40(-/0) which marked the onset of borospherene chemistry. Here, we present a joint photoelectron spectroscopic and first-principles study of B37(-) and B38(-), which are in the transition size range between the 2D borophene-type clusters and the 3D borospherenes...
March 21, 2017: Nanoscale
https://www.readbyqxmd.com/read/28320909/theoretical-and-computational-studies-of-non-equilibrium-and-non-statistical-dynamics-in-the-gas-phase-in-the-condensed-phase-and-at-interfaces
#14
Riccardo Spezia, Emilio Martínez-Nuñez, Saulo Vazquez, William L Hase
In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28320908/reaction-and-relaxation-at-surface-hotspots-using-molecular-dynamics-and-the-energy-grained-master-equation-to-describe-diamond-etching
#15
David R Glowacki, W J Rodgers, Robin Shannon, Struan H Robertson, Jeremy N Harvey
The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'hotspots' that form on the surface of diamond during the chemical vapour deposition process...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28320294/solid-gas-biocatalysis
#16
REVIEW
L M Kulishova, D O Zharkov
Solid/gas biocatalysis is a nontraditional reaction system that employs the ability of some enzymes, being in the solid state, to catalyze reactions of substrates in the gas phase. Manipulation of the reaction parameters (temperature and pressure) in the solid/gas system allows precise control over the thermodynamic activity of water and substrate and creation of a controlled microenvironment for the enzyme, making it an appropriate model for enzymology studies. Owing to such advantages as high stability of dry enzymes and cofactors and easy fractionation of gas mixtures, solid/gas biotechnology has already found several industrial applications...
February 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28319669/cell-adhesion-on-dynamic-supramolecular-surfaces-probed-by-fluid-force-microscopy-based-single-cell-force-spectroscopy
#17
Shrikrishnan Sankaran, Leena Jaatinen, Jenny Brinkmann, Tomaso Zambelli, Janos Vörös, Pascal Jonkheijm
Biomimetic and stimuli-responsive cell-material interfaces are actively being developed to study and control various cell-dynamics phenomena. Since cells naturally reside in the highly dynamic and complex environment of the extracellular matrix, attempts are being made to replicate these conditions in synthetic biomaterials. Supramolecular chemistry, dealing with noncovalent interactions, has recently provided possibilities to incorporate such dynamicity and responsiveness in various types of architectures...
March 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28319378/computational-study-of-13-c-nmr-chemical-shift-anisotropy-patterns-in-c20h10-and-c20h10-4-insights-into-their-variation-upon-planarization-and-formation-of-concentric-aromatic-species-in-the-smaller-isolated-pentagon-structural-motif
#18
Alvaro Muñoz-Castro, Wilson Caimanque-Aguilar, Cesar Morales-Verdejo
Corannulene, C20H10, exhibits a concave surface in the ground state that is able to experience a bowl-to-bowl inversion through a planar conformation. Such a structure is the smaller example resembling an isolated-pentagon motif, as a relevant fragment in fullerene chemistry. Here, we explored the differences between bowl and planar conformations involving both energetic and (13)C NMR properties, for the neutral and tetraanionic species by using density functional theory (DFT) methods. This allows us to understand the variation of the chemical environment at the carbon atoms upon planarization of this representive motif...
March 24, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28318267/magnetic-microlassos-for-reversible-cargo-capture-transport-and-release
#19
Tao Yang, Tonguc Onur Tasci, Keith B Neeves, Ning Wu, David W M Marr
Microbot propulsion has seen increasing interest in recent years as artificial methods that overcome the well-established reversible and challenging nature of microscale fluid mechanics. While controlled movement is an important feature of microbot action, many envisioned applications also involve cargo transport where microbots must be able to load and unload contents on command while tolerating complex solution chemistry. Here we introduce a physical method that uses flexible and linked superparamagnetic colloidal chains, which can form closed rings or "lassos" in the presence of a planar rotating magnetic field...
March 20, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28317998/supramolecular-electrode-assemblies-for-bioelectrochemistry
#20
Theodoros Laftsoglou, Lars J C Jeuken
For more than three decades, the field of bioelectrochemistry has provided novel insights into the catalytic mechanisms of enzymes, the principles that govern biological electron transfer, and has elucidated the basic principles for bioelectrocatalytic systems. Progress in biochemistry, bionanotechnology, and our ever increasing ability to control the chemistry and structure of electrode surfaces has enabled the study of ever more complex systems with bioelectrochemistry. This feature article highlights developments over the last decade, where supramolecular approaches have been employed to develop electrode assemblies that increase enzyme loading on the electrode or create more biocompatible environments for membrane enzymes...
March 20, 2017: Chemical Communications: Chem Comm
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